U.S. patent application number 13/540935 was filed with the patent office on 2012-12-20 for polymerase compositions and methods.
This patent application is currently assigned to LIFE TECHNOLOGIES CORPORATION. Invention is credited to Amy CASTILLO, Cheng-Yao CHEN, Stephen P. HENDRICKS, Daniel MAZUR, Xinzhan PENG, Marian PERIS, Michael PHELAN.
Application Number | 20120322057 13/540935 |
Document ID | / |
Family ID | 42781937 |
Filed Date | 2012-12-20 |
United States Patent
Application |
20120322057 |
Kind Code |
A1 |
HENDRICKS; Stephen P. ; et
al. |
December 20, 2012 |
POLYMERASE COMPOSITIONS AND METHODS
Abstract
Disclosed herein are modified polymerase compositions exhibiting
altered polymerase activity, which can be useful in a variety of
biological applications. Also disclosed herein are methods of
making and using such compositions. In some embodiments, the
compositions exhibit altered properties that can enhance their
utility in a variety of biological applications. Such altered
properties, can include, for example, altered nucleotide binding
affinities, altered nucleotide incorporation kinetics, altered
photostability and/or altered nanoparticle tolerance, as well as a
range of other properties as disclosed herein.
Inventors: |
HENDRICKS; Stephen P.; (Los
Gatos, CA) ; PHELAN; Michael; (Hayward, CA) ;
PERIS; Marian; (Belmont, CA) ; CHEN; Cheng-Yao;
(Carlsbad, CA) ; MAZUR; Daniel; (San Diego,
CA) ; PENG; Xinzhan; (Carlsbad, CA) ;
CASTILLO; Amy; (Houston, TX) |
Assignee: |
LIFE TECHNOLOGIES
CORPORATION
Carlsbad
CA
|
Family ID: |
42781937 |
Appl. No.: |
13/540935 |
Filed: |
July 3, 2012 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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12748359 |
Mar 26, 2010 |
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13540935 |
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61164324 |
Mar 27, 2009 |
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61184770 |
Jun 5, 2009 |
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61242771 |
Sep 15, 2009 |
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61245457 |
Sep 24, 2009 |
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61263974 |
Nov 24, 2009 |
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61289388 |
Dec 22, 2009 |
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61293618 |
Jan 8, 2010 |
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61293616 |
Jan 8, 2010 |
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61299919 |
Jan 29, 2010 |
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61299917 |
Jan 29, 2010 |
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61307356 |
Feb 23, 2010 |
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Current U.S.
Class: |
435/6.1 ;
435/194; 435/243; 435/91.5; 536/23.2 |
Current CPC
Class: |
G01N 21/6428 20130101;
G01N 33/582 20130101; C12N 9/1252 20130101; C12Y 207/07007
20130101; C12N 9/1241 20130101; C07H 19/20 20130101; C12Q 1/6818
20130101; G01N 2021/6432 20130101; C12N 9/96 20130101; C12Y 207/07
20130101; C12Q 1/6869 20130101 |
Class at
Publication: |
435/6.1 ;
435/194; 536/23.2; 435/243; 435/91.5 |
International
Class: |
C12N 9/12 20060101
C12N009/12; C12Q 1/68 20060101 C12Q001/68; C12N 1/00 20060101
C12N001/00; C12P 19/34 20060101 C12P019/34; C12N 15/54 20060101
C12N015/54; C12N 15/63 20060101 C12N015/63 |
Claims
1. A DNA polymerase having a photostability that is at least about
80% under standard photostability assay conditions.
2. The DNA polymerase of claim 1, wherein the polymerase comprises
an amino acid sequence that is at least about 95% identical to the
amino acid sequence of SEQ ID NO: 7.
3. The DNA polymerase of claim 2, further comprising one or more
amino acid substitutions selected from the group consisting of:
D9A, E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A,
Q377A, S385G, H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370
W, H370Y, H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A,
E371Q, E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R,
K372A, K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R,
K380A, K380Q, K380W, K380Y, K380F, D507H, D507G, D507E, D507T,
D5075, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F, K509H,
K509G, K509D, K509R, K509E, K509T, K5095, K509R, K509A, K509Q,
K509W, K509Y and K509F, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 7.
4. The DNA polymerase of claim 1, wherein the polymerase further
comprises a mutation reducing 3' to 5' exonuclease activity.
5. The DNA polymerase of claim 4, wherein the mutation comprises
one or more amino acid substitutions at positions selected from the
group consisting of: 2, 9, 11, 12, 58, 59, 63, 162, 166, 377 and
385.
6. The DNA polymerase of claim 1, wherein the polymerase further
comprises a mutation increasing the branching ratio of the enzyme
with a labeled nucleotide.
7. The DNA polymerase of claim 6, wherein the mutation comprises
one or more amino acid substitutions at positions selected from the
group consisting of: 370, 371, 372, 373, 374, 375, 376 and 377.
8. The DNA polymerase of claim 1, wherein the polymerase further
comprises a mutation increasing the primer extension activity.
9. The DNA polymerase of claim 8, wherein the mutation comprises
one or more amino acid substitutions selected from the group
consisting of: 129 and 339.
10. The DNA polymerase of claim 1, wherein the polymerase further
comprises a mutation increasing the affinity of the polymerase for
a particular labeled nucleotide.
11. The DNA polymerase of claim 10, wherein the mutation comprises
one or more amino acid substitutions selected from the group
consisting of: 370, 371, 372, 373, 374, 375, 376, 507 and 509.
12. A nucleic acid molecule encoding the DNA polymerase of claim 1,
wherein the nucleic acid molecule is DNA or RNA.
13. A vector comprising a DNA encoding the polymerase of claim
2.
14. An isolated host cell comprising the nucleic acid molecule of
claim 12.
15. An isolated host cell comprising the vector of claim 13.
16. A method for obtaining a polymerase comprising: purifying the
polymerase from the isolated host cell of claim 15.
17. A method for performing a primer extension reaction,
comprising: contacting a modified polymerase comprising an amino
acid sequence that is at least 90% identical to the amino acid
sequence of SEQ ID NO: 7 with a nucleic acid molecule and a
nucleotide under conditions where the nucleotide is incorporated
into the nucleic acid molecule by the polymerase.
18. The method of claim 17, wherein the at least one nucleotide is
a labeled nucleotide, and the label of the nucleotide emits a
signal during incorporation of the nucleotide.
19. The method of claim 18, further comprising detecting the signal
emitted by the nucleotide label.
20. The method of claim 19, further comprising analyzing the
detected signal to determine the identity of the incorporated
nucleotide.
21. The method of claim 17, wherein the modified polymerase
exhibits a t.sub.-1 value for a labeled nucleotide that is equal to
or greater than the t.sub.-1 value of a reference Phi-29 polymerase
comprising the amino acid sequence of SEQ ID NO: 1 for the same
nucleotide.
22. The method of claim 17, wherein the modified polymerase
exhibits a t.sub.pol value for a labeled nucleotide that is equal
to or greater than the t.sub.pol value of a reference Phi-29
polymerase comprising the amino acid sequence of SEQ ID NO: 1 for
the same nucleotide.
23. The method of claim 17, wherein the modified polymerase
exhibits a residence time for a labeled nucleotide that is equal to
or greater than the residence time of a reference Phi-29 polymerase
comprising the amino acid sequence of SEQ ID NO: 1 for the same
nucleotide.
24. The method of claim 17, wherein the modified polymerase has a
photostability of at least about 80% under standard photostability
assay conditions.
25. The method of claim 17, wherein the modified polymerase has a
nanoparticle tolerance of at least about 80% under standard
tolerance assay conditions.
26. The method of claim 18, wherein the labeled nucleotide
comprises a nucleotide label linked to the base, sugar or phosphate
group of the nucleotide.
27. The method of claim 18, wherein the labeled nucleotide is a
reversible terminator.
28. The method of claim 18, wherein the modified polymerase is
linked to a label.
29. The method of claim 27, wherein the label of the modified
polymerase and the nucleotide label are capable of undergoing FRET
with each other.
30. A modified DNA polymerase having an increased branching ratio
in the presence of labeled nucleotides relative to a B103
polymerase comprising the amino acid sequence of SEQ ID NO: 7.
31. The modified DNA polymerase of claim 30, wherein the polymerase
comprises an amino acid sequence that is at least about 95%
identical to the amino acid sequence of SEQ ID NO: 7.
32. The modified DNA polymerase of claim 31, further comprising one
or more amino acid mutations selected from the group consisting of:
T365G, T365F, T365G, T365S, T365K, T365R, T365A, T365Q, T365W,
T365Y, T365H, H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370
W, H370Y, H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A,
E371Q, E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R,
K372A, K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R,
K380A, K380Q, K380W, K380Y, K380F, A481E, A481F, A481G, A481S,
A481R, A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G,
D507E, D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y,
D507F, K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R,
K509A, K509Q, K509W, K509Y and K509F, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 7.
33. The modified DNA polymerase of claim 32, further comprising the
amino acid mutation D166A and having reduced exonuclease activity
relative to a DNA polymerase having the amino acid sequence of SEQ
ID NO: 7.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. Nonprovisional
application Ser. No. 12/748,359, filed Mar. 26, 2010, which claims
the filing date benefit of U.S. Provisional Application Nos.
61/164,324, filed on Mar. 27, 2009; 61/184,770, filed on Jun. 5,
2009; 61/242,771, filed on Sep. 15, 2009; 61/245,457, filed on Sep.
24, 2009; 61/263,974, filed on Nov. 24, 2009; 61/289,388; filed on
Dec. 22, 2009; 61/293,618, filed on Jan. 8, 2010; 61/293,616, filed
on Jan. 8, 2010; 61/299,919, filed on Jan. 29, 2010; 61/299,917,
filed on Jan. 29, 2010; 61/307,356, filed on Feb. 23, 2010. The
contents of each of the foregoing patent applications are
incorporated by reference in their entirety.
[0002] The instant application contains a Sequence Listing which
has been submitted via EFS-Web and is hereby incorporated by
reference in its entirety. Said ASCII copy, created on Jun. 24,
2010, is named LT00052.txt, and is 77,540 bytes in size.
FIELD
[0003] The disclosure relates generally to polymerase compositions
and methods. More particularly, the disclosure relates to modified
polymerases and their use in biological applications including, for
example, nucleotide incorporation, primer extension and single
molecule sequencing reactions.
BACKGROUND
[0004] The polymerases typically catalyze nucleic acid synthesis
against an existing polynucleotide template using Watson-Crick base
pairing interactions, and are useful in a variety of biological
applications. Such applications frequently involve the use of
labels to visualize one or more components or products of the
polymerase reaction. For example, "sequencing by synthesis"
applications typically involve the monitoring of polymerase
activity in real time by detecting signals emitted by labels
associated with one or more components of the polymerase reaction.
However, many labels cannot be employed in such assays because
their presence inhibits polymerase activity. For example, although
nanoparticles can exhibit superior quantum yield, size tunability,
brightness and resistance to photobleaching compared to
conventional organic, e.g., dye, labels, their utility in
polymerase-based assays is hampered by the sensitivity of many
polymerases to the presence of nanoparticles. Furthermore, many
polymerases can also exhibit loss of polymerase activity upon
exposure to excitation radiation, thus hampering their use in
assays involving labels that require excitation to be detectable.
This problem can be exacerbated in the presence of nanoparticles,
resulting in further loss of polymerase activity.
[0005] Yet another set of problems revolves around the kinetic
behavior of the polymerase towards nucleotide substrates. Analysis
of polymerase activity can be complicated by undesirable behavior
such as, for example, the tendency of a given polymerase to
dissociate from the template; to bind and/or incorporate the
incorrect, e.g., non Watson-Crick base-paired, nucleotide; or to
release the correct, e.g., Watson-Crick based paired, nucleotide
without incorporation. In addition, some applications may require
the use of polymerases exhibiting increased residence times or
branching ratios for particular nucleotides, so as to increase the
duration during which labeled nucleotide incorporation can be
detected. Finally, although many biological applications require
the use of labeled nucleotides, many polymerases do not incorporate
such nucleotides efficiently, thus limiting the utility of such
polymerase-nucleotide combinations in these applications. These and
other desirable properties can be enhanced via suitable selection,
engineering and/or modification of a polymerase of choice.
[0006] It is therefore desirable to develop polymerases having
increased tolerance for the presence of both organic (e.g.,
conventional dye) and inorganic (e.g., nanoparticle-based) labels,
as well as polymerases that retain higher levels of polymerase
activity following exposure to excitation radiation. There is also
a need for polymerases that exhibit improved reaction kinetics with
a particular set of labeled nucleotides. Accordingly, there remains
a need in the art for improved polymerase compositions, and methods
of use thereof, which can permit polynucleotide synthesis with
higher efficiency while allowing the use of an expanded repertoire
of excitation and/or labeling strategies.
SUMMARY
[0007] Provided herein are novel polymerak compositions, methods of
making such compositions and methods of using such compositions in
various biological applications.
[0008] In some embodiments, the present disclosure relates to a
modified DNA polymerase having a photostability that is at least
about 80% under standard photostability assay conditions.
[0009] In some embodiments, the present disclosure relates to a
modified DNA polymerase having a primer extension activity that is
at least about 105%, 110%, 125%, 150%, 175%, 200%, 250%, 375%,
500%, 750% or 1000% relative to the primer extension activity of a
wild type Phi-29 polymerase comprising the amino acid sequence of
SEQ ID NO: 1 under standard photostability assay conditions.
[0010] In some embodiments, the present disclosure relates to a
modified DNA polymerase having a nanoparticle tolerance that is at
least about 80% under standard nanoparticle tolerance assay
conditions.
[0011] In some embodiments, the present disclosure relates to a
modified DNA polymerase having a primer extension activity that is
at least about 105%, 110%, 125%, 150%, 175%, 200%, 250%, 375%,
500%, 750% or 1000% relative to the primer extension activity of a
wild type Phi-29 polymerase comprising the amino acid sequence of
SEQ ID NO: 1 under standard nanoparticle tolerance assay
conditions.
[0012] In some embodiments, the present disclosure relates to a
modified DNA polymerase having a primer extension activity that is
at least about 105%, 110%, 125%, 150%, 175%, 200%, 250%, 375%,
500%, 750% or 1000% relative to the primer extension activity of a
wild type Phi-29 polymerase comprising the amino acid sequence of
SEQ ID NO: 1 under standard nanoparticle tolerance assay
conditions.
[0013] In some embodiments, the disclosure relates to a nucleic
acid molecule encoding any one, some or all of the modified DNA
polymerases of the present disclosure. The nucleic acid molecule
can optionally be DNA or RNA.
[0014] In some embodiments, the disclosure relates to a vector
comprising a DNA encoding any one, some or all of the modified DNA
polymerases as provided herein.
[0015] In some embodiments, the disclosure relates to an isolated
host cell comprising a vector including a DNA encoding any one,
some or all of the modified DNA polymerases of the present
disclosure.
[0016] In some embodiments, the disclosure relates to a method for
obtaining the modified DNA polymerases of the present disclosure.
Optionally, the method comprises purifying the modified DNA
polymerase from an isolated host cell comprising a vector including
a DNA encoding a modified DNA polymerase of the present
disclosure.
[0017] In some embodiments, the disclosure relates to a method for
performing a primer extension reaction, comprising: contacting a
modified DNA polymerase as provided herein with a nucleic acid
molecule and a nucleotide under conditions where the nucleotide is
incorporated into the nucleic acid molecule by the modified DNA
polymerase. Optionally, the nucleotide is a labeled nucleotide, and
the label of the nucleotide emits a signal during incorporation of
the at least one nucleotide. Optionally, the method further
comprises detecting the signal emitted by the nucleotide label.
Optionally, the method further comprises analyzing the detected
signal to determine the identity of the incorporated
nucleotide.
[0018] In some embodiments, the disclosure relates to a modified
DNA polymerase having an increased branching ratio in the presence
of labeled nucleotides relative to a DNA polymerase having the
amino acid sequence of SEQ ID NO: 7. In some embodiments, the
modified DNA polymerase comprising an amino acid sequence that is
at least about 95% identical to the amino acid sequence of SEQ ID
NO: 7. Optionally, the modified DNA polymerase further includes the
amino acid mutation H370R.
DETAILED DESCRIPTION OF THE DRAWINGS
[0019] The following figures form part of the present specification
and are included to further demonstrate certain aspects of the
disclosure by way of illustrating non-limiting embodiments and
examples. The disclosure may be better understood by reference to
one or more of these figures in combination with the detailed
description of specific embodiments presented herein.
[0020] FIG. 1 depicts one exemplary theoretical model of the
various stages in binding of a polymerase to a nucleic acid
molecule and a nucleotide substrate, followed by dissociation of
the nucleotide substrate in unaltered state (i.e., a non-productive
event) or by incorporation of the nucleotide into the nucleic acid
molecule.
[0021] FIG. 2 depicts an expression vector, pTTQ-B104-exo minus,
comprising the amino acid sequence of SEQ ID NO: 8 fused downstream
of an isopropyl .beta.-D-1-thiogalactopyranoside (IPTG) promoter in
the expression vector pTTQ.
[0022] FIG. 3 depicts the results of an assay measuring the
fractional extension activity, i.e., the fraction of nucleic acid
templates that are extended by at least one nucleotide in a
polymerase reaction, of an exemplary modified polymerase comprising
the amino acid sequence of SEQ ID NO: 8, and two exemplary
reference polymerases comprising the amino acid sequences of SEQ ID
NO: 15 and SEQ ID NO: 20, respectively.
[0023] FIG. 4 depicts the results of an assay measuring the
exonuclease activity of T7 DNA polymerase, an exemplary reference
polymerase, and of an exemplary modified variant comprising the
amino acid sequence of SEQ ID NO: 7.
[0024] FIG. 5 depicts the results of an assay measuring the
nanoparticle tolerance of an exemplary modified polymerase
comprising the amino acid sequence of SEQ ID NO: 19, and an
exemplary reference polymerase comprising the amino acid sequence
of SEQ ID NO: 20.
[0025] FIG. 6 depicts the results of an assay measuring the
photostability of an exemplary modified polymerase comprising the
amino acid sequence of SEQ ID NO: 19, and an exemplary reference
polymerase comprising the amino acid sequence of SEQ ID NO: 20.
[0026] FIG. 7 depicts time traces of fluorescence at 550 nm from
three different stopped-flow assay systems, each comprising a
mutant Phi-29 polymerase and terminally labeled nucleotide
triphosphates (panel A); terminally labeled nucleotide
tetraphosphates (panel B) and terminally labeled nucleotide
hexaphosphates (panel C).
[0027] FIG. 8 depicts time traces of fluorescence at 550 nm from
two different stopped-flow assay systems, each comprising different
mutant Phi-29 polymerase (panels A and B, respectively) and
terminally labeled nucleotide hexaphosphates.
[0028] FIG. 9 provides a graphical depiction of the various
reaction components included in the real-time single molecule
sequencing reaction of Example 10.
[0029] FIG. 10 depicts exemplary portions of fluorescence time
traces detected at 550 and 647 nm from a single-molecule real time
sequencing reaction comprising a mutant Phi-29 polymerase and
terminally-labeled nucleotide hexaphosphates.
[0030] FIG. 11 depicts the general structure of a dye-labeled
nucleotide hexaphosphate that can be used in conjunction with the
labeled polymerase conjugates disclosed herein.
DETAILED DESCRIPTION OF THE SEQUENCE LISTINGS
[0031] SEQ ID NO: 1 comprises the amino acid sequence of an
exemplary polymerase of the bacteriophage Phi-29.
[0032] SEQ ID NO: 2 comprises the amino acid sequence of a
consensus motif named Motif 1, also known as Motif A, which can be
found within various polymerases including polymerases isolated
from bacteriophages of the family of Phi-29-like
bacteriophages.
[0033] SEQ ID NO: 3 comprises the amino acid sequence of a
consensus motif named Motif 2a, also known as Motif B, which can be
found within various polymerases including polymerases isolated
from bacteriophages of the family of Phi-29-like
bacteriophages.
[0034] SEQ ID NO: 4 comprises the amino acid sequence of a
consensus motif named Motif 3, also known as Motif C, which can be
found within various polymerases including polymerases isolated
from bacteriophages of the family of Phi-29-like
bacteriophages.
[0035] SEQ ID NO: 5 comprises the amino acid sequence of a
consensus motif named Motif 4, we can be found within various
polymerases including polymerases isolated from bacteriophages of
the family of Phi-29-like bacteriophages.
[0036] SEQ ID NO: 6 comprises the amino acid sequence of an
exemplary polymerase of the bacteriophage B103, a member of the
Phi-29-like family of bacteriophages SEQ ID NO: 7 comprises the
amino acid sequence of an exemplary modified polymerase according
to the present disclosure.
[0037] SEQ ID NO: 8 comprises the amino acid sequence of another
exemplary modified polymerase according to the present
disclosure.
[0038] SEQ ID NO: 9 comprises the nucleotide sequence of an
exemplary polynucleotide encoding the modified polymerase
comprising the amino acid sequence of SEQ ID NO: 7.
[0039] SEQ ID NO: 10 comprises the nucleotide sequence of a second
exemplary polynucleotide encoding the modified polymerase
comprising the amino acid sequence of SEQ ID NO: 7.
[0040] SEQ ID NO: 11 comprises the nucleotide sequence of an
exemplary polynucleotide encoding the modified polymerase
comprising the amino acid sequence of SEQ ID NO: 8.
[0041] SEQ ID NO: 12 comprises the nucleotide sequence of a second
exemplary polynucleotide encoding the modified polymerase
comprising the amino acid sequence of SEQ ID NO: 8.
[0042] SEQ ID NO: 13 comprises the amino acid sequence of a
polymerase of the bacteriophage M2Y, a member of the Phi-29-like
family of bacteriophages.
[0043] SEQ ID NO: 14 comprises the amino acid sequence of a
polymerase of the bacteriophage Nf, a member of the Phi-29-like
family of bacteriophages.
[0044] SEQ ID NO: 15 comprises the amino acid sequence of a
polymerase of RB69.
[0045] SEQ ID NO: 16 comprises the amino acid sequence of an
exemplary peptide linker, named "H-linker", useful in linking tags
or labels to a protein sequence of interest.
[0046] SEQ ID NO: 17 comprises the amino acid sequence of another
exemplary peptide linker, named "F-linker", useful in linking tags
or labels to a protein sequence of interest.
[0047] SEQ ID NO: 18 comprises the amino acid sequence of an
exemplary His-tagged version of a protein comprising the amino acid
sequence of SEQ ID NO: 7.
[0048] SEQ ID NO: 19 comprises the amino acid sequence of another
exemplary His-tagged version of a protein comprising the amino acid
sequence of SEQ ID NO: 7.
[0049] SEQ ID NO: 20 comprises the amino acid sequence of HP1, a
Phi-29 polymerase peptide that lacks exonuclease activity and
comprises an N-terminal His-tag, an intervening linker sequence,
and the D12A and D66A mutations.
[0050] SEQ ID NO: 21 comprises the nucleotide sequence of an
exemplary oligonucleotide primer used to construct a
primer:template duplex for use in assays for fractional extension
activity as disclosed, for example, in Example 3.
[0051] SEQ ID NOS: 22-25 each comprises the nucleotide sequence of
an exemplary polynucleotide template used to construct a
primer:template duplex for use in assays for fractional extension
activity as disclosed, for example, in Example 3.
[0052] SEQ ID NO: 26 comprises the nucleotide sequence of an
exemplary oligonucleotide primer used to construct a
primer:template duplex for use in nucleotide incorporation assays
to evaluate polymerase reaction kinetics as disclosed, for example,
in Example 7.
[0053] SEQ ID NOS: 27-30 each comprises the nucleotide sequence of
an exemplary polynucleotide template used to construct a
primer:template duplex for use in nucleotide incorporation assays
as disclosed, for example, in Example 7.
[0054] SEQ ID NO: 31 comprises the nucleotide sequence of an
exemplary oligonucleotide primer used to construct a
primer:template duplex for use in nucleotide incorporation assays
to evaluate polymerase reaction kinetics as disclosed, for example,
in Example 8.
[0055] SEQ ID NOS: 32-35 each comprise the nucleotide sequence of
an exemplary polynucleotide template used to construct a
primer:template duplex for use in nucleotide incorporation assays
as disclosed, for example, in Example 8.
[0056] SEQ ID NO: 36 comprises the nucleotide sequence of an
exemplary oligonucleotide primer used to construct a
primer-template duplex for use in a real time single molecule
sequencing assay, as disclosed, for example, in Example 10.
[0057] SEQ ID NO: 37 comprises the nucleotide sequence of an
exemplary polynucleotide template used to construct a
primer-template duplex for use in a real time single molecule
sequencing assay, as disclosed, for example, in Example 10.
[0058] SEQ ID NO: 38 comprises the nucleotide sequence of an
exemplary hairpin template used for three-color nucleotide
incorporation reaction as described, for example, in Example
11.
[0059] SEQ ID NO: 39 comprises the nucleotide sequence of an
exemplary polynucleotide template used for a four-color nucleotide
incorporation reaction as described, for example, in Example
11.
[0060] SEQ ID NO: 40 comprises the nucleotide sequence of an
exemplary oligonucleotide primer used for a four-color nucleotide
incorporation reaction as described, for example, in Example
11.
[0061] SEQ ID NO: 41 comprises the predicted nucleotide sequence
that will be synthesized in a four-color nucleotide incorporation
reaction using the primer of SEQ ID NO: 40 in conjunction with the
template of SEQ ID NO: 39 as described, for example, in Example
11.
[0062] SEQ ID NO: 42 comprises the amino acid sequence of a
modified B103 polymerase comprising the amino acid sequence of SEQ
ID NO: 8 and further including the mutation H370R as well as a
biotinylation site and His tag fused to the N-terminus of the
polymerase.
[0063] SEQ ID NO: 43 comprises the nucleotide sequence of a
fluorescein-labeled oligonucleotide primer used to measure primer
extension activity of a polymerase sample according to an exemplary
assay, as described in Example 13.
[0064] SEQ ID NO: 44 comprises the nucleotide sequence of an
exemplary polynucleotide template used in a stopped-flow assay for
nucleotide incorporation kinetics as described, for example, in
Example 12.
[0065] SEQ ID NO: 45 comprises the nucleotide sequence of an
exemplary oligonucleotide primer used in a stopped-flow assay for
nucleotide incorporation kinetics as described, for example, in
Example 12.
[0066] SEQ ID NO: 46 comprises the nucleotide sequence of an
exemplary polynucleotide template used in a stopped-flow assay for
nucleotide incorporation kinetics as described, for example, in
Example 12.
[0067] SEQ ID NO: 47 comprises the nucleotide sequence of an
exemplary oligonucleotide primer used in a stopped-flow assay for
nucleotide incorporation kinetics as described, for example, in
Example 12.
DETAILED DESCRIPTION
[0068] The present disclosure provides for compositions, methods
and systems relating to modified polymerases and their use in
various biological applications. More particularly, provided herein
are novel polymerases having altered polymerase activity, label
tolerance, photostability and/or nucleotide incorporation kinetics
as compared to their unmodified counterparts, which can be useful
in a wide variety of biological applications.
[0069] Unless defined otherwise, all technical and scientific terms
used herein have the same meaning as is commonly understood by one
of ordinary skill in the art to which these inventions belong. All
patents, patent applications, published applications, treatises and
other publications referred to herein, both supra and infra, are
incorporated by reference in their entirety. If a definition and/or
description is set forth herein that is contrary to or otherwise
inconsistent with any definition set forth in the patents, patent
applications, published applications, and other publications that
are herein incorporated by reference, the definition and/or
description set forth herein prevails over the definition that is
incorporated by reference. The citation of any publication is for
its disclosure prior to the filing date and should not be construed
as an admission that the present invention is not entitled to
antedate such publication by virtue of prior invention.
[0070] The practice of the present disclosure will employ, unless
otherwise indicated, conventional techniques of molecular biology,
microbiology and recombinant DNA techniques, which are within the
skill of the art. Such techniques are explained fully in the
literature. See, for example, Sambrook, J., and Russell, D. W.,
2001, Molecular Cloning: A Laboratory Manual, Third Edition;
Ausubel, F. M., et al., eds., 2002, Short Protocols In Molecular
Biology, Fifth Edition.
[0071] Unless otherwise indicated, the numbering of any amino acid
residues described herein will be relative to the sequence of a
B103 polymerase having the amino acid sequence of SEQ ID NO: 6.
However, the skilled artisan will appreciate that the actual
position within a modified polymerase according to the present
disclosure may vary. For example, the modified polymerase may
comprise one or more deletions or additions within its sequence,
thereby altering the numbering of the corresponding amino acid
residue in the modified polymerase relative to the B103 polymerase
having SEQ ID NO: 6.
[0072] Throughout this disclosure, various amino acid mutations,
including, for example, amino acid substitutions are referenced
using the amino acid single letter code, and indicating the
position of the residue within a reference amino acid sequence. In
the case of amino acid substitutions, the identity of the
substituent is also indicated using the amino acid single letter
code. For example, the amino acid substitution F383L, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6,
indicates an amino acid substitution wherein a leucine (L) residue
is substituted for the normally occurring phenylalanine (F) residue
at amino acid position 383 of the amino acid sequence of SEQ ID NO:
6.
[0073] As used herein, the terms "link", "linked", "linkage" and
variants thereof comprise any type of fusion, bond, adherence or
association that is of sufficient stability to withstand use in the
particular biological application of interest. Such linkage can
comprise, for example, covalent, ionic, hydrogen, dipole-dipole,
hydrophilic, hydrophobic, or affinity bonding, bonds or
associations involving van der Waals forces, mechanical bonding,
and the like. Optionally, such linkage can occur between a
combination of different molecules, including but not limited to:
between a nanoparticle and a protein; between a protein and a
label; between a linker and a functionalized nanoparticle; between
a linker and a protein; and the like. Some examples of linkages can
be found, for example, in Hermanson, G., Bioconjugate Techniques,
Second Edition (2008); Aslam, M., Dent, A., Bioconjugation: Protein
Coupling Techniques for the Biomedical Sciences, London: Macmillan
(1998); Aslam, M., Dent, A., Bioconjugation: Protein Coupling
Techniques for the Biomedical Sciences, London: Macmillan
(1998).
[0074] As used herein, the term "linker" and its variants comprises
any composition, including any molecular complex or molecular
assembly, that serves to link two or more compounds.
[0075] As used herein, the term "polymerase" and its variants
comprise any enzyme that can catalyze the polymerization of
nucleotides (including analogs thereof) into a nucleic acid strand.
Typically but not necessarily such nucleotide polymerization can
occur in a template-dependent fashion. Such polymerases can include
without limitation naturally occurring polymerases and any subunits
and truncations thereof, mutant polymerases, variant polymerases,
recombinant, fusion or otherwise engineered polymerases, chemically
modified polymerases, synthetic molecules or assemblies, and any
analogs, derivatives or fragments thereof that retain the ability
to catalyze such polymerization. Optionally, the polymerase can be
a mutant polymerase comprising one or more mutations involving the
replacement of one or more amino acids with other amino acids, the
insertion or deletion of one or more amino acids from the
polymerase, or the linkage of parts of two or more polymerases.
Typically, the polymerase comprises one or more active sites at
which nucleotide binding and/or catalysis of nucleotide
polymerization can occur. Some exemplary polymerases include
without limitation DNA polymerases (such as for example Phi-29 DNA
polymerase, reverse transcriptases and E. coli DNA polymerase) and
RNA polymerases. The term "polymerase" and its variants, as used
herein, also refers to fusion proteins comprising at least two
portions linked to each other, where the first portion comprises a
peptide that can catalyze the polymerization of nucleotides into a
nucleic acid strand and is linked to a second portion that
comprises a second polypeptide, such as, for example, a reporter
enzyme or a processivity-enhancing domain. One exemplary embodiment
of such a polymerase is Phusion.RTM. DNA polymerase (New England
Biolabs), which comprises a Pyrococcus-like polymerase fused to a
processivity-enhancing domain as described, for example, in U.S.
Pat. No. 6,627,424.
[0076] As used herein, the term "polymerase activity" and its
variants, when used in reference to a given polymerase, comprises
any in vivo or in vitro enzymatic activity characteristic of a
given polymerase that relates to catalyzing the polymerization of
nucleotides into a nucleic acid strand, e.g., primer extension
activity, and the like. Typically, but not necessarily such
nucleotide polymerization occurs in a template-dependent fashion.
In addition to such polymerase activity, the polymerase can
typically possess other enzymatic activities, for example, 3' to 5'
exonuclease activity.
[0077] As used herein, the term "nucleotide" and its variants
comprises any compound that can bind selectively to, or can be
polymerized by, a polymerase. Typically, but not necessarily,
selective binding of the nucleotide to the polymerase is followed
by polymerization of the nucleotide into a nucleic acid strand by
the polymerase; occasionally however the nucleotide may dissociate
from the polymerase without becoming incorporated into the nucleic
acid strand, an event referred to herein as a "non-productive"
event. Such nucleotides include not only naturally occurring
nucleotides but also any analogs, regardless of their structure,
that can bind selectively to, or can be polymerized by, a
polymerase. While naturally occurring nucleotides typically
comprise base, sugar and phosphate moieties, the nucleotides of the
present disclosure can include compounds lacking any one, some or
all of such moieties. In some embodiments, the nucleotide can
optionally include a chain of phosphorus atoms comprising three,
four, five, six, seven, eight, nine, ten or more phosphorus atoms.
In some embodiments, the phosphorus chain can be attached to any
carbon of a sugar ring, such as the 5' carbon. The phosphorus chain
can be linked to the sugar with an intervening O or S. In one
embodiment, one or more phosphorus atoms in the chain can be part
of a phosphate group having P and O. In another embodiment, the
phosphorus atoms in the chain can be linked together with
intervening O, NH, S, methylene, substituted methylene, ethylene,
substituted ethylene, CNH.sub.2, C(O), C(CH.sub.2),
CH.sub.2CH.sub.2, or C(OH)CH.sub.2R (where R can be a 4-pyridine or
1-imidazole). In one embodiment, the phosphorus atoms in the chain
can have side groups having O, BH.sub.3, or S. In the phosphorus
chain, a phosphorus atom with a side group other than O can be a
substituted phosphate group. In the phosphorus chain, phosphorus
atoms with an intervening atom other than O can be a substituted
phosphate group. Some examples of nucleotide analogs are described
in Xu, U.S. Pat. No. 7,405,281. In some embodiments, the nucleotide
comprises a label and referred to herein as a "labeled nucleotide";
the label of the labeled nucleotide is referred to herein as a
"nucleotide label". In some embodiments, the label can be in the
form of a fluorescent dye attached to the terminal phosphate group,
i.e., the phosphate group most distal from the sugar. Some examples
of nucleotides that can be used in the disclosed methods and
compositions include, but are not limited to, ribonucleotides,
deoxyribonucleotides, modified ribonucleotides, modified
deoxyribonucleotides, ribonucleotide polyphosphates,
deoxyribonucleotide polyphosphates, modified ribonucleotide
polyphosphates, modified deoxyribonucleotide polyphosphates,
peptide nucleotides, modified peptide nucleotides,
metallonucleosides, phosphonate nucleosides, and modified
phosphate-sugar backbone nucleotides, analogs, derivatives, or
variants of the foregoing compounds, and the like. In some
embodiments, the nucleotide can comprise non-oxygen moieties such
as, for example, thio- or borano-moieties, in place of the oxygen
moiety bridging the alpha phosphate and the sugar of the
nucleotide, or the alpha and beta phosphates of the nucleotide, or
the beta and gamma phosphates of the nucleotide, or between any
other two phosphates of the nucleotide, or any combination
thereof.
[0078] As used herein, the term "nucleotide incorporation" and its
variants comprises polymerization of one or more nucleotides into a
nucleic acid strand.
[0079] As used herein, the term "biological activity" and its
variants, when used in reference to a biomolecule (such as, for
example, an enzyme) refers to any in vivo or in vitro activity that
is characteristic of the biomolecule itself, including the
interaction of the biomolecule with one or more targets. For
example, biological activity can optionally include the selective
binding of an antibody to an antigen, the enzymatic activity of an
enzyme, and the like. Such activity can also include, without
limitation, binding, fusion, bond formation, association, approach,
catalysis or chemical reaction, optionally with another biomolecule
or with a target molecule.
[0080] As used herein, the term "biologically active fragment" and
its variants refers to any fragment, derivative or analog of a
biomolecule that possesses an in vivo or in vitro activity that is
characteristic of the biomolecule itself. For example, the
biomolecule can be an antibody that is characterized by
antigen-binding activity, or an enzyme characterized by the ability
to catalyze a particular biochemical reaction, etc. Biologically
active fragments can optionally exist in vivo, such as, for
example, fragments which arise from post transcriptional processing
or which arise from translation of alternatively spliced RNAs, or
alternatively can be created through engineering, bulk synthesis,
or other suitable manipulation. Biologically active fragments
include fragments expressed in native or endogenous cells as well
as those made in expression systems such as, for example, in
bacterial, yeast, insect or mammalian cells. Because biomolecules
often exhibit a range of physiological properties and because such
properties can be attributable to different portions of the
biomolecule, a useful biologically active fragment can be a
fragment of a biomolecule that exhibits a biological activity in
any biological assay. In some embodiments, the fragment or analog
possesses 10%, 40%, 60%, 70%, 80% or 90% or greater of the activity
of the biomolecule in any in vivo or in vitro assay of
interest.
[0081] The term "modification" or "modified" and their variants, as
used herein with reference to a protein, comprise any change in the
structural, biological and/or chemical properties of the protein,
particularly a change in the amino acid sequence of the protein. In
some embodiments, the modification can comprise one or more amino
acid mutations, including without limitation amino acid additions,
deletions and substitutions (including both conservative and
non-conservative substitutions).
[0082] As used herein, the terms "identical" or "percent identity,"
and their variants, when used in the context of two or more nucleic
acid or polypeptide sequences, refer to two or more sequences or
subsequences that are the same or have a specified percentage of
amino acid residues or nucleotides that are the same, when compared
and aligned for maximum correspondence, as measured using any one
or more of the following sequence comparison algorithms:
Needleman-Wunsch (see, e.g., Needleman, Saul B.; and Wunsch,
Christian D. (1970). "A general method applicable to the search for
similarities in the amino acid sequence of two proteins" Journal of
Molecular Biology 48 (3):443-53); Smith-Waterman (see, e.g., Smith,
Temple F.; and Waterman, Michael S., "Identification of Common
Molecular Subsequences" (1981) Journal of Molecular Biology
147:195-197); or BLAST (Basic Local Alignment Search Tool; see,
e.g., Altschul S F, Gish W, Miller W, Myers E W, Lipman D J, "Basic
local alignment search tool" (1990) J Mol Biol 215
(3):403-410).
[0083] The terms "resonance energy transfer" and "RET" and their
variants, as used herein, refer to a radiationless transmission of
excitation energy from a first moiety, termed a donor moiety, to a
second moiety termed an acceptor moiety. One type of RET includes
Forster Resonance Energy Transfer (FRET), in which a fluorophore
(the donor) in an excited state transfers its energy to a proximal
molecule (the acceptor) by nonradiative dipole-dipole interaction.
See, e.g., Forster, T. "Intermolecular Energy Migration and
Fluorescence", Ann. Phys., 2:55-75, 1948; Lakowicz, J. R.,
Principles of Fluorescence Spectroscopy, 2nd ed. Plenum, New York.
367-394., 1999. RET also comprises luminescence resonance energy
transfer, bioluminescence resonance energy transfer,
chemiluminescence resonance energy transfer, and similar types of
energy transfer not strictly following the Forster's theory, such
as nonoverlapping energy transfer occurring when nonoverlapping
acceptors are utilized. See, for example, Anal. Chem. 2005, 77:
1483-1487.
[0084] The term "conservative" and its variants, as used herein
with reference to any change in amino acid sequence, refers to an
amino acid mutation wherein one or more amino acids is substituted
by another amino acid having highly similar properties. For
example, one or more amino acids comprising nonpolar or aliphatic
side chains (for example, glycine, alanine, valine, leucine,
isoleucine or proline) can be substituted for each other.
Similarly, one or more amino acids comprising polar, uncharged side
chains (for example, serine, threonine, cysteine, methionine,
asparagine or glutamine) can be substituted for each other.
Similarly, one or more amino acids comprising aromatic side chains
(for example, phenylalanine, tyrosine or tryptophan) can be
substituted for each other. Similarly, one or more amino acids
comprising positively charged side chains (for example, lysine,
arginine or histidine) can be substituted for each other.
Similarly, one or more amino acids comprising negatively charged
side chains (for example, aspartic acid or glutamic acid) can be
substituted for each other. In some embodiments, the modified
polymerase is a variant that comprises one or more of these
conservative amino acid substitutions, or any combination thereof.
In some embodiments, conservative substitutions for leucine
include: alanine, isoleucine, valine, phenylalanine, tryptophan,
methionine, and cysteine. In other embodiments, conservative
substitutions for asparagine include: arginine, lysine, aspartate,
glutamate, and glutamine.
[0085] The term "primer extension activity" and its variants, as
used herein, when used in reference to a given polymerase,
comprises any in vivo or in vitro enzymatic activity characteristic
of a given polymerase that relates to catalyzing nucleotide
incorporation onto the terminal 3'OH end of an extending nucleic
acid molecule. Typically but not necessarily such nucleotide
incorporation occurs in a template-dependent fashion. The primer
extension activity is typically quantified as the total number of
nucleotides incorporated (as measured by, e.g., radiometric or
other suitable assay) by a unit amount of polymerase (in moles) per
unit time (seconds) under a particular set of reaction
conditions.
[0086] The terms "His tag" or "His-tag" and their variants as used
herein refers to a stretch of amino acids comprising multiple
histidine residues. Typically, the His tag can bind to metal ions,
for example, Zn.sup.2+, Ni.sup.2+, Co.sup.2+, or Cu.sup.2+ ions.
Optionally, the His tag comprises 2, 3, 4, 5, 6, 7, 8 or more
histidine residues. In some embodiments, the His tag is fused to
the N- or C-terminus of a protein; alternatively, it can be fused
at any suitable location within the protein.
[0087] As used herein, the term "biotin moiety" and its variants
comprises biotin
(cis-hexahydro-2-oxo-1H-thieno[3,4]imidazole-4-pentanoic acid) and
any derivatives and analogs thereof, including biotin-like
compounds. Such compounds include, for example, biotin-e-N-lysine,
biocytin hydrazide, amino or sulfhydryl derivatives of
2-iminobiotin and biotinyl-.di-elect cons.-aminocaproic
acid-N-hydroxysuccinimide ester, sulfosuccinimideiminobiotin,
biotinbromoacetylhydrazide, p-diazobenzoyl biocytin,
3-(N-maleimidopropionyl)biocytin, and the like. "Biotin moiety"
also comprises biotin variants that can specifically bind to an
avidin moiety.
[0088] The term "biotinylated" and its variants, as used herein,
refer to any covalent or non-covalent adduct of biotin with other
moieties such as biomolecules, e.g., proteins, nucleic acids
(including DNA, RNA, DNA/RNA chimeric molecules, nucleic acid
analogs and peptide nucleic acids), proteins (including enzymes,
peptides and antibodies), carbohydrates, lipids, etc.
[0089] The terms "avidin" and "avidin moiety" and their variants,
as used herein, comprises the native egg-white glycoprotein avidin,
as well as any derivatives, analogs and other non-native forms of
avidin, that can specifically bind to biotin moieties. In some
embodiments, the avidin moiety can comprise deglycosylated forms of
avidin, bacterial streptavidins produced by selected strains of
Streptomyces, e.g., Streptomyces avidinii, to truncated
streptavidins, and to recombinant avidin and streptavidin as well
as to derivatives of native, deglycosylated and recombinant avidin
and of native, recombinant and truncated streptavidin, for example,
N-acyl avidins, e.g., N-acetyl, N-phthalyl and N-succinyl avidin,
and the commercial products ExtrAvidin.RTM., Captavidin.RTM.,
Neutravidin.RTM. and Neutralite Avidin.RTM.. All forms of
avidin-type molecules, including both native and recombinant avidin
and streptavidin as well as derivatized molecules, e.g.
nonglycosylated avidins, N-acyl avidins and truncated
streptavidins, are encompassed within the terms "avidin" and
"avidin moiety". Typically, but not necessarily, avidin exists as a
tetrameric protein, wherein each of the four tetramers is capable
of binding at least one biotin moiety.
[0090] As used herein, the term "biotin-avidin bond" and its
variants refers to a specific linkage formed between a biotin
moiety and an avidin moiety. Typically, a biotin moiety can bind
with high affinity to an avidin moiety, with a dissociation
constant K.sub.d typically in the order of 10.sup.-14 to 10.sup.-15
mol/L. Typically, such binding occurs via non-covalent
interactions.
[0091] The term "label" and its variants, as used herein, comprises
any optically detectable moiety and includes any moiety that can be
detected using, for example, fluorescence, luminescence and/or
phosphorescence spectroscopy, Raman scattering, or diffraction.
Exemplary labels according to the present disclosure include
fluorescent and luminescent moieties as well as quenchers thereof.
Some typical labels include without limitation nanoparticles and
organic dyes.
[0092] The present disclosure relates to compositions and methods
comprising modified polymerases derived from Phi-29 and/or
Phi-29-like phages, wherein the modified polymerases exhibit
altered polymerase activity, photostability, label tolerance,
kinetics for nucleotide binding and/or nucleotide incorporation
kinetics. For example, in some embodiments the disclosure relates
to polymerase compositions, methods of making such compositions and
methods of using such compositions in various biological
applications. The compositions and related methods described herein
represent significant advances over the art. For example, in some
embodiments, the disclosed compositions and methods can permit
nucleic acid synthesis with improved kinetics for real-time
visualization of polymerase activity. In some embodiments, the
disclosed compositions and methods can permit polymerization of
nucleotides (including labeled nucleotide analogs) with increased
tolerance for the presence of labeled moieties, for example
nanoparticles. In some embodiments, the disclosed compositions and
methods can permit increased primer extension activity in
conjunction with use of higher intensities or duration of exposure
to excitation radiation. Such compositions and methods can
facilitate, for example, applications involving nucleic acid
synthesis, including applications requiring direct monitoring of
polymerase activity in vitro or in vivo, such as real-time single
molecule sequencing.
[0093] In some embodiments, the present disclosure relates to a
modified DNA polymerase having a photostability that is at least
about 80% under standard photostability assay conditions. In some
embodiments, the modified DNA polymerase comprises an amino acid
sequence that is at least about 80%, 85%, 90%, 95%, 97%, 98% or 99%
identical to the amino acid sequence of SEQ ID NO: 7.
[0094] In some embodiments, the present disclosure relates to a
modified DNA polymerase having a primer extension activity that is
at least about 105%, 110%, 125%, 150%, 175%, 200%, 250%, 375%,
500%, 750% or 1000% relative to the primer extension activity of a
wild type Phi-29 polymerase comprising the amino acid sequence of
SEQ ID NO: 1 under standard photostability assay conditions.
[0095] In some embodiments, the disclosure relates to a modified
DNA polymerase comprising an amino acid sequence that is at least
about 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the amino
acid sequence of SEQ ID NO: 7, and further including one or more
amino acid mutations that increase the photostability of the
enzyme. In some embodiments, the one or more amino acid mutations
increase the photostability of the modified DNA polymerase by at
least about 5%, 10%, 25%, 50%, 75%, 100%, 125%, 250%, 500%, 750% or
1000%.
[0096] In some embodiments, the present disclosure relates to a
modified DNA polymerase having a nanoparticle tolerance that is at
least about 80% under standard nanoparticle tolerance assay
conditions. In some embodiments, the modified DNA polymerase
comprises an amino acid sequence that is at least about 80%, 85%,
90%, 95%, 97%, 98% or 99% identical to the amino acid sequence of
SEQ ID NO: 7 or SEQ ID NO: 8.
[0097] In some embodiments, the disclosure relates to a modified
DNA polymerase comprising an amino acid sequence that is at least
about 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the amino
acid sequence of SEQ ID NO: 7, and further including one or more
amino acid mutations that increase the nanoparticle tolerance of
the enzyme. In some embodiments, the one or more amino acid
mutations increase the nanoparticle tolerance of the modified DNA
polymerase by at least about 5%, 10%, 25%, 50%, 75%, 100%, 125%,
250%, 500%, 750% or 1000%.
[0098] In some embodiments, the present disclosure relates to a
modified DNA polymerase having a primer extension activity that is
at least about 105%, 110%, 125%, 150%, 175%, 200%, 250%, 375%,
500%, 750% or 1000% relative to the primer extension activity of a
wild type Phi-29 polymerase comprising the amino acid sequence of
SEQ ID NO: 1 under standard nanoparticle tolerance assay
conditions.
[0099] In some embodiments, the disclosure relates to a modified
DNA polymerase comprising an amino acid sequence that is at least
about 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the amino
acid sequence of SEQ ID NO: 7, and further including one or more
amino acid mutations that increase the primer extension activity of
the enzyme. In some embodiments, the one or more amino acid,
mutations increase the primer extension activity of the modified
DNA polymerase by at least about 5%, 10%, 25%, 50%, 75%, 100%,
125%, 250%, 500%, 750% or 1000%.
[0100] In some embodiments, the present disclosure relates to a
modified DNA polymerase comprising an amino acid sequence that is
at least about 85%, 90%, 95%, 97% or 99% identical to the amino
acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8. In some embodiments,
the modified DNA polymerase has a nanoparticle tolerance that is at
least about 80% under standard nanoparticle tolerance assay
conditions. In some embodiments, the modified DNA polymerase has a
photostability that is at least about 80% under standard
photostability assay conditions.
[0101] In some embodiments, the present disclosure relates to a
modified DNA polymerase having a primer extension activity that is
at least about 105%, 110%, 125%, 150%, 175%, 200%, 250%, 375%,
500%, 750% or 1000% relative to the primer extension activity of a
wild type Phi-29 polymerase comprising the amino acid sequence of
SEQ ID NO: 1 under standard nanoparticle tolerance assay
conditions.
[0102] In some embodiments, the present disclosure relates to a
modified DNA polymerase comprising an amino acid sequence that is
at least about 85%, 90%, 95%, 97% or 99% identical to the amino
acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8. The modified DNA
polymerases of the present disclosure can further comprise one or
more amino acid substitutions selected from the group consisting
of: D9A, E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A,
Q377A, S385G, H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370
W, H370Y, H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A,
E371Q, E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R,
K372A, K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R,
K380A, K380Q, K380W, K380Y, K380F, D507H, D507G, D507E, D507T,
D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F, K509H,
K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A, K509Q,
K509W, K509Y and K509F, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 7.
[0103] Optionally, the modified DNA polymerases of the present
disclosure can further comprise a mutation reducing 3' to 5'
exonuclease activity. The mutation reducing 3' to 5' exonuclease
activity of the modified DNA polymerase can optionally include one
or more amino acid substitutions at positions selected from the
group consisting of: 2, 9, 11, 12, 58, 59, 63, 162, 166, 377 and
385. In some embodiments, the one or more amino acid substitutions
can be selected from the group consisting of: D9A, E11A, E11I,
T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and S385G,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 7.
[0104] In some embodiments, the modified DNA polymerases of the
present disclosure can further comprise a mutation increasing the
branching ratio of the polymerase in the presence of a labeled
nucleotide. Optionally, the modified DNA polymerase comprises an
amino acid sequence that is at least about 80%, 85%, 90%, 95%, 97%,
98% or 99% identical to the amino acid sequence of SEQ ID NO: 7,
and further comprises one or more mutations increasing the
branching ratio of the modified DNA polymerase. In some
embodiments, the one or more mutations comprise one or more amino
acid substitutions at positions selected from the group consisting
of: 370, 371, 372, 373, 374, 375, 376 and 377. In some embodiments,
the one or more mutations can be selected from the group consisting
of: H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, D507H, D507G, D507E, D507T, D507S,
D507R, D507A, D507R, D507Q, D507W, D507Y; D507F, K509H, K509G,
K509D, K509R, K509E, K509T, K509S, K509R, K509A, K509Q, K509W,
K509Y and K509F, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the modified
DNA polymerase comprises an amino acid sequence that is at least
about 85%, 90%, 95%, 97% or 99% identical to the amino acid
sequence of SEQ ID NO: 7 or SEQ ID NO: 8 and further includes the
amino acid substitution H370R. In some embodiments, the presence of
the amino acid substitution H370R increases the branching ratio of
the modified polymerase by at least about 5%, 10%, 25%, 50%, 75%,
100%, 150%, 200%, 250%, 500%, 750%, 1000% or greater.
[0105] In some embodiments, the modified DNA polymerases of the
present disclosure can further comprise a mutation increasing the
primer extension activity. Optionally, the mutation increasing the
primer extension activity of the modified DNA polymerase comprises
one or more amino acid substitutions at positions selected from the
group consisting of: 129 and 339, wherein the numbering is relative
to the amino acid sequence of SEQ ID NO: 7.
[0106] In some embodiments, the modified DNA polymerases of the
present disclosure can further comprise a mutation that increases
the nucleotide binding affinity of the polymerase for a particular
labeled nucleotide. Optionally, the mutation increasing the
nucleotide binding affinity for a particular labeled nucleotide
comprises one or more amino acid substitutions at positions
selected from the group consisting of: 370, 371, 372, 373, 374,
375, 376, 507 and 509. In some embodiments, the one or more amino
acid substitutions can be selected from the group consisting of:
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, D507H, D507G, D507E, D507T, D507S,
D507R, D507A, D507R, D507Q, D507W, D507Y, D507F, K509H, K509G,
K509D, K509R, K509E, K509T, K509S, K509R, K509A, K509Q, K509W,
K509Y and K509F, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7.
[0107] In some embodiments, the disclosure relates to a nucleic
acid molecule encoding any one, some or all of the modified DNA
polymerases of the present disclosure. The nucleic acid molecule
can optionally be DNA or RNA.
[0108] In some embodiments, the disclosure relates to a vector
comprising a DNA encoding any one, some or all of the modified DNA
polymerases of the present disclosure.
[0109] In some embodiments, the disclosure relates to an isolated
host cell comprising a vector including a DNA encoding any one,
some or all of the modified DNA polymerases of the present
disclosure.
[0110] In one embodiment, the disclosure relates to compositions
and methods relating to modified polymerases comprising one or more
modifications relative to a reference polymerase. In some
embodiments, the reference polymerase is a Phi-29 polymerase
comprising the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO:
20. In some embodiments, the reference polymerase is a B103
polymerase comprising the amino acid sequence of SEQ ID NO: 6.
[0111] In some embodiments, the modified polymerase is an isolated
variant of a B103 polymerase comprising the amino acid sequence of
SEQ ID NO: 6, wherein the variant comprises an amino acid sequence
that is at least 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to
the amino acid sequence of SEQ ID NO: 7.
[0112] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%
or 99% identical to the amino acid sequence of SEQ ID NO: 7 or SEQ
ID NO: 8.
[0113] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95% or 99% identical
to the amino acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8, and
further comprises any one, two, three or more modifications at
amino acid positions 2, 9, 12, 14, 15, 58, 59, 63, 129, 166, 246,
247, 339, 370, 371, 372, 373, 374, 375, 376, 377, 380, 383, 384,
385, 455, 507 and 509, or any combinations thereof, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 7.
In some embodiments, the modifications can include deletions,
additions and substitutions. The substitutions can be conservative
or non-conservative substitutions.
[0114] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95% or 99% identical
to the amino acid sequence of SEQ ID NO: 7 and comprises any one,
two, three or more mutations selected from the group consisting of:
D9A, E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A,
Q377A, S385G, H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370
W, H370Y, H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A,
E371Q, E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R,
K372A, K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R,
K380A, K380Q, K380W, K380Y, K380F, D507H, D507G, D507E, D507T,
D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F, K509H,
K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A, K509Q,
K509W, K509Y and K509F, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 7. In some embodiments, the
modified polymerase comprises any one, two, three or more of these
amino acid substitutions.
[0115] In some embodiments, the modified polymerase comprises one
or more amino acid substitutions selected from the group consisting
of: D9A, E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A,
Q377A and S385G, and further comprises one or more amino acid
substitutions selected from the group consisting of: H370G, H370T,
H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y, H370F, E371G,
E371H, E371T, E371S, E371K, E371R, E371A, E371Q, E371W, E371Y,
E371F, K372G, K372E, K372T, K372S, K372R, K372A, K372Q, K372W,
K372Y, K372F, K380E, K380T, K380S, K380R, K380A, K380Q, K380W,
K380Y, K380F, D507H, D507G, D507E, D507T, D507S, D507R, D507A,
D507R, D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R,
K509E, K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F,
wherein the numbering is relative to the sequence of SEQ ID NO:
7.
[0116] In some embodiments, the modified polymerase comprises one
or more modifications resulting in an alteration (for example, an
increase or decrease) in polymerase activity relative to the
polymerase activity of a reference polymerase.
[0117] In some embodiments, the modified polymerase comprises one
or more modifications resulting in a change in the kinetic behavior
of the polymerase in vitro or in vivo. For example, the
modification(s) may result in a change (for example, an increase or
decrease) in one or more of the following activities or properties
of the polymerase, relative to the corresponding activity or
property of a reference polymerase: specific activity as measured
in a primer extension assay; specific activity as measured in a
nucleotide incorporation assay (including assays for incorporation
of naturally occurring nucleotides and nucleotide analogs);
exonuclease activity (including, for example, 3' to 5' exonuclease
activity); ability to bind one or more substrates (including
naturally occurring nucleotides and nucleotide analogs); yield of
synthesized nucleic acid product; processivity; fidelity of nucleic
acid synthesis; rate of nucleic acid synthesis; binding affinity
for one or more particular nucleotides (including naturally
occurring nucleotides and nucleotide analogs); K.sub.m for one or
more substrates (including naturally occurring nucleotides,
nucleotide analogs and/or template strand); k.sub.cat or V.sub.max,
t.sub.pol, t.sub.-1, k.sub.pol, or k.sub.-1 for one or more
nucleotides (including naturally occurring nucleotides and
nucleotide analogs); binding affinity for one or more nucleotides
(including naturally occurring nucleotides and nucleotide analogs);
residence time of one or more nucleotides (including naturally
occurring nucleotides and nucleotide analogs) within one or more
polymerase active sites; rate of binding for one or more
nucleotides (including naturally occurring nucleotides and
nucleotide analogs); rate of nucleotide release (in either altered
or unaltered state) from the polymerase active site, including, for
example, rate of product release; average template read length in
presence of nucleotides (including naturally occurring nucleotides
and nucleotide analogs); stability of the polymerase under a given
set of conditions, including photostability and chemical stability;
tolerance for the presence of labels (including both organic
labels, e.g., dyes, and inorganic labels, e.g., nanoparticles); and
photostability.
[0118] In some embodiments, the modification(s) result in an
alteration (e.g., increase or decrease) of any one, some or all of
the above activities or properties or properties relative to the
corresponding activity or property of a reference polymerase.
[0119] The reference polymerase can be any suitable polymerase
whose polymerase activity can be measured and compared to the
activity of a modified polymerase of the present disclosure. In
some embodiments, the reference polymerase can be the unmodified
counterpart of the modified polymerase. In some embodiments, the
reference polymerase is a naturally occurring polymerase. The
naturally occurring polymerase can in some embodiments be derived
from Phi-29 or the Phi-29-like family of bacteriophages, including
Phi-29, B103 and RB69; alternatively, it can be a non-Phi-29-like
polymerase, including, for example, T7 DNA polymerase, Taq DNA
polymerase or E. coli DNA polymerase. In some embodiments, the
reference polymerase can be a Phi-29 polymerase. (See, for example,
U.S. Pat. Nos. 5,001,050; 5,198,543 and 5,576,204 to Blanco et
al.). In some embodiments, the reference polymerase is wild type
Phi-29 polymerase having the amino acid sequence of SEQ ID NO: 1,
or a His-tagged version of Phi-29 polymerase having the amino acid
sequence of SEQ ID NO: 20. In some embodiments, the reference
polymerase can be a B103 polymerase comprising the amino acid
sequence of SEQ ID NO: 6. In some embodiments, the reference
polymerase can be a variant of a B103 polymerase comprising the
amino acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the reference polymerase is an RB69 polymerase having
the amino acid sequence of SEQ ID NO: 15. In some embodiments, the
reference polymerase can comprise the amino acid sequence of SEQ ID
NO: 13. In some embodiments, the reference polymerase can comprise
the amino acid sequence of SEQ ID NO: 14. (See, for example, Meijer
et al., "Phi-29 family of phages" Microbiol. & Mol. Biol. Revs.
65(2):261-287 (2001)).
[0120] In some embodiments, the reference polymerase is the same
polymerase in unmodified form. In some embodiments, the reference
polymerase is a polymerase having the amino acid sequence of SEQ ID
NO: 1 or SEQ ID NO: 20. In some embodiments, the reference
polymerase comprises the amino acid sequence of SEQ ID NO: 6. In
some embodiments, the reference polymerase is RB69 polymerase
comprising the amino acid sequence of SEQ ID NO: 15.
[0121] In some embodiments, the modified polymerase exhibits an
increase or decrease in the branching ratio in the presence of a
particular nucleotide, for example, a labeled nucleotide analog,
relative to the unmodified polymerase, or relative to any other
reference polymerase such as, for example, a Phi-29 polymerase
having the amino acid sequence of SEQ ID NO: 1.
[0122] In some embodiments, the modified polymerase exhibits an
increase in the t.sub.-1 value for a particular nucleotide, for
example, a labeled nucleotide analog, relative to an unmodified
counterpart.
[0123] In some embodiments, the modified polymerase exhibits a
t.sub.-1 value for a labeled nucleotide that is equal to or greater
than the value for the same nucleotide of a reference Phi-29
polymerase comprising the amino acid sequence of SEQ ID NO: 1.
[0124] In some embodiments, the modified polymerase exhibits an
increase in the t.sub.pol value for a particular nucleotide, for
example, a labeled nucleotide analog, relative to an unmodified
counterpart.
[0125] In some embodiments, the modified polymerase exhibits a
t.sub.pol value for a labeled nucleotide that is equal to or lesser
than the t.sub.pol value for the same nucleotide of a reference
Phi-29 polymerase comprising the amino acid sequence of SEQ ID NO:
1.
[0126] In some embodiments, the modified polymerase exhibits an
increase in residence time for a particular nucleotide, for
example, a labeled nucleotide analog, relative to an unmodified
counterpart.
[0127] In some embodiments, the modified polymerase exhibits a
residence time for a labeled nucleotide that is equal to or greater
than the residence time for the same nucleotide of a reference
Phi-29 polymerase comprising the amino acid sequence of SEQ ID NO:
1.
[0128] In some embodiments, the modified polymerase exhibits an
increase in photostability relative to an unmodified
counterpart.
[0129] In some embodiments, the modified polymerase exhibits a
photostability that is greater than the photostability of a
reference Phi-29 polymerase comprising the amino acid sequence of
SEQ ID NO: 1.
[0130] In some embodiments, the modified polymerase exhibits an
increase in nanoparticle tolerance relative to an unmodified
counterpart.
[0131] In some embodiments, the modified polymerase exhibits a
nanoparticle tolerance that is greater than the nanoparticle
tolerance of a reference Phi-29 polymerase comprising the amino
acid sequence of SEQ ID NO: 1.
[0132] In some embodiments, the modified polymerase is operably
linked to a detectable label. In some embodiments, the detectable
label is a nanoparticle.
[0133] Also provided herein are polynucleotides encoding the
modified polymerases of the present disclosure, and isolated host
cells comprising one or more of these polynucleotides.
[0134] Also provided herein are vectors comprising one or more
polynucleotides encoding the modified polymerases of the present
disclosure, and isolated host cells comprising these vectors. In
some embodiments, the vectors further comprise a promoter operably
linked to the polynucleotide encoding the modified polymerase. The
promoter can be constitutive or inducible. The host cell comprising
the polynucleotide encoding the modified polymerase can be
eukaryotic or prokaryotic.
[0135] Also provided are methods for producing one or more modified
polymerases of the present disclosure, comprising: culturing a host
cell comprising a polynucleotide that encodes a modified polymerase
under conditions that are suitable for the host cell to produce the
active modified polymerase. Optionally, the method can include the
step of purifying the modified polymerase from the isolated host
cells. Also disclosed herein is an active modified polymerase
produced by this method.
[0136] Also provided herein are methods for nucleotide
incorporation, comprising: contacting a modified polymerase of the
present disclosure with a target nucleic acid molecule and with at
least one nucleotide under conditions where the at least one
labeled nucleotide is incorporated by the modified polymerase into
an extending nucleic acid molecule. In some embodiments, the
modified polymerase can comprise an amino acid sequence at least
90%, 95%, 97,%, 98% or 99% identical to the amino acid sequence of
SEQ ID NO: 7 or SEQ ID NO: 8. In some embodiments, the at least one
nucleotide can be a labeled nucleotide. In some embodiments, the
labeled nucleotide comprises a nucleotide operably linked to a
detectable label, referred to herein as a nucleotide label. In some
embodiments, the nucleotide label can emits one or more signals
indicative of incorporation of the labeled nucleotide. In some
embodiments, the method can further comprise the step of detecting
the incorporation of the labeled nucleotide by detecting the one or
more signals emitted by the nucleotide label. In some embodiments,
the incorporation is a productive or non-productive
incorporation.
[0137] Also provided herein is a method for determining a
nucleotide sequence of a single nucleic acid molecule, comprising:
(a) conducting a nucleotide polymerization reaction comprising a
target nucleic acid molecule, a modified polymerase and at least
one labeled nucleotide, which reaction results in the incorporation
of one or more labeled nucleotides by the modified polymerase and
the generation of one or more detectable signals indicative of one
or more nucleotide incorporations; (b) detecting a time sequence of
nucleotide incorporations; and (c) determining the identity of one
or more incorporated nucleotides, thereby determining some or all
of the nucleotide sequence of the target nucleic acid molecule. In
some embodiments, the determination of nucleotide sequence can
occur in real or near real time. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 80%,
85%, 90%, 95%, 97%, 98% or 99% identical to the amino acid sequence
of SEQ ID NO: 8, and can optionally further include one or more
amino acid mutations selected from the group consisting of: T365G,
T365F, T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y,
T365H, H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W,
H370Y, H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A,
E371Q, E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R,
K372A, K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R,
K380A, K380Q, K380W, K380Y, K380F, A481E, A481F, A481G, A481S,
A481R, A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G,
D507E, D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y,
D507F, K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R,
K509A, K509Q, K509W, K509Y and K509F, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 7. Typically,
this modified polymerase can exhibit increase branching ratio
and/or increased photostability and/or increased nanoparticle
tolerance relative to a reference polymerase having the amino acid
sequence of SEQ ID NO: 7. Optionally, the modified polymerase can
further include one or more mutations reducing 3' to 5' exonuclease
activity selected from the group consisting of: D9A, E11A, E11I,
T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and S385G,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 7. In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%
or 99% identical to the amino acid sequence of SEQ ID NO: 1, and
can optionally further include an amino acid substitution at
position 383, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 1.
[0138] Also disclosed herein is a method for determining a
nucleotide sequence of a single nucleic acid molecule, comprising
the steps of: (a) conducting a polymerase reaction comprising a
polymerase and at least one labeled nucleotide, such that one or
more labeled nucleotides interact successively with the polymerase,
thereby generating or causing to be generated one or more
detectable signals indicative of one or more polymerase-nucleotide
interactions, and where the polymerase comprises the amino acid
sequence of SEQ ID NO: 7 or SEQ ID NO: 8; (b) detecting a time
sequence of polymerase-nucleotide interactions; and (c) determining
the identity of the one or more labeled nucleotides that interact
with the polymerase during the one or more polymerase-nucleotide
interactions, thereby determining some or all of the nucleotide
sequence of a single nucleic acid molecule. In some embodiments,
the determination of nucleotide sequence can occur in real or near
real time. In some embodiments, the modified polymerase can
comprise an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98% or 99% identical to the amino acid sequence of SEQ ID
NO: 8. In some embodiments, the modified polymerase can further
comprise one or more amino acid substitutions selected from the
group consisting of: T365G, T365F, T365G, T365S, T365K, T365R,
T365A, T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K,
H370R, H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T,
E371S, E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G,
K372E, K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F,
K380E, K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F,
A481E, A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q,
A481W, A481Y, D507H, D507G, D507E, D507T, D507S, D507R, D507A,
D507R, D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R,
K509E, K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 7. Typically, this modified polymerase can exhibit increase
branching ratio and/or increased photostability and/or increased
nanoparticle tolerance relative to a reference polymerase having
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 7.
[0139] In some embodiments, the modified polymerase can comprise an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%
or 99% identical to the amino acid sequence of SEQ ID NO: 1, and
further comprise one or more amino acid substitutions increasing
the branching ratio of the enzyme. Optionally, the one or more
amino acid substitutions can include replacement of the lysine
residue at position 373 of SEQ ID NO: 1 with any amino acid other
than lysine.
[0140] In some embodiments of the methods of the present
disclosure, the modified polymerase can exhibit a t.sub.-1 value
for a labeled nucleotide that is equal to or greater than the
t.sub.-1 value for the same nucleotide of a reference Phi-29
polymerase comprising the amino acid sequence of SEQ ID NO: 1.
[0141] In some embodiments of the methods of the present
disclosure, the modified polymerase can exhibit a t.sub.pol value
for a labeled nucleotide that is equal to or lesser than the
t.sub.pol value for the same nucleotide of a reference Phi-29
polymerase comprising the amino acid sequence of SEQ ID NO: 1.
[0142] In some embodiments of the methods of the present
disclosure, the modified polymerase can exhibit a residence time
for a labeled nucleotide that is equal to or greater than the
residence time for the same nucleotide of a reference Phi-29
polymerase comprising the amino acid sequence of SEQ ID NO: 1.
[0143] In some embodiments of the methods of the present
disclosure, the modified polymerase can exhibit a photostability
that is equal to or greater than the photostability of a reference
Phi-29 polymerase comprising the amino acid sequence of SEQ ID NO:
1.
[0144] In some embodiments of the methods of the present
disclosure, the modified polymerase can exhibit a nanoparticle
tolerance that is equal to or greater than the nanoparticle
tolerance of a reference Phi-29 polymerase comprising the amino
acid sequence of SEQ ID NO: 1.
[0145] In some embodiments of the methods of the present
disclosure, the labeled nucleotide can comprise a nucleotide label
operably linked to the nucleotide. In some embodiments, the
nucleotide label can be operably linked to the base, sugar or
phosphate group of the nucleotide.
[0146] In some embodiments of the methods of the present
disclosure, the labeled nucleotide can be a reversible terminator.
In some embodiments, the modified polymerase can be operably linked
to a detectable label. In some embodiments, the label of the
modified polymerase and the nucleotide label can be capable of
undergoing FRET with each other. Typically, FRET between the
polymerase label and the nucleotide label results in the emission
of one or more FRET signals. Optionally, the one or more FRET
signals can be detected and analyzed to determine the occurrence of
a polymerase-nucleotide interaction, or the base identity of the
underlying nucleotide.
[0147] Although the polymerases differ from organism to organism,
such polymerases are typically capable of template-dependent
nucleic acid synthesis and share several highly conserved domains.
Various studies have examined the phylogenetic relationships among
various polymerases. See, e.g., Bernad, A., et al., "Structural and
functional relationships between prokaryotic and eukaryotic DNA
polymerases" EMBO J. 6(13):4219-4225 (1987); Braithwaite, D. K.
& Ito, J., "Compilation, alignment, and phylogenetic
relationships of DNA polymerases" Nucl. Acids Res. 21:787-802
(1993); Steitz et al., "DNA polymerases: structural diversity and
common mechanisms" J. Biol. Chem. 274:17395-17398 (1999). Based on
such studies, polymerases have been classified into the Family A
DNA polymerases (based on homology to the product of the polA gene
encoding E. coli DNA polymerase I); the Family B DNA polymerases
(based on homology to the product of the polB gene encoding E. coli
DNA polymerase II); and the Family C DNA polymerases (based on
homology to the product of the polC gene encoding E. coli DNA
polymerase III alpha subunit). The Family B DNA polymerases can
include the DNA polymerase of the bacteriophage Phi-29, (also known
as .PHI.29 or phi29) of the Podoviridae family of phages.
[0148] In some embodiments, the modified polymerase can be a
modified Phi-29-like polymerase comprising an amino acid sequence
that is at least 80%, 85%, 90%, 95%, or 99% identical to the amino
acid sequence of SEQ ID NO: 1:
TABLE-US-00001 (SEQ ID NO: 1) MKHMPRKMYS CDFETTTKVE DCRVWAYGYM
NIEDHSEYKI GNSLDEFMAW VLKVQADLYF 70 80 90 100 110 120 HNLKFDGAFI
INWLERNGFK WSADGLPNTY NTIISRMGQW YMIDICLGYK GKRKIHTVIY 130 140 150
160 170 180 DSLKKLPFPV KKIAKDFKLT VLKGDIDYHK ERPVGYKITP EEYAYIKNDI
QIIAEALLIQ 190 200 210 220 230 240 FKQGLDRMTA GSDSLKGFKD IITTKKFKKV
FPTLSLGLDK EVRYAYRGGF TWLNDRFKEK 250 260 270 280 290 300 EIGEGMVFDV
NSLYPAQMYS RLLPYGEPIV FEGKYVWDED YPLHIQHIRC EFELKEGYIP 310 320 330
340 350 360 TIQIKRSRFY KGNEYLKSSG GEIADLWLSN VDLELMKEHY DLYNVEYISG
LKFKATTGLF 370 380 390 400 410 420 KDFIDKWTYI KTTSEGAIKQ LAKLMLNSLY
GKFASNPDVT GKVPYLKENG ALGFRLGEEE 430 440 450 460 470 480 TKDPVYTPMG
VFITAWARYT TITAAQACYD RIIYCDTDSI HLTGTEIPDV IKDIVDPKKL 490 500 510
520 530 540 GYWAHESTFK RAKYLRQKTY IQDIYMKEVD GKLVEGSPDD YTDIKFSVKC
AGMTDKIKKE 550 560 570 VTFENFKVGF SRKMKPKPVQ VPGGVVLVDD TFTIK
[0149] In some embodiments, the reference polymerase can comprise
an amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%,
99% or 100% identical to the amino acid sequence of SEQ ID NO:
1.
[0150] In some embodiments, the polymerase can be a mutant Phi-29
polymerase that retains nucleotide polymerization activity but
lacks the 3'.fwdarw.5' or 5'.fwdarw.3' exonuclease activity. For
example, mutant Phi-29 polymerases having exonuclease-minus
activity, or reduced exonuclease activity, can include the amino
acid sequence of SEQ ID NO: 1 and further comprise one or more
amino acid substitutions at positions selected from the group
consisting of: 12, 14, 15, 62, 66, 165 and 169 (wherein the
numbering is relative to the amino acid sequence of wild type
Phi-29). In some embodiments, the polymerase is a phi29 polymerase
comprising the amino acid sequence of SEQ ID NO: 1 and one or more
of the following amino acid substitutions: D12A, E14I, E14A, T15I,
N62D, D66A, Y165F, Y165C, and D169A, wherein the numbering is
relative to SEQ ID NO:. 1. In some embodiments, the reference
polymerase can comprise an amino acid sequence that is at least
70%, 80%, 85%, 90%, 95%, 99% or 100% identical to the amino acid
sequence of SEQ ID NO: 1 and further comprise one or more of the
following amino acid substitutions: D12A, E14I, E14A, T15I, N62D,
D66A, Y165F, Y165C, and D169A, wherein the numbering is relative to
SEQ ID NO: 1. In some embodiments, the polymerase is a phi29
polymerase comprising the amino acid sequence of SEQ ID NO: 1 and
one or both of the following amino acid substitutions: D12A and
D66A. In some embodiments, the reference polymerase can comprise an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 99%
or 100% identical to the amino acid sequence of SEQ ID NO: 1 and
further comprise one or both of the following amino acid
substitutions: D12A and D66A, wherein the numbering is relative to
SEQ ID NO: 1. See, e.g., Blanco, U.S. Pat. Nos. 5,001,050,
5,198,543, and 5,576,204; and Hardin PCT/US2009/31027 with an
International filing date of Jan. 14, 2009. Optionally, the
polymerase can further include a biotinylation site or His tag as
described herein.
[0151] In some embodiments, the modified polymerase can comprise an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 99%
or 100% identical to the amino acid sequence of SEQ ID NO: 1 and
further include one or more amino acid mutations at positions
selected from the group consisting of: 132, 135, 250, 266, 332,
342, 368, 370, 371, 372, 373, 375, 379, 380, 383, 387, 390, 458,
478, 480, 484, 486, and 512, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 1. In some embodiments, the
modified polymerase can comprise an amino acid deletion, wherein
the deletion includes some of all of the amino acids spanning
positions 306 to 311.
[0152] In some embodiments, the reference polymerase can comprise
an amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 1
and further include one or more amino acid mutations at positions
selected from the group consisting of: 132, 135, 250, 266, 332,
342, 368, 371, 375, 379, 380, 383, 387, 390, 458, 478, 480, 484,
486, 510 and 512, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 1.
[0153] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 99%
or 100% identical to the amino acid sequence of SEQ ID NO: 1 and
further includes one or more amino acid mutations selected from the
group consisting of: K132A, K135A, K135D, K135E, V250A, V250C,
Y266F, D332Y, L342G, T368D, T368E, T368F, K370A, K371E, T372D,
T372E, T372R, T372K, E375A, E375F, E375H, E375K, E375Q, E375R,
E375S, E375W, E375Y, K379A, Q380A, K383E, K383H, K383L, K383R,
N387Y, Y390F, D458N, K478D, K478E, K478R, L480K, L480R, A484E,
E486A, E486D, K512A K512D, K512E, K512R, K512Y,
K371E/K383E/N387Y/D458N, Y266F/Y390F, Y266F/Y390F/K379A/Q380A,
K379A/Q380A, E375Y/Q380A/K383R, E375Y/Q380A/K383H,
E375Y/Q380A/K383L, E375Y/Q380A/V250A, E375Y/Q380A/V250C,
E375Y/K512Y/T368F, E375Y/K512Y/T368F/A484E, K379A/E375Y,
K379A/K383R, K379A/K383H, K379A/K383L, K379A/Q380A, V250A/K379A,
V250A/K379A/Q380A, V250C/K379A/Q380A, K132A/K379A and deletion of
some or all of the amino acid residues spanning R306 to K311,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 1.
[0154] Also disclosed herein is a method for single molecule
sequencing in real time, comprising: contacting a modified Phi-29
polymerase according to the present disclosure with labeled
nucleotide under conditions where the labeled nucleotides are
incorporated by the polymerase onto the end of an extending nucleic
acid molecule, accompanied by the emission of a signal indicative
of a nucleotide incorporation; detecting a time sequence of
nucleotide incorporations; and analyzing the time sequence of
nucleotide incorporations to determine a polynucleotide
sequence.
[0155] In some embodiments, the reference polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 99%
or 100% identical to the amino acid sequence of SEQ ID NO: 1 and
further includes one or more amino acid mutations selected from the
group consisting of: K132A, K135A, K135D, K135E, V250A, V250C,
Y266F, D332Y, L342G, T368D, T368E, T368F, K370A, K371E, T372D,
T372E, T372R, T372K, T373A, T373F, 1373H, T373K, T373Q, T373R,
T373S, T373W, T373Y, T373E, E375A, E375F, E375H, E375K, E375Q,
E375R, E375S, E375W, E375Y, K379A, Q380A, K383E, K383H, K383L,
K383R, N387Y, Y390F, D458N, K478D, K478E, K478R, L480K, L480R,
A484E, E486A, E486D, K510A, K510F, K510H, K510K, K510Q, K510R,
K510S, K510W, K510Y, K510E, K512A K512D, K512E, K512R, K512Y,
K371E/K383E/N387Y/D458N, Y266F/Y390F, Y266F/Y390F/K379A/Q380A,
K379A/Q380A, E375Y/Q380A/K383R, E375Y/Q380A/K383H,
E375Y/Q380A/K383L, E375Y/Q380A/V250A, E375Y/Q380A/V250C,
E375Y/K512Y/T368F, E375Y/K512Y/T368F/A484E, K379A/E375Y,
K379A/K383R, K379A/K383H, K379A/K383L, K379A/Q380A, V250A/K379A,
V250A/K379A/Q380A, V250C/K379A/Q380A, K132A/K379A and deletion of
some or all of the amino acid residues spanning R306 to K311,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 1.
[0156] Without being bound to any particular theory, it is thought
that the domain comprising amino acid residues 304-314 of the amino
acid sequence of SEQ ID NO: 3 (Phi-29 polymerase), or homologs
thereof, can reduce or otherwise interfere with DNA initiation
and/or elongation by inhibiting access to the Phi-29 polymerase
active site, and that this region must be displaced in order to
allow access to the active site. See, e.g., Kamtekar et al., "The
.PHI.29 DNA polymerase:protein primer structure suggests a model
for the initiation to elongation transition", EMBO J., 25:1335-1343
(2005).
[0157] In some embodiments, the modified polymerase is derived from
a polymerase of any member of the Phi-29-like family of phages. The
Phi-29-like phages are a genus of phages that are related to Phi-29
that includes the phages PZA, .PHI.15, BS32, B103, M2Y (M2), Nf1
and GA-1. Phages of this group have been sub-classified into three
groups based on serological properties, DNA and/or polymerase maps
and partial or complete DNA sequences, and share several
characteristics in common. For example, such phages can typically
undergo protein-primed DNA replication. See, for example, Meijer et
al., "Phi-29 family of phages" Microbiol. & Mol. Biol. Revs.
65(2):261-287 (2001).
[0158] The genome of the Phi-29-like phage B103, including a gene
encoding a B103 DNA polymerase, has been sequenced. See, e.g.,
Pecenkova et al., "Bacteriophage B103: complete DNA sequence of its
genome and relationship to other Bacillus phages" Gene 199:157-163
(1999). The DNA polymerase of B103 is homologous to the DNA
polymerase of Phi-29 and of other Phi-29-like phages. Collectively,
these polymerases share several, highly conserved regions. See,
e.g., Meijer et al., "Phi-29 family of phages" Microbiol. &
Mol. Biol. Revs. 65(2):261-287 (2001). These conserved regions are
typically characterized by several conserved amino acid motifs.
See, e.g., Blanco et al., Gene 100:27-38 (1991); Blasco et al.,
".PHI.29 DNA polymerase. Active Site" J. Biol. Chem.
268:16763-16770 (1993) (describing regions of sequence homology and
mutational analysis of consensus regions of Phi-29 and Phi-29-like
DNA polymerases); Berman et al., "Structures of phi29 DNA
polymerase complexed with substrate: the mechanism of translocation
in B-family polymerases", EMBO J., 26:3494-3505 (2007).
Site-directed mutagenesis indicates that these three regions can
include an evolutionarily conserved polymerase active site.
[0159] Collectively, the polymerases of these phages share several
highly conserved regions. See, e.g., Meijer et al., "Phi-29 family
of phages" Microbiol. & Mol. Biol. Rev. 65(2):261-287 (2001).
The conserved regions are typically characterized by the following
amino acid motifs:
TABLE-US-00002 Dx.sub.2SLYP (SEQ ID NO: 2)
[0160] The consensus sequence of SEQ ID NO: 2 represents the
consensus amino acid sequence for a motif known as region 1, also
named motif A.
TABLE-US-00003 Kx.sub.3NSxYG (SEQ ID NO: 3)
[0161] The consensus sequence of SEQ ID NO: 3 represents the
consensus amino acid sequence for the motif known as region 2a,
also named motif B.
TABLE-US-00004 YGDTDS (SEQ ID NO: 4)
[0162] The consensus sequence of SEQ ID NO: 4 represents the
consensus amino acid sequence for the motif known as region 3, also
named motif C.
TABLE-US-00005 KxY (SEQ ID NO: 5)
[0163] The consensus sequence of SEQ ID NO: 5 represents the
consensus amino acid sequence for the motif known as region 4. See,
e.g., Blanco et al., Gene 100:27-38 (1991); Blasco et al., ".PHI.29
DNA polymerase Active Site" J. Biol. Chem. 268:16763-16770 (1993)
(describing regions of sequence homology and mutational analysis of
consensus regions of Phi-29 and Phi-29-like DNA polymerases).
[0164] Site-directed mutagenesis indicates that these motifs can
include one or more evolutionarily conserved polymerase active
sites.
[0165] In some embodiments, the modified polymerase is
[0166] In some embodiments, the modified polymerase is derived from
a Phi-29-like polymerase and comprises an amino acid sequence that
is at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100%
identical to the amino acid sequence of SEQ ID NO: 6 as
follows:
TABLE-US-00006 (SEQ ID NO: 6) 1 mprkmfscdf etttklddcr vwaygymeig
nldnykigns ldefmqwvme iqadlyfhnl 61 kfdgafivnw lehhgfkwsn
eglpntynti iskmgqwymi dicfgykgkr klhtviydsl 121 kklpfpvkki
akdfqlpllk gdidyhaerp vgheitpeey eyikndieii araldiqfkq 181
gldrmtagsd slkgfkdils tkkfnkvfpk lslpmdkeir rayrggftwl ndkykekeig
241 egmvfdvnsl ypsqmysrpl pygapivfqg kyekdeqypl yiqrirfefe
lkegyiptiq 301 ikknpffkgn eylknsgaep velyltnvdl eliqehyemy
nveyidgfkf rektglfkef 361 idkwtyvkth ekgakkqlak lmfdslygkf
asnpdvtgkv pylkedgslg frvgdeeykd 421 pvytpmgvfi tawarfttit
aaqacydrii ycdtdsihlt gtevpeiikd ivdpkklgyw 481 ahestfkrak
ylrqktyiqd iyakevdgkl iecspdeatt tkfsvkcagm tdtikkkvtf 541
dnfrvgfsst gkpkpvqvng gvvlvdsvft ik
[0167] In some embodiments, the modified polymerase is derived from
a polymerase of the Phi-29-like phages and comprises an amino acid
sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or
100% identical to the amino acid sequence, wherein the modified
polymerase comprises an amino acid sequence that is at least 80%,
85%, 90%, 95%, 97%, 98% or 99% identical to the amino acid sequence
of SEQ ID NO: 6, or any biologically active fragment thereof.
[0168] In some embodiments, the modified polymerase is homologous
to a polymerase of one or more of the following organisms: B103,
Phi-29, GA-1, PZA, Phi-15, BS32, M2Y, Nf, G1, Cp-1, PRD1, PZE, SF5,
Cp-5, Cp-7, PR4, PR5, PR722, or L17. See, e.g., Meijer et al.,
"Phi-29 family of phages," Microbiol. & Mol. Biol. Revs.
65(2):261-287 (2001).
[0169] In some embodiments, the modified polymerase is derived from
a B103 polymerase having the amino acid sequence of SEQ ID NO: 6
and further comprises one or more mutations in the amino acid
sequence of SEQ ID NO: 6. In some embodiments, the one or more
mutations can include, for example, substitution, chemical
modification, addition, deletion and/or inversion of one or more
amino acid residues, or any combination of the foregoing.
[0170] For example, in some embodiments, the modified polymerase
comprises the amino acid sequence of SEQ ID NO: 6, and further
comprises one or more amino acid mutations (e.g., amino acid
substitutions, additions, deletions) that increases polymerase
activity, reduces 3' to 5' exonuclease activity, increases the
branching ratio of the polymerase with a particular labeled
nucleotide, and/or increases the residence time of a particular
labeled nucleotide within the polymerase active site. The
modification can include, for example, one or more amino acid
substitutions, additions, deletions or chemical modifications.
[0171] For example, in some embodiments, the modified polymerase
includes one or more amino acid mutations that increase the
polymerase activity of the modified polymerase relative to a
reference polymerase having the amino acid sequence of SEQ ID NO:
6. For example, in some embodiments, the modified polymerase
comprises an amino acid mutation at position 383, at position 384,
or at both positions 383 and 384, wherein the numbering is relative
to the amino acid sequence of SEQ ID NO: 6. In some embodiments,
the modified polymerase comprises the amino acid substitutions
F383L and D384N, and exhibits increased polymerase activity
relative to the reference polymerase having the amino acid sequence
of SEQ ID NO: 6. Typically, such mutants exhibit increased
polymerase activity relative to the unmodified protein having the
amino acid sequence of SEQ ID NO: 6.
[0172] In some embodiments, the modified polymerase having
increased polymerase activity relative to the reference polymerase
of SEQ ID NO: 6 comprises an amino acid sequence that is at least
80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the amino acid
sequence of SEQ ID NO: 6, or any biologically active fragment
thereof, wherein the amino acid at position 383 is not
phenylalanine (F), where the numbering is relative to the amino
acid sequence of SEQ ID NO: 6.
[0173] In some embodiments, the modified polymerase comprises the
amino acid sequence of SEQ ID NO: 6, and further comprises an amino
acid substitution at position 383, wherein the numbering is
relative to a B103 polymerase having the amino acid sequence of SEQ
ID NO: 6. In some embodiments, the modified polymerase is a variant
of B103 polymerase that comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the amino
acid sequence of SEQ ID NO: 6, or any biologically active fragment
thereof, wherein the modified polymerase further comprises the
amino acid mutation F383L.
[0174] In some embodiments, the modified polymerase is a variant of
a B103 polymerase that comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the amino
acid sequence of SEQ ID NO: 6, or any biologically active fragment
thereof, wherein the amino acid at position 384 is not aspartic
acid (D), where the numbering is relative to the amino acid
sequence of SEQ ID NO: 6.
[0175] In some embodiments, the modified polymerase comprises the
amino acid sequence of SEQ ID NO: 6 and further comprises an amino
acid substitution at position 384, wherein the numbering is
relative to a B103 polymerase having the amino acid sequence of SEQ
ID NO: 6. In some embodiments, the modified polymerase is a variant
of B103 polymerase that comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the amino
acid sequence of SEQ ID NO: 6, or any biologically active fragment
thereof, wherein the modified polymerase further comprises the
amino acid mutation D384N.
[0176] In some embodiments, the modified polymerase is a variant of
B103 polymerase, or any biologically active fragment thereof,
having the amino acid sequence of SEQ ID NO: 6, wherein the
modified variant further comprises amino acid substitutions at
positions 383 and 384, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6. In some embodiments, the
modified polymerase comprises the amino acid substitutions F383L
and D384N, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 6. The amino acid sequence of this modified
polymerase can be represented as follows:
TABLE-US-00007 (SEQ ID NO: 7) 1 mprkmfscdf etttklddcr vwaygymeig
nldnykigns ldefmqwvme iqadlyfhnl 61 kfdgafivnw lehhgfkwsn
eglpntynti iskmgqwymi dicfgykgkr klhtviydsl 121 kklpfpvkki
akdfqlpllk gdidyhaerp vgheitpeey eyikndieii araldiqfkq 181
gldrmtagsd slkgfkdils tkkfnkvfpk lslpmdkeir rayrggftwl ndkykekeig
241 egmvfdvnsl ypsqmysrpl pygapivfqg kyekdeqypl yiqrirfefe
lkegyiptiq 301 ikknpffkgn eylknsgaep velyltnvdl eliqehyemy
nveyidgfkf rektglfkef 361 idkwtyvkth ekgakkqlak lmlnslygkf
asnpdvtgkv pylkedgslg frvgdeeykd 421 pvytpmgvfi tawarfttit
aaqacydrii ycdtdsihlt gtevpeiikd ivdpkklgyw 481 ahestfkrak
ylrqktyiqd iyakevdgkl iecspdeatt tkfsvkcagm tdtikkkvtf 541
dnfrvgfsst gkpkpvqvng gvvlvdsvft ik
[0177] In some embodiments, the modified B103 polymerase comprises
an amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%,
98% or 99% identical to the amino acid sequence of SEQ ID NO: 7, or
any biologically active fragment thereof. Typically, a modified
polymerase having the amino acid sequence of SEQ ID NO: 7 will
exhibit increased polymerase activity (e.g., primer extension
activity) relative to the unmodified reference polymerase having
the amino acid sequence of SEQ ID NO: 6.
[0178] In some embodiments, the modified polymerase comprises one
or more modifications resulting in altered exonuclease activity
(for example 3' to 5' exonuclease activity) as compared to a
reference polymerase (for example, an unmodified counterpart). In
some embodiments, the modification comprises an amino acid
substitution. In some embodiments, the modified polymerase lacks 3'
to 5' exonuclease activity, or lacks 5' to 3' exonuclease activity,
or both.
[0179] Mutations that reduce or eliminate 3' to 5' exonuclease
activity have been described, for example, in Phi-29 polymerase at
various residues. See, e.g., de Vega et al., "Primer-terminus
stabilization at the 3'-5' exonuclease active site of .PHI.29 DNA
polymerase. Involvement of two amino acid residues highly conserved
in proofreading DNA polymerases" EMBO J., 15(5):1182-1192 (1996);
Soengas et al., "Site-directed mutagenesis at the Exo III motif of
.PHI..sub.29 DNA polymerase; overlapping structural domains for the
3'-5' exonuclease and strand-displacement activities" EMBO J.,
11(11):4227-4237 (1992); Blanco et al., U.S. Pat. Nos. 5,001,050,
5,198,543 and 5,576,204.
[0180] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 75%, 85%, 90%, 95% or 99%
identical to any one of the amino acid sequences SEQ ID NO: 6, SEQ
ID NO: 7 and SEQ ID NO: 8, or to any biologically active fragment
thereof, and further comprises one or more amino acid
substitutions, additions or deletions at one or more positions
selected from the group consisting of: 2, 9, 11, 12, 58, 59, 63,
162, 166, 377 and 385, wherein the numbering is relative to SEQ ID
NO: 6. In some embodiments, this modified polymerase can exhibit
reduced exonuclease activity relative to an unmodified
counterpart.
[0181] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 75%, 85%, 90%, 95% or 99%
identical to any one of the amino acid sequences SEQ ID NO: 6 or
SEQ ID NO: 7, or to any biologically active fragment thereof, and
further comprises the amino acid mutation D166A, wherein the
numbering is relative to SEQ ID NO: 6. In some embodiments, this
modified polymerase can exhibit reduced 3' to 5' exonuclease
activity relative to a reference polymerase having the amino acid
sequence of SEQ ID NO: 7.
[0182] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 75%, 85%, 90%, 95% or 99%
identical to any one of the amino acid sequences SEQ ID NO: 6, SEQ
ID NO: 7 and SEQ ID NO: 8, or to any biologically active fragment
thereof, and further comprises one or more amino acid substitutions
selected from the group consisting of: D9A, E11A, E11I, T12I, H58R,
N59D, D63A, Y162F, Y162C, D166A, Q377A and S385G, wherein the
numbering is relative to SEQ ID NO: 6. In some embodiments, this
modified polymerase can exhibit reduced exonuclease activity
relative to an unmodified counterpart.
[0183] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 75%, 85%, 90%, 95% or 99%
identical to any one of the amino acid sequences SEQ ID NO: 6, SEQ
ID NO: 7 and SEQ ID NO: 8, or to any biologically active fragment
thereof, and further comprises one or more amino acid substitutions
selected from the group consisting of: D9A, E11A, E11I, T12I, H58R,
N59D, D63A, Y162F, Y162C, Q377A and S385G, wherein the numbering is
relative to SEQ ID NO: 6. Typically, this modified polymerase can
exhibit reduced 3' to 5' exonuclease activity relative to an
unmodified counterpart.
[0184] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95% or 99% identical
to the amino acid sequence of SEQ ID NO: 6 and further comprises an
amino acid substitution wherein the amino acid residue at position
9 is replaced with an alanine ("A") residue, wherein the numbering
is relative to the amino acid sequence of SEQ ID NO: 6.
[0185] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95% or 99% identical
to the amino acid sequence of SEQ ID NO: 6 and further comprises
one or more of the amino acid substitutions D9A, E11A, T12I, H58R,
N59D, D63A, D166A, Q377A, S385G, or any combination thereof,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 6. In some embodiments, the modified polymerase comprises
any one, two, three, four, five or all of these mutations. In some
embodiments, the modified polymerase comprises the amino acid
substitutions D9A and D63A. In some embodiments, the modified
polymerase comprises the amino acid substitutions N59D and T12I.
Typically, this polymerase will exhibit reduced 3' to 5'
exonuclease activity relative to an unmodified counterpart.
[0186] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95% or 99% identical
to the amino acid sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID
NO: 8 and comprises any one, two, three or more of the mutations
described herein.
[0187] Optionally, the modification(s) reducing 3' to 5'
exonuclease activity can be combined with additional
modification(s) that increase polymerase activity. Modifications
increasing polymerase activity include, for example, the amino acid
substitutions F383L and D384N.
[0188] In one embodiment, the modified polymerase comprises the
amino acid sequence of SEQ ID NO: 6 and further comprises the amino
acid substitution D166A, which reduces the 3' to 5' exonuclease
activity, in combination with the amino acid substitutions F383L
and D384N, which increase the polymerase activity of the modified
polymerase, relative to the unmodified protein having the amino
acid sequence of SEQ ID NO: 6. The amino acid sequence of this
triple mutant polymerase is the amino acid sequence of SEQ ID NO:
8, below:
TABLE-US-00008 (SEQ ID NO: 8) 1 mprkmfscdf etttklddcr vwaygymeig
nldnykigns ldefmqwvme iqadlyfhnl 61 kfdgafivnw lehhgfkwsn
eglpntynti iskmgqwymi dicfgykgkr klhtviydsl 121 kklpfpvkki
akdfqlpllk gdidyhaerp vgheitpeey eyiknaieii araldiqfkq 181
gldrmtagsd slkgfkdils tkkfnkvfpk lslpmdkeir rayrggftwl ndkykekeig
241 egmvfdvnsl ypsqmysrpl pygapivfqg kyekdeqypl yiqrirfefe
lkegyiptiq 301 ikknpffkgn eylknsgaep velyltnvdl eliqehyemy
nveyidgfkf rektglfkef 361 idkwtyvkth ekgakkqlak lmlnslygkf
asnpdvtgkv pylkedgslg frvgdeeykd 421 pvytpmgvfi tawarfttit
aaqacydrii ycdtdsihlt gtevpeiikd ivdpkklgyw 481 ahestfkrak
ylrqktyiqd iyakevdgkl iecspdeatt tkfsvkcagm tdtikkkvtf 541
dnfrvgfsst gkpkpvqvng gvvlvdsvft ik
[0189] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%,
97%, 98% or 99% identical to the amino acid sequence of SEQ ID NO:
8, or any biologically active fragment thereof. Typically, the
modified polymerase of SEQ ID NO: 8 will exhibit reduced
exonuclease activity relative to a reference polymerase comprising
the amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 6, SEQ ID NO: 7
or SEQ ID NO: 13.
[0190] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 75%, 85%, 90%, 95% or 99%
identical to any one of the amino acid sequences SEQ ID NO: 6, SEQ
ID NO: 7 and SEQ ID NO: 8, or to any biologically active fragment
thereof, and further comprises one or more modifications resulting
in altered (e.g., increased or decreased) branching ratio and/or
nucleotide binding affinity (K.sub.D) as compared to a reference
polymerase. For example, mutations that may affect branching ratio
and/or nucleotide binding affinity can include mutations (e.g.,
amino acid substitutions, additions or deletions) at positions
selected from the group consisting of: 370, 371, 372, 373, 374,
375, 376 and 377, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 6. In some embodiments, the mutation
comprises one or more of the amino acid substitutions selected from
the group consisting of H370G, H370T, H370S, H370K, H370R, H370A,
H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T, E371S, E371K,
E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E, K372T,
K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E, K380T,
K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, D507H, D507G,
D507E, D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y,
D507F, K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R,
K509A, K509Q, K509W, K509Y and K509F, wherein the numbering is
relative to the sequence of SEQ ID NO: 6.
[0191] In some embodiments, the polymerase further comprises one or
more mutations reducing the exonuclease activity as described
herein such as, for example, the amino acid substitution D166A.
[0192] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 75%, 85%, 90%, 95% or 99%
identical to any one of the amino acid sequences SEQ ID NO: 6, SEQ
ID NO: 7 and SEQ ID NO: 8, or to any biologically active fragment
thereof, and further comprises one or more modifications resulting
in altered (e.g., increased or decreased) primer extension activity
as compared to a reference polymerase. For example, mutations that
may affect primer extension activity can include mutations (e.g.,
amino acid substitutions, additions or deletions) at positions
selected from the group consisting of: 129 and 339, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the mutation comprises one or more of the
amino acid substitutions selected from the group consisting of: In
some embodiments, the polymerase further comprises one or more
mutations reducing the exonuclease activity as described herein
such as, for example, the amino acid substitution D166A.
[0193] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 75%, 85%, 90%, 95% or 99%
identical to any one of the amino acid sequences SEQ ID NO: 6, SEQ
ID NO: 7 and SEQ ID NO: 8, or to any biologically active fragment
thereof, and further comprises one or more modifications resulting
in altered (e.g., increased or decreased) t.sub.pol or k.sub.pol
values as compared to a reference polymerase. For example,
mutations that may affect t.sub.pol or k.sub.pol values can include
mutations (e.g., amino acid substitutions, additions or deletions)
at position 380, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 6. In some embodiments, the mutation
comprises one or more of the amino acid substitutions selected from
the group consisting of: K380E, K380T, K380S, K380R, K380A, K380Q,
K380W, K380Y and K380F, and results in an increased t.sub.pol value
(or decreased k.sub.pol value) relative to the unmodified
counterpart. In some embodiments, the polymerase further comprises
one or more mutations reducing the exonuclease activity as
described herein such as, for example, the amino acid substitution
D166A.
[0194] In some embodiments, the modified polymerase is a variant of
a B103 polymerase comprising the amino acid sequence of SEQ ID NO:
6, SEQ ID NO: 7 or SEQ ID NO: 8, wherein the variant further
comprises any one, two, three or more modifications at amino acid
positions 2, 9, 12, 14, 15, 58, 59, 63, 129, 166, 246, 247, 339,
370, 371, 372,373, 374, 375, 376, 377, 380, 383, 384, 385, 455,
507, 509, or any combinations thereof, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 6. In some
embodiments, the modifications can include deletions, additions and
substitutions. The substitutions can be conservative or
non-conservative substitutions.
[0195] In some embodiments, the modified polymerase is a variant of
a B103 polymerase comprising the amino acid sequence of SEQ ID NO:
6, SEQ ID NO: 7 or SEQ ID NO: 8, wherein the variant further
comprises any one, two, three or more modifications at amino acid
positions selected from the group consisting of: 2, 9, 12, 14, 15,
58, 59, 61, 63, 98, 129, 166, 176, 185, 186, 187, 195, 208, 246,
247, 248, 251, 252, 256, 300, 302, 310, 339, 357, 360, 362, 367,
368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380, 383,
384, 385, 386, 387, 389, 390, 392, 399, 411, 419, 430, 455, 475,
477, 481, 483, 493, 494, 497, 507, 509, 511, 526, 528, 529, 531,
535, 552, 555, 567, 569 and 572, wherein the numbering is relative
to the amino acid sequence of SEQ ID NO: 6. In some embodiments,
the modifications can include deletions, additions and
substitutions. The substitutions can be conservative or
non-conservative substitutions. Optionally, this modified
polymerase comprises the amino acid substitution H370R. In some
embodiments, the polymerase further comprises one or more mutations
reducing the exonuclease activity as described herein such as, for
example, the amino acid substitution D166A. Typically, this
modified polymerase can exhibit increased branching ratio,
increased nucleotide binding affinity, increased photostability
and/or increased nanoparticle tolerance relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 7.
[0196] In some embodiments, the modified polymerase comprises one
or more amino acid substitutions at any one, two, three or more
positions selected from the group consisting of: 2, 9, 12, 58, 59,
63, 129, 166, 246, 247, 339, 370, 371, 372, 373, 374, 375, 376,
377, 380, 383, 384, 385, 455, 507 and 509, or any combinations
thereof.
[0197] In some embodiments, the modified polymerase is a variant of
B103 polymerase that comprises an amino acid sequence that is at
least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to
any one of the amino acid sequences SEQ ID NO: 6, SEQ ID NO: 7 and
SEQ ID NO: 8, or to any biologically active fragment thereof, and
further comprises a modification at residue at position 2, wherein
the numbering is relative to a B103 polymerase having the amino
acid sequence of SEQ ID NO: 6. The modification can include, for
example, one or more amino acid substitutions, additions, deletions
or chemical modifications. In some embodiments, the modified
polymerase comprises a proline (P) residue at position 2.
[0198] In some embodiments, the modified polymerase is a variant of
B103 polymerase that comprises an amino acid sequence that is at
least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to
any one of the amino acid sequences SEQ ID NO: 6, SEQ ID NO: 7 and
SEQ ID NO: 8, or to any biologically active fragment thereof, and
further comprises an amino acid modification at position 370,
wherein the numbering is relative to a B103 polymerase having the
amino acid sequence of SEQ ID NO: 6. In some embodiments, the amino
acid at position 370 is any amino acid other than threonine (T) or
histidine (H). In some embodiments, the amino acid at position 370
of the modified polymerase is glutamic acid (E), serine (S), lysine
(K), arginine (R), alanine (A), glutamine (Q), tryptophan (W),
tyrosine (Y), phenylalanine (F) or any other natural or non-natural
amino acid, other than threonine (T) modified polymerase is a
variant of B103 polymerase that comprises an amino acid sequence
that is at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99%
identical to any one of the amino acid sequences SEQ ID NO: 6, SEQ
ID NO: 7 and SEQ ID NO: 8, or to any biologically active fragment
thereof, and further comprises an amino acid substitution selected
from the group consisting of: H370E, H370K, H370G, H370T, H370S,
H370K, H370R, H370A, H370Q, H370 W, H370Y and H370F, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO:
6.
[0199] In some embodiments, the modified polymerase is a variant of
B103 polymerase that comprises an amino acid sequence that is at
least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to
any one of the amino acid sequences SEQ ID NO: 6, SEQ ID NO: 7 and
SEQ ID NO: 8, or to any biologically active fragment thereof, and
further comprises an amino acid modification at position 371,
wherein the numbering is relative to a B103 polymerase having the
amino acid sequence of SEQ ID NO: 7. The modification can include,
for example, one or more amino acid substitutions, additions,
deletions or chemical modifications. In some embodiments, the
modified polymerase is a variant of B103 polymerase that comprises
an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%,
95%, 97%, 98% or 99% identical to any one of the amino acid
sequences SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8, or to any
biologically active fragment thereof, wherein the amino acid at
position 371 is any amino acid other than serine (S). In some
embodiments, the modified polymerase comprises a glutamic acid (E)
residue at position 371. In some embodiments, the amino acid at
position 371 is any amino acid other than serine (S) or glutamic
acid (E). In some embodiments, the amino acid at position 371 of
the modified polymerase is glycine (G), histidine (H), lysine (K),
arginine (R), alanine (A), glutamine (Q), tryptophan (W), tyrosine
(Y), phenylalanine (F) or any other natural or non-natural amino
acid, other than serine (S). In some embodiments, the modified
polymerase is a variant of B103 polymerase that comprises an amino
acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,
98% or 99% identical to any one of the amino acid sequences SEQ ID
NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8, or to any biologically active
fragment thereof, and further comprises one or more amino acid
substitutions selected from the group consisting of E371G, E371H,
E371T, E371S, E371K, E371R, E371A, E371Q, E371W, E371Y and E371F,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 6.
[0200] In some embodiments, the modified polymerase is a variant of
B103 polymerase that comprises an amino acid sequence that is at
least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to
any one of the amino acid sequences SEQ ID NO: 6, SEQ ID NO: 7 and
SEQ ID NO: 8, or to any biologically active fragment thereof, and
further comprises an amino acid modification at position 372,
wherein the numbering is relative to a B103 polymerase having the
amino acid sequence of SEQ ID NO: 7. The modification can include,
for example, one or more amino acid substitutions, additions,
deletions or chemical modifications. In some embodiments, the
modified polymerase is a variant of B103 polymerase that comprises
an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%,
95%, 97%, 98% or 99% identical to any one of the amino acid
sequences SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8, or to any
biologically active fragment thereof, wherein the amino acid at
position 372 is any amino acid other than glutamic acid (E). In
some embodiments, the modified polymerase comprises a lysine (K)
residue at position 372. In some embodiments, the amino acid at
position 372 is any amino acid other than glutamic acid (E) or
lysine (K). In some embodiments, the amino acid at position 372 of
the modified polymerase is glycine (G), histidine (H), serine (S),
arginine (R), alanine (A), glutamine (Q), tryptophan (W), tyrosine
(Y), phenylalanine (F) or any other natural or non-natural amino
acid, other than glutamic acid (E). In some embodiments, the
modified polymerase is a variant of B103 polymerase that comprises
an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%,
95%, 97%, 98% or 99% identical to any one of the amino acid
sequences SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8, or to any
biologically active fragment thereof, and further comprises one or
more amino acid substitutions selected from the group consisting
of: K372G, K372E, K372T, K372S, K372R, K372A, K372Q, K372W, K372Y
and K372F, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 6.
[0201] In some embodiments, the modified polymerase is a variant of
B103 polymerase that comprises an amino acid sequence that is at
least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to
any one of the amino acid sequences SEQ ID NO: 6, SEQ ID NO: 7 and
SEQ ID NO: 8, or to any biologically active fragment thereof, and
further comprises an amino acid modification at position 380,
wherein the numbering is relative to a B103 polymerase having the
amino acid sequence of SEQ ID NO: 7. The modification can include,
for example, one or more amino acid substitutions, additions,
deletions or chemical modifications. In some embodiments, the amino
acid at position 380 can be any amino acid other than lysine (K).
In some embodiments, the amino acid at position 380 of the modified
polymerase is glycine (G), histidine (H), serine (S), arginine (R),
alanine (A), glutamine (Q), tryptophan (W), tyrosine (Y),
phenylalanine (F) or any other natural or non-natural amino acid,
other than lysine (K). In some embodiments, the modified polymerase
is a variant of B103 polymerase that comprises an amino acid
sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or
99% identical to any one of the amino acid sequences SEQ ID NO: 6,
SEQ ID NO: 7 and SEQ ID NO: 8, or to any biologically active
fragment thereof, and further comprises one or more amino acid
substitutions selected from the group consisting of: K380E, K380T,
K380S, K380R, K380A, K380Q, K380W, K380Y and K380F, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO:
6.
[0202] In some embodiments, the modified polymerase is a variant of
B103 polymerase that comprises an amino acid sequence that is at
least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to
any one of the amino acid sequences SEQ ID NO: 6, SEQ ID NO: 7 and
SEQ ID NO: 8, or to any biologically active fragment thereof, and
further comprises an amino acid modification at position 507,
wherein the numbering is relative to a B103 polymerase having the
amino acid sequence of SEQ ID NO: 7. The modification can include,
for example, one or more amino acid substitutions, additions,
deletions or chemical modifications. In some embodiments, the amino
acid at position 507 can be any amino acid other than aspartic acid
(D). In some embodiments, the modified polymerase comprises a
histidine (H) residue at position D. In some embodiments, the amino
acid at position 380 of the modified polymerase is glycine (G),
histidine (H), serine (S), arginine (R), alanine (A), glutamine
(Q), tryptophan (W), tyrosine (Y), phenylalanine (F) or any other
natural or non-natural amino acid, other than aspartic acid (D). In
some embodiments, the modified polymerase is a variant of B103
polymerase that comprises an amino acid sequence that is at least
70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to any one
of the amino acid sequences SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID
NO: 8, or to any biologically active fragment thereof, and further
comprises one or more amino acid substitutions selected from the
group consisting of: D507H, D507G, D507E, D507T, D507S, D507R,
D507A, D507R, D507Q, D507W, D507Y and D507F, wherein the numbering
is relative to the amino acid sequence of SEQ ID NO: 6.
[0203] In some embodiments, the modified polymerase is a variant of
B103 polymerase that comprises an amino acid sequence that is at
least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to
any one of the amino acid sequences SEQ ID NO: 6, SEQ ID NO: 7 and
SEQ ID NO: 8, or to any biologically active fragment thereof, and
further comprises an amino acid modification at position 509,
wherein the numbering is relative to a B103 polymerase having the
amino acid sequence of SEQ ID NO: 7. The modification can include,
for example, one or more amino acid substitutions, additions,
deletions or chemical modifications. In some embodiments, the amino
acid at position 509 can be any amino acid other than lysine (K).
In some embodiments, the amino acid at position 509 of the modified
polymerase is glycine (G), histidine (H), serine (S), arginine (R),
alanine (A), glutamine (Q), tryptophan (W), tyrosine (Y),
phenylalanine (F) or any other natural or non-natural amino acid,
other than lysine (K). In some embodiments, the modified polymerase
is a variant of B103 polymerase that comprises an amino acid
sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or
99% identical to any one of the amino acid sequences SEQ ID NO: 6,
SEQ ID NO: 7 and SEQ ID NO: 8, or to any biologically active
fragment thereof, and further comprises one or more amino acid
substitutions selected from the group consisting of: K509H, K509G,
K509D, K509R, K509E, K509T, K509S, K509R, K509A, K509Q, K509W,
K509Y and K509F, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 6.
[0204] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95% or 99% identical
to the amino acid sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID
NO: 8 and comprises any one, two, three or more of the mutations
selected from the group consisting of: D9A, E11A, T12I, H58R, N59D,
D63A, D166A, Q377A, S385G, T365G, T365F, T365G, T365S, T365K,
T365R, T365A, T365Q, T365W, T365Y, T365H, H370G, H370T, H370S,
H370K, H370R, H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H,
E371T, E371S, E371K, E371R, E371A, E371Q, E371W, E371Y, E371F,
K372G, K372E, K372T, K372S, K372R, K372A, K372Q, K372W, K372Y,
K372F, K380E, K380T, K380S, K380R, K380A, K380Q, K380W, K380Y,
K380F, F383L, D384N, A481E, A481F, A481G, A481S, A481R, A481K,
A481A, A481T, A481Q, A481W, A481Y, D507H, D507G, D507E, D507T,
D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F, K509H,
K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A, K509Q,
K509W, K509Y and K509F, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6, 7 or 8, respectively.
[0205] In some embodiments, the modified polymerase comprises one
or more amino acid substitutions selected from the group consisting
of: D9A, E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A,
Q377A and S385G, and further includes one or more amino acid
substitutions selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, F383L, D384N, A481E, A481F, A481G,
A481S, A481R, A481K, A481A, A481T, A481Q, A481W, A481Y, D507H,
D507G, D507E, D507T, D507S, D507R, D507A, D507R, D507Q, D507W,
D507Y, D507F, K509H, K509G, K509D, K509R, K509E, K509T, K509S,
K509R, K509A, K509Q, K509W, K509Y and K509F, wherein the numbering
is relative to the sequence of SEQ ID NO: 6.
[0206] In some embodiments, the modified polymerase comprises one,
or more amino acid substitutions selected from the group consisting
of: D9A, E11A, T12I, H58R, N59D, D63A, D166A, Q377A and S385G, and
further comprises amino acid substitutions at two or more positions
selected from the group consisting of: 370, 372 and 507.
[0207] In some embodiments, the modified polymerase comprises one
or more amino acid substitutions selected from the group consisting
of: D9A, E11A, T12I, H58R, N59D, D63A, D166A, Q377A and S385G, and
further comprises the amino acid substitutions K372Y and D507H.
[0208] In some embodiments, the modified polymerase comprises one
or more amino acid substitutions selected from the group consisting
of: D9A, E11A, T12I, H58R, N59D, D63A, D166A, Q377A and S385G, and
further comprises the amino acid substitutions H370R and D507H.
[0209] In some embodiments, the modified polymerase comprises one
or more amino acid substitutions selected from the group consisting
of: D9A, E11A, T12I, H58R, N59D, D63A, D166A, Q377A and S385G, and
further comprises two or more amino acid substitutions selected
from the group consisting of: H370R, K372Y and D507H.
[0210] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95%, 97%, 98% or 99%
identical to the amino acid sequence of SEQ ID NO: 7 and further
comprises an amino acid mutation at one, two, three or more amino
acid positions selected from the group consisting of: 9, 11, 12,
58, 59, 63, 162, 162, 166, 377 and 385, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 6. Typically,
such a modified polymerase will exhibit reduced 3' to 5'
exonuclease activity relative to reference polymerase having the
amino acid sequence of SEQ ID NO: 7.
[0211] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95%, 97%, 98% or 99%
identical to the amino acid sequence of SEQ ID NO: 7 and further
comprises one, two, three or more amino acid mutations selected
from the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D,
D63A, Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering
is relative to the amino acid sequence of SEQ ID NO: 6. In some
embodiments, the modified polymerase comprises any one, two, three,
four, five or all of these mutations. In some embodiments, the
modified polymerase comprises the amino acid substitution D166A. In
some embodiments, the modified polymerase comprises the amino acid
substitutions D9A and D63A. In some embodiments, the modified
polymerase comprises the amino acid substitutions N59D and T12I.
Typically, such modified polymerases will exhibit reduced 3' to 5'
exonuclease activity relative to reference polymerase having the
amino acid sequence of SEQ ID NO: 7.
[0212] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 7
and further comprises an amino acid substitution at one or more
positions selected from the group consisting of: 2, 73, 107, 147,
221, 318, 339, 359, 372, 405, 503, 511, 544 and 550, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
Typically, this modified polymerase can exhibit increased
photostability and/or increased nanoparticle tolerance relative to
a reference polymerase having the amino acid sequence of SEQ ID NO:
7.
[0213] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 7
and further includes a mutation at position 370. In some
embodiments, the mutation is selected from the group consisting of:
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y and
H370F, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 6. Optionally, this modified polymerase comprises the
amino acid mutation H370R. Typically, this modified polymerase can
exhibit an increased branching ratio and/or increased nucleotide
binding affinity relative to a reference polymerase having the
amino acid sequence of SEQ ID NO: 7.
[0214] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 7
and further includes a mutation at position 365, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the mutation is selected from the group
consisting of: T365H, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W and T365Y, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6. Optionally, this modified
polymerase comprises the amino acid mutation T365F. Typically, this
modified polymerase can exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 7.
[0215] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 7
and further includes a mutation at position 372, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the mutation is selected from the group
consisting of: K372G, K372E, K372T, K372S, K372R, K372A, K372Q,
K372W, K372Y and K372F, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6. Optionally, this modified
polymerase comprises the amino acid mutation K372Y. Typically, this
modified polymerase can'exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 7.
[0216] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 7
and further includes a mutation at position 481, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the mutation is selected from the group
consisting of: A481E, A481F, A481G, A481S, A481R, A481K, A481A,
A481T, A481Q, A481W and A481Y, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 6. Optionally, this modified
polymerase comprises the amino acid mutation A481E. Typically, this
modified polymerase can exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 7.
[0217] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 7
and further includes a mutation at position 509, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the mutation is selected from the group
consisting of: K509E, K509F, K509G, K509S, K509R, K509K, K509A,
K509T, K509Q, K509W and K509Y, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 6. Optionally, this modified
polymerase comprises the amino acid mutation K509Y. Typically, this
modified polymerase can exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 7.
[0218] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
7 and further includes an amino acid mutation at any one, two,
three or more positions selected from the group consisting of: 9,
12, 14, 15, 58, 59, 61, 63, 98, 129, 176, 185, 186, 187, 195, 208,
246, 247, 248, 251, 252, 256, 300, 302, 310, 357, 360, 362, 365,
367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380,
383, 384, 385, 386, 387, 389, 390, 392, 399, 411, 419, 430, 455,
475, 477, 481, 483, 493, 494, 497, 507, 509, 511, 526, 528, 529,
531, 535, 544, 555, 567, 569 and 572, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 6. In some
embodiments, the modifications can include deletions, additions and
substitutions. The substitutions can be conservative or
non-conservative substitutions. Optionally, this modified
polymerase comprises the amino acid substitution H370R. In some
embodiments, the polymerase further comprises one or more mutations
reducing the exonuclease activity as described herein such as, for
example, the amino acid substitution D166A. Typically, this
modified polymerase can exhibit increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 7.
[0219] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
7 and further comprises an amino acid mutation at any one, two,
three or more positions selected from the group consisting of: 2,
9, 12, 14, 15, 58, 59, 61, 63, 73, 98, 107, 129, 147, 166, 176,
185, 186, 187, 195, 208, 221, 246, 247, 248, 251, 252, 256, 300,
302, 310, 318, 339, 357, 359, 360, 362, 367, 368, 369, 370, 371,
372, 373, 374, 375, 376, 377, 378, 380, 383, 384, 385, 386, 387,
389, 390, 392, 399, 405, 411, 419, 430, 455, 475, 477, 481, 483,
493, 494, 497, 503, 507, 509, 511, 526, 528, 529, 531, 535, 544,
550, 552, 555, 567, 569 and 572, wherein the numbering is relative
to the amino acid sequence of SEQ ID NO: 6. In some embodiments,
the modifications can include deletions, additions and
substitutions. The substitutions can be conservative or
non-conservative substitutions. Optionally, this modified
polymerase comprises the amino acid substitution H370R. In some
embodiments, the polymerase further comprises one or more mutations
reducing the exonuclease activity as described herein such as, for
example, the amino acid substitution D166A. Typically, this
modified polymerase can exhibit increased branching ratio,
increased nucleotide binding affinity, increased photostability
and/or increased nanoparticle tolerance relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 7.
[0220] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 7
and further includes any one, two, three or more amino acid
mutations selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, F383L, D384N, A481E, A481F, A481G,
A481S, A481R, A481K, A481A, A481T, A481Q, A481W, A481Y, D507H,
D507G, D507E, D507T, D507S, D507R, D507A, D507R, D507Q, D507W,
D507Y, D507F, K509H, K509G, K509D, K509R, K509E, K509T, K509S,
K509R, K509A, K509Q, K509W, K509Y and K509F, wherein the numbering
is relative to the amino acid sequence of SEQ ID NO: 6. In some
embodiments, the modified polymerase comprises the amino acid
mutations Typically, this modified polymerase can exhibit an
increased branching ratio and/or increased nucleotide binding
affinity relative to a reference polymerase having the amino acid
sequence of SEQ ID NO: 7. Optionally, the modified polymerase can
further include one or more mutations reducing 3' to 5' exonuclease
activity selected from the group consisting of: D9A, E11A, E11I,
T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and S385G,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 6.
[0221] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 7
and further includes amino acid mutations at positions 372 and 509,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 7. In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 7
and further includes the amino acid substitutions E372Y and K509Y,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 7. In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 7
and further includes amino acid mutations at positions 365, 372 and
509, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 7. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98%, 99% or 100% identical to the amino acid sequence of
SEQ ID NO: 7 and further includes the amino acid substitutions
T365F, E372Y and K509Y, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 7. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 7 and further includes amino acid
mutations at positions 365, 372, 481 and 509, wherein the numbering
is relative to the amino acid sequence of SEQ ID NO: 7. In some
embodiments, the modified polymerase comprises an amino acid
sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100%
identical to the amino acid sequence of SEQ ID NO: 7 and further
includes the amino acid substitutions T365F, E372Y, A481E and
K509Y, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 6. Typically, such modified polymerases can exhibit
an increased branching ratio and/or increased nucleotide binding
affinity relative to a reference polymerase having the amino acid
sequence of SEQ ID NO: 7. Optionally, the modified polymerase can
further include one or more mutations reducing 3' to 5' exonuclease
activity selected from the group consisting of: D9A, E11A, E11I,
T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and S385G,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 7.
[0222] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
7 and further comprises the amino acid mutation H370R. Optionally,
the polymerase can further comprise any one, two, three or more
amino acid mutations selected from the group consisting of: S2P,
Q73H, R107K, T147A, K221R, V318A, L339M, D359E, E372K, D405E,
V503N, K511I, A544R, M550T, E371G, E371H, E371T, E371S, E371K,
E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E, K372T,
K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E, K380T,
K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, D507H, D507G,
D507E, D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y,
D507F, K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R,
K509A, K509Q, K509W, K509Y and K509F, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 6. Typically,
this modified polymerase can exhibit increase branching ratio
and/or increased photostability and/or increased nanoparticle
tolerance relative to a reference polymerase having the amino acid
sequence of SEQ ID NO: 7. Optionally, the modified polymerase can
further include one or more mutations reducing 3' to 5' exonuclease
activity selected from the group consisting of: D9A, E11A, E11I,
T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and S385G,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 7.
[0223] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
7 and further includes an amino acid mutation selected from the
group: H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W,
H370Y and H370F, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. Typically, this modified polymerase
can exhibit an increase t.sub.-1 value in the presence of the
dye-labeled nucleotides relative to a reference polymerase having
the amino acid sequence of SEQ ID NO: 7. In some embodiments, the
t.sub.-1 value of the modified polymerase is increased by at least
about 105%, 110%, 125%, 150%, 175%, 200%, 250%, 500%, 750%, or
1000% relative to the reference polymerase. Optionally, the
modified polymerase can further include one or more mutations
reducing 3' to 5' exonuclease activity selected from the group
consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A, Y162F,
Y162C, D166A, Q377A and S385G, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include any one, two, three or more amino
acid mutations selected from the group consisting of: S2P, Q73H,
T147A, K221R, V318A, L339M, D359E, I-1370R, E372K, D405E, V503A,
K511I, A544R and M550T, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 7. In some embodiments, the
t.sub.-1 value is increased in the presence of the dye-labeled
nucleotide AF647-C6-dG6P. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 7 and further includes the amino acid
mutation H370R, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 7.
[0224] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
7 and further includes an amino acid mutation selected from the
group: K380G, K380E, K380T, K380S, K380R, K380A, K380Q, K380W,
K380Y and K380F, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. Typically, this modified polymerase
can exhibit an increased t.sub.pol value in the presence of the
dye-labeled nucleotides relative to a reference polymerase having
the amino acid sequence of SEQ ID NO: 7. In some embodiments, the
t.sub.pol value of the modified polymerase is increased by at least
about 105%, 110%, 125%, 150%, 175%, 200%, 250%, 500%, 750%, or
1000% relative to the reference polymerase. Optionally, the
modified polymerase can further include one or more mutations
reducing 3' to 5' exonuclease activity selected from the group
consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A, Y162F,
Y162C, D166A, Q377A and S385G, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include any one, two, three or more amino
acid mutations selected from the group consisting of: S2P, Q73H,
T147A, K221R, V318A, L339M, D359E, H370R, E372K, D405E, V503A,
K511I, A544R and M550T, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6. In some embodiments, the
t.sub.pol value is increased in the presence of the dye-labeled
nucleotide AF647-C6-dG6P. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 7 and further includes the amino acid
mutation K380R, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 7.
[0225] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
7 and further comprises any one, two, three or more amino acid
mutations selected from the group consisting of: S2P, Q73H, T147A,
K221R, V318A, L339M, D359E, H370R, E372K, D405E, V503A, K511I,
A544R and M550T, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 6. Optionally, the modified polymerase
can further comprise one, two or three amino acid mutations
selected from the group: T365G, T365F, T365G, T365S, T365K, T365R,
T365A, T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K,
H370R, H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T,
E371S, E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G,
K372E, K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F,
K380E, K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F,
A481E, A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q,
A481W, A481Y, D507H, D507G, D507E, D507T, D507S, D507R, D507A,
D507R, D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R,
K509E, K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 6. Typically, this modified polymerase can exhibit increase
branching ratio and/or increased photostability and/or increased
nanoparticle tolerance relative to a reference polymerase having
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 7.
[0226] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
1 and further includes an amino acid mutation selected from the
group: T373G, T373E, T373T, T373S, T373R, T373A, K T373Q, T373W,
T373Y and T373F, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 1. Typically, this modified polymerase
can exhibit an increased t.sub.-1 value in the presence of the
dye-labeled nucleotides relative to a reference polymerase having
the amino acid sequence of SEQ ID NO: 1. In some embodiments, the
t.sub.-1 value of the modified polymerase is increased by at least
about 105%, 110%, 125%, 150%, 175%, 200%, 250%, 500%, 750%, or
1000% relative to the reference polymerase. Optionally, the
modified polymerase can further include one or more mutations
reducing 3' to 5' exonuclease activity selected from the group
consisting of: D12A, E14I, E14A, T15I, N62D, D66A, Y165F, Y165C,
and D169A, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 1. In some embodiments, the t.sub.-1 value
is increased in the presence of the dye-labeled nucleotide
AF647-C6-dG6P. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 70%, 80%, 85%,
90%, 95%, 97%, 98%, 99% or 100% identical to the amino acid
sequence of SEQ ID NO: 7 and further includes the amino acid
mutation T373R, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 1. In some embodiments, the modified
polymerase further includes the mutations D12A and D66A.
[0227] Also disclosed herein are exemplary nucleotide sequences
(polynucleotides) encoding the modified polymerases of the present
disclosure.
[0228] In some embodiments, the nucleotide sequence encodes a
modified polymerase having or comprising an amino acid sequence
that is at least 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to
the amino acid sequence of SEQ ID NO: 7.
[0229] In some embodiments, the nucleotide sequence encoding the
modified polymerase having the amino acid sequence of SEQ ID NO: 7
comprises the following nucleotide sequence:
TABLE-US-00009 (SEQ ID NO: 9)
atgcctcgcaaaatgtttagctgcgattttgaaaccaccaccaaactggatgattgtcgtgtttgggcc
tatggctatatggaaattggcaacctggataattataaaatcggcaatagcctggatgaatttatgcag
tgggttatggaaattcaggccgatctgtattttcataacctgaaatttgatggtgcctttattgtgaat
tggctggaacatcatggctttaaatggtctaatgaaggcctgccgaatacctataacaccatcattagc
aaaatgggccagtggtatatgattgatatttgctttggctataaaggcaaacgtaaactgcataccgtg
atttatgatagcctgaaaaaactgccgtttccggtgaaaaaaatcgccaaagatttccaattaccttta
ctgaagggtgatattgattatcatgcagaacgtccggttggtcatgaaattacaccggaagaatatgaa
tacatcaagaatgatattgaaattattgcccgtgccctggatattcagtttaaacagggtctggatcgt
atgaccgcaggtagcgattctctgaaaggctttaaagatattctgagcaccaaaaaatttaacaaagtg
tttccgaaactgagcctgccgatggataaagaaattcgtcgtgcctatcgtggtggttttacctggctg
aatgataaatataaagaaaaagaaattggcgaaggcatggtttttgatgttaatagcctgtatccgagc
cagatgtatagccgtccgctgccgtatggtgcaccgattgtgtttcagggcaaatatgaaaaagatgaa
cagtatccgctgtatattcagcgcatccgctttgaatttgaactgaaagaaggctatatcccgaccatc
cagattaaaaaaaatccgttttttaaaggcaacgaatatctgaaaaatagcggtgcagaaccggttgaa
ctgtatctgaccaatgtggatctggaactgatccaggaacattatgaaatgtacaacgtggaatatatt
gatggttttaaatttcgcgaaaaaaccggtctgtttaaagagttcattgataaatggacctatgtgaaa
acccatgaaaaaggtgcaaaaaaacagctggccaaactgatgttgaattccctgtatggcaaatttgca
agcaatccggatgttaccggtaaagttccgtatctgaaagaagatggtagcctgggttttcgtgttggt
gatgaagaatataaagatccggtttataccccgatgggtgtttttattaccgcatgggcacgttttacc
accattaccgcagcacaggcatgttatgaccgcattatttattgcgataccgatagcattcatctgacc
ggcaccgaagttccggaaattattaaagatattgttgatccgaaaaaactgggttattgggcacatgaa
agcacctttaaacgtgcaaaatatctgcgccagaaaacctatattcaggatatttatgccaaagaagtg
gacggtaaactgattgaatgttctccggatgaagcaaccaccacaaaatttagcgttaaatgcgcaggt
atgaccgataccattaaaaaaaaagtgacctttgataactttcgtgtgggttttagcagcaccggtaaa
ccgaaaccggttcaggttaatggtggtgttgttctggttgatagcgtgtttaccattaaataa
[0230] In some embodiments, the nucleotide sequence of the modified
polymerase comprises a polynucleotide that is at least 80%, 85%,
90%, 95%, 97%, 98% or 99% identical to the nucleotide sequence of
SEQ ID NO: 9.
[0231] In some embodiments, the modified polymerase comprising the
amino acid sequence of SEQ ID NO: 7 can be encoded by the following
nucleotide sequence:
TABLE-US-00010 (SEQ ID NO: 10)
ATGCCTAGAAAAATGTTTAGTTGTGACTTTGAGACGACTACAAAGTTAGACGATTGTCGTGTATGGGCA
TATGGCTATATGGAAATCGGTAATCTCGACAACTACAAGATTGGAAATAGCTTAGATGAATTCATGCAG
TGGGTTATGGAAATTCAAGCTGATTTATATTTCCACAATCTAAAATTTGACGGTGCTTTCATTGTAAAC
TGGTTAGAGCATCATGGTTTTAAGTGGTCAAACGAAGGGTTACCGAATACTTATAACACAATAATATCA
AAAATGGGTCAATGGTATATGATTGACATATGTTTCGGCTATAAGGGAAAACGGAAATTACATACAGTG
ATATACGACAGCTTAAAGAAATTGCCGTTCCCAGTAAAGAAAATAGCGAAAGATTTTCAATTACCGTTA
TTGAAGGGTGACATTGATTACCACGCTGAACGTCCTGTTGGACATGAGATAACACCCGAAGAATACGAG
TATATTAAGAACGACATAGAAATTATCGCACGTGCACTTGACATTCAATTTAAACAGGGTTTAGACCGA
ATGACAGCTGGGAGCGATAGCCTTAAAGGGTTTAAGGACATACTTAGCACCAAGAAATTTAACAAGGTG
TTTCCTAAGCTTAGCCTACCAATGGATAAAGAAATAAGGCGAGCTTATCGTGGTGGCTTCACATGGTTA
AACGATAAATACAAAGAAAAAGAGATTGGTGAAGGTATGGTGTTTGACGTTAACAGCCTATACCCCAGT
CAGATGTATTCCCGACCACTCCCGTACGGAGCGCCAATCGTATTCCAAGGAAAGTATGAGAAAGATGAG
CAATATCCGCTCTATATACAGCGTATCAGATTTGAGTTTGAATTGAAAGAGGGCTATATACCCACAATT
CAGATTAAGAAAAATCCCTTTTTTAAGGGTAATGAGTATCTTAAAAACAGTGGCGCTGAGCCTGTTGAA
CTATATCTTACTAATGTAGATTTAGAATTAATACAGGAACACTACGAAATGTATAACGTTGAGTATATT
GACGGATTTAAATTCCGTGAAAAGACTGGATTATTCAAAGAGTTTATTGATAAATGGACATATGTAAAA
ACTCATGAAAAGGGAGCTAAGAAACAATTGGCTAAGCTAATGTTGAATAGTCTCTATGGTAAATTTGCA
AGTAACCCTGACGTTACAGGTAAAGTCCCTTATTTAAAAGAAGATGGGAGCCTTGGTTTCCGTGTTGGT
GATGAGGAATATAAAGACCCTGTTTATACACCTATGGGTGTGTTTATAACGGCATGGGCTAGATTTACA
ACTATAACAGCGGCACAAGCGTGTTACGATAGAATTATATATTGTGACACTGATAGTATACATTTAACA
GGTACAGAAGTACCAGAAATAATAAAGGATATTGTTGATCCAAAAAAGTTAGGGTACTGGGCGCATGAA
AGCACATTTAAGAGAGCAAAATATTTACGTCAGAAAACGTATATTCAAGACATATATGCGAAAGAGGTT
GACGGTAAATTGATAGAGTGTTCACCTGATGAAGCTACGACAACTAAATTCAGTGTGAAATGTGCCGGA
ATGACTGACACTATCAAAAAGAAAGTCACATTTGATAACTTTAGAGTTGGTTTCAGTAGCACGGGTAAA
CCTAAACCAGTTCAAGTTAATGGCGGGGTAGTGTTGGTTGATAGTGTGTTTACGATTAAA
[0232] In some embodiments, the nucleotide sequence of the modified
polymerase comprises a polynucleotide that is at least 80%, 85%,
90%, 95%, 97%, 98% or 99% identical to the nucleotide sequence of
SEQ ID NO: 10.
[0233] In some embodiments, the polynucleotide encodes a modified
polymerase having or comprising an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the amino
acid sequence of SEQ ID NO: 7.
[0234] In some embodiments, the modified polymerase comprising the
amino acid sequence of SEQ ID NO: 8 can be encoded by the following
nucleotide sequence:
TABLE-US-00011 (SEQ ID NO: 11)
atgcctcgcaaaatgtttagctgcgattttgaaaccaccaccaaactggatgattgtcgtgtttgggcc
tatggctatatggaaattggcaacctggataattataaaatcggcaatagcctggatgaatttatgcag
tgggttatggaaattcaggccgatctgtattttcataacctgaaatttgatggtgcctttattgtgaat
tggctggaacatcatggctttaaatggtctaatgaaggcctgccgaatacctataacaccatcattagc
aaaatgggccagtggtatatgattgatatttgctttggctataaaggcaaacgtaaactgcataccgtg
atttatgatagcctgaaaaaactgccgtttccggtgaaaaaaatcgccaaagatttccaattaccttta
ctgaagggtgatattgattatcatgcagaacgtccggttggtcatgaaattacaccggaagaatatgaa
tacatcaagaatgctattgaaattattgcccgtgccctggatattcagtttaaacagggtctggatcgt
atgaccgcaggtagcgattctctgaaaggctttaaagatattctgagcaccaaaaaatttaacaaagtg
tttccgaaactgagcctgccgatggataaagaaattcgtcgtgcctatcgtggtggttttacctggctg
aatgataaatataaagaaaaagaaattggcgaaggcatggtttttgatgttaatagcctgtatccgagc
cagatgtatagccgtccgctgccgtatggtgcaccgattgtgtttcagggcaaatatgaaaaagatgaa
cagtatccgctgtatattcagcgcatccgctttgaatttgaactgaaagaaggctatatcccgaccatc
cagattaaaaaaaatccgttttttaaaggcaacgaatatctgaaaaatagcggtgcagaaccggttgaa
ctgtatctgaccaatgtggatctggaactgatccaggaacattatgaaatgtacaacgtggaatatatt
gatggttttaaatttcgcgaaaaaaccggtctgtttaaagagttcattgataaatggacctatgtgaaa
acccatgaaaaaggtgcaaaaaaacagctggccaaactgatgttgaattccctgtatggcaaatttgca
agcaatccggatgttaccggtaaagttccgtatctgaaagaagatggtagcctgggttttcgtgttggt
gatgaagaatataaagatccggtttataccccgatgggtgtttttattaccgcatgggcacgttttacc
accattaccgcagcacaggcatgttatgaccgcattatttattgcgataccgatagcattcatctgacc
ggcaccgaagttccggaaattattaaagatattgttgatccgaaaaaactgggttattgggcacatgaa
agcacctttaaacgtgcaaaatatctgcgccagaaaacctatattcaggatatttatgccaaagaagtg
gacggtaaactgattgaatgttctccggatgaagcaaccaccacaaaatttagcgttaaatgcgcaggt
atgaccgataccattaaaaaaaaagtgacctttgataactttcgtgtgggttttagcagcaccggtaaa
ccgaaaccggttcaggttaatggtggtgttgttctggttgatagcgtgtttaccattaaataa
[0235] In some embodiments, the nucleotide sequence of the modified
polymerase comprises a polynucleotide that is at least 80%, 85%,
90%, 95%, 97%, 98% or 99% identical to the nucleotide sequence of
SEQ ID NO: 11.
[0236] In some embodiments, the modified polymerase comprising the
amino acid sequence of SEQ ID NO: 8 can be encoded by the following
nucleotide sequence:
TABLE-US-00012 (SEQ ID NO: 12)
ATGCCTAGAAAAATGTTTAGTTGTGACTTTGAGACGACTACAAAGTTAGACGATTGTCGTGTATGGGCA
TATGGCTATATGGAAATCGGTAATCTCGACAACTACAAGATTGGAAATAGCTTAGATGAATTCATGCAG
TGGGTTATGGAAATTCAAGCTGATTTATATTTCCACAATCTAAAATTTGACGGTGCTTTCATTGTAAAC
TGGTTAGAGCATCATGGTTTTAAGTGGTCAAACGAAGGGTTACCGAATACTTATAACACAATAATATCA
AAAATGGGTCAATGGTATATGATTGACATATGTTTCGGCTATAAGGGAAAACGGAAATTACATACAGTG
ATATACGACAGCTTAAAGAAATTGCCGTTCCCAGTAAAGAAAATAGCGAAAGATTTTCAATTACCGTTA
TTGAAGGGTGACATTGATTACCACGCTGAACGTCCTGTTGGACATGAGATAACACCCGAAGAATACGAG
TATATTAAGAACGCCATAGAAATTATCGCACGTGCACTTGACATTCAATTTAAACAGGGTTTAGACCGA
ATGACAGCTGGGAGCGATAGCCTTAAAGGGTTTAAGGACATACTTAGCACCAAGAAATTTAACAAGGTG
TTTCCTAAGCTTAGCCTACCAATGGATAAAGAAATAAGGCGAGCTTATCGTGGTGGCTTCACATGGTTA
AACGATAAATACAAAGAAAAAGAGATTGGTGAAGGTATGGTGTTTGACGTTAACAGCCTATACCCCAGT
CAGATGTATTCCCGACCACTCCCGTACGGAGCGCCAATCGTATTCCAAGGAAAGTATGAGAAAGATGAG
CAATATCCGCTCTATATACAGCGTATCAGATTTGAGTTTGAATTGAAAGAGGGCTATATACCCACAATT
CAGATTAAGAAAAATCCCTTTTTTAAGGGTAATGAGTATCTTAAAAACAGTGGCGCTGAGCCTGTTGAA
CTATATCTTACTAATGTAGATTTAGAATTAATACAGGAACACTACGAAATGTATAACGTTGAGTATATT
GACGGATTTAAATTCCGTGAAAAGACTGGATTATTCAAAGAGTTTATTGATAAATGGACATATGTAAAA
ACTCATGAAAAGGGAGCTAAGAAACAATTGGCTAAGCTAATGTTGAATAGTCTCTATGGTAAATTTGCA
AGTAACCCTGACGTTACAGGTAAAGTCCCTTATTTAAAAGAAGATGGGAGCCTTGGTTTCCGTGTTGGT
GATGAGGAATATAAAGACCCTGTTTATACACCTATGGGTGTGTTTATAACGGCATGGGCTAGATTTACA
ACTATAACAGCGGCACAAGCGTGTTACGATAGAATTATATATTGTGACACTGATAGTATACATTTAACA
GGTACAGAAGTACCAGAAATAATAAAGGATATTGTTGATCCAAAAAAGTTAGGGTACTGGGCGCATGAA
AGCACATTTAAGAGAGCAAAATATTTACGTCAGAAAACGTATATTCAAGACATATATGCGAAAGAGGTT
GACGGTAAATTGATAGAGTGTTCACCTGATGAAGCTACGACAACTAAATTCAGTGTGAAATGTGCCGGA
ATGACTGACACTATCAAAAAGAAAGTCACATTTGATAACTTTAGAGTTGGTTTCAGTAGCACGGGTAAA
CCTAAACCAGTTCAAGTTAATGGCGGGGTAGTGTTGGTTGATAGTGTGTTTACGATTAAA
[0237] In some embodiments, the nucleotide sequence of the modified
polymerase comprises a polynucleotide that is at least 80%, 85%,
90%, 95%, 97%, 98% or 99% identical to the nucleotide sequence of
SEQ ID NO: 12.
[0238] In some embodiments, the polynucleotide encodes a modified
polymerase having or comprising an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the amino
acid sequence of SEQ ID NO: 8, wherein the modified polymerase
comprises any residue other than aspartic acid (D) at position 166,
the numbering being relative to the amino acid sequence of SEQ ID
NO: 8. In some embodiments, the residue at position 166 is alanine
(A).
[0239] In some embodiments, the polynucleotide encodes a modified
polymerase having or comprising an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the amino
acid sequence of SEQ ID NO: 8.
[0240] As the skilled artisan will appreciate, due to the
degeneracy of the genetic code, many different polynucleotides can
encode the modified polymerases disclosed herein, all of which are
within the scope of the present disclosure. An exemplary list of
the various nucleotide "codons" or "triplets" that may encode a
given amino acid is provided in Table 1, below:
TABLE-US-00013 TABLE 1 Amino Acid SLC DNA codons Isoleucine I ATT,
ATC, ATA Leucine L CTT, CTC, CTA, CTG, TTA, TTG Valine V GTT, GTC,
GTA, GTG Phenylalanine F TTT, TTC Methionine M ATG Cysteine C TGT,
TGC Alanine A GCT, GCC, GCA, GCG Glycine G GGT, GGC, GGA, GGG
Proline P CCT, CCC, CCA, CCG Threonine T ACT, ACC, ACA, ACG Serine
S TCT, TCC, TCA, TCG, AGT, AGC Tyrosine Y TAT, TAC Tryptophan W TGG
Glutamine Q CAA, CAG Asparagine N AAT, AAC Histidine H CAT, CAC
Glutamic acid E GAA, GAG Aspartic acid D GAT, GAC Lysine K AAA, AAG
Arginine R CGT, CGC, CGA, CGG, AGA, AGG Stop codons Stop TAA, TAG,
TGA
[0241] Table 1 lists the twenty naturally occurring amino acids
commonly found in proteins, along with the single-letter code
("SLC") typically used to represent these amino acids in protein
databases. The nucleotide codons that typically encode each amino
acid are also listed. As shown in Table 1, 3 of the 64 possible
3-letter combinations of the nucleic acid coding units T, C, A and
G can be used to encode one of the three stop codons (TAA, TAG and
TGA) that typically signals the end of a sequence. The remaining 61
combinations can be used to encode one of the twenty
naturally-occurring amino acids, as indicated in Table 1. As the
skilled artisan will readily appreciate, the corresponding peptide
sequence encoded by any given polynucleotide sequence can typically
be determined unambiguously. Because most amino acids have multiple
codons, however, a number of different polynucleotide sequences can
encode the same protein sequence.
[0242] As indicated in Table 1, most of the naturally occurring
amino acids are coded for by multiple codons. Because codon
preference can vary from species to species, selection or synthesis
of a polynucleotide sequence, and its expression in a given species
can optionally be optimized by selecting for codons that are highly
preferred, or provide optimal translation efficiency or overall
expression levels, in the species of choice. See, for example,
Kudla et al., Science 324:255-258 (2009). In some embodiments the
polynucleotide may be homologous to polynucleotides having the
nucleotide sequence of SEQ ID NO: 9, 10, 11 or 12, and contain
"silent" or "synonymous" mutations that do not alter the peptide
sequence of the encoded peptide product.
[0243] In some embodiments, the polynucleotide is an artificial or
recombinant nucleic acid molecule that hybridizes to a nucleic acid
molecule having the nucleotide sequence of SEQ ID NO: 9, SEQ ID NO:
10, SEQ ID NO: 11 or SEQ ID NO: 12 under highly stringent
conditions over substantially the entire length of the nucleic acid
molecule. Hybridization, or association of nucleic acid molecules
due to hydrogen bonding, base stacking, solvent exclusion and the
like are well known in the art and have been extensively described.
See, e.g., Hanes et al., Gene Probes (Oxford University Press
1995); Tijssen, Laboratory Techniques in Biochemistry and Molecular
Biology (Elsevier, 1993). In one exemplary method, the
polynucleotide is greater than 100 nucleotides in length and is
subjected to high-stringency hybridization conditions comprising
50% formalin with 1 mg of heparin at 42.degree. C. overnight. In
some embodiments, the polynucleotide can also be subjected to a
high-stringency wash following hybridization. In some embodiments,
the high stringency wash can comprise one wash with 0.2.times..SSC
at 65.degree. C. for 15 minutes. In some embodiments, the
polynucleotide can be subjected to extremely stringent conditions
selected to be equal to the thermal melting point (T.sub.m) for a
particular polynucleotide sequence. The T.sub.m, is the temperature
(under defined ionic strength and pH) at which 50% of the test
sequence hybridizes to a perfectly matched probe. For the purposes
of the present invention, generally, "highly stringent"
hybridization and wash conditions are selected to be about
5.degree. C. lower than the T.sub.m for the specific sequence at a
defined ionic strength and pH.
[0244] In some embodiments, disclosed herein is a polynucleotide
encoding modified polymerases, wherein the polynucleotide
specifically hybridizes to a probe nucleic acid having the
nucleotide sequence of SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11
or SEQ ID NO: 12 under stringent, highly stringent or extremely
stringent conditions. A polynucleotide is said to specifically
hybridize to a probe nucleic acid when it hybridizes at least 50%
as well to the probe as to the perfectly matched complementary
target, i.e., with a signal to noise ratio at least half as high as
hybridization of the probe to the target under conditions in which
the perfectly matched probe binds to the perfectly matched
complementary target with a signal to noise ratio that is at least
about 5-10 times as high as that observed for hybridization to any
of the unmatched target nucleic acids.
[0245] The skilled artisan will also appreciate that many variants
of the disclosed nucleotide and/or amino acid sequences are within
the scope and spirit of the present disclosure. For example,
modified polymerases comprising one or more conservative mutations
of the disclosed amino acid sequences and are functionally similar
to the modified polymerases explicitly disclosed herein are also
disclosed. In some embodiments, the modified polymerases of the
present disclosure can be a variant of the various modified
polymerases disclosed herein and additionally contain one or more
conservative mutations.
[0246] In some embodiments, the modified polymerase is a variant of
a polymerase comprising the amino acid sequence of SEQ ID NO: 7,
wherein the variant polymerase further comprises one or more amino
acid substitutions within one or more amino acid motifs selected
from the group consisting of: a motif comprising the amino acid
sequence of SEQ ID NO: 2; a motif comprising the amino acid
sequence of SEQ ID NO: 3; a motif comprising the amino acid
sequence of SEQ ID NO: 4; and a motif comprising the amino acid
sequence of SEQ ID NO: 5. In some embodiments, the one or more
substitutions are conservative mutations. In some embodiments, the
one or more substitutions are non-conservative mutations.
[0247] In some embodiments, the modified polymerase is derived from
a M2 polymerase (also known as M2Y DNA polymerase) having the amino
acid sequence of the SEQ ID NO: 13 as follows:
TABLE-US-00014 (SEQ ID NO: 13) 1 msrkmfscdf etttklddcr vwaygymeig
nldnykigns ldefmqwvme iqadlyfhnl 61 kfdgafivnw leqhgfkwsn
eglpntynti iskmgqwymi dicfgykgkr klhtviydsl 121 kklpfpvkki
akdfqlpllk gdidyhterp vgheitpeey eyikndieii araldiqfkq 181
gldrmtagsd slkgfkdils tkkfnkvfpk lslpmdkeir kayrggftwl ndkykekeig
241 egmvfdvnsl ypsqmysrpl pygapivfqg kyekdeqypl yiqrirfefe
lkegyiptiq 301 ikknpffkgn eylknsgvep velyltnvdl eliqehyely
nveyidgfkf rektglfkdf 361 idkwtyvkth eegakkqlak lmlnslygkf
asnpdvtgkv pylkddgslg frvgdeeykd 421 pvytpmgvfi tawarfttit
aaqacydrii ycdtdsihlt gtevpeiikd ivdpkklgyw 481 ahestfkrak
ylrqktyiqd iyvkevdgkl kecspdeatt tkfsvkcagm tdtikkkvtf 541
dnfavgfssm gkpkpvqvng gvvlvdsvft ik
[0248] In some embodiments, the modified polymerase can comprise an
amino acid sequence that is at least 85%, 90%, 95%, 97%, 98% or 99%
or 100% identical to the amino acid of SEQ ID NO: 13. In some
embodiments, the modified polymerase can have a nanoparticle
tolerance that is at least about 5%, 10%, 25%, 37.5%, 50%, 75%,
100%, 110%, 125%, 150%, 200%, 250%, 500%, 750%, 1,000%, 5,000% or
10,000 relative to the nanoparticle tolerance of a reference Phi-29
polymerase having the amino acid sequence of SEQ ID NO: 1. In some
embodiments, the modified polymerase has a photostability that is
at least about 5%, 10%, 25%, 37.5%, 50%, 75%, 100%, 110%, 125%,
150%, 200%, 250%, 500%, 750%, 1,000%, 5,000% or 10,000 relative to
the photostability of a reference Phi-29 polymerase having the
amino acid sequence of SEQ ID NO: 1.
[0249] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95%, 97%, 98% or 99%
identical to the amino acid sequence of SEQ ID NO: 13 and further
comprises an amino acid mutation at one, two, three or more amino
acid positions selected from the group consisting of: 9, 11, 12,
58, 59, 63, 162, 162, 166, 377 and 385, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 6. Typically,
such a modified polymerase will exhibit reduced 3' to 5'
exonuclease activity relative to reference polymerase having the
amino acid sequence of SEQ ID NO: 13.
[0250] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95%, 97%, 98% or 99%
identical to the amino acid sequence of SEQ ID NO: 13 and further
comprises one, two, three or more amino acid mutations selected
from the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D,
D63A, Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering
is relative to the amino acid sequence of SEQ ID NO: 6. In some
embodiments, the modified polymerase comprises any one, two, three,
four, five or all of these mutations. In some embodiments, the
modified polymerase comprises the amino acid substitution D166A. In
some embodiments, the modified polymerase comprises the amino acid
substitutions D9A and D63A. In some embodiments, the modified
polymerase comprises the amino acid substitutions N59D and T12I.
Typically, such modified polymerases will exhibit reduced 3' to 5'
exonuclease activity relative to reference polymerase having the
amino acid sequence of SEQ ID NO: 13.
[0251] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 13
and further comprises an amino acid substitution at one or more
positions selected from the group consisting of: 2, 73, 147, 221,
318, 339, 359, 372, 405, 503, 511, 544 and 550, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
Typically, this modified polymerase can exhibit increased
photostability and/or increased nanoparticle tolerance relative to
a reference polymerase having the amino acid sequence of SEQ ID NO:
13.
[0252] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 13
and further includes a mutation at position 370. In some
embodiments, the mutation is selected from the group consisting of:
H370G, H370T, H370S, H370K, H370R, I-1370A, H370Q, H370 W, H370Y
and H370F, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 6. Optionally, this modified polymerase
comprises the amino acid mutation H370R. Typically, this modified
polymerase can exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 13.
[0253] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 13
and further includes a mutation at position 365, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the mutation is selected from the group
consisting of: T365H, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W and T365Y, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6. Optionally, this modified
polymerase comprises the amino acid mutation T365F. Typically, this
modified polymerase can exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 13.
[0254] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 13
and further includes a mutation at position 372, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the mutation is selected from the group
consisting of: K372G, K372E, K372T, K372S, K372R, K372A, K372Q,
K372W, K372Y and K372F, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6. Optionally, this modified
polymerase comprises the amino acid mutation K372Y. Typically, this
modified polymerase can exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 13.
[0255] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 13
and further includes a mutation at position 481, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the mutation is selected from the group
consisting of: A481E, A481F, A481G, A481S, A481R, A481K, A481A,
A481T, A481Q, A481W and A481Y, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 6. Optionally, this modified
polymerase comprises the amino acid mutation A481E. Typically, this
modified polymerase can exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 13.
[0256] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 13
and further includes a mutation at position 509, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the mutation is selected from the group
consisting of: K509E, K509F, K509G, K509S, K509R, K509K, K509A,
K509T, K509Q, K509W and K509Y, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 6. Optionally, this modified
polymerase comprises the amino acid mutation K509Y. Typically, this
modified polymerase can exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 13.
[0257] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 13
and further includes any one, two, three or more amino acid
mutations selected from the group consisting of: S2P, Q73H, T147A,
K221R, V318A, L339M, D359E, E372K, D405E, V503A, K511I, A544R and
M550T, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 6. Typically, this modified polymerase can exhibit
increased photostability and/or increased nanoparticle tolerance
relative to a reference polymerase having the amino acid sequence
of SEQ ID NO: 13.
[0258] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
13 and further includes an amino acid mutation at any one, two,
three or more positions selected from the group consisting of: 9,
12, 14, 15, 58, 59, 61, 63, 98, 129, 176, 185, 186, 187, 195, 208,
246, 247, 248, 251, 252, 256, 300, 302, 310, 357, 360, 362, 365,
367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380,
383, 384, 385, 386, 387, 389, 390, 392, 399, 411, 419, 430, 455,
475, 477, 481, 483, 493, 494, 497, 507, 509, 511, 526, 528, 529,
531, 535, 544, 555, 567, 569 and 572, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 6. In some
embodiments, the modifications can include deletions, additions and
substitutions. The substitutions can be conservative or
non-conservative substitutions. Optionally, this modified
polymerase comprises the amino acid substitution H370R. In some
embodiments, the polymerase further comprises one or more mutations
reducing the exonuclease activity as described herein such as, for
example, the amino acid substitution D166A. Typically, this
modified polymerase can exhibit increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 13.
[0259] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
13 and further comprise amino acid mutations at any one, two, three
or more positions selected from the group consisting of: 2, 9, 12,
14, 15, 58, 59, 61, 63, 73, 98, 129, 147, 166, 176, 185, 186, 187,
195, 208, 221, 246, 247, 248, 251, 252, 256, 300, 302, 310, 318,
339, 357, 359, 360, 362, 367, 368, 369, 370, 371, 372, 373, 374,
375, 376, 377, 378, 380, 383, 384, 385, 386, 387, 389, 390, 392,
399, 405, 411, 419, 430, 455, 475, 477, 481, 483, 493, 494, 497,
503, 507, 509, 511, 526, 528, 529, 531, 535, 544, 550, 552, 555,
567, 569 and 572, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 6. In some embodiments, the
modifications can include deletions, additions and substitutions.
The substitutions can be conservative or non-conservative
substitutions. Optionally, this modified polymerase comprises the
amino acid substitution H370R. In some embodiments, the polymerase
further comprises one or more mutations reducing the exonuclease
activity as described herein such as, for example, the amino acid
substitution D166A. Typically, this modified polymerase can exhibit
increased branching ratio, increased nucleotide binding affinity,
increased photostability and/or increased nanoparticle tolerance
relative to a reference polymerase having the amino acid sequence
of SEQ ID NO: 13.
[0260] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 13
and further includes any one, two, three or more amino acid
mutations selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, A481E, A481F, A4810, A481S, A481R,
A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G, D507E,
D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F,
K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A,
K509Q, K509W, K509Y and K509F, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 6. In some embodiments, the
modified polymerase comprises the amino acid mutations Typically,
this modified polymerase can exhibit an increased branching ratio
and/or increased nucleotide binding affinity relative to a
reference polymerase having the amino acid sequence of SEQ ID NO:
13. Optionally, the modified polymerase can further include one or
more mutations reducing 3' to 5' exonuclease activity selected from
the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A,
Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 6.
[0261] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 13
and further includes amino acid mutations at positions 372 and 509,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 6. In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 13
and further includes the amino acid substitutions E372Y and K509Y,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 6. In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 13
and further includes amino acid mutations at positions 365, 372 and
509, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 6. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98%, 99% or 100% identical to the amino acid sequence of
SEQ ID NO: 13 and further includes the amino acid substitutions
T365F, E372Y and K509Y, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 13 and further includes amino
acid mutations at positions 365, 372, 481 and 509, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the modified polymerase comprises an amino
acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%, 99% or
100% identical to the amino acid sequence of SEQ ID NO: 13 and
further includes the amino acid substitutions T365F, E372Y, A481E
and K509Y, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 6. Typically, such modified polymerases can
exhibit an increased branching ratio and/or increased nucleotide
binding affinity relative to a reference polymerase having the
amino acid sequence of SEQ ID NO: 13. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y'162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 6.
[0262] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
13 and further comprises the amino acid mutation H370R. Optionally,
the polymerase can further comprise any one, two, three or more
amino acid mutations selected from the group consisting of:
[0263] S2P, Q73H, R107K, T147A, K221R, V318A, L339M, D359E, E372K,
D405E, V503A, K511I, A544R, M550T, E371G, E371H, E371T, E371S,
E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E,
K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E,
K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, D507H,
D507G, D507E, D507T, D507S, D507R, D507A, D507R, D507Q, D507W,
D507Y, D507F, K509H, K509G, K509D, K509R, K509E, K509T, K509S,
K509R, K509A, K509Q, K509W, K509Y and K509F, wherein the numbering
is relative to the amino acid sequence of SEQ ID NO: 6. Typically,
this modified polymerase can exhibit increase branching ratio
and/or increased photostability and/or increased nanoparticle
tolerance relative to a reference polymerase having the amino acid
sequence of SEQ ID NO: 13. Optionally, the modified polymerase can
further include one or more mutations reducing 3' to 5' exonuclease
activity selected from the group consisting of: D9A, E11A, E11I,
T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and S385G,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 6.
[0264] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
13 and further includes the amino acid mutation H370R, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the modified polymerase comprises an amino
acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 13
and further comprises any one, two, three or more amino acid
mutations selected from the group consisting of: S2P, Q73H, T147A,
K221R, V318A, L339M, D359E, H370R, E372K, D405E, V503A, K511I,
A544R and M550T, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 6. Optionally, the modified polymerase
can further comprise one, two or three amino acid mutations
selected from the group: T365G, T365F, T365G, T365S, T365K, T365R,
T365A, T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K,
H370R, H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T,
E371S, E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G,
K372E, K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F,
K380E, K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F,
A481E, A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q,
A481W, A481Y, D507H, D507G, D507E, D507T, D5075, D507R, D507A,
D507R, D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R,
K509E, K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 6. Typically, this modified polymerase can exhibit increase
branching ratio and/or increased photostability and/or increased
nanoparticle tolerance relative to a reference polymerase having
the amino acid sequence of SEQ ID NO: 13. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 6.
[0265] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
13 and further includes an amino acid mutation selected from the
group: H370G, I-1370T, H370S, I-1370K, H370R, H370A, H370Q, H370 W,
H370Y and H370F, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. Typically, this modified polymerase
can exhibit an increase t.sub.-1 value in the presence of the
dye-labeled nucleotides relative to a reference polymerase having
the amino acid sequence of SEQ ID NO: 13. In some embodiments, the
t.sub.-1 value of the modified polymerase is increased by at least
about 105%, 110%, 125%, 150%, 175%, 200%, 250%, 500%, 750%, or
1000% relative to the reference polymerase. Optionally, the
modified polymerase can further include one or more mutations
reducing 3' to 5' exonuclease activity selected from the group
consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A, Y162F,
Y162C, D166A, Q377A and S385G, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include any one, two, three or more amino
acid mutations selected from the group consisting of: S2P, Q73H,
T147A, K221R, V318A, L339M, D359E, H370R, E372K, D405E, V503A,
K51I, A544R and M550T, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6. In some embodiments, the
t.sub.-1 value is increased in the presence of the dye-labeled
nucleotide AF647-C6-dG6P. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 7 and further includes the amino acid
mutation H370R, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 7.
[0266] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
13 and further includes an amino acid mutation selected from the
group: K380G, K380E, K380T, K380S, K380R, K380A, K380Q, K380W,
K380Y and K380F, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. Typically, this modified polymerase
can exhibit an increased t.sub.pol value in the presence of the
dye-labeled nucleotides relative to a reference polymerase having
the amino acid sequence of SEQ ID NO: 13. In some embodiments, the
t.sub.pol value of the modified polymerase is increased by at least
about 105%, 110%, 125%, 150%, 175%, 200%, 250%, 500%, 750%, or
1000% relative to the reference polymerase. Optionally, the
modified polymerase can further include one or more mutations
reducing 3' to 5' exonuclease activity selected from the group
consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A, Y162F,
Y162C, D166A, Q377A and S385G, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include any one, two, three or more amino
acid mutations selected from the group consisting of: S2P, Q73H,
T147A, K221R, V318A, L339M, D359E, H370R, E372K, D405E, V503A,
K5111, A544R and M550T, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 7. In some embodiments, the
t.sub.pol value is increased in the presence of the dye-labeled
nucleotide AF647-C6-dG6P. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 7 and further includes the amino acid
mutation K380R, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 7.
[0267] In some embodiments, the modified polymerase is derived from
a bacteriophage Nf polymerase having the amino acid sequence of the
SEQ ID NO: 14 as follows:
TABLE-US-00015 (SEQ ID NO: 14) 1 msrkmfscdf etttklddcr vwaygymeig
nldnykigns ldefmqwvme iqadlyfhnl 61 kfdgafivnw leqhgfkwsn
eglpntynti iskmgqwymi dicfgyrgkr klhtviydsl 121 kklpfpvkki
akdfqlpllk gdidyhterp vgheitpeey eyikndieii araldiqfkq 181
gldrmtagsd slkgfkdils tkkfnkvfpk lslpmdkeir kayrggftwl ndkykekeig
241 egmvfdvnsl ypsqmysrpl pygapivfqg kyekdeqypl yiqrirfefe
lkegyiptiq 301 ikknpffkgn eylknsgvep velyltnvdl eliqehyely
nveyidgfkf rektglfkdf 361 idkwtyvkth eegakkqlak lmlnslygkf
asnpdvtgkv pylkddgslg frvgdeeykd 421 pvytpmgvfi tawarfttit
aaqacydrii ycdtdsihlt gtevpeiikd ivdpkklgyw 481 ahestfkrak
ylrqktyiqd iyvkevdgkl kecspdeatt tkfsvkcagm tdtikkkvtf 541
dnfavgfssm gkpkpvqvng gvvlvdsvft ik
[0268] In some embodiments, the modified polymerase can comprise an
amino acid sequence that is at least 85%, 90%, 95%, 97%, 98% or 99%
or 100% identical to the amino acid of SEQ ID NO: 14. In some
embodiments, the modified polymerase can have a nanoparticle
tolerance that is at least about 5%, 10%, 25%, 37.5%, 50%, 75%,
100%, 110%, 125%, 150%, 200%, 250%, 500%, 750%, 1,000%, 5,000% or
10,000 relative to the nanoparticle tolerance of a reference Phi-29
polymerase having the amino acid sequence of SEQ ID NO: 1. In some
embodiments, the modified polymerase has a photostability that is
at least about 5%, 10%, 25%, 37.5%, 50%, 75%, 100%, 110%, 125%,
150%, 200%, 250%, 500%, 750%, 1,000%, 5,000% or 10,000 relative to
the photostability of a reference Phi-29 polymerase having the
amino acid sequence of SEQ ID NO: 1.
[0269] In some embodiments, the modified Nf polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95%, 97%, 98% or 99%
identical to the amino acid sequence of SEQ ID NO: 14 and further
comprises an amino acid mutation at one, two, three or more amino
acid positions selected from the group consisting of: 9, 11, 12,
58, 59, 63, 162, 162, 166, 377 and 385, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 6. Typically,
such a modified polymerase will exhibit reduced 3' to 5'
exonuclease activity relative to reference polymerase having the
amino acid sequence of SEQ ID NO: 14.
[0270] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95%, 97%, 98% or 99%
identical to the amino acid sequence of SEQ ID NO: 14 and further
comprises one, two, three or more amino acid mutations selected
from the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D,
D63A, Y162F, Y 162C, D166A, Q377A and S385G, wherein the numbering
is relative to the amino acid sequence of SEQ ID NO: 6. In some
embodiments, the modified polymerase comprises any one, two, three,
four, five or all of these mutations. In some embodiments, the
modified polymerase comprises the amino acid substitution D166A. In
some embodiments, the modified polymerase comprises the amino acid
substitutions D9A and D63A. In some embodiments, the modified
polymerase comprises the amino acid substitutions N59D and T12I.
Typically, such modified polymerases will exhibit reduced 3' to 5'
exonuclease activity relative to reference polymerase having the
amino acid sequence of SEQ ID NO: 14.
[0271] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 14
and further comprises an amino acid substitution at one or more
positions selected from the group consisting of: 2, 73, 107, 147,
221, 318, 339, 359, 372, 405, 503, 511, 544 and 550, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
Typically, this modified polymerase can exhibit increased
photostability and/or increased nanoparticle tolerance relative to
a reference polymerase having the amino acid sequence of SEQ ID NO:
14.
[0272] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 14
and further includes a mutation at position 370. In some
embodiments, the mutation is selected from the group consisting of:
H370G, H370T, I-1370S, H370K, H370R, H370A, H370Q, H370 W, H370Y
and I-1370F, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 6. Optionally, this modified polymerase
comprises the amino acid mutation H370R. Typically, this modified
polymerase can exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 14.
[0273] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 14
and further includes a mutation at position 365, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the mutation is selected from the group
consisting of: T365H, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W and T365Y, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6. Optionally, this modified
polymerase comprises the amino acid mutation T365F. Typically, this
modified polymerase can exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 14.
[0274] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 14
and further includes a mutation at position 372, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the mutation is selected from the group
consisting of: K372G, K372E, K372T, K372S, K372R, K372A, K372Q,
K372W, K372Y and K372F, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6. Optionally, this modified
polymerase comprises the amino acid mutation K372Y. Typically, this
modified polymerase can exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 14.
[0275] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 14
and further includes a mutation at position 481, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the mutation is selected from the group
consisting of: A481E, A481F, A481G, A481S, A481R, A481K, A481A,
A481T, A481Q, A481W and A481Y, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 6. Optionally, this modified
polymerase comprises the amino acid mutation A481E. Typically, this
modified polymerase can exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 14.
[0276] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 14
and further includes a mutation at position 509, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the mutation is selected from the group
consisting of: K509E, K509F, K509G, K509S, K509R, K509K, K509A,
K509T, K509Q, K509W and K509Y, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 6. Optionally, this modified
polymerase comprises the amino acid mutation K509Y. Typically, this
modified polymerase can exhibit an increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 14.
[0277] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 14
and further includes any one, two, three or more amino acid
mutations selected from the group consisting of: S2P, Q73H, R107K,
T147A, K221R, V318A, L339M, D359E, E372K, D405E, V503A, K511I,
A544R and M550T, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 6. Typically, this modified polymerase
can exhibit increased photostability and/or increased nanoparticle
tolerance relative to a reference polymerase having the amino acid
sequence of SEQ ID NO: 14.
[0278] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
14 and further includes an amino acid mutation at any one, two,
three or more positions selected from the group consisting of: 9,
12, 14, 15, 58, 59, 61, 63, 98, 129, 176, 185, 186, 187, 195, 208,
246, 247, 248, 251, 252, 256, 300, 302, 310, 357, 360, 362, 365,
367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380,
383, 384, 385, 386, 387, 389, 390, 392, 399, 411, 419, 430, 455,
475, 477, 481, 483, 493, 494, 497, 507, 509, 511, 526, 528, 529,
531, 535, 544, 555, 567, 569 and 572, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 6. In some
embodiments, the modifications can include deletions, additions and
substitutions. The substitutions can be conservative or
non-conservative substitutions. Optionally, this modified
polymerase comprises the amino acid substitution H370R. In some
embodiments, the polymerase further comprises one or more mutations
reducing the exonuclease activity as described herein such as, for
example, the amino acid substitution D166A. Typically, this
modified polymerase can exhibit increased branching ratio and/or
increased nucleotide binding affinity relative to a reference
polymerase having the amino acid sequence of SEQ ID NO: 14.
[0279] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
14 and further comprise amino acid mutations at any one, two, three
or more positions selected from the group consisting of: 2, 9, 12,
14, 15, 58, 59, 61, 63, 73, 98, 107, 129, 147, 166, 176, 185, 186,
187, 195, 208, 221, 246, 247, 248, 251, 252, 256, 300, 302, 310,
318, 339, 357, 359, 360, 362, 367, 368, 369, 370, 371, 372, 373,
374, 375, 376, 377, 378, 380, 383, 384, 385, 386, 387, 389, 390,
392, 399, 405, 411, 419, 430, 455, 475, 477, 481, 483, 493, 494,
497, 503, 507, 509, 511, 526, 528, 529, 531, 535, 544, 550, 552,
555, 567, 569 and 572, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6. In some embodiments, the
modifications can include deletions, additions and substitutions.
The substitutions can be conservative or non-conservative
substitutions. Optionally, this modified polymerase comprises the
amino acid substitution H370R. In some embodiments, the polymerase
further comprises one or more mutations reducing the exonuclease
activity as described herein such as, for example, the amino acid
substitution D166A. Typically, this modified polymerase can exhibit
increased branching ratio, increased nucleotide binding affinity,
increased photostability and/or increased nanoparticle tolerance
relative to a reference polymerase having the amino acid sequence
of SEQ ID NO: 14.
[0280] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 14
and further includes any one, two, three or more amino acid
mutations selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
I-1370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, A481E, A481F, A481G, A481S, A481R,
A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G, D507E,
D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F,
K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A,
K509Q, K509W, K509Y and K509F, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 6. In some embodiments, the
modified polymerase comprises the amino acid mutations Typically,
this modified polymerase can exhibit an increased branching ratio
and/or increased nucleotide binding affinity relative to a
reference polymerase having the amino acid sequence of SEQ ID NO:
14. Optionally, the modified polymerase can further include one or
more mutations reducing 3' to 5' exonuclease activity selected from
the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A,
Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 6.
[0281] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 14
and further includes amino acid mutations at positions 372 and 509,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 6. In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 14
and further includes the amino acid substitutions E372Y and K509Y,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 6. In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 14
and further includes amino acid mutations at positions 365, 372 and
509, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 6. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98%, 99% or 100% identical to the amino acid sequence of
SEQ ID NO: 14 and further includes the amino acid substitutions
T365F, E372Y and K509Y, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 14 and further includes amino
acid mutations at positions 365, 372, 481 and 509, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the modified polymerase comprises an amino
acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%, 99% or
100% identical to the amino acid sequence of SEQ ID NO: 14 and
further includes the amino acid substitutions T365F, E372Y, A481E
and K509Y, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 6. Typically, such modified polymerases can
exhibit an increased branching ratio and/or increased nucleotide
binding affinity relative to a reference polymerase having the
amino acid sequence of SEQ ID NO: 14. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 6.
[0282] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
14 and further comprises the amino acid mutation H370R. Optionally,
the polymerase can further comprise any one, two, three or more
amino acid mutations selected from the group consisting of: S2P,
Q73H, R107K, T147A, K221R, V318A, L339M, D359E, E372K, D405E,
V503A, K511I, A544R, M550T, E371G, E371H, E371T, E371S, E371K,
E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E, K372T,
K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E, K380T,
K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, D507H, D507G,
D507E, D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y,
D507F, K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R,
K509A, K509Q, K509W, K509Y and K509F, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 6. Typically,
this modified polymerase can exhibit increase branching ratio
and/or increased photostability and/or increased nanoparticle
tolerance relative to a reference polymerase having the amino acid
sequence of SEQ ID NO: 14.
[0283] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
14 and further includes the amino acid mutation H370R, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 6.
In some embodiments, the modified polymerase comprises an amino
acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%, 98%,
99% or 100% identical to the amino acid sequence of SEQ ID NO: 14
and further comprises any one, two, three or more amino acid
mutations selected from the group consisting of: S2P, Q73H, T147A,
K221R, V318A, L339M, D359E, H370R, E372K, D405E, V503A, K511I,
A544R and M550T, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 6. Optionally, the modified polymerase
can further comprise one, two or three amino acid mutations
selected from the group: T365G, T365F, T365G, T365S, T365K, T365R,
T365A, T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K,
H370R, H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T,
E371S, E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G,
K372E, K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F,
K380E, K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F,
A481E, A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q,
A481W, A481Y, D507H, D507G, D507E, D507T, D507S, D507R, D507A,
D507R, D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R,
K509E, K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 6. Typically, this modified polymerase can exhibit increase
branching ratio and/or increased photostability and/or increased
nanoparticle tolerance relative to a reference polymerase having
the amino acid sequence of SEQ ID NO: 14. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 6.
[0284] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
14 and further includes an amino acid mutation selected from the
group: H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W,
H370Y and H370F, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. Typically, this modified polymerase
can exhibit an increase t.sub.-1 value in the presence of the
dye-labeled nucleotides relative to a reference polymerase having
the amino acid sequence of SEQ ID NO: 14. In some embodiments, the
t.sub.-1 value of the modified polymerase is increased by at least
about 105%, 110%, 125%, 150%, 175%, 200%, 250%, 500%, 750%, or
1000% relative to the reference polymerase. Optionally, the
modified polymerase can further include one or more mutations
reducing 3' to 5' exonuclease activity selected from the group
consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A, Y162F,
Y162C, D166A, Q377A and S385G, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include any one, two, three or more amino
acid mutations selected from the group consisting of: S2P, Q73H,
T147A, K221R, V318A, L339M, D359E, H370R, E372K, D405E, V503A,
K511I, A544R and M550T, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 7. In some embodiments, the
t.sub.-1 value is increased in the presence of the dye-labeled
nucleotide AF647-C6-dG6P. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 14 and further includes the amino acid
mutation H370R, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 7.
[0285] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
14 and further includes an amino acid mutation selected from the
group: K380G, K380E, K380T, K380S, K380R, K380A, K380Q, K380W,
K380Y and K380F, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. Typically, this modified polymerase
can exhibit an increased t.sub.pol value in the presence of the
dye-labeled nucleotides relative to a reference polymerase having
the amino acid sequence of SEQ ID NO: 14. In some embodiments, the
t.sub.pol value of the modified polymerase is increased by at least
about 105%, 110%, 125%, 150%, 175%, 200%, 250%, 500%, 750%, or
1000% relative to the reference polymerase. Optionally, the
modified polymerase can further include one or more mutations
reducing 3' to 5' exonuclease activity selected from the group
consisting of: D9A, E11A, E111, T12I, H58R, N59D, D63A, Y162F,
Y162C, D166A, Q377A and S385G, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include any one, two, three or more amino
acid mutations selected from the group consisting of: S2P, Q73H,
T147A, K221R, V318A, L339M, D359E, H370R, E372K, D405E, V503A,
K511I, A544R and M550T, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 6. In some embodiments, the
t.sub.pol value is increased in the presence of the dye-labeled
nucleotide AF647-C6-dG6P. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 7 and further includes the amino acid
mutation K380R, wherein the numbering is relative to the amino acid
sequence of SEQ ID NO: 7.
[0286] In some embodiments, the modified polymerase is derived from
an RB69 polymerase having the amino acid sequence of the SEQ ID NO:
15 as follows:
TABLE-US-00016 (SEQ ID NO: 15)
MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKR-
ME
DIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD-
LL
NSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFDIPYV-
YN
RIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGK-
LK
YDGPISKLRESNHQRYISYNIIDVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNK-
VI
PQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVY-
SC
SPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKI-
KK
LSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLN-
EV
CGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMF-
MD
REAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEE-
SL
QEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLP-
LR
EGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDF
[0287] In some embodiments, the modified polymerase can comprise an
amino acid sequence that is at least 85%, 90%, 95%, 97%, 98% or 99%
identical to the amino acid of SEQ ID NO: 15.
[0288] In some embodiments, the modified polymerases disclosed
herein, as well as the modified polymerases encoded by the
polynucleotides of the present disclosure, can exhibit (or can be
further engineered or evolved to exhibit) an altered polymerase
activity in a particular biological assay of interest as compared
to a reference counterpart. Some examples of evolved polymerases
having altered functions or activities can be found, for example,
in U.S. Provisional Application No. 61/020,995, filed Jan. 14,
2008; International PCT Application No. WO 2008/091847, published
Jul. 23, 2009; U.S. Publication No. 2007/0196846 A1, published Aug.
23, 2007; U.S. Publication No. 2008/0108082, published May 8, 2008;
and U.S. Publication No. 2009/0176233, published Jul. 9, 2009.
[0289] In some embodiments, a vector comprises a polynucleotide
encoding a modified polymerase of the present disclosure. In some
embodiments, the vector is a cosmid, plasmid, virus, phage or the
like. In some embodiments, the vector is an expression vector. In
some embodiments, the modified polymerases of the present
disclosure can be produced by a suitable expression vector/host
cell system. For example, a modified polymerase can be encoded by
suitable recombinant expression vectors carrying inserted sequences
of the modified polymerase. The polymerase sequence can be linked
to a suitable expression vector. The polymerase sequence can be
inserted in-frame into the suitable expression vector. The suitable
expression vector can replicate in a phage host, or a prokaryotic
or eukaryotic host cell. The suitable expression vector can
replicate autonomously in the host cell, or can be inserted into
the host cell's genome and be replicated as part of the host
genome. The suitable expression vector can carry a selectable
marker that confers resistance to drugs (e.g., kanamycin,
ampicillin, tetracycline, chloramphenicol, or the like) or a
requirement for a nutrient. The suitable expression vector can have
one or more restriction sites for inserting the nucleic acid
molecule of interest. The suitable expression vector can include
expression control sequences for regulating transcription and/or
translation of the encoded sequence. The expression control
sequences can include: promoters (e.g., inducible or constitutive),
enhancers, transcription terminators, and secretion signals. The
expression vector can be a plasmid, cosmid, virus, phage, and the
like. The expression vector can enter a host cell which can
replicate the vector, produce an RNA transcript of the inserted
sequence, and/or produce protein encoded by the inserted sequence.
Methods for preparing suitable recombinant expression vectors and
expressing the RNA and/or protein encoded by the inserted sequences
are well known (Sambrook et al, Molecular Cloning (1989)). In some
embodiments, the polynucleotide comprises the nucleotide sequence
of SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11 or SEQ ID NO: 12, or
a nucleotide sequence that is at least 80%, 85%, 90%, 95%, 97% or
99% identical to any of these nucleotide sequences. In some
embodiments, the polynucleotide is cloned into the expression
vector pTTQ, which allows expression of the polypeptide encoded by
the polynucleotide from the pTAC promoter (Stark, J. J. R., Gene,
51, pp. 255-267, 1987).
[0290] In some embodiments, the modified polymerase can be
homologous to a naturally occurring polymerase; alternatively, it
can be a biologically active fragment, mutant or other derivative
of a naturally occurring polymerase. Typically, the polymerase will
elongate a pre-existing nucleic acid, for example, a primer, by
polymerizing nucleotides on to the 3' end of the molecule; for
example, the polymerase can catalyze transfer of a nucleoside
monophosphate from a nucleoside triphosphate (or analog thereof) to
the 3' hydroxyl group of the polymerization initiation site. The
polymerase can bind a target nucleic acid molecule, which may or
may not be base-paired with a polymerization initiation site (e.g.,
primer). The polymerase can bind a nucleotide. The polymerase can
mediate incorporation of a nucleotide (or analog thereof) on to a
polymerization initiation site (e.g., terminal 3'OH of a primer).
The polymerase can mediate cleavage between the .alpha. and .beta.
phosphate groups. The polymerase can mediate phosphodiester bond
formation. The polymerase can mediate release of the polyphosphate
product.
[0291] In some embodiments, the modified polymerase can be linked
to a label to form a labeled polymerase that retains polymerase
activity. In some embodiments, the label is an organic label. In
some embodiments, the label is an inorganic label, for example a
nanoparticle. The nanoparticle can be a nanocrystal or a quantum
dot. In some embodiments, the nanoparticle or quantum dot, or
populations thereof, can comprise a surface layer including
multiple functional groups such as, for example, dipeptides,
tripeptides, monodentate thiols, or polydentate thiols as well as
mixtures of dipeptides, tripeptides, monodentate thiols, or
polydentate thiols with hydrophobic ligands like TDPA, OPA, TOP,
and/or TOPO.
[0292] In some embodiments, the modified polymerase is linked to an
energy transfer moiety. The energy transfer moiety can in some
embodiments be a RET or FRET moiety. In some embodiments, the
energy transfer moiety is a donor moiety. Exemplary methods of
attaching labels to a polymerase can be found, for example, in U.S.
Provisional Application No. 61/184,770, filed Jun. 5, 2009.
[0293] In some embodiments, the polymerase can be further modified
to comprise intact subunits, biologically-active fragments and/or
fusion variants of any polymerases disclosed herein, as well as
mutated, truncated, modified, genetically engineered or fusion
variants of such polymerases. The modifications of a modified
polymerase can include amino acid substitutions, insertions, or
deletions. In some embodiments, the modified polymerases can be
isolated from a cell, or generated using recombinant DNA technology
or chemical synthesis methods. In another embodiment, the modified
polymerases can be expressed in prokaryote, eukaryote, viral, or
phage organisms. In some embodiments, the modified polymerases can
be post-translationally modified proteins or fragments thereof.
[0294] The polymerases disclosed herein can also be derived from
any subunits, mutated, modified, truncated, genetically engineered
or fusion variants of a polymerase having the amino acid sequence
of SEQ ID NO: 7 or SEQ ID NO: 8 (wherein the mutation involves the
replacement of one or more or many amino acids with other amino
acids, the insertion or deletion of one or more or many amino
acids, or the conjugation of parts of one or more polymerases).
[0295] In some embodiments, the modified polymerase is a fusion
protein comprising some or all of the amino acid sequence of SEQ ID
NO: 7 or SEQ ID NO: 8.
[0296] In some embodiments, the modified polymerase can be
attached, fused or otherwise associated with a moiety that
facilitates purification of the polymerase, isolation of the
polymerase and/or linkage of the polymerase to one or more labels.
For example, in some embodiments the moiety can be an enzymatic
recognition site, an epitope or an affinity tag that facilitates
purification of the polymerase. In some embodiments, the tag is an
affinity tag. The affinity tag can be selected from: a His tag, a
GST tag, an HA tag, a SNAP-tag, and the like. In some embodiments,
the modified polymerase can comprise a plurality of 6-His tags (SEQ
ID NO: 48), a plurality of GST tags, a plurality of HA tags, and
combinations thereof. Such tags can be inserted into any suitable
position within the polymerase sequence. In some embodiments, the
modified polymerase comprises one or more tags that are fused
in-frame with the polymerase amino acid sequence at the N-terminal,
the C-terminal end, or anywhere in between. Typically, the presence
of the tag does not affect polymerase activity.
[0297] In some embodiments, the affinity tag is a His tag. For
example, in some embodiments the His tag can include a stretch of
amino acids comprising multiple histidine residues. In some
embodiments, the His tag comprises a 6-His tag (SEQ ID NO: 48)
(hexahistidine tag [SEQ ID NO: 48]). The His tag can optionally
bind to one or more metal atom of a label. In one exemplary
embodiment, the His tag binds to bound metal ions on the surface of
a nanoparticle, for example, Ni.sup.2+, Co.sup.2+, or Cu.sup.2+
ions, thus linking the polymerase to the nanoparticle. In some
embodiments, the His tag comprises 2, 3, 4, 5, 6, 7, 8 or more
histidine residues. In some embodiments, the His tag is fused to
the N- or C-terminus of the protein; alternatively, it can be fused
at any suitable location within the open reading frame of the
protein.
[0298] In some embodiments, the His tag may be fused directly with
the protein; alternatively, a linker comprising various lengths of
amino acid residues can be placed between the protein and the His
tag. The linker can be flexible or rigid.
[0299] In some embodiments, the His tag can facilitate purification
of the polymerase. For example, His tagged polymerase can be
purified from a raw bacterial lysate by contacting the lysate with
any suitable affinity medium comprising bound metal ions to which
the histidine residues of the His tag can chelate. The bound metal
ions can comprise either nickel or cobalt, to which the
polyhistidine-tag binds with micromolar affinity. Suitable affinity
media include Ni Sepharose (such as, for example, that provided by
GE Healthcare), NTA-agarose (such as, for example, that provided by
Qiagen), HisPur.RTM. resin (Thermo Scientific, Pierce Protein
Products, Rockford, Ill.), or Talon.RTM. resin (Clontech, Mountain
View, Calif.). The affinity matrix can be washed with suitable
buffers, e.g., phosphate buffers, to remove proteins that do not
specifically interact with the cobalt or nickel ion. Washing
efficiency can be improved by the addition of 20 mM imidazole. In
some embodiments, the protein(s) can be eluted from the matrix. In
some embodiments, the proteins can be eluted with 150-300 mM
imidazole). The purity and amount of purified polymerase can be
assessed using suitable methods, e.g., SDS-PAGE, size exclusion
chromatography, mass spectrometry and/or Western blotting.
[0300] In some embodiments, the His tag can be followed by a
suitable amino acid sequence that facilitates removal of the His
tag using a suitable endopeptidase. Alternatively, the His tag may
be removed using a suitable exopeptidase, for example the Qiagen
TAGZyme exopeptidase.
[0301] In addition to facilitating purification of the polymerase,
the His tag can also facilitate binding of the His tagged
polymerase to the nanoparticle comprising one or more bound metal
ions via chelation bonding. Exemplary methods of conjugation of a
His tagged polymerase to a nanoparticle are described, for example,
in U.S. Provisional Application No. 61/184,770, filed Jun. 5, 2009
(Attorney Docket: LT00003 PRO).
[0302] In some embodiments, the amino acid sequence of a modified
polymerase fused to a peptide sequence that encodes a stretch of
amino acid acids capable of functioning as a peptide linker to
facilitate the formation of a linkage between the modified
polymerase and another reactive moiety. This peptide linker
sequence can be fused to the N-terminus, the C-terminus or any
suitable position between the N-terminus and the C-terminus of the
modified polymerase.
[0303] In some embodiments, the peptide linker can comprise the
amino acid sequence: LLGAAAKGAAAKGSAA (SEQ ID NO: 16).
[0304] This linker is hereinafter referred to as the "H-linker".
Without being bound to any particular theory of operation, it has
been suggested that this linker comprises a helix-forming peptide
that can effectively separate different functional domains of a
fusion protein or conjugate. See, for example, Arai et al., Protein
Engineering 14(8): 529-532 (2001); Marqusee & Baldwin, Proc.
Natl. Acad. Sci. USA, 84: 8898-8902 (1987).
[0305] In some embodiments, the peptide linker can comprise the
amino acid sequence: LLGGGGSGGGGSAAAGSAA (SEQ ID NO: 17)
[0306] This linker is hereinafter referred to as the "F-linker".
See, for example, Arai et al., Protein Engineering 14(8): 529-532
(2001); Alfthan et al., Protein Engineering 8(7): 725-731
(1995).
[0307] In some embodiments, the modified polymerase comprises a
modified N-terminal His tagged version of a B103 polymerase,
wherein the modified polymerase comprises the following amino acid
sequence:
TABLE-US-00017 (SEQ ID NO: 18) 10 20 30 40 50 60 MNHLVHHHHH
HIEGRHMELG TLEGSMPRKM FSCDFETTTK LDDCRVWAYG YMEIGNLDNY 70 80 90 100
110 120 KIGNSLDEFM QWVMEIQADL YFHNLKFDGA FIVNWLEHHG FKWSNEGLPN
TYNTIISKMG 130 140 150 160 170 180 QWYMIDICFG YKGKRKLHTV IYDSLKKLPF
PVKKIAKDFQ LPLLKGDIDY HAERPVGHEI 190 200 210 220 230 240 TPEEYEYIKN
DIEIIARALD IQFKQGLDRM TAGSDSLKGF KDILSTKKFN KVFPKLSLPM 250 260 270
280 290 300 DKEIRRAYRG GFTWLNDKYK EKEIGEGMVF DVNSLYPSQM YSRPLPYGAP
IVFQGKYEKD 310 320 330 340 350 360 EQYPLYIQRI RFEFELKEGY IPTIQIKKNP
FFKGNEYLKN SGAEPVELYL TNVDLELIQE 370 380 390 400 410 420 HYEMYNVEYI
DGFKFREKTG LFKEFIDKWT YVKTHEKGAK KQLAKLMLNS LYGKFASNPD 430 440 450
460 470 480 VTGKVPYLKE DGSLGFRVGD EEYKDPVYTP MGVFITAWAR FTTITAAQAC
YDRIIYCDTD 490 500 510 520 530 540 SIHLTGTEVP EIIKDIVDPK KLGYWAHEST
FKRAKYLRQK TYIQDIYAKE VDGKLIECSP 550 560 570 580 590 DEATTTKFSV
KCAGMTDTIK KKVTFDNFRV GFSSTGKPKP VQVNGGVVLV DSVFTIK
[0308] In some embodiments, the modified polymerase can comprise an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 99%
or 100% identical to the amino acid sequence of SEQ ID NO: 18. In
some embodiments, the modified polymerase further comprises the
amino acid substitution D191A, wherein the numbering is relative to
SEQ ID NO: 18.
[0309] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95% or 99% identical
to the amino acid sequence of SEQ ID NO: 18 and comprises any one,
two, three or more of the mutations described herein.
[0310] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95% or 99% identical
to the amino acid sequence of SEQ ID NO: 18 and further comprises
one or more amino acid substitutions selected from the group
consisting of: D34A, E36A, H83R, N84D, D88A, D191A, Q402A and
S410G, and further comprises one or more amino acid substitutions
selected from the group consisting of: H395G, H395T, H395S, H395K,
H395R, H395A, H395Q, H395W, H395Y, H395F, E396G, E396H, E396T,
E396S, E396K, E396R, E396A, E396Q, E396W, E396Y, E396F, K397G,
K397E, K397T, K397S, K397R, K397A, K397Q, K397W, K397Y, K397F,
K405E, K405T, K405S, K405R, K405A, K405Q, K405W, K405Y, K405F,
D532H, D532G, D532E, D532T, D532S, D532R, D532A, D532R, D532Q,
D532W, D532Y, D532F, K534H, K534G, K534D, K534R, K534E, K534T,
K534S, K534R, K534A, K534Q, K534W, K534Y and K534F, wherein the
numbering is relative to the sequence of SEQ ID NO: 18.
[0311] In some embodiments, the modified polymerase comprising the
amino acid sequence of SEQ ID NO: 18 further comprises one or more
amino acid substitutions selected from the group consisting of:
D34A, E36A, H83R, N84D, D88A, D191A, Q402A and S410G, and further
comprises amino acid substitutions at two or more positions
selected from the group consisting of: 395, 397 and 532, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
18.
[0312] In some embodiments, the modified polymerase comprises the
amino acid sequence of comprises one or more amino acid
substitutions selected from the group consisting of: D34A, E36A,
H83R, N84D, D88A, D191A, Q402A and S410G, and further comprises the
amino acid substitutions K397Y and D532H, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 18.
[0313] In some embodiments, the modified polymerase comprises one
or more amino acid substitutions selected from the group consisting
of: D34A, E36A, H83R, N84D, D88A, D191A, Q402A and S410G, and
further comprises the amino acid substitutions H395R and D532H,
wherein the numbering is relative to the amino acid sequence of SEQ
ID NO: 18.
[0314] In some embodiments, the modified polymerase comprises one
or more amino acid substitutions selected from the group consisting
of: D34A, E36A, H83R, N84D, D88A, D191A, Q402A and S410G, and
further comprises two or more amino acid substitutions selected
from the group consisting of: H395R, K397Y and D532H, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO:
18.
[0315] In some embodiments, the modified polymerase comprises a
modified N-terminal His tagged version of a B103 polymerase,
wherein the modified polymerase comprises the following amino acid
sequence:
TABLE-US-00018 (SEQ ID NO: 19) 10 20 30 40 50 60 MHHHHHHKHM
PRKMFSCDFE TTTKLDDCRV WAYGYMEIGN LDNYKIGNSL DEFMQWVMEI 70 80 90 100
110 120 QADLYFHNLK FDGAFIVNWL EHHGFKWSNE GLPNTYNTII SKMGQWYMID
ICFGYKGKRK 130 140 150 160 170 180 LHTVIYDSLK KLPFPVKKIA KDFQLPLLKG
DIDYHAERPV GHEITPEEYE YIKNDIEIIA 190 200 210 220 230 240 RALDIQFKQG
LDRMTAGSDS LKGFKDILST KKFNKVFPKL SLPMDKEIRR AYRGGFTWLN 250 260 270
280 290 300 DKYKEKEIGE GMVFDVNSLY PSQMYSRPLP YGAPIVFQGK YEKDEQYPLY
IQRIRFEFEL 310 320 330 340 350 360 KEGYIPTIQI KKNPFFKGNE YLKNSGAEPV
ELYLTNVDLE LIQEHYEMYN VEYIDGFKFR 370 380 390 400 410 420 EKTGLFKEFI
DKWTYVKTHE KGAKKQLAKL MLNSLYGKFA SNPDVTGKVP YLKEDGSLGF 430 440 450
460 470 480 RVGDEEYKDP VYTPMGVFIT AWARFTTITA AQACYDRIIY CDTDSIHLTG
TEVPEIIKDI 490 500 510 520 530 540 VDPKKLGYWA HESTFKRAKY LRQKTYIQDI
YAKEVDGKLI ECSPDEATTT KFSVKCAGMT 550 560 570 580 DTIKKKVTFD
NFRVGFSSTG KPKPVQVNGG VVLVDSVFTI K
[0316] In some embodiments, the modified polymerase can comprise an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 99%
or 100% identical to the amino acid sequence of SEQ ID NO: 19. In
some embodiments, the modified polymerase further comprises the
amino acid substitution D175A, wherein the numbering is relative to
SEQ ID NO: 19.
[0317] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95% or 99% identical
to the amino acid sequence of SEQ ID NO: 19 and comprises any one,
two, three or more of the mutations described herein.
[0318] In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 85%, 90%, 95% or 99% identical
to the amino acid sequence of SEQ ID NO: 19 and further comprises
any one, two, three or more of the mutations selected from the
group consisting of: D18A, E20A, H67R, N68D, D72A, D175A, Q386A,
S394G, H379G, H379T, H379S, H379K, H379R, H379A, H379Q, H379W,
H379Y, H379F, E379G, E380H, E380T, E380S, E380K, E380R, E380A,
E380Q, E380 W, E380Y, E380F, K381G, K381E, K381T, K381S, K381R,
K381A, K381Q, K381W, K381Y, K381F, K389E, K389T, K389S, K389R,
K389A, K389Q, K389W, K389Y, K389F, D516H, D516G, D516E, D516T,
D516S, D516R, D516A, D516R, D516Q, D516W, D516Y D516F, K518H,
K518G, K518D, K518R, K518E, K518T, K518S, K518R, K518A, K518Q,
K518W, K518Y and K518F, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 19.
[0319] In some embodiments, the modified polymerase comprises one
or more amino acid substitutions selected from the group consisting
of: D18A, E20A, H67R, N68D, D72A, D175A, Q386A and S394G, and
further comprises one or more amino acid substitutions selected
from the group consisting of: H379G, H379T, H379S, H379K, H379R,
H379A, H379Q, H379W, H379Y, H379F, E379G, E380H, E380T, E380S,
E380K, E380R, E380A, E380Q, E380 W, E380Y, E380F, K381G, K381E,
K381T, K381S, K381R, K381A, K381Q, K381W, K381Y, K381F, K389E,
K389T, K389S, K389R, K389A, K389Q, K389W, K389Y, K389F, D516H,
D516G, D516E, D516T, D516S, D516R, D516A, D516R, D516Q, D516W,
D516Y D516F, K518H, K518G, K518D, K518R, K518E, K518T, K518S,
K518R, K518A, K518Q, K518W, K518Y and K518F, wherein the numbering
is relative to the sequence of SEQ ID NO: 19.
[0320] In some embodiments, the modified polymerase comprises one
or more amino acid substitutions selected from the group consisting
of: D18A, E20A, H67R, N68D, D72A, D175A, Q386A and S394G and
further comprises amino acid substitutions at two or more positions
selected from the group consisting of: 379, 380 and 516, wherein
the numbering is relative to the sequence of SEQ ID NO: 19.
[0321] In some embodiments, the modified polymerase comprises one
or more amino acid substitutions selected from the group consisting
of: D18A, E20A, H67R, N68D, D72A, D175A, Q386A and S394G, and
further comprises the amino acid substitutions K381Y and D516H,
wherein the numbering is relative to the sequence of SEQ ID NO:
19.
[0322] In some embodiments, the modified polymerase comprises one
or more amino acid substitutions selected from the group consisting
of: D18A, E20A, H67R, N68D, D72A, D175A, Q386A and S394G, and
further comprises the amino acid substitutions H379R and D516H,
wherein the numbering is relative to the sequence of SEQ ID NO:
19.
[0323] In some embodiments, the modified polymerase comprises one
or more amino acid substitutions selected from the group consisting
of: D18A, E20A, H67R, N68D, D72A, D175A, Q386A and S394G, and
further comprises two or more amino acid substitutions selected
from the group consisting of: H379R, K381Y and D516H, wherein the
numbering is relative to the sequence of SEQ ID NO: 19.
[0324] In some embodiments, one or more activities or properties of
a modified polymerase comprising an amino acid sequence that is at
least %, 90%, 95% or 99% identical to the amino acid sequence of
SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 18 or SEQ ID NO: 19 can be
altered (e.g., increased or decreased) relative to the
corresponding one or more activities or properties of an exemplary
reference polymerase having an amino acid sequence that is at least
70%, 80%, 85%, 90%, 95%, 99% or 100% identical to the following
amino acid sequence:
TABLE-US-00019 (SEQ ID NO: 20) MNHLVHHHHH HIEGRHMELG TLEGSMKHMP
RKMYSCAFET TTKVEDCRVW AYGYMNIEDH 70 80 90 100 110 120 SEYKIGNSLD
EFMAWVLKVQ ADLYFHNLKF AGAFIINWLE RNGFKWSADG LPNTYNTIIS 130 190 150
160 170 180 RMGQWYMIDI CLGYKGKRKI HTVIYDSLKK LPFPVKKIAK DFKLTVLKGD
IDYHKERPVG 190 200 210 220 230 240 YKITPEEYAY IKNDIQIIAE ALLIQFKQGL
DRMTAGSDSL KGFKDIITTK KFKKVFPTLS 250 260 270 280 290 300 LGLDKEVRYA
YRGGFTWLND RFKEKEIGEG MVFDVNSLYP AQMYSRLLPY GEPIVFEGKY 310 320 330
340 350 360 VWDEDYPLHI QHIRCEFELK EGYIPTIQIK RSRFYKGNEY LKSSGGEIAD
LWLSNVDLEL 370 380 390 400 410 420 MKEHYDLYNV EYISGLKFKA TTGLFKDFID
KWTYIKTTSE GAIKQLAKLM LNSLYGKFAS 430 440 450 460 470 480 NPDVTGKVPY
LKENGALGFR LGEEETKDPV YTPMGVFITA WARYTTITAA QACYDRIIYC 490 500 510
520 530 540 DTDSIHLTGT EIPDVIKDIV DPKKLGYWAH ESTFKRAKYL RQKTYIQDIY
MKEVDGKLVE 550 560 570 580 590 600 GSPDDYTDIK FSVKCAGMTD KIKKEVTFEN
FKVGFSRKMK PKPVQVPGGV VLVDDTFTIK
[0325] This fusion polymerase of amino acid sequence of SEQ ID NO:
20 is herein variously referred to as "HP1" or "HP-1". See, e.g.,
U.S. Provisional Application No. 61/184,770, filed Jun. 5, 2009.
This reference polymerase typically comprises a Phi-29 polymerase
peptide that lacks exonuclease activity and comprises an N-terminal
His-tag, an intervening linker sequence, and the D12A and D66A
mutations.
[0326] In some embodiments, the reference polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 99%
or 100% identical to the amino acid sequence of SEQ ID NO: 20
(HP-1).
[0327] In one embodiment, the polymerase can be a fusion protein
comprising the amino acid sequence of a nucleic acid-dependent
polymerase (the polymerase portion) linked to the amino acid
sequence of a second enzyme or a biologically active fragment
thereof (the second enzyme portion). The second enzyme portion of
the fusion protein may be linked to the amino or carboxyl end of
the polymerase portion, or may be inserted within the polymerase
portion. The polymerase portion of the fusion protein may be linked
to the amino or carboxyl end of the second enzyme portion, or may
be inserted within the second enzyme portion. In some embodiments,
the polymerase and second enzyme portions can be linked to each
other in a manner which does not significantly interfere with
polymerase activity of the fusion or with the ability of the fusion
to bind nucleotides, or does not significantly interfere with the
activity of the second enzyme portion. In the fusion protein, the
polymerase portion or the second enzyme portions can be linked with
at least one energy transfer donor moiety. The fusion protein can
be a recombinant protein having a polymerase portion and a second
enzyme portion. In some embodiments, the fusion protein can include
a polymerase portion chemically linked to the second enzyme
portion.
[0328] In some embodiments, the polymerase can be a modified
polymerase having certain desired characteristics, such as an
evolved polymerase selected from a directed or non-directed
molecular evolution procedure. The evolved polymerase can exhibit
modulated characteristics or functions, such as changes in:
affinity, specificity, or binding rates for substrates (e.g.,
target molecules, polymerization initiation sites, or nucleotides);
binding stability to the substrates (e.g., target molecules,
polymerization initiation sites, or nucleotides); nucleotide
incorporation rate; nucleotide analog permissiveness; exonuclease
activity (e.g., 3'.fwdarw.5' or 5'.fwdarw.3'); rate of extension;
processivity; fidelity; stability; or sensitivity and/or
requirement for temperature, chemicals (e.g., DTT), salts, metals,
pH, or electromagnetic energy (e.g., excitation or emitted energy).
Many examples of evolved polymerases having altered functions or
activities can be found in U.S. provisional patent application No.
61/020,995, filed Jan. 14, 2008.
[0329] Methods for creating and selecting proteins and enzymes
having the desired characteristics are known in the art, and
include: oligonucleotide-directed mutagenesis in which a short
sequence is replaced with a mutagenized oligonucleotide;
error-prone polymerase chain reaction in which low-fidelity
polymerization conditions are used to introduce point mutations
randomly across a sequence up to about 1 kb in length (R. C.
Caldwell, et al., 1992 PCR Methods and Applications 2:28-33; H.
Gramm, et al., 1992 Proc. Natl. Acad. Sci. USA 89:3576-3580); and
cassette mutagenesis in which a portion of a sequence is replaced
with a partially randomized sequence (A. R. Oliphant, et al., 1986
Gene 44:177-183; J. D. Hermes, et al., 1990 Proc. Natl. Acad. Sci.
USA 87:696-700; A. Arkin and D. C. Youvan 1992 Proc. Natl. Acad.
Sci. USA 89:7811-7815; E. R. Goldman and D. C. Youvan 1992
Bio/Technology 10:1557-1561; Delagrave et al., 1993 Protein
Engineering 6: 327-331; Delagrave et al., 1993 Bio/Technology 11:
1548-155); and domain shuffling.
[0330] Methods for creating evolved antibody and antibody-like
polypeptides can be adapted for creating evolved polymerases, and
include applied molecular evolution formats in which an
evolutionary design algorithm is applied to achieve specific mutant
characteristics. Many library formats can be used for evolving
polymerases including: phage libraries (J. K. Scott and G. P. Smith
1990 Science 249:386-390; S. E. Cwirla, et al. 1990 Proc. Natl.
Acad. Sci. USA 87:6378-6382; J. McCafferty, et al. 1990 Nature
348:552-554) and lad (M. G. Cull, et al., 1992 Proc. Natl. Acad.
Sci. USA 89:1865-1869).
[0331] Another adaptable method for evolving polymerases employs
recombination (crossing-over) to create the mutagenized
polypeptides, such as recombination between two different plasmid
libraries (Caren et al. 1994 Bio/Technology 12: 517-520), or
homologous recombination to create a hybrid gene sequence
(Calogero, et al., 1992 FEMS Microbiology Lett. 97: 41-44; Galizzi
et al., WO91/01087). Another recombination method utilizes host
cells with defective mismatch repair enzymes (Radman et al.,
WO90/07576). Other methods for evolving polymerases include random
fragmentation, shuffling, and re-assembly to create mutagenized
polypeptides (published application No. U.S. 2008/0261833,
Stemmer). Adapting these mutagenesis procedures to generate evolved
polymerases is well within the skill of the art.
[0332] In some embodiments, the polymerase can be fused with, or
otherwise engineered to include, DNA-binding or other domains from
other proteins that are capable of modulating DNA polymerase
activity. For example, fusion of suitable portions of the
Single-Stranded DNA Binding Protein (SSBP), thioredoxin and/or T7
DNA polymerase to bacterial or viral DNA polymerases has been shown
to enhance both the processivity and fidelity of the DNA
polymerase. Similarly, other groups have described efforts to
engineer polymerases so as to broaden their substrate range. See,
e.g., Ghadessy et al, Nat. Biotech., 22 (6):755-759 (2004).
Similarly, the conjugates of the present disclosure can optionally
comprise any polymerase engineered to provide suitable performance
characteristics, including for example a polymerase fused to intact
SSBP or fragments thereof, or to domains from other DNA-binding
proteins (such as the herpes simplex virus UL42 protein.)
[0333] In some embodiments, a blend of different conjugates, each
of which comprises a polymerase of unique sequence and
characteristics, can be used according to the methods described
herein. Use of such conjugate blends can additionally increase the
fidelity and processivity of DNA synthesis. For example, use of a
blend of processive and non-processive polymerases has been shown
to result in increased overall read length during DNA synthesis, as
described in U.S. Published App. No. 2004/0197800. Alternatively,
conjugates comprising polymerases of different affinities for
specific acceptor-labeled nucleotides can be used so as to achieve
efficient incorporation of all four nucleotides.
[0334] In some embodiments, the polymerase can comprise the amino
acid sequence of any polymerase disclosed in U.S. Provisional
Application Nos. 61/242,771, filed on Sep. 15, 2009; 61/263,974,
filed on Nov. 24, 2009 and 61/299,919, filed on Jan. 29, 2010, or
any variant thereof.
[0335] In some embodiments, the polymerases of the present
disclosure can be isolated from a cell, or generated using
recombinant DNA technology or chemical synthesis methods. In
another embodiment, the polymerases can be expressed in prokaryote,
eukaryote, viral, or phage organisms. In another embodiment, the
polymerases can be post-translationally modified proteins or
fragments thereof.
[0336] In some embodiments, the polymerases of the present
disclosure can be recombinant proteins that are produced by a
suitable expression vector/host cell system. The polymerases can be
encoded by suitable recombinant expression vectors carrying
inserted nucleotide sequences of the polymerases. In some
embodiments, the polymerase sequence can be linked to a suitable
expression vector. The polymerase sequence can be inserted in-frame
into the suitable expression vector. The suitable expression vector
can replicate in a phage host, or a prokaryotic or eukaryotic host
cell. The suitable expression vector can replicate autonomously in
the host cell, or can be inserted into the host cell's genome and
be replicated as part of the host genome. The suitable expression
vector can carry a selectable marker which confers resistance to
drugs (e.g., kanamycin, ampicillin, tetracycline, chloramphenicol,
or the like), or confers a nutrient requirement. The suitable
expression vector can have one or more restriction sites for
inserting the nucleic acid molecule of interest. The suitable
expression vector can include expression control sequences for
regulating transcription and/or translation of the encoded
sequence. The expression control sequences can include: promoters
(e.g., inducible or constitutive), enhancers, transcription
terminators, and secretion signals. The expression vector can be a
plasmid, cosmid, or phage vector. The expression vector can enter a
host cell which can replicate the vector, produce an RNA transcript
of the inserted sequence, and/or produce protein encoded by the
inserted sequence. The recombinant polymerase can include an
affinity tag for enrichment or purification, including a poly-amino
acid tag (e.g., poly His tag), GST, and/or HA sequence tag. Methods
for preparing suitable recombinant expression vectors and
expressing the RNA and/or protein encoded by the inserted sequences
are well known (Sambrook et al, Molecular Cloning (1989)).
[0337] In some embodiments, the present disclosure relates to
modified polymerases exhibiting altered kinetics of nucleotide
binding, nucleotide incorporation and/or primer extension. For
example, in some embodiments, the modified polymerases of the
present disclosure comprise one or more modifications resulting in
a change in the kinetic behavior of the polymerase in vitro or in
vivo. For example, the modification(s) may result in a change (for
example, an increase or decrease) in one or more of the following
activities or properties of the polymerase, relative to the
corresponding activity or property of a reference polymerase:
specific activity as measured in a primer extension assay; specific
activity as measured in a nucleotide incorporation assay (including
assays for incorporation of naturally occurring nucleotides and
nucleotide analogs); exonuclease activity (including, for example,
3' to 5' exonuclease activity); ability to bind one or more
substrates (including naturally occurring nucleotides and
nucleotide analogs); yield of synthesized nucleic acid product;
processivity; fidelity of nucleic acid synthesis; rate of nucleic
acid synthesis; binding affinity for one or more particular
nucleotides (including naturally occurring nucleotides and
nucleotide analogs); K.sub.m for one or more substrates (including
naturally occurring nucleotides, nucleotide analogs and/or template
strand); k.sub.cat or V.sub.max, t.sub.pol, t.sub.-1, k.sub.pol, or
k.sub.-1 for one or more nucleotides (including naturally occurring
nucleotides and nucleotide analogs); residence time of one or more
nucleotides (including naturally occurring nucleotides and
nucleotide analogs) within one or more polymerase active sites;
rate of binding for one or more nucleotides (including naturally
occurring nucleotides and nucleotide analogs); rate of nucleotide
release (in either altered or unaltered state) from the polymerase
active site, including, for example, rate of product release;
average template read length in presence of nucleotides (including
naturally occurring nucleotides and nucleotide analogs); nucleotide
binding specificity for one or more particular nucleotides
(including naturally occurring nucleotides and nucleotide analogs);
accessibility of one or more polymerase active sites by one or more
nucleotides (including naturally occurring nucleotides and
nucleotide analogs); steric inhibition of nucleotide entry into a
polymerase active site (including, for example, inhibition of entry
of naturally occurring nucleotides and nucleotide analogs);
complementarity of a polymerase active site with one or more
natural, unnatural or non-complementary nucleotides (including
naturally occurring nucleotides and nucleotide analogs) as compared
to that of complementary nucleotides; ability to discriminate
between correct and incorrect nucleotides (including naturally
occurring nucleotides and nucleotide analogs); frequency of
incorporation of non-complementary nucleotides as compared to that
of complementary nucleotides (including naturally occurring
nucleotides and nucleotide analogs); branching ratio for one or
more nucleotides (including naturally occurring nucleotides and
nucleotide analogs); stability, for example at elevated
temperatures; observed performance in a particular biological
assay; complementarity with one or more natural or non-natural
features of a nucleotide (including naturally occurring nucleotides
and nucleotide analogs); tolerance of the polymerase for various
chemical and/or physical stresses, as well as the stability of the
polymerase under a given set of conditions, including
photostability and chemical stability; tolerance for the presence
of labels (including both organic labels, e.g., dyes, and inorganic
labels, e.g., nanoparticles); and photostability.
[0338] In some embodiments, the modified polymerases and/or
polynucleotides of the present disclosure can exhibit an altered
kinetic behavior with one or more nucleotide substrates, including,
for example, labeled nucleotide analogs, relative to an unmodified
counterpart. For example, in some embodiments, the modified
polymerase can exhibit altered kinetics of polymerization,
including, for example, polymerization of substrates comprising
labeled nucleotide analogs. In some embodiments, the modified
polymerase can exhibit an altered K.sub.m value for a substrate,
particularly a labeled nucleotide analog. In some embodiments, the
polymerase can be engineered to exhibit altered K.sub.cat/K.sub.m,
and/or V.sub.max/K.sub.m for a substrate, particularly a labeled
nucleotide analog. In some embodiments, the K.sub.cat/K.sub.m the
V.sub.max/K.sub.m, or both, are increased relative to the wild type
polymerase. In some embodiments, the modified polymerase can
exhibit an altered K.sub.m, K.sub.D, t.sub.-1, t.sub.pol,
nucleotide residence time for one or more nucleotides, for example
a labeled nucleotide analog.
[0339] The kinetic activity of an enzyme can be modeled using
various methods. Some exemplary theories of enzyme kinetics and
associated models can be found, for example, in Berg at al.,
Biochemistry, 5th Ed. (W.H. Freeman, 2007); Fersht, Enzyme
Structure & Mechanism, 5th Ed. (W.H. Freeman, 1985). Without
being bound by any particular theory, the Michaelis-Menten theory
provides an non-limiting exemplary theoretical model for enzymatic
activity. This model is based on the assumption that an
enzyme-substrate reaction typically proceeds as follows:
E + S .rarw. .fwdarw. k 1 k - 1 ES .fwdarw. k 2 E + P
##EQU00001##
[0340] Where E=free enzyme; S=free substrate; P=product and
ES=enzyme-substrate complex, k.sub.1 is the rate constant for the
association of substrate (S) and enzyme (E) to form an
enzyme-substrate complex (ES); k.sub.2 is the rate constant for the
dissociation of the enzyme-substrate complex (ES) into product
(i.e., altered substrate) and free enzyme, and k.sub.-1 is the rate
constant for the dissociation of the enzyme-substrate complex, ES,
into unaltered substrate and enzyme.
[0341] The equilibrium dissociation constant for the dissociation
of the enzyme-substrate complex, ES, into unaltered substrate and
enzyme, K.sub.D, can be determined as the ratio of k.sub.-1 and
k.sub.1. Mathematically, this relationship can be represented
as:
K.sub.D=k.sub.-1/k.sub.1
[0342] K.sub.D can also be expressed as a ratio of the equilibrium
concentrations of enzyme, substrate and enzyme-substrate
complex:
K.sub.D=[E][S]/[ES]
[0343] The Michaelis-Menten equation describes the rate of initial
enzymatic activity, .nu., as a function of substrate
concentration:
.nu.=V.sub.max[S]/(K.sub.m+[S])
[0344] where the variables can be defined as follows:
[0345] .nu. is the reaction rate, measured as amount of product
formed per time interval.
[0346] [S] is the concentration of uncombined, i.e., free,
substrate.
[0347] V.sub.max is maximal enzyme velocity, extrapolated to
maximum substrate concentrations, i.e., rate when enzyme is
saturated with substrate (also referred to as enzymatic "rate");
and
[0348] K.sub.m is the so-called Michaelis-Menten constant, can be
defined as (k.sub.2+k.sub.-1)/k.sub.1. K.sub.m is typically related
to the dissociation constant, and provides an indication of the
affinity of the enzyme for a particular substrate (and hence the
stability of the enzyme-substrate complex). In the most simple
case, when k.sub.2<<k.sub.1, product formation is very slow
compared to the rate of formation of enzyme-substrate complex (ES),
i.e., product formation is the rate limiting step, then K.sub.m can
equal or approximate the equilibrium dissociation constant of the
enzyme-substrate complex, K.sub.D, and thus can describe the
binding affinity of the substrate for the enzyme. Typically,
K.sub.m can be measured as the substrate concentration at which the
reaction rate is half the maximum enzyme velocity, V.sub.max.
[0349] V.sub.max, k.sub.cat and E.sub.T, the total enzyme
concentration (i.e., the concentration of active sites), can be
mathematically related in the following equation:
k.sub.cat=V.sub.max/E.sub.T
[0350] For a polymerase reaction involving incorporation of a
nucleotide onto the end of an extending nucleic acid molecule, the
enzyme-substrate interactions can be more complex because they
involve enzymatic interactions with the nucleic acid molecule as
well as the nucleotide. A typical exemplary reaction can be
represented by the following pathway:
E + NA n n .revreaction. E NA n .revreaction. E NA n + N - P .rarw.
.fwdarw. k - 1 E NA n N - P .fwdarw. k pol .rarw. >>>
.fwdarw. E + NA n + 1 + ( P i ) n ##EQU00002##
[0351] A more detailed representation of this exemplary theoretical
model is also depicted in FIG. 1. As depicted above and in FIG. 1,
the nucleotide incorporation reaction pathway can typically begin
with the initial association of the enzyme with a nucleic acid
molecule comprising "n" nucleotide subunits (represented above and
in FIG. 1 as "NA.sub.n") to form an enzyme-nucleic acid complex,
represented as ENA.sub.n. The ENA.sub.n complex can also associate
with a nucleotide, represented above and in FIG. 1 as "N-P"
although this representation is in no way intended to restrict the
nucleotide to any particular structure or any particular number of
phosphate groups, as opposed to other forms of nucleotides and
nucleotide analogs, which are also included. This association of
the ENA.sub.n complex with the nucleotide results in the formation
of a ternary complex, represented as ENA.sub.nN-P. This ternary
complex can in some instances dissociate with rate constant
k.sub.-1 to yield an enzyme-nucleic acid complex, ENA.sub.n,
comprising enzyme bound to nucleic acid, and unaltered nucleotide,
N-P (a so-called "non-productive incorporation"). Alternatively, in
some instances the ternary complex can undergo a productive
incorporation wherein the nucleic acid molecule is extended by one
nucleotide moiety with the liberation of a polyphosphate moiety.
During this productive incorporation, the polymerase can undergo a
conformational change from the so-called "open" form to the
"closed" form wherein the nucleotide is positioned in the
polymerase active site; the resulting complex comprising the
polymerase in "closed" conformation is represented as
E*NA.sub.nN-P. This complex can give rise to an intermediate
complex comprising the "closed"-form polymerase, an extended
nucleic acid and a polyphosphate group; this intermediate complex
can be represented as E*NA.sub.n+1(Pi).sub.n, wherein the
polyphosphate moiety is represented herein and in FIG. 1 as
(Pi).sub.n. The polymerase of the complex can undergo a reverse
conformational change from the "closed" to "open" form, resulting
in a complex comprising "open"-form polymerase, extended nucleic
acid and polyphosphate moiety (ENA.sub.n+1(Pi).sub.n). Release of
the polyphosphate moiety ((Pi).sub.n) results in a complex
comprising polymerase and extended nucleic acid, which can in some
instances associate with another nucleotide to form a ternary
complex that can undergo another productive incorporation.
[0352] Although the polyphosphate moiety is represented herein and
in FIG. 1 as (Pi).sub.n, this representation is in no way intended
to restrict the polyphosphate moiety to monophosphates or inorganic
phosphate. In some embodiments, for example, the nucleotide can be
a phosphate-labeled nucleotide analog and the liberated moiety can
comprise any one, two, three, four, five, six, seven, eight, nine,
ten or more phosphate groups linked to a label, e.g., a dye moiety.
The number of phosphate groups in the liberated polyphosphate will
depend on the number of phosphates in the polyphosphate chain of
the nucleotide substrate. A more complete description of this
theoretical model of polymerase activity can be found, for example,
in Patel et al., "Pre-Steady-State Kinetic Analysis of Processive
DNA Replication Including Complete Characterization of an
Exonuclease-Deficient Mutant" Biochemistry 30:511-525 (1991).
[0353] In FIG. 1, the step involving productive incorporation is
further depicted as separated into three sub-steps, with the first
sub-step involving formation of the ternary complex, ENA.sub.nN-P,
and the second sub-step involves the conversion of ENA.sub.nN-P to
E*NA.sub.nN-P.sub.n, wherein the enzyme has undergone a
conformational change from "open" form (E) to "closed" form (E*).
The third sub-step, the so-called "chemistry" step, typically
involves the conversion of E*NA.sub.nN-P to E*NA.sub.n+1(Pi).sub.n,
wherein the nucleic acid is extended by a single nucleotide moiety,
with the formation of a polyphosphate by-product, denoted as
(Pi).sub.n. In some embodiments, the E'NA.sub.n+1(Pi).sub.n complex
can dissociate to form free enzyme, extended nucleic acid, and free
polyphosphate (E+NA.sub.n+1+(Pi).sub.n); alternatively, the
polyphosphate may dissociate from the complex while the enzyme
remains associated with the extended nucleic acid and can in some
embodiments catalyze a subsequent nucleotide incorporation. FIG. 1
also depicts a window wherein FRET activity can occur using
embodiments wherein any suitable combination of components selected
from the group consisting of the nucleic acid molecule, the
nucleotide, the primer and the polymerase are labeled with moieties
capable of undergoing FRET with each other. In some embodiments,
the polymerase is labeled with one member of a FRET donor:acceptor
pair and the incoming nucleotide is labeled with another member of
the FRET pair.
[0354] In some embodiments, the above reaction involves a
polymerase, any suitable nucleic acid molecule (represented above
as NA.sub.n) and any suitable nucleotide. In some embodiments, the
nucleotide can be a polyphosphate-comprising nucleotide,
represented above as N-P. Any suitable polyphosphate-comprising
nucleotide can be used, including, for example labeled
deoxynucleotide polyphosphates comprising tri-, tetra-, penta-
hexa-phosphate, hepta-phosphate, octa-phosphate, nona-phosphate,
deca-phosphate, and undeca-phosphate moieties, as well as
deoxynucleotide polyphosphates comprising twelve or more phosphate
groups.
[0355] Theoretically, each step of this reaction pathway is
associated with specific rate constants, dissociation constants,
and associated kinetic parameters. In one exemplary embodiment, one
or more of these kinetic parameters can be measured in a
"stopped-flow" assay using suitable techniques. See, for example,
M. P. Roettger, Biochemistry 47:9718-9727 (2008); M. Bakhtina
Biochemistry 48:3197-320 (2009); Ahn et al, Biochemistry
36:1100-1107 (1997).
[0356] Without intending to be bound to any particular theory of
reaction mechanism, it can be surmised that in some cases which
indicates the rate of dissociation of the ternary complex
(ENA.sub.nN-P) into enzyme-nucleic acid complex (ENA.sub.n) and
free, unaltered nucleotide (N-P), is significantly lower than
k.sub.pol, which indicates the rate at which the ternary complex
(ENA.sub.nN-P) converts to the intermediate complex
(E*NA.sub.n+1(Pi).sub.n), then it can be expected that
non-productive incorporation events will predominate over
productive incorporation events. Conversely, when k.sub.pol is
significantly lower than k.sub.-1 then it can be expected that
productive incorporations will predominate over non-productive
incorporations.
[0357] In some embodiments, the polymerases, nucleotides, and
reaction conditions, can be screened for their suitability for use
in the disclosed nucleotide binding, nucleotide incorporation
and/or primer extension methods, using well known screening
techniques. For example, the suitable polymerase may be capable of
binding nucleotides and/or incorporating nucleotides. In some
embodiments, the reaction kinetics for nucleotide binding,
association, incorporation, and/or dissociation rates, can be
determined using rapid kinetics techniques (e.g., stopped-flow or
quench flow techniques). Using stopped-flow or quench flow
techniques, the binding kinetics of a nucleotide can be estimated
by calculating the 1/k.sub.d value. Stopped-flow techniques which
analyze absorption and/or fluorescence spectroscopy properties of
the nucleotide binding, incorporation, or dissociation rates to a
polymerase are well known in the art (Kumar and Patel 1997
Biochemistry 36:13954-13962; Tsai and Johnson 2006 Biochemistry
45:9675-9687; Hanzel, U.S. published patent application No.
2007/0196846). Other methods include quench flow (Johnson 1986
Methods Enzymology 134:677-705), time-gated fluorescence decay time
measurements (Korlach, U.S. Pat. No. 7,485,424), plate-based assays
(Clark, U.S. published patent application No. 2009/0176233), and
X-ray crystal structure analysis (Berman 2007 EMBO Journal
26:3494). Nucleotide incorporation by a polymerase can also be
analyzed by gel separation of the primer extension products.
[0358] In some embodiments, the modified polymerase exhibits
altered (e.g., increased or decreased) levels of primer extension
activity. For example, the modified polymerase may exhibit
increased primer extension activity in the presence of labeled
nucleotides, relative to an unmodified counterpart. In some
embodiments, the primer extension activity of the modified
polymerase is at least about 5%, 10%, 25%, 37.5%, 50%, 75%, 100%,
110%, 125%, 150%, 200%, 250%, 500%, 750%, 1,000%, 5,000% or 10,000%
of the primer extension activity of a reference polymerase under
identical reaction conditions. In some embodiments, the reference
polymerase is the unmodified counterpart of the modified
polymerase. In some embodiments, the reference polymerase is a
Phi-29 polymerase having the amino acid sequence of SEQ ID NO: 1.
In some embodiments, the reference polymerase is a B103 polymerase
having the amino acid sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ
ID NO: 8. In some embodiments, the modified polymerase comprises
the amino acid sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other
variant form of the polymerase having the amino acid sequence of
SEQ ID NO: 7. In some embodiments, the nucleotide substrate is a
natural nucleotide. In some embodiments, the nucleotide substrate
is a labeled nucleotide analog. The polymerase can be at least 80%,
85%, 97%, 98% or 99% identical to the amino acid sequence of SEQ ID
NO: 7 or SEQ ID NO: 8. In some embodiments, the modified polymerase
comprises one or more amino acid substitutions at positions
selected from the group consisting of: 2, 9, 12, 58, 59, 63, 129,
166, 246, 247, 339, 370, 371, 372, 373, 374, 375, 376, 377, 380,
383, 384, 385, 455, 507 and 509, or any combinations thereof. In
some embodiments, the modified polymerase comprises an amino acid
sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or
100% identical to the amino acid sequence of SEQ ID NO: 7 and
further includes amino acid mutations at any one, two, three or
more positions selected from the group consisting of: 2, 9, 12, 14,
15, 58, 59, 61, 63, 73, 98, 107, 129, 147, 166, 176, 185, 186, 187,
195, 208, 221, 246, 247, 248, 251, 252, 256, 300, 302, 310, 318,
339, 357, 359, 360, 362, 367, 368, 369, 370, 371, 372, 373, 374,
375, 376, 377, 378, 380, 383, 384, 385, 386, 387, 389, 390, 392,
399, 405, 411, 419, 430, 455, 475, 477, 481, 483, 493, 494, 497,
503, 507, 509, 511,526, 528, 529, 531, 535, 544, 550, 552, 555,
567, 569 and 572, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the
modifications can include deletions, additions and substitutions.
The substitutions can be conservative or non-conservative
substitutions. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98%, 99% or 100% identical to the amino acid sequence of
SEQ ID NO: 7 and further includes any one, two, three or more amino
acid mutations selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
I-1370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, A481E, A481F, A481G, A481S, A481R,
A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G, D507E,
D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F,
K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A,
K509Q, K509W, K509Y and K509F, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G; wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 7. Optionally, this modified polymerase comprises the
amino acid substitution H370R.
[0359] The primer extension activity can be measured using any
suitable assay that provides a quantitative indication of the
amount of extension product obtained using defined reaction
conditions comprising a known concentration of polymerase.
Regardless of which assay is used, differences in primer extension
activity between two samples, when obtained using identical
reaction conditions, can be evaluated by simply comparing levels of
observed primer activity obtained from each sample. Optionally, the
observed primer extension activity can normalized for amount of
polymerase by dividing the amount of incorporated radioactivity by
the polymerase concentration in the reaction mixture, to allow
comparison between reactions containing different polymerase
concentrations.
[0360] In one exemplary embodiment, the primer extension activity
of a polymerase can be measured using a radiometric assay that
measures incorporation of a radioactively labeled nucleotide into
acid-insoluble material in a polymerase reaction. The amount of
incorporated radioactivity indicates the total number of
nucleotides incorporated. See, e.g., Wu et al., Gene Biotechnology,
2nd Ed., CRC Press; Sambrook, J., Fritsch; E F, and Maniatis, T.
(1989) Molecular Cloning A Laboratory Manual, 2nd ed., Cold Spring
Harbor Laboratory Press, Cold Spring Harbor, N.Y.
[0361] In another exemplary embodiment, levels of primer extension
activity in a sample can be measured by monitoring the fluorescence
intensity change over time during extension of a
fluorescein-labeled hairpin oligonucleotide. One such exemplary
assay is described in Example 13, herein.
[0362] In another exemplary embodiment, the primer extension
activity can be quantified by quantifying the amount of
pyrophosphate liberated after performing primer extension under
standard tolerance assay conditions for 5 minutes. One such
exemplary assay is described in Example 5.
[0363] In another exemplary embodiment, the primer extension
activity can be quantified by measuring the fraction of extended
primer within a population of primer-template duplexes. One such
exemplary assay using standard photostability assay conditions is
provided in Example 6. In this exemplary embodiment, the template
comprised a radioactive (.sup.32P) moiety or fluorescent (TAMRA)
label to permit visualization of polymerase reaction products
(e.g., extended primer). Primer extension products were resolved on
a gel, and the primer extension activity was quantified as the
proportion (%) of extended primer relative to total starting primer
by adding the intensities of all bands observed within a single
lane as measured by densitometric analysis.
[0364] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) K.sub.m value for any
particular nucleotide substrate of interest, for example a labeled
nucleotide analog, relative to an unmodified counterpart. In some
embodiments, the modified polymerase exhibits a K.sub.m value for a
particular nucleotide substrate that is at least about 5%, 10%,
25%, 37.5%, 50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%,
750%, 1,000%, 5,000% or 10,000% as high as the K.sub.m value of a
reference polymerase for the same nucleotide substrate. In some
embodiments, the reference polymerase is the unmodified counterpart
of the modified polymerase. In some embodiments, the reference
polymerase is a Phi-29 polymerase having the amino acid sequence of
SEQ ID NO: 1. In some embodiments, the reference polymerase is a
B103 polymerase having the amino acid sequence of SEQ ID NO: 6, SEQ
ID NO: 7 or SEQ ID NO: 8. In some embodiments, the modified
polymerase comprises the amino acid sequence of SEQ ID NO: 7, SEQ
ID NO: 8, or any other variant form of the polymerase having the
amino acid sequence of SEQ ID NO: 7. In some embodiments, the
nucleotide substrate is a natural nucleotide. In some embodiments,
the nucleotide substrate is a labeled nucleotide analog. The
polymerase can be at least 80%, 85%, 97%, 98% or 99% identical to
the amino acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the modified polymerase comprises one or more amino
acid substitutions at positions selected from the group consisting
of: 2, 9, 12, 58, 59, 63, 129, 166, 246, 247, 339, 370, 371, 372,
373, 374, 375, 376, 377, 380, 383, 384, 385, 455, 507 and 509, or
any combinations thereof. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 7 and further includes amino acid
mutations at any one, two, three or more positions selected from
the group consisting of: 2, 9, 12, 14, 15, 58, 59, 61, 63, 73, 98,
107, 129, 147, 166, 176, 185, 186, 187, 195, 208, 221, 246, 247,
248, 251, 252, 256, 300, 302, 310, 318, 339, 357, 359, 360, 362,
367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380,
383, 384, 385, 386, 387, 389, 390, 392, 399, 405, 411, 419, 430,
455, 475, 477, 481, 483, 493, 494, 497, 503, 507, 509, 511, 526,
528, 529, 531, 535, 544, 550, 552, 555, 567, 569 and 572, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. In some embodiments, the modifications can include deletions,
additions and substitutions. The substitutions can be conservative
or non-conservative substitutions. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 7 and further includes any one,
two, three or more amino acid mutations selected from the group
consisting of: T365G, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K, H370R,
H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T, E371S,
E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E,
K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E,
K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, A481E,
A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q, A481W,
A481Y, D507H, D507G, D507E, D507T, D507S, D507R, D507A, D507R,
D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R, K509E,
K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. Optionally, the modified polymerase can further include one or
more mutations reducing 3' to 5' exonuclease activity selected from
the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A,
Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 7. Optionally,
this modified polymerase comprises the amino acid substitution
H370R.
[0365] In some embodiments, the modified polymerase comprises one
or more modifications that alter the t.sub.-1 value of the modified
polymerase for a given nucleotide, for example a labeled nucleotide
analog, as compared to the t.sub.-1 value of an unmodified
counterpart for the same nucleotide. In some embodiments, the
t.sub.-1 value can be defined as the average time required for the
nucleotide (e.g., a labeled nucleotide analog) to dissociate in
unaltered form from the enzyme-template-nucleotide ternary complex
(ENA.sub.nN-P) during nucleic acid polymerization, wherein the
dissociation can be represented through the following reaction:
E NA n + N - P .fwdarw. .rarw. k - 1 E NA n N - P ##EQU00003##
[0366] Typically, t.sub.-1 can be calculated as the reciprocal of
k.sub.-1, the rate constant for the dissociation reaction, and thus
t.sub.-1 can be mathematically represented as 1/k.sub.-1. In some
embodiments, the modified polymerase comprises one, two or more
modifications that increase the t.sub.-1 value of the polymerase
for a particular nucleotide substrate, particularly a labeled
nucleotide analog. Such increase in the t.sub.-1 value typically
correlates with a decreased rate of dissociation of the
enzyme-template-nucleotide ternary complex, which can in some cases
increase the duration during which the nucleotide remains
associated with the polymerase and template in the ternary complex.
This can be helpful in various biological applications, including
nucleic acid sequencing, which require or otherwise involve
visualization of the labeled nucleotide analog when in proximity
with or bound to the polymerase active site.
[0367] A variety of methods are available to measure the rate of
nucleotide dissociation, k.sub.-1 (and the corresponding t.sub.-1
value). Typically, the k.sub.-1 value is measured using
stopped-flow fluorescence measurements, and fitting the resulting
fluorescence traces to a single exponential function of the
form:
Fluorescence=A.sub.1*e.sup.-k-1*t+C [Equation (1)]
[0368] where A.sub.1 represents the corresponding fluorescence
amplitude, C is an offset constant, and k.sub.-1 is the observed
rate constant for the fluorescence transition. See, e.g., Bakhtina,
Biochemistry 48:3197-3208 (2009).
[0369] In one exemplary method, a non-extendible primed template is
formed by annealing a primer comprising a dideoxynucleotide at its
3' end with a template oligonucleotide that further protrudes a few
nucleotides downstream from the 3' end of the primer, and comprises
a donor fluorophore at its 5' end. This non-extendible primed
template is then contacted with a nucleotide comprising an acceptor
fluorophore attached to the terminal phosphate group (also referred
to herein as the "omega" phosphate group) to form a ternary
complex. The ternary complex is then contacted with unlabeled
("cold") nucleotides, and the dissociation of the omega-labeled
nucleotide from the ternary complex is monitored as a function of
donor fluorescence where typically dissociation is correlated with
an increase in donor fluorescence. The fluorescence traces are then
fitted into a function of the form of Equation (1) to determine the
k.sub.-1 and the corresponding t.sub.-1 values for the
polymerase.
[0370] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) t.sub.-1 value for a given
nucleotide substrate, for example a labeled nucleotide analog,
relative to an unmodified counterpart. In some embodiments, the
modified polymerase exhibits a t.sub.pol value for a particular
nucleotide substrate that is at least about 5%, 10%, 25%, 37.5%,
50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%, 750%, 1,000%,
5,000% or 10,000% as high as the L.sub.1 value of a reference
polymerase for the same nucleotide substrate. In some embodiments,
the reference polymerase is the unmodified counterpart of the
modified polymerase. In some embodiments, the reference polymerase
is a Phi-29 polymerase having the amino acid sequence of SEQ ID NO:
1. In some embodiments, the reference polymerase is a B103
polymerase having the amino acid sequence of SEQ ID NO: 6, SEQ ID
NO: 7 or SEQ ED NO: 8. In some embodiments, the nucleotide
substrate is a natural nucleotide. In some embodiments, the
nucleotide substrate is a labeled nucleotide analog. In some
embodiments, the modified polymerase comprises the amino acid
sequence of SEQ ID NO: 7, SEQ ID NO: 8 or any other variant form of
the polymerase having the amino acid sequence of SEQ ID NO: 7. In
some embodiments, the modified polymerase is at least 80%, 85%,
97%, 98% or 99% identical to the amino acid sequence of SEQ ID NO:
7 or SEQ ID NO: 8. In some embodiments, the modified polymerase
comprises one or more amino acid substitutions at positions
selected from the group consisting of: 2, 9, 12, 58, 59, 63, 129,
166, 246, 247, 370, 371, 372, 373, 374, 375, 376, 377, 380, 383,
384, 385, 455, 507 and 509, or any combinations thereof.
[0371] In one exemplary assay, the L.sub.1 value of the modified
polymerase is measured with respect to an exemplary labeled
nucleotide analog comprising a fluorophore, e.g., an Alexa Fluor
647 moiety, attached to the terminal phosphate of a deoxynucleotide
tetraphosphate via a suitable linker. Some non-limiting examples of
labeled nucleotides and methods of using such nucleotides in
polymerase-based applications can be found, inter alia, in U.S.
Pat. Nos. 7,244,566 issued Jul. 17, 2007; 7,223,541 issued May 29,
2007; 7,052,839 issued May 30, 2006; 7,244,566 issued Jul. 17,
2007; 7,393,640 issued Jul. 1, 2008; 7,033,762 issued Apr. 25,
2006; 7,256,019 issued Aug. 14, 2007; 7,041,812 issued May 9, 2006;
7,452,698 issued Nov. 18, 2008 and 7,078,499 issued Jul. 18, 2006;
as well as in U.S. Published Application Nos. 2004/0048300
published Mar. 11, 2004; 2008/0132692 published Jun. 5, 2008;
2009/0081686, published Mar. 26, 2009; 2008/0131952, published Jun.
5, 2008; and 2007/0292679, published Dec. 20, 2007.
[0372] In some embodiments, the modified polymerase has a t.sub.-1
value for a nucleotide substrate that is greater than or equal to
the t.sub.-1 value for the same nucleotide substrate of a Phi-29
polymerase comprising the amino acid sequence of SEQ ID NO: 1 and
further comprising an amino acid substitution at one or more
residues selected from the group consisting of: 132, 250, 342, 373,
375, 379, 380, 383, 510 and 512, wherein the numbering is relative
to the amino acid of SEQ ID NO: 1. In some embodiments, the
modified polymerase has a t.sub.-1 value for a given nucleotide
that is greater than or equal to the t.sub.-1 for the same
nucleotide of a Phi-29 polymerase comprising the amino acid
sequence of SEQ ID NO: 1 and further comprising one or more amino
acid substitutions selected from the group consisting of: K132A,
V250A, L342G, T373R, E375Y, T373R, K379A, Q380A, D510H and
K512Y.
[0373] In some embodiments, the modified polymerase comprises the
amino acid sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other
variant of the polymerase having the amino acid sequence of SEQ ID
NO: 7. In some embodiments, the modified polymerase is at least
80%, 85%, 97%, 98% or 99% identical to the amino acid sequence of
SEQ ID NO: 7 and can in some embodiments comprise an amino acid
substitutions at one or more positions selected from the group
consisting of: 2, 9, 12, 58, 59, 63, 129, 166, 246, 247, 339, 370,
371, 372, 373, 374, 375, 376, 377, 380, 383, 384, 385, 455, 507 and
509, or any combinations thereof. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 7 and further includes amino acid
mutations at any one, two, three or more positions selected from
the group consisting of: 2, 9, 12, 14, 15, 58, 59, 61, 63, 73, 98,
107, 129, 147, 166, 176, 185, 186, 187, 195, 208, 221, 246, 247,
248, 251, 252, 256, 300, 302, 310, 318, 339, 357, 359, 360, 362,
367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380,
383, 384, 385, 386, 387, 389, 390, 392, 399, 405, 411, 419, 430,
455, 475, 477, 481, 483, 493, 494, 497, 503, 507, 509, 511, 526,
528, 529, 531, 535, 544, 550, 552, 555, 567, 569 and 572, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. In some embodiments, the modifications can include deletions,
additions and substitutions. The substitutions can be conservative
or non-conservative substitutions. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 7 and further includes any one,
two, three or more amino acid mutations selected from the group
consisting of: T365G, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K, H370R,
H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T, E371S,
E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E,
K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E,
K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, A481E,
A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q, A481W,
A481Y, D507H, D507G, D507E, D507T, D507S, D507R, D507A, D507R,
D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R, K509E,
K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. Optionally, the modified polymerase can further include one or
more mutations reducing 3' to 5' exonuclease activity selected from
the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A,
Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 7. Optionally,
this modified polymerase comprises the amino acid substitution
H370R.
[0374] Another useful parameter of enzymatic activity is k.sub.cat,
also known as the turnover number. Typically, k.sub.cat equals the
number of times each enzyme site converts substrate to product per
unit time, i.e., the maximal number of molecules of substrate
converted to product per enzyme active site per unit time (e.g.,
second).
[0375] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) k.sub.cat value for a given
nucleotide substrate, for example a labeled nucleotide analog,
relative to an unmodified counterpart. In some embodiments, the
modified polymerase exhibits a k.sub.cat value for a particular
nucleotide substrate that is at least about 5%, 10%, 25%, 37.5%,
50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%, 750%, 1,000%,
5,000% or 10,000% as high as the k.sub.cat value of a reference
polymerase for the same nucleotide substrate. In some embodiments,
the reference polymerase is the unmodified counterpart of the
modified polymerase. In some embodiments, the reference polymerase
is a Phi-29 polymerase having the amino acid sequence of SEQ ID NO:
1. In some embodiments, the reference polymerase is a B103
polymerase having the amino acid sequence of SEQ ID NO: 6, SEQ ID
NO: 7 or SEQ ID NO: 8. In some embodiments, the nucleotide
substrate is a natural nucleotide. In some embodiments, the
nucleotide substrate is a labeled nucleotide analog. In some
embodiments, the modified polymerase comprises the amino acid
sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other variant form
of the polymerase having the amino acid sequence of SEQ ID NO: 7.
In some embodiments, the modified polymerase can be at least 80%,
85%, 97%, 98% or 99% identical to the amino acid sequence of SEQ ID
NO: 7 or SEQ ID NO: 8. In some embodiments, the modified polymerase
comprises one or more amino acid substitutions at positions
selected from the group consisting of: 2, 9, 12, 58, 59, 63, 129,
166, 246, 247, 339, 370, 371, 372, 373, 374, 375, 376, 377, 380,
383, 384, 385, 455, 507 and 509, or any combinations thereof. In
some embodiments, the modified polymerase comprises an amino acid
sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or
100% identical to the amino acid sequence of SEQ ID NO: 7 and
further includes amino acid mutations at any one, two, three or
more positions selected from the group consisting of: 2, 9, 12, 14,
15, 58, 59, 61, 63, 73, 98, 107, 129, 147, 166, 176, 185, 186, 187,
195, 208, 221, 246, 247, 248, 251, 252, 256, 300, 302, 310, 318,
339, 357, 359, 360, 362, 367, 368, 369, 370, 371, 372, 373, 374,
375, 376, 377, 378, 380, 383, 384, 385, 386, 387, 389, 390, 392,
399, 405, 411, 419, 430, 455, 475, 477, 481, 483, 493, 494, 497,
503, 507, 509, 511, 526, 528, 529, 531, 535, 544, 550, 552, 555,
567, 569 and 572, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the
modifications can include deletions, additions and substitutions.
The substitutions can be conservative or non-conservative
substitutions. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98%, 99% or 100% identical to the amino acid sequence of
SEQ ID NO: 7 and further includes any one, two, three or more amino
acid mutations selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, A481E, A481F, A481G, A481S, A481R,
A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G, D507E,
D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F,
K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A,
K509Q, K509W, K509Y and K509F, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 7. Optionally, this modified polymerase comprises the
amino acid substitution H370R.
[0376] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) specificity for a given
nucleotide substrate, for example a labeled nucleotide analog,
relative to an unmodified counterpart. In some embodiments, the
modified polymerase exhibits a specificity for a particular
nucleotide substrate that is at least about 5%, 10%, 25%, 37.5%,
50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%, 750%, 1,000%,
5,000% or 10,000% as high as the specificity of a reference
polymerase for the same nucleotide substrate. In some embodiments,
the reference polymerase is the unmodified counterpart of the
modified polymerase. In some embodiments, the reference polymerase
is a Phi-29 polymerase having the amino acid sequence of SEQ ID NO:
1. In some embodiments, the reference polymerase is a B103
polymerase having the amino acid sequence of SEQ ID NO: 6, SEQ ID
NO: 7 or SEQ ID NO: 8. In some embodiments, the nucleotide
substrate is a natural nucleotide. In some embodiments, the
nucleotide substrate is a labeled nucleotide analog. In some
embodiments, the modified polymerase comprises the amino acid
sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other variant form
of the polymerase having the amino acid sequence of SEQ ID NO: 7.
In some embodiments, the modified polymerase can be at least 80%,
85%, 97%, 98% or 99% identical to the amino acid sequence of SEQ ID
NO: 7 or SEQ ID NO: 8. In some embodiments, the modified polymerase
comprises one or more amino acid substitutions at positions
selected from the group consisting of: 2, 9, 12, 58, 59, 63, 129,
166, 246, 247, 370, 371, 372, 373, 374, 375, 376, 377, 380, 383,
384, 385, 455, 507 and 509, or any combinations thereof.
[0377] Without being bound to any particular theory, according to
some theories the specificity of the enzyme can be defined
mathematically as the ratio
k.sub.cat/K.sub.m=k.sub.catk.sub.1/(k.sub.-1+k.sub.2). It has the
dimension M.sup.-1s.sup.-1, with large values typically indicating
high specificity. In some embodiments, the modified polymerase
exhibits an altered (e.g., increased or decreased)
k.sub.cat/K.sub.m ratio for a given nucleotide substrate, for
example a labeled nucleotide analog, relative to an unmodified
counterpart. In some embodiments, the modified polymerase exhibits
a k.sub.cat/K.sub.m ratio for a particular nucleotide substrate
that is at least about 5%, 10%, 25%, 37.5%, 50%, 75%, 100%, 110%,
125%, 150%, 200%, 250%, 500%, 750%, 1,000%, 5,000% or 10,000% as
high as the k.sub.cat/K.sub.m ratio of a reference polymerase for
the same nucleotide substrate. In some embodiments, the reference
polymerase is the unmodified counterpart of the modified
polymerase. In some embodiments, the reference polymerase is a
Phi-29 polymerase having the amino acid sequence of SEQ ID NO: 1.
In some embodiments, the reference polymerase is a B103 polymerase
having the amino acid sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ
ID NO: 8. In some embodiments, the nucleotide substrate is a
natural nucleotide. In some embodiments, the nucleotide substrate
is a labeled nucleotide analog. In some embodiments, the modified
polymerase comprises the amino acid sequence of SEQ ID NO: 7, SEQ
ID NO: 8, or any other variant of the polymerase having the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the modified
polymerase can be at least 80%, 85%, 97%, 98% or 99% identical to
the amino acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the modified polymerase comprises one or more amino
acid substitutions at positions selected from the group consisting
of: 2, 9, 12, 58, 59, 63, 129, 166, 246, 247, 370, 371, 372, 373,
374, 375, 376, 377, 380, 383, 384, 385, 455, 507 and 509, or any
combinations thereof. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 70%, 80%, 85%,
90%, 95%, 97%, 98%, 99% or 100% identical to the amino acid
sequence of SEQ ID NO: 7 and further includes amino acid mutations
at any one, two, three or more positions selected from the group
consisting of: 2, 9, 12, 14, 15, 58, 59, 61, 63, 73, 98, 107, 129,
147, 166, 176, 185, 186, 187, 195, 208, 221, 246, 247, 248, 251,
252, 256, 300, 302, 310, 318, 339, 357, 359, 360, 362, 367, 368,
369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380, 383, 384,
385, 386, 387, 389, 390, 392, 399, 405, 411, 419, 430, 455, 475,
477, 481, 483, 493, 494, 497, 503, 507, 509, 511, 526, 528, 529,
531, 535, 544, 550, 552, 555, 567, 569 and 572, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 7.
In some embodiments, the modifications can include deletions,
additions and substitutions. The substitutions can be conservative
or non-conservative substitutions. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 7 and further includes any one,
two, three or more amino acid mutations selected from the group
consisting of: T365G, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K, H370R,
H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T, E371S,
E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E,
K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E,
K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, A481E,
A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q, A481W,
A481Y, D507H, D507G, D507E, D507T, D507S, D507R, D507A, D507R,
D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R, K509E,
K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. Optionally, the modified polymerase can further include one or
more mutations reducing 3' to 5' exonuclease activity selected from
the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A,
Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 7. Optionally,
this modified polymerase comprises the amino acid substitution
H370R.
[0378] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) V.sub.max/K.sub.m value for
a given nucleotide substrate, for example a labeled nucleotide
analog, relative to an unmodified counterpart. In some embodiments,
the modified polymerase exhibits a V.sub.max/K.sub.m value for a
particular nucleotide substrate that is at least about 5%, 10%,
25%, 37.5%, 50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%,
750%, 1,000%, 5,000% or 10,000% as high as the V.sub.max/K.sub.m
value of a reference polymerase for the same nucleotide substrate.
In some embodiments, the reference polymerase is the unmodified
counterpart of the modified polymerase. In some embodiments, the
reference polymerase is a Phi-29 polymerase having the amino acid
sequence of SEQ ID NO: 1. In some embodiments, the reference
polymerase is a B103 polymerase having the amino acid sequence of
SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO: 8. In some embodiments,
the nucleotide substrate is a natural nucleotide. In some
embodiments, the nucleotide substrate is a labeled nucleotide
analog. In some embodiments, the modified polymerase comprises the
amino acid sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other
variant of the polymerase having the amino acid sequence of SEQ ID
NO: 7. In some embodiments, the modified polymerase can be at least
80%, 85%, 97%, 98% or 99% identical to the amino acid sequence of
SEQ ID NO: 7 or SEQ ID NO: 8. In some embodiments, the modified
polymerase comprises one or more amino acid substitutions at
positions selected from the group consisting of: 2, 9, 12, 58, 59,
63, 129, 166, 246, 247, 339, 370, 371, 372, 373, 374, 375, 376,
377, 380, 383, 384, 385, 455, 507 and 509, or any combinations
thereof. In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
7 and further includes amino acid mutations at any one, two, three
or more positions selected from the group consisting of: 2, 9, 12,
14, 15, 58, 59, 61, 63, 73, 98, 107, 129, 147, 166, 176, 185, 186,
187, 195, 208, 221, 246, 247, 248, 251, 252, 256, 300, 302, 310,
318, 339, 357, 359, 360, 362, 367, 368, 369, 370, 371, 372, 373,
374, 375, 376, 377, 378, 380, 383, 384, 385, 386, 387, 389, 390,
392, 399, 405, 411, 419, 430, 455, 475, 477, 481, 483, 493, 494,
497, 503, 507, 509, 511, 526, 528, 529, 531, 535, 544, 550, 552,
555, 567, 569 and 572, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 7. In some embodiments, the
modifications can include deletions, additions and substitutions.
The substitutions can be conservative or non-conservative
substitutions. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98%, 99% or 100% identical to the amino acid sequence of
SEQ ID NO: 7 and further includes any one, two, three or more amino
acid mutations selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, A481E, A481F, A481G, A481S, A481R,
A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G, D507E,
D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F,
K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A,
K509Q, K509W, K509Y and K509F, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 7. Optionally, this modified polymerase comprises the
amino acid substitution H370R.
[0379] In some embodiments, the modified polymerase comprises one
or more modifications that alter the t.sub.pol value of the
modified polymerase for a given nucleotide, for example a labeled
nucleotide analog, as compared to the t.sub.pol value of an
unmodified counterpart for the same nucleotide. The t.sub.pol value
can be defined as the average time for the incorporation reaction
to occur from the enzyme-template-nucleotide ternary complex
according to the following reaction:
E NA n N - P .fwdarw. k pol .rarw. E + NA n + 1 + ( P i ) n
##EQU00004##
[0380] Typically, t.sub.pol can be calculated as the reciprocal of
k.sub.pol, the rate constant for the above reaction, and thus
t.sub.pol can be mathematically represented as 1/k.sub.pol. In some
embodiments, the modified polymerase comprises one, two or more
modifications that decrease the t.sub.pol value of the polymerase
for a particular nucleotide substrate, particularly a labeled
nucleotide analog. Such decrease in the t.sub.pol value typically
correlates with an increased rate of the forward reaction in which
the enzyme-template-nucleotide ternary complex undergoes a
productive incorporation, thereby producing an extended nucleic
acid molecule. This increase in forward rate can be helpful in
various biological applications, including nucleic acid sequencing,
which require or otherwise involve visualization of the labeled
nucleotide analog when in proximity with or bound to the polymerase
active site.
[0381] A variety of methods are available to measure k.sub.pol (and
the corresponding t.sub.pol value). In one exemplary method as
taught in MP Roettger (2008 Biochemistry 47:9718-9727); M. Bakhtina
2009 Biochemistry 48:3197-320), the k.sub.pd value of a polymerase
can be measured in a stopped-flow experiment by fitting the
fluorescence trace data to a general double exponential function of
the form:
Fluorescence=A.sub.1*e.sup.-k1*t+A.sub.2*e.sup.-kpol*t+C [Equation
(2)]
[0382] where A.sub.1 and A.sub.2 represent corresponding
fluorescence amplitudes, C is an offset constant, and k.sub.1 and
k.sub.pol are the observed rate constants for the fast and slow
phases of the reaction, respectively. Plotting the concentration
dependence of the rates and amplitudes for the fast and slow phases
can afford a definition of the rate constants k.sub.1 and k.sub.pol
in a two-step binding process.
[0383] In one exemplary stopped-flow method, the an extendible
primed template is formed by annealing a primer with a template
oligonucleotide that extends a further few nucleotides downstream
from the 3' end of the primer, and comprises a donor fluorophore at
its 5' end. This extendible primed template is contacted with a
nucleotide comprising an acceptor fluorophore attached to the
terminal ("omega") phosphate group to initiate the nucleotide
incorporation reaction. The reaction progress is monitored as a
function of donor fluorescence where typically the reaction
progress is correlated with an initial dip in donor fluorescence
followed by a recovery in donor fluorescence. Based on these
fluorescence measurements, the k.sub.pol value can be determined by
fitting the fluorescence traces to a function having the form of
Equation (2), and the t.sub.pol value can be calculated as the
reciprocal of the k.sub.pol value.
[0384] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) t.sub.pol value for a given
nucleotide substrate, for example a labeled nucleotide analog,
relative to an unmodified counterpart. In some embodiments, the
modified polymerase exhibits a t.sub.pol value for a particular
nucleotide substrate that is at least about 5%, 10%, 25%, 37.5%,
50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%, 750%, 1,000%,
5,000% or 10,000% as high as the t.sub.pol value of a reference
polymerase for the same nucleotide substrate. In some embodiments,
the reference polymerase is the unmodified counterpart of the
modified polymerase. In some embodiments, the reference polymerase
is a Phi-29 polymerase having the amino acid sequence of SEQ ID NO:
1. In some embodiments, the reference polymerase is a B103
polymerase having the amino acid sequence of SEQ ID NO: 6, SEQ ID
NO: 7 or SEQ ID NO: 8. In some embodiments, the nucleotide
substrate is a natural nucleotide. In some embodiments, the
nucleotide substrate is a labeled nucleotide analog. In some
embodiments, the modified polymerase comprises the amino acid
sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other variant of the
polymerase having the amino acid sequence of SEQ ID NO: 7. In some
embodiments, the modified polymerase can be at least 80%, 85%, 97%,
98% or 99% identical to the amino acid sequence of SEQ ID NO: 7 or
SEQ ID NO: 8. In some embodiments, the modified polymerase
comprises one or more amino acid substitutions at positions
selected from the group consisting of: 2, 9, 12, 58, 59, 63, 129,
166, 246, 247, 339, 370, 371, 372, 373, 374, 375, 376, 377, 380,
383, 384, 385, 455, 507 and 509, or any combinations thereof. In
some embodiments, the modified polymerase comprises an amino acid
sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or
100% identical to the amino acid sequence of SEQ ID NO: 7 and
further includes amino acid mutations at any one, two, three or
more positions selected from the group consisting of: 2, 9, 12, 14,
15, 58, 59, 61, 63, 73, 98, 107, 129, 147, 166, 176, 185, 186, 187,
195, 208, 221, 246, 247, 248, 251, 252, 256, 300, 302, 310, 318,
339, 357, 359, 360, 362, 367, 368, 369, 370, 371, 372, 373, 374,
375, 376, 377, 378, 380, 383, 384, 385, 386, 387, 389, 390, 392,
399, 405, 411, 419, 430, 455, 475, 477, 481, 483, 493, 494, 497,
503, 507, 509, 511, 526, 528, 529, 531, 535, 544, 550, 552, 555,
567, 569 and 572, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the
modifications can include deletions, additions and substitutions.
The substitutions can be conservative or non-conservative
substitutions. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98%, 99% or 100% identical to the amino acid sequence of
SEQ ID NO: 7 and further includes any one, two, three or more amino
acid mutations selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, A481E, A481F, A481G, A481S, A481R,
A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G, D507E,
D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F,
K509H, K5090, K509D, K509R, K509E, K509T, K509S, K509R, K509A,
K509Q, K509W, K509Y and K509F, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 7. Optionally, this modified polymerase comprises the
amino acid substitution H370R.
[0385] Any suitable method of measuring t.sub.pol may be used. In
one exemplary assay, the t.sub.pol value of the modified polymerase
is measured with respect to an exemplary labeled nucleotide analog
comprising an Alexa Fluor 647 moiety attached to the terminal
("omega") phosphate of a deoxynucleotide tetraphosphate via a
6-carbon linker. See, for example, U.S. Pat. No. 7,041,812, issued
May 9, 2006.
[0386] In some embodiments, the modified polymerase has a t.sub.pol
value for a nucleotide that is less than or equal to the t.sub.pol
value for the same nucleotide of a Phi-29 polymerase comprising the
amino acid sequence of SEQ ID NO: 1 and further comprising an amino
acid substitution at one or more positions selected from the group
consisting of: 132, 250, 342, 373 375, 379, 380, 383, 510 and 512,
wherein the numbering is relative to the amino acid of SEQ ID NO:
1. In some embodiments, the modified polymerase has a t.sub.pol
value for a given nucleotide that is greater than or equal to the
t.sub.pol value for the same nucleotide of a Phi-29 polymerase
comprising the amino acid sequence of SEQ ID NO: 1 and further
comprising one or more amino acid substitutions selected from the
group consisting of: K132A, V250A, L342G, T373R, E375Y, K379A,
Q380A, D510H and K512Y.
[0387] In some embodiments, the ratio of t.sub.-1/t.sub.pol values
for the modified polymerase is at least about 0.5, more typically
at least about 1.0, even more typically at least about 1.2, 1.3,
1.5, 1.75, 2.0, 2.5, 5.0, 7.5, 10, 12.5, 25, 50, or 100. In some
embodiments, the modified polymerase exhibits an altered (e.g.,
increased or decreased) ratio of t.sub.-1/t.sub.pol values for a
given nucleotide substrate, for example a labeled nucleotide
analog, relative to an unmodified counterpart. In some embodiments,
the modified polymerase exhibits a t.sub.-1/t.sub.pol ratio for a
particular nucleotide substrate that is at least about 5%, 10%,
25%, 37.5%, 50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%,
750%, 1,000%, 5,000% or 10,000% as high as the t.sub.-1/t.sub.o
ratio of a reference polymerase for the same nucleotide substrate.
In some embodiments, the reference polymerase is the unmodified
counterpart of the modified polymerase. In some embodiments, the
reference polymerase is a Phi-29 polymerase having the amino acid
sequence of SEQ ID NO: 1. In some embodiments, the reference
polymerase is a B103 polymerase having the amino acid sequence of
SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO: 8. In some embodiments,
the nucleotide substrate is a natural nucleotide. In some
embodiments, the nucleotide substrate is a labeled nucleotide
analog. In some embodiments, the modified polymerase comprises the
amino acid sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other
variant of the polymerase having the amino acid sequence of SEQ ID
NO: 7. In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 97%, 98% or 99%
identical to the amino acid sequence of SEQ ID NO: 7 or SEQ ID NO:
8. In some embodiments, the modified polymerase comprises one or
more amino acid substitutions at positions selected from the group
consisting of: 2, 9, 12, 58, 59, 63, 129, 166, 246, 247, 339, 370,
371, 372, 373, 374, 375, 376, 377, 380, 383, 384, 385, 455, 507 and
509, or any combinations thereof. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 7 and further includes amino acid
mutations at any one, two, three or more positions selected from
the group consisting of: 2, 9, 12, 14, 15, 58, 59, 61, 63, 73, 98,
107, 129, 147, 166, 176, 185, 186, 187, 195, 208, 221, 246, 247,
248, 251, 252, 256, 300, 302, 310, 318, 339, 357, 359, 360, 362,
367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380,
383, 384, 385, 386, 387, 389, 390, 392, 399, 405, 411, 419, 430,
455, 475, 477, 481, 483, 493, 494, 497, 503, 507, 509, 511, 526,
528, 529, 531, 535, 544, 550, 552, 555, 567, 569 and 572, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. In some embodiments, the modifications can include deletions,
additions and substitutions. The substitutions can be conservative
or non-conservative substitutions. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 7 and further includes any one,
two, three or more amino acid mutations selected from the group
consisting of: T365G, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K, H370R,
H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T, E371S,
E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E,
K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E,
K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, A481E,
A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q, A481W,
A481Y, D507H, D507G, D507E, D507T, D507S, D507R, D507A, D507R,
D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R, K509E,
K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. Optionally, the modified polymerase can further include one or
more mutations reducing 3' to 5' exonuclease activity selected from
the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A,
Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 7. Optionally,
this modified polymerase comprises the amino acid substitution
H370R.
[0388] In one embodiment, stopped-flow techniques can be used to
screen and select mutant polymerases having a t.sub.pol value
(e.g.,) for a particular labeled nucleotide that is less than the
t.sub.-1 (e.g., 1/k.sub.-1) value of the polymerase for the same
labeled nucleotide. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 97%,
98% or 99% identical to the amino acid sequence of SEQ ID NO: 7 or
SEQ ID NO: 8. In some embodiments, the modified polymerase
comprises one or more amino acid substitutions at positions
selected from the group consisting of: 2, 9, 12, 58, 59, 63, 129,
166, 246, 247, 339, 370, 371, 372, 373, 374, 375, 376, 377, 380,
383, 384, 385, 455, 507 and 509, or any combinations thereof. In
some embodiments, the polymerase comprises the amino acid sequence
of SEQ ID NO: 8, and optionally further comprises the amino acid
substitution H370R. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 70%, 80%, 85%,
90%, 95%, 97%, 98%, 99% or 100% identical to the amino acid
sequence of SEQ ID NO: 7 and further includes amino acid mutations
at any one, two, three or more positions selected from the group
consisting of: 2, 9, 12, 14, 15, 58, 59, 61, 63, 73, 98, 107, 129,
147, 166, 176, 185, 186, 187, 195, 208, 221, 246, 247, 248, 251,
252, 256, 300, 302, 310, 318, 339, 357, 359, 360, 362, 367, 368,
369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380, 383, 384,
385, 386, 387, 389, 390, 392, 399, 405, 411, 419, 430, 455, 475,
477, 481, 483, 493, 494, 497, 503, 507, 509, 511, 526, 528, 529,
531, 535, 544, 550, 552, 555, 567, 569 and 572, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 7.
In some embodiments, the modifications can include deletions,
additions and substitutions. The substitutions can be conservative
or non-conservative substitutions. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 7 and further includes any one,
two, three or more amino acid mutations selected from the group
consisting of: T365G, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K, H370R,
H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T, E371S,
E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E,
K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E,
K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, A481E,
A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q, A481W,
A481Y, D507H, D507G, D507E, D507T, D507S, D507R, D507A, D507R,
D507Q, D507W, D507Y, D507F, K509H, K5090, K509D, K509R, K509E,
K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. Optionally, the modified polymerase can further include one or
more mutations reducing 3' to 5' exonuclease activity selected from
the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A,
Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 7. Optionally,
this modified polymerase comprises the amino acid substitution
H370R.
[0389] For example, some Phi-29 or B103 polymerases (wild-type or
mutant) exhibit t.sub.pol values which are less than t.sub.-1
values, in the presence of nucleotide tetraphosphate or
hexaphosphate molecules.
[0390] In another embodiment, polymerases can be modified by
binding it to a chemical compound or an antibody, in order to
inhibit nucleotide incorporation.
[0391] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) ratio of k.sub.cat/K.sub.d
value values for a given nucleotide substrate, for example a
labeled nucleotide analog, relative to an unmodified counterpart.
In some embodiments, the modified polymerase exhibits a
k.sub.cat/K.sub.d ratio for a particular nucleotide substrate that
is at least about 5%, 10%, 25%, 37.5%, 50%, 75%, 100%, 110%, 125%,
150%, 200%, 250%, 500%, 750%, 1,000%, 5,000% or 10,000% as high as
the k.sub.cat/K.sub.d ratio of a reference polymerase for the same
nucleotide substrate. In some embodiments, the reference polymerase
is the unmodified counterpart of the modified polymerase. In some
embodiments, the reference polymerase is a Phi-29 polymerase having
the amino acid sequence of SEQ ID NO: 1. In some embodiments, the
reference polymerase is a B103 polymerase having the amino acid
sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the nucleotide substrate is a natural nucleotide. In
some embodiments, the nucleotide substrate is a labeled nucleotide
analog.
[0392] In some embodiments, the modified polymerase comprises the
amino acid sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other
variant of the polymerase having the amino acid sequence of SEQ ID
NO: 7. In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 97%, 98% or 99%
identical to the amino acid sequence of SEQ ID NO: 7 or SEQ ID NO:
8. In some embodiments, the modified polymerase comprises one or
more amino acid substitutions at positions selected from the group
consisting of: 2, 9, 12, 58, 59, 63, 129, 166, 246, 247, 339, 370,
371, 372, 373, 374, 375, 376, 377, 380, 383, 384, 385, 455, 507 and
509, or any combinations thereof. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 7 and further includes amino acid
mutations at any one, two, three or more positions selected from
the group consisting of: 2, 9, 12, 14, 15, 58, 59, 61, 63, 73, 98,
107, 129, 147, 166, 176, 185, 186, 187, 195, 208, 221, 246, 247,
248, 251, 252, 256, 300, 302, 310, 318, 339, 357, 359, 360, 362,
367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380,
383, 384, 385, 386, 387, 389, 390, 392, 399, 405, 411, 419, 430,
455, 475, 477, 481, 483, 493, 494, 497, 503, 507, 509, 511, 526,
528, 529, 531, 535, 544, 550, 552, 555, 567, 569 and 572, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. In some embodiments, the modifications can include deletions,
additions and substitutions. The substitutions can be conservative
or non-conservative substitutions. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 7 and further includes any one,
two, three or more amino acid mutations selected from the group
consisting of: T365G, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K, H370R,
H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T, E371S,
E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E,
K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E,
K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, A481E,
A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q, A481W,
A481Y, D507H, D507G, D507E, D507T, D507S, D507R, D507A, D507R,
D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R, K509E,
K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. Optionally, the modified polymerase can further include one or
more mutations reducing 3' to 5' exonuclease activity selected from
the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A,
Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 7. Optionally,
this modified polymerase comprises the amino acid substitution
H370R.
[0393] In some embodiments, the polymerase can be selected to
exhibit a reduced K.sub.sub for a substrate, particularly a labeled
nucleotide analog. In some embodiments, the polymerase can comprise
one or more mutations resulting in altered K.sub.cat/K.sub.sub
and/or V.sub.max/K.sub.sub for a particular labeled nucleotide. In
some embodiments, the K.sub.cat/K.sub.sub the V.sub.max/K.sub.sub,
or both, are increased as compared to the wild type polymerase.
[0394] In some embodiments, the modified polymerase exhibits a
K.sub.cat/K.sub.sub and/or V.sub.max/K.sub.sub ratio for a
particular nucleotide substrate that is at least about 5%, 10%,
25%, 37.5%, 50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%,
750%, 1,000%, 5,000% or 10,000% as high as the K.sub.cat/K.sub.sub
and/or V.sub.max/K.sub.sub ratio of a reference polymerase for the
same nucleotide substrate. In some embodiments, the reference
polymerase is the unmodified counterpart of the modified
polymerase. In some embodiments, the reference polymerase is a
Phi-29 polymerase having the amino acid sequence of SEQ ID NO: 1.
In some embodiments, the reference polymerase is a B103 polymerase
having the amino acid sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ
ID NO: 8. In some embodiments, the nucleotide substrate is a
natural nucleotide. In some embodiments, the nucleotide substrate
is a labeled nucleotide analog.
[0395] In some embodiments, the modified polymerase comprises the
amino acid sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other
variant of the polymerase having the amino acid sequence of SEQ ID
NO: 7. In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 80%, 85%, 97%, 98% or 99%
identical to the amino acid sequence of SEQ ID NO: 7 or SEQ ID NO:
8. In some embodiments, the modified polymerase comprises one or
more amino acid substitutions at positions selected from the group
consisting of: 2, 9, 12, 58, 59, 63, 129, 166, 246, 247, 339, 370,
371, 372, 373, 374, 375, 376, 377, 380, 383, 384, 385, 455, 507 and
509, or any combinations thereof. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 7 and further includes amino acid
mutations at any one, two, three or more positions selected from
the group consisting of: 2, 9, 12, 14, 15, 58, 59, 61, 63, 73, 98,
107, 129, 147, 166, 176, 185, 186, 187, 195, 208, 221, 246, 247,
248, 251, 252, 256, 300, 302, 310, 318, 339, 357, 359, 360, 362,
367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380,
383, 384, 385, 386, 387, 389, 390, 392, 399, 405, 411, 419, 430,
455, 475, 477, 481, 483, 493, 494, 497, 503, 507, 509, 511, 526,
528, 529, 531, 535, 544, 550, 552, 555, 567, 569 and 572, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. In some embodiments, the modifications can include deletions,
additions and substitutions. The substitutions can be conservative
or non-conservative substitutions. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 7 and further includes any one,
two, three or more amino acid mutations selected from the group
consisting of: T365G, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K, H370R,
H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T, E371S,
E371K, E371R, E371A, E37.1Q, E371W, E371Y, E371F, K372G, K372E,
K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E,
K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, A481E,
A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q, A481W,
A481Y, D507H, D507G, D507E, D507T, D507S, D507R, D507A, D507R,
D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R, K509E,
K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. Optionally, the modified polymerase can further include one or
more mutations reducing 3' to 5' exonuclease activity selected from
the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A,
Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 7. Optionally,
this modified polymerase comprises the amino acid substitution
H370R.
[0396] In some embodiments, the modified polymerase exhibits, or
can be further modified, selected, mutated, evolved or otherwise
engineered to exhibit either increased or decreased residence times
for one or more nucleotides, particularly for a labeled nucleotide
analog. The residence time indicates the duration for which the
nucleotide dwells within the active site of the polymerase.
[0397] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) residence for a given
nucleotide substrate, for example a labeled nucleotide analog,
relative to an unmodified counterpart. In some embodiments, the
modified polymerase exhibits a residence time for a particular
nucleotide substrate that is at least about 5%, 10%, 25%, 37.5%,
50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%, 750%, 1,000%,
5,000% or 10,000% as high as the residence time of a reference
polymerase for the same nucleotide substrate. In some embodiments,
the reference polymerase is the unmodified counterpart of the
modified polymerase. In some embodiments, the reference polymerase
is a Phi-29 polymerase having the amino acid sequence of SEQ ID NO:
1. In some embodiments, the reference polymerase is a B103
polymerase having the amino acid sequence of SEQ ID NO: 6, SEQ ID
NO: 7 or SEQ ID NO: 8. In some embodiments, the nucleotide
substrate is a natural nucleotide. In some embodiments, the
nucleotide substrate is a labeled nucleotide analog. In some
embodiments, the modified polymerase comprises the amino acid
sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other variant of the
polymerase having the amino acid sequence of SEQ ID NO: 7. In some
embodiments, the modified polymerase can be at least 80%, 85%, 97%,
98% or 99% identical to the amino acid sequence of SEQ ID NO: 7 or
SEQ ID NO: 8. In some embodiments, the modified polymerase
comprises one or more amino acid substitutions at positions
selected from the group consisting of: 2, 9, 12, 58, 59, 63, 129,
166, 246, 247, 339, 370, 371, 372, 373, 374, 375, 376, 377, 380,
383, 384, 385, 455, 507 and 509, or any combinations thereof. In
some embodiments, the modified polymerase comprises an amino acid
sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or
100% identical to the amino acid sequence of SEQ ID NO: 7 and
further includes amino acid mutations at any one, two, three or
more positions selected from the group consisting of: 2, 9, 12, 14,
15, 58, 59, 61, 63, 73, 98, 107, 129, 147, 166, 176, 185, 186, 187,
195, 208, 221, 246, 247, 248, 251, 252, 256, 300, 302, 310, 318,
339, 357, 359, 360, 362, 367, 368, 369, 370, 371, 372, 373, 374,
375, 376, 377, 378, 380, 383, 384, 385, 386, 387, 389, 390, 392,
399, 405, 411, 419, 430, 455, 475, 477, 481, 483, 493, 494, 497,
503, 507, 509, 511, 526, 528, 529, 531, 535, 544, 550, 552, 555,
567, 569 and 572, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the
modifications can include deletions, additions and substitutions.
The substitutions can be conservative or non-conservative
substitutions. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98%, 99% or 100% identical to the amino acid sequence of
SEQ ID NO: 7 and further includes any one, two, three or more amino
acid mutations selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
H370G, I-1370T, H370S, H370K, I-1370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, A481E, A481F, A481G, A481S, A481R,
A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G, D507E,
D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F,
K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A,
K509Q, K509W, K509Y and K509F, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 7. Optionally, this modified polymerase comprises the
amino acid substitution H370R.
[0398] In some embodiments, the modified polymerase has a residence
time for a particular nucleotide substrate that is between about 20
msec and about 300 msec, typically between about 55 msec and about
100 msec. In some embodiments, the residence time of the selected,
mutated, modified, evolved or otherwise engineered polymerase for
the nucleotide substrate can be between about 1.5 and about 4 times
the residence time of a reference polymerase for the same
nucleotide substrate. Some exemplary polymerases exhibiting altered
residence times for labeled nucleotides are disclosed in U.S. Pub.
No. 20080108082, published May 8, 2008.
[0399] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) 1/(k.sub.pol+k.sub.-1) value
for a given nucleotide substrate, for example a labeled nucleotide
analog, relative to an unmodified counterpart. In some embodiments,
the modified polymerase exhibits a 1/(k.sub.pol+k.sub.-1) value for
a particular nucleotide substrate that is at least about 5%, 10%,
25%, 37.5%, 50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%,
750%, 1,000%, 5,000% or 10,000% as high as the
1/(k.sub.pol+k.sub.-1) value of a reference polymerase for the same
nucleotide substrate. In some embodiments, the reference polymerase
is the unmodified counterpart of the modified polymerase. In some
embodiments, the reference polymerase is a Phi-29 polymerase having
the amino acid sequence of SEQ ID NO: 1. In some embodiments, the
reference polymerase is a B103 polymerase having the amino acid
sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the nucleotide substrate is a natural nucleotide. In
some embodiments, the nucleotide substrate is a labeled nucleotide
analog. In some embodiments, the modified polymerase comprises the
amino acid sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other
variant of the polymerase having the amino acid sequence of SEQ ID
NO: 7. In some embodiments, the modified polymerase can be at least
80%, 85%, 97%, 98% or 99% identical to the amino acid sequence of
SEQ ID NO: 7 or SEQ ID NO: 8. In some embodiments, the modified
polymerase comprises one or more amino acid substitutions at
positions selected from the group consisting of: 2, 9, 12, 58, 59,
63, 129, 166, 246, 247, 339, 339, 370, 371, 372, 373, 374, 375,
376, 377, 380, 383, 384, 385, 455, 507 and 509, or any combinations
thereof. In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
7 and further includes amino acid mutations at any one, two, three
or more positions selected from the group consisting of: 2, 9, 12,
14, 15, 58, 59, 61, 63, 73, 98, 107, 129, 147, 166, 176, 185, 186,
187, 195, 208, 221, 246, 247, 248, 251, 252, 256, 300, 302, 310,
318, 339, 357, 359, 360, 362, 367, 368, 369, 370, 371, 372, 373,
374, 375, 376, 377, 378, 380, 383, 384, 385, 386, 387, 389, 390,
392, 399, 405, 411, 419, 430, 455, 475, 477, 481, 483, 493, 494,
497, 503, 507, 509, 511, 526, 528, 529, 531, 535, 544, 550, 552,
555, 567, 569 and 572, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 7. In some embodiments, the
modifications can include deletions, additions and substitutions.
The substitutions can be conservative or non-conservative
substitutions. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98%, 99% or 100% identical to the amino acid sequence of
SEQ ID NO: 7 and further includes any one, two, three or more amino
acid mutations selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, A481E, A481F, A481G, A481S, A481R,
A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G, D507E,
D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F,
K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A,
K509Q, K509W, K509Y and K509F, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 7. Optionally, this modified polymerase comprises the
amino acid substitution H370R.
[0400] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) rate of binding for a given
nucleotide substrate, for example a labeled nucleotide analog,
relative to an unmodified counterpart. In some embodiments, the
modified polymerase exhibits a rate of binding for a particular
nucleotide substrate that is at least about 5%, 10%; 25%, 37.5%,
50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%, 750%, 1,000%,
5,000% or 10,000% as high as the rate of binding of a reference
polymerase for the same nucleotide substrate. In some embodiments,
the reference polymerase is the unmodified counterpart of the
modified polymerase. In some embodiments, the reference polymerase
is a Phi-29 polymerase having the amino acid sequence of SEQ ID NO:
1. In some embodiments, the reference polymerase is a B103
polymerase having the amino acid sequence of SEQ ID NO: 6, SEQ ID
NO: 7 or SEQ ID NO: 8. In some embodiments, the nucleotide
substrate is a natural nucleotide. In some embodiments, the
nucleotide substrate is a labeled nucleotide analog. In some
embodiments, the modified polymerase comprises the amino acid
sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other variant of the
polymerase having the amino acid sequence of SEQ ID NO: 7. In some
embodiments, the modified polymerase can be at least 80%, 85%, 97%,
98% or 99% identical to the amino acid sequence of SEQ ID NO: 7 or
SEQ ID NO: 8. In some embodiments, the modified polymerase
comprises one or more amino acid substitutions at positions
selected from the group consisting of: 2, 9, 12, 58, 59, 63, 129,
166, 246, 247, 339, 370, 371, 372, 373, 374, 375, 376, 377, 380,
383, 384, 385, 455, 507 and 509, or any combinations thereof. In
some embodiments, the modified polymerase comprises an amino acid
sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or
100% identical to the amino acid sequence of SEQ ID NO: 7 and
further includes amino acid mutations at any one, two, three or
more positions selected from the group consisting of: 2, 9, 12, 14,
15, 58, 59, 61, 63, 73, 98, 107, 129, 147, 166, 176, 185, 186, 187,
195, 208, 221, 246, 247, 248, 251, 252, 256, 300, 302, 310, 318,
339, 357, 359, 360, 362, 367, 368, 369, 370, 371, 372, 373, 374,
375, 376, 377, 378, 380, 383, 384, 385, 386, 387, 389, 390, 392,
399; 405, 411, 419, 430, 455, 475, 477, 481, 483, 493, 494, 497,
503, 507, 509, 511, 526, 528, 529, 531, 535, 544, 550, 552, 555,
567, 569 and 572, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the
modifications can include deletions, additions and substitutions.
The substitutions can be conservative or non-conservative
substitutions. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98%, 99% or 100% identical to the amino acid sequence of
SEQ ID NO: 7 and further includes any one, two, three or more amino
acid mutations selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, A481E, A481F, A481G, A481S, A481R,
A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G, D507E,
D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F,
K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A,
K509Q, K509W, K509Y and K509F, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 7. Optionally, this modified polymerase comprises the
amino acid substitution H370R.
[0401] In some embodiments, the modified polymerase exhibits, or
can be further modified, selected, mutated, evolved or otherwise
engineered to exhibit an altered branching ratio for one or more
nucleotide substrates, particularly for labeled nucleotide analogs.
The term "branching" and its variants, when used in reference to a
polymerase, typically refers to binding of the appropriate
nucleotide to the polymerase without productive incorporation of
the nucleotide into an extending nucleic acid molecule by the
polymerase. In some applications, for example single molecule
sequencing, such behavior can be undesirable because it can
complicate analysis of the reaction as it progresses and/or render
it difficult to distinguish between productive and non-productive
incorporations, and it is therefore desirable to alter the
branching ratio to minimize such complications. The complications
posed by branching behavior during single molecule sequencing
analysis are described, for example, in Rank, U.S. Published Patent
Application No. 2008/0108082; Hanzel, U.S. Published Patent
Application No. 2007/0196846; Clark, U.S. Published Patent
Application No. 2009/0176233; and Bjornsen, U.S. Published Patent
Application No. 2009/0286245.
[0402] Without being bound to any particular theory, in some
embodiments, the branching ratio can be defined as the fraction
(expressed as a percentage ratio) of events involving the formation
of an enzyme-template-nucleotide ternary complex, ENAN-P, that
actually result in productive incorporation of the nucleotide into
an extending nucleic acid molecule. Alternatively, in some
embodiments, the branching ratio can be defined as the fraction of
the nucleotides that bind to, and dissociate from, the polymerase
active site without being incorporated to the extending nucleic
acid molecule.
[0403] One exemplary mathematical measure for branching ratio can
be represented as follows:
Branching ratio=k.sub.pol/(k.sub.pol+k.sub.-1)
[0404] Without intending to be bound to any particular theory, in
some cases this measure of branching ratio,
k.sub.pol/(K.sub.pol+k.sub.-1), can provides an indication of the
fraction (expressed as a percentage) of nucleotide binding events
(i.e., events wherein the nucleotide binds to the polymerase to
form a ternary enzyme-template-nucleotide complex) that result in
productive incorporation. In some applications, it can be desirable
to increase the branching ratio as much as possible, ideally to 1.0
(wherein a value of 1.0 indicates that every bound nucleotide
becomes incorporated into the extending nucleic acid molecule).
[0405] In some embodiments, the branching ratio (measured as
k.sub.pol/(k.sub.pol+k.sub.-1)) of the modified polymerase for a
particular nucleotide substrate, for example, a labeled nucleotide
analog, can be between about 0.25 and 1.00, typically between about
0.6 and about 0.99. In some embodiments, the branching ratio of the
modified polymerase for a particular nucleotide substrate, for
example a labeled nucleotide analog, is greater than 0.95,
typically greater than about 0.97, 0.98, 0.99 or 0.999.
[0406] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) branching ratio for a given
nucleotide substrate, for example a labeled nucleotide analog,
relative to an unmodified counterpart. In some embodiments, the
modified polymerase exhibits a branching ratio for a particular
nucleotide substrate that is at least about 5%, 10%, 25%, 37.5%,
50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%, 750%, 1,000%,
5,000% or 10,000% as high as the branching ratio of a reference
polymerase for the same nucleotide substrate. In some embodiments,
the reference polymerase is the unmodified counterpart of the
modified polymerase. In some embodiments, the reference polymerase
is a Phi-29 polymerase having the amino acid sequence of SEQ ID NO:
1. In some embodiments, the reference polymerase is a B103
polymerase having the amino acid sequence of SEQ ID NO: 6, SEQ ID
NO: 7 or SEQ ID NO: 8. In some embodiments, the nucleotide
substrate is a natural nucleotide. In some embodiments, the
nucleotide substrate is a labeled nucleotide analog. In some
embodiments, the modified polymerase comprises the amino acid
sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other variant of the
polymerase having the amino acid sequence of SEQ ID NO: 7. In some
embodiments, the modified polymerase can be at least 80%, 85%, 97%,
98% or 99% identical to the amino acid sequence of SEQ ID NO: 7 or
SEQ ID NO: 8. In some embodiments, the modified polymerase
comprises one or more amino acid substitutions at positions
selected from the group consisting of: 2, 9, 12, 58, 59, 63, 129,
166, 246, 247, 339, 370, 371, 372, 373, 374, 375, 376, 377, 380,
383, 384, 385, 455, 507 and 509, or any combinations thereof. In
some embodiments, the modified polymerase comprises an amino acid
sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or
100% identical to the amino acid sequence of SEQ ID NO: 7 and
further includes amino acid mutations at any one, two, three or
more positions selected from the group consisting of: 2, 9, 12, 14,
15, 58, 59, 61, 63, 73, 98, 107, 129, 147, 166, 176, 185, 186, 187,
195, 208, 221, 246, 247, 248, 251, 252, 256, 300, 302, 310, 318,
339, 357, 359, 360, 362, 367, 368, 369, 370, 371, 372, 373, 374,
375, 376, 377, 378, 380, 383, 384, 385, 386, 387, 389, 390, 392,
399, 405, 411, 419, 430, 455, 475, 477, 481, 483, 493, 494, 497,
503, 507, 509, 511, 526, 528, 529, 531, 535, 544, 550, 552, 555,
567, 569 and 572, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the
modifications can include deletions, additions and substitutions.
The substitutions can be conservative or non-conservative
substitutions. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98%, 99% or 100% identical to the amino acid sequence of
SEQ ID NO: 7 and further includes any one, two, three or more amino
acid mutations selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, A481E, A481F, A481G, A481S, A481R,
A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G, D507E,
D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F,
K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A,
K509Q, K509W, K509Y and K509F, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 7. Optionally, this modified polymerase comprises the
amino acid substitution H370R.
[0407] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased)
k.sub.pol/(k.sub.pol+k.sub.-1) value for a given nucleotide
substrate, for example a labeled nucleotide analog, relative to an
unmodified counterpart. In some embodiments, the modified
polymerase exhibits a k.sub.pol/(k.sub.pol+K.sub.-1) value for a
particular nucleotide substrate that is at least about 5%, 10%,
25%, 37.5%, 50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%,
750%, 1,000%, 5,000% or 10,000% as high as the
k.sub.pol/(k.sub.pol+k.sub.-1) value of a reference polymerase for
the same nucleotide substrate. In some embodiments, the reference
polymerase is the unmodified counterpart of the modified
polymerase. In some embodiments, the reference polymerase is a
Phi-29 polymerase having the amino acid sequence of SEQ ID NO: 1.
In some embodiments, the reference polymerase is a B103 polymerase
having the amino acid sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ
ID NO: 8. In some embodiments, the nucleotide substrate is a
natural nucleotide. In some embodiments, the nucleotide substrate
is a labeled nucleotide analog. In some embodiments, the modified
polymerase comprises the amino acid sequence of SEQ ID NO: 7, SEQ
ID NO: 8, or any other variant of the polymerase having the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the modified
polymerase can be at least 80%, 85%, 97%, 98% or 99% identical to
the amino acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the modified polymerase comprises one or more amino
acid substitutions at positions selected from the group consisting
of: 2, 9, 12, 58, 59, 63, 129, 166, 246, 247, 339, 370, 371, 372,
373, 374, 375, 376, 377, 380, 383, 384, 385, 455, 507 and 509, or
any combinations thereof. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 7 and further includes amino acid
mutations at any one, two, three or more positions selected from
the group consisting of: 2, 9, 12, 14, 15, 58, 59, 61, 63, 73, 98,
107, 129, 147, 166, 176, 185, 186, 187, 195, 208, 221, 246, 247,
248, 251, 252, 256, 300, 302, 310, 318, 339, 357, 359, 360, 362,
367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380,
383, 384, 385, 386, 387, 389, 390, 392, 399, 405, 411, 419, 430,
455, 475, 477, 481, 483, 493, 494, 497, 503, 507, 509, 511, 526,
528, 529, 531, 535, 544, 550, 552, 555, 567, 569 and 572, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. In some embodiments, the modifications can include deletions,
additions and substitutions. The substitutions can be conservative
or non-conservative substitutions. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 7 and further includes any one,
two, three or more amino acid mutations selected from the group
consisting of: T365G, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K, H370R,
H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T, E371S,
E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E,
K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E,
K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, A481E,
A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q, A481W,
A481Y, D5071-1, D507G, D507E, D507T, D507S, D507R, D507A, D507R,
D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R, K509E,
K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. Optionally, the modified polymerase can further include one or
more mutations reducing 3' to 5' exonuclease activity selected from
the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A,
Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 7. Optionally,
this modified polymerase comprises the amino acid substitution
H370R.
[0408] In some embodiments, the modified polymerase exhibits, or
can be further modified, selected, mutated, evolved or otherwise
engineered to exhibit either increased or decreased processivity
for one or more nucleotide substrates, particularly for labeled
nucleotide analogs. The processivity is the number of nucleotides
incorporated for a single binding event between the polymerase and
the target molecule base-paired with the polymerization initiation
site.
[0409] In some embodiments, the processivity of the modified
polymerase with one or more labeled nucleotide analogs can be
between about 10 and 10,000 nucleotides, typically between about 10
and 100 nucleotides. For example, the processivity of the modified
polymerase may be about 1, 5, 10, 20, 25, 50, 100, 250, 500, 750,
1000, 2000, 5000, or 10,000 or more nucleotides incorporated with a
single binding event.
[0410] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) processivity for a given
nucleotide substrate, for example a labeled nucleotide analog,
relative to an unmodified counterpart. In some embodiments, the
modified polymerase exhibits a processivity for a particular
nucleotide substrate that is at least about 5%, 10%, 25%, 37.5%,
50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%, 750%, 1,000%,
5,000% or 10,000% as high as the processivity of a reference
polymerase for the same nucleotide substrate. In some embodiments,
the reference polymerase is the unmodified counterpart of the
modified polymerase. In some embodiments, the reference polymerase
is a Phi-29 polymerase having the amino acid sequence of SEQ ID NO:
1. In some embodiments, the reference polymerase is a B103
polymerase having the amino acid sequence of SEQ ID NO: 6, SEQ ID
NO: 7 or SEQ ID NO: 8. In some embodiments, the nucleotide
substrate is a natural nucleotide. In some embodiments, the
nucleotide substrate is a labeled nucleotide analog. In some
embodiments, the modified polymerase comprises the amino acid
sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other variant of the
polymerase having the amino acid sequence of SEQ ID NO: 7. In some
embodiments, the modified polymerase can be at least 80%, 85%, 97%,
98% or 99% identical to the amino acid sequence of SEQ ID NO: 7 or
SEQ ID NO: 8. In some embodiments, the modified polymerase
comprises one or more amino acid substitutions at positions
selected from the group consisting of: 2, 9, 12, 58, 59, 63, 129,
166, 246, 247, 339, 370, 371, 372, 373, 374, 375, 376, 377, 380,
383, 384, 385, 455, 507 and 509, or any combinations thereof.
[0411] Without being bound to any particular theory, under some
models one exemplary mathematical expression for processivity can
be represented as follows:
Processivity=k.sub.pol/(k.sub.-1 (EDNA))
[0412] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) k.sub.pol/(k.sub.-1 (EDNA))
value for a given nucleotide substrate, for example a labeled
nucleotide analog, relative to an unmodified counterpart. In some
embodiments, the modified polymerase exhibits a k.sub.pol/(k.sub.-1
(EDNA)) value for a particular nucleotide substrate that is at
least about 5%, 10%, 25%, 37.5%, 50%, 75%, 100%, 110%, 125%, 150%,
200%, 250%, 500%, 750%, 1,000%, 5,000% or 10,000% as high as the
k.sub.pol/(k.sub.-1 (EDNA)) value of a reference polymerase for the
same nucleotide substrate. In some embodiments, the reference
polymerase is the unmodified counterpart of the modified
polymerase. In some embodiments, the reference polymerase is a
Phi-29 polymerase having the amino acid sequence of SEQ ID NO: 1.
In some embodiments, the reference polymerase is a B103 polymerase
having the amino acid sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ
ID NO: 8. In some embodiments, the nucleotide substrate is a
natural nucleotide. In some embodiments, the nucleotide substrate
is a labeled nucleotide analog. In some embodiments, the modified
polymerase comprises the amino acid sequence of SEQ ID NO: 7, SEQ
ID NO: 8, or any other variant of the polymerase having the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the modified
polymerase can be at least 80%, 85%, 97%, 98% or 99% identical to
the amino acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the modified polymerase comprises one or more amino
acid substitutions at positions selected from the group consisting
of: 2, 9, 12, 58, 59, 63, 129, 166, 246, 247, 339, 370, 371, 372,
373, 374, 375, 376, 377, 380, 383, 384, 385, 455, 507 and 509, or
any combinations thereof. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 7 and further includes amino acid
mutations at any one, two, three or more positions selected from
the group consisting of: 2, 9, 12, 14, 15, 58, 59, 61, 63, 73, 98,
107, 129, 147, 166, 176, 185, 186, 187, 195, 208, 221, 246, 247,
248, 251, 252, 256, 300, 302, 310, 318, 339, 357, 359, 360, 362,
367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380,
383, 384, 385, 386, 387, 389, 390, 392, 399, 405, 411, 419, 430,
455, 475, 477, 481, 483, 493, 494, 497, 503, 507, 509, 511, 526,
528, 529, 531, 535, 544, 550, 552, 555, 567, 569 and 572, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. In some embodiments, the modifications can include deletions,
additions and substitutions. The substitutions can be conservative
or non-conservative substitutions. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 7 and further includes any one,
two, three or more amino acid mutations selected from the group
consisting of: T365G, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K, H370R,
H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T, E371S,
E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E,
K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E,
K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, A481E,
A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q, A481W,
A481Y, D507H, D507G, D507E, D507T, D507S, D507R, D507A, D507R,
D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R, K509E,
K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. Optionally, the modified polymerase can further include one or
more mutations reducing 3' to 5' exonuclease activity selected from
the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A,
Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 7. Optionally,
this modified polymerase comprises the amino acid substitution
H370R.
[0413] In some embodiments, the modified polymerase exhibits, or
can be further modified, selected, mutated, evolved or otherwise
engineered to extend an increased or decreased fractional extension
activity, defined as fraction of nucleic acid templates that are
extended by at least one nucleotide in a polymerase reaction under
defined reaction conditions. In a typical embodiment, fractional
extension efficiency is determined using reaction conditions
comprising 50 mM Tris, pH 7.5, 50 mM NaCl, 5 mM DTT, 100 nM
polymerase, 100 nM primer-template duplex, 2 mM MnCl.sub.2 and 5
.mu.M of nucleotides at 37.degree. C. (for eukaryotic or bacterial
polymerases) or 23.degree. C. (for B103-like and Phi29-like
polymerases) for 30 seconds. In some embodiments, the extended
fraction can be measured as the percentage of total primed nucleic
acid templates that are extended by one or more nucleotides under
such reaction conditions. In some embodiments, the fractional
extension activity of the modified polymerase is increased or
decreased relative to the fractional extension activity of a
reference polymerase under identical reaction conditions. In some
embodiments, the reference polymerase can be a Phi-29 polymerase
having the amino acid sequence of SEQ ID NO: 1. In some
embodiments, the reference polymerase is a B103 polymerase having
the amino acid sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO:
8. In some embodiments, the nucleotide substrate is a natural
nucleotide. In some embodiments, the nucleotide substrate is a
labeled nucleotide analog. In some embodiments, the modified
polymerase comprises the amino acid sequence of SEQ ID NO: 7, SEQ
ID NO: 8, or any other variant of the polymerase having the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the modified
polymerase can be at least 80%, 85%, 97%, 98% or 99% identical to
the amino acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the modified polymerase comprises one or more amino
acid substitutions at positions selected from the group consisting
of: 2, 9, 12, 58, 59, 63, 129, 166, 246, 247, 339, 370, 371, 372,
373, 374, 375, 376, 377, 380, 383, 384, 385, 455, 507 and 509, or
any combinations thereof, and exhibits increased or decreased
fractional extension activity as compared to a reference
polymerase, e.g., an unmodified counterpart. In some embodiments,
the modified polymerase comprises an amino acid sequence that is at
least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to
the amino acid sequence of SEQ ED NO: 7 and further includes amino
acid mutations at any one, two, three or more positions selected
from the group consisting of: 2, 9, 12, 14, 15, 58, 59, 61, 63, 73,
98, 107, 129, 147, 166, 176, 185, 186, 187, 195, 208, 221, 246,
247, 248, 251, 252, 256, 300, 302, 310, 318, 339, 357, 359, 360,
362, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378,
380, 383, 384, 385, 386, 387, 389, 390, 392, 399, 405, 411, 419,
430, 455, 475, 477,481,483,493,494,497,503,507,509, 511, 526, 528,
529, 531, 535, 544, 550, 552, 555, 567, 569 and 572, wherein the
numbering is relative to the amino acid sequence of SEQ ID NO: 7.
In some embodiments, the modifications can include deletions,
additions and substitutions. The substitutions can be conservative
or non-conservative substitutions. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 7 and further includes any one,
two, three or more amino acid mutations selected from the group
consisting of: T365G, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K, H370R,
H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T, E371S,
E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E,
K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E,
K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, A481E,
A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q, A481W,
A481Y, D507H, D507G, D507E, D507T, D507S, D507R, D507A, D507R,
D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R, K509E,
K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. Optionally, the modified polymerase can further include one or
more mutations reducing 3' to 5' exonuclease activity selected from
the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A,
Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 7. Optionally,
this modified polymerase comprises the amino acid substitution
H370R.
[0414] In some embodiments, the modified polymerase exhibits, or
can be further modified, selected, mutated, evolved or otherwise
engineered to exhibit either increased or decreased ease of entry
of nucleotides, particularly labeled nucleotide analogs, into the
polymerase active site. In some embodiments, the modified
polymerase exhibits an altered (e.g., increased or decreased)
degree of steric inhibition of nucleotide entry to the active site
relative to the degree of steric inhibition exhibited by a
reference polymerase. In some embodiments, the reference polymerase
is a Phi-29 polymerase having the amino acid sequence of SEQ ID NO:
1. In some embodiments, the reference polymerase is a B103
polymerase having the amino acid sequence of SEQ ID NO: 6, SEQ ID
NO: 7 or SEQ ID NO: 8. In some embodiments, the nucleotide
substrate is a natural nucleotide. In some embodiments, the
nucleotide substrate is a labeled nucleotide analog. In some
embodiments, the modified polymerase comprises the amino acid
sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other variant of the
polymerase having the amino acid sequence of SEQ ID NO: 7. In some
embodiments, the modified polymerase can be at least 80%, 85%, 97%,
98% or 99% identical to the amino acid sequence of SEQ ID NO: 7 or
SEQ ID NO: 8. In some embodiments, the modified polymerase
comprises one or more amino acid substitutions at positions
selected from the group consisting of: 2, 9, 12, 58, 59, 63, 129,
166, 246, 247, 339, 370, 371, 372, 373, 374, 375, 376, 377, 380,
383, 384, 385, 455, 507 and 509, or any combinations thereof. In
some embodiments, the modified polymerase comprises an amino acid
sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or
100% identical to the amino acid sequence of SEQ ID NO: 7 and
further includes amino acid mutations at any one, two, three or
more positions selected from the group consisting of: 2, 9, 12, 14,
15, 58, 59, 61, 63, 73, 98, 107, 129, 147, 166, 176, 185, 186, 187,
195, 208, 221, 246, 247, 248, 251, 252, 256, 300, 302, 310, 318,
339, 357, 359, 360, 362, 367, 368, 369, 370, 371, 372, 373, 374,
375, 376, 377, 378, 380, 383, 384, 385, 386, 387, 389, 390, 392,
399, 405, 411, 419, 430, 455, 475, 477, 481, 483, 493, 494, 497,
503, 507, 509, 511, 526, 528, 529, 531, 535, 544, 550, 552, 555,
567, 569 and 572, wherein the numbering is relative to the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the
modifications can include deletions, additions and substitutions.
The substitutions can be conservative or non-conservative
substitutions. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98%, 99% or 100% identical to the amino acid sequence of
SEQ ID NO: 7 and further includes any one, two, three or more amino
acid mutations selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, A481E, A481F, A481G, A481S, A481R,
A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G, D507E,
D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F,
K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A,
K509Q, K509W, K509Y and K509F, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 7. Optionally, this modified polymerase comprises the
amino acid substitution H370R.
[0415] In some embodiments, the modified polymerase exhibits, or
can be further modified, selected, mutated, evolved or otherwise
engineered to exhibit either increased or decreased rate of
incorporation of one or more nucleotide substrates, particularly
for labeled nucleotide analogs. In some embodiments, the rate of
nucleotide incorporation of the modified polymerase with one or
more nucleotide substrates is greater than or equal to one
nucleotide per second, 5 nucleotides per second, 10 nucleotides per
second, 20 nucleotides per second, 30 nucleotides per second, 40
nucleotides per second, 50 nucleotides per second, 100 nucleotides,
or 200 nucleotides per second. In some embodiments, the rate of
nucleotide incorporation is one nucleotide per 2, 3, 4, or 5
seconds.
[0416] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) rate of nucleotide
incorporation for a given nucleotide substrate, for example a
labeled nucleotide analog, relative to an unmodified counterpart.
In some embodiments, the modified polymerase exhibits a rate of
nucleotide incorporation for a particular nucleotide substrate that
is at least about 5%, 10%, 25%, 37.5%, 50%, 75%, 100%, 110%, 125%,
150%, 200%, 250%, 500%, 750%, 1,000%, 5,000% or 10,000% as high as
the rate of nucleotide incorporation of a reference polymerase for
the same nucleotide substrate. In some embodiments, the reference
polymerase is the unmodified counterpart of the modified
polymerase. In some embodiments, the reference polymerase is a
Phi-29 polymerase having the amino acid sequence of SEQ ID NO: 1.
In some embodiments, the reference polymerase is a B103 polymerase
having the amino acid sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ
ID NO: 8. In some embodiments, the nucleotide substrate is a
natural nucleotide. In some embodiments, the nucleotide substrate
is a labeled nucleotide analog. In some embodiments, the modified
polymerase comprises the amino acid sequence of SEQ ID NO: 7, SEQ
ID NO: 8, or any other variant of the polymerase having the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the modified
polymerase can be at least 80%, 85%, 97%, 98% or 99% identical to
the amino acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the modified polymerase comprises one or more amino
acid substitutions at positions selected from the group consisting
of: 2, 9, 12, 58, 59, 63, 129, 166, 246, 247, 339, 370, 371, 372,
373, 374, 375, 376, 377, 380, 383, 384, 385, 455, 507 and 509, or
any combinations thereof. In some embodiments, the modified
polymerase comprises an amino acid sequence that is at least 70%,
80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the amino
acid sequence of SEQ ID NO: 7 and further includes amino acid
mutations at any one, two, three or more positions selected from
the group consisting of: 2, 9, 12, 14, 15, 58, 59, 61, 63, 73, 98,
107, 129, 147, 166, 176, 185, 186, 187, 195, 208, 221, 246, 247,
248, 251, 252, 256, 300, 302, 310, 318, 339, 357, 359, 360, 362,
367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 380,
383, 384, 385, 386, 387, 389, 390, 392, 399, 405, 411, 419, 430,
455, 475, 477, 481, 483, 493, 494, 497, 503, 507, 509, 511, 526,
528, 529, 531, 535, 544, 550, 552, 555, 567, 569 and 572, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. In some embodiments, the modifications can include deletions,
additions and substitutions. The substitutions can be conservative
or non-conservative substitutions. In some embodiments, the
modified polymerase comprises an amino acid sequence that is at
least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the
amino acid sequence of SEQ ID NO: 7 and further includes any one,
two, three or more amino acid mutations selected from the group
consisting of: T365G, T365F, T365G, T365S, T365K, T365R, T365A,
T365Q, T365W, T365Y, T365H, H370G, H370T, H370S, H370K, H370R,
H370A, H370Q, H370 W, H370Y, H370F, E371G, E371H, E371T, E371S,
E371K, E371R, E371A, E371Q, E371W, E371Y, E371F, K372G, K372E,
K372T, K372S, K372R, K372A, K372Q, K372W, K372Y, K372F, K380E,
K380T, K380S, K380R, K380A, K380Q, K380W, K380Y, K380F, A481E,
A481F, A481G, A481S, A481R, A481K, A481A, A481T, A481Q, A481W,
A481Y, D507H, D507G, D507E, D507T, D507S, D507R, D507A, D507R,
D507Q, D507W, D507Y, D507F, K509H, K509G, K509D, K509R, K509E,
K509T, K509S, K509R, K509A, K509Q, K509W, K509Y and K509F, wherein
the numbering is relative to the amino acid sequence of SEQ ID NO:
7. Optionally, the modified polymerase can further include one or
more mutations reducing 3' to 5' exonuclease activity selected from
the group consisting of: D9A, E11A, E11I, T12I, H58R, N59D, D63A,
Y162F, Y162C, D166A, Q377A and S385G, wherein the numbering is
relative to the amino acid sequence of SEQ ID NO: 7. Optionally,
this modified polymerase comprises the amino acid substitution
H370R.
[0417] In one embodiment, polymerases exhibiting reduced nucleotide
incorporation rates include mutant phi29 polymerase having lysine
substituted with leucine, arginine, histidine or other amino acids
(Castro 2009 Nature Structural and Molecular Biology 16:212-218).
In some embodiments, the polymerase can be selected to exhibit
either reduced or enhanced rates of incorporation for
polyphosphate-comprising nucleotides comprising a label bonded to
the terminal phosphate.
[0418] In some embodiments, the polymerase can be selected,
mutated, modified, evolved or otherwise engineered to exhibit high
fidelity with low error rates. The fidelity of a polymerase may be
measured using assays well known in the art (Lundburg et al., 1991
Gene, 108:1-6). Typically, the fidelity of a polymerase is measured
as the error rate, i.e., the frequency of incorporation of a
nucleotide in a manner that violates the widely known Watson-Crick
base pairing rules. The accuracy or fidelity of DNA polymerization
can be influenced not only by the polymerase activity of a given
enzyme, but also by the 3'-5' exonuclease activity of a polymerase.
The error rate of the polymerase can be one error per about 100, or
about 250, or about 500, or about 1000, or about 1500 incorporated
nucleotides. High fidelity polymerases include those exhibiting
error rates of about 5.times.10.sup.-6 per base pair or lower
rates. By suitable selection and engineering of the polymerase, the
error rate of the single-molecule sequencing methods disclosed
herein can be further improved. In some embodiments, the polymerase
can be further engineered or modified, e.g., via glycosylation, so
as to enhance peptide stability and/or performance.
[0419] In some embodiments, the selection of the polymerase can be
determined by the level of fidelity desired, such as the error rate
per nucleotide incorporation. The frequency of misincorporation
(f.sub.mis) can be defined as the ratio between the
k.sub.cat/K.sub.d values for correct and incorrect nucleotides.
Fidelity, i.e. the number of correct incorporation events before a
mismatch occurs, can be expressed as 1/f.sub.mis.
[0420] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) fidelity in the presence of
a given nucleotide substrate, for example a labeled nucleotide
analog, relative to an unmodified counterpart. In some embodiments,
the modified polymerase exhibits a fidelity in the presence of a
particular nucleotide substrate that is at least about 5%, 10%,
25%, 37.5%, 50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%,
750%, 1,000%, 5,000% or 10,000% as high as the fidelity exhibited
by a reference polymerase in the presence of the same nucleotide
substrate. In some embodiments, the reference polymerase is the
unmodified counterpart of the modified polymerase. In some
embodiments, the reference polymerase is a Phi-29 polymerase having
the amino acid sequence of SEQ ID NO: 1. In some embodiments, the
reference polymerase is a B103 polymerase having the amino acid
sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the nucleotide substrate is a natural nucleotide. In
some embodiments, the nucleotide substrate is a labeled nucleotide
analog. In some embodiments, the modified polymerase comprises the
amino acid sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other
variant of the polymerase having the amino acid sequence of SEQ ID
NO: 7. In some embodiments, the modified polymerase can be at least
80%, 85%, 97%, 98% or 99% identical to the amino acid sequence of
SEQ ID NO: 7 or SEQ ID NO: 8. In some embodiments, the modified
polymerase comprises one or more amino acid substitutions at
positions selected from the group consisting of: 2, 9, 12, 58, 59,
63, 129, 166, 246, 247, 339, 370, 371, 372, 373, 374, 375, 376,
377, 380, 383, 384, 385, 455, 507 and 509, or any combinations
thereof. In some embodiments, the modified polymerase comprises an
amino acid sequence that is at least 70%, 80%, 85%, 90%, 95%, 97%,
98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:
7 and further includes amino acid mutations at any one, two, three
or more positions selected from the group consisting of: 2, 9, 12,
14, 15, 58, 59, 61, 63, 73, 98, 107, 129, 147, 166, 176, 185, 186,
187, 195, 208, 221, 246, 247, 248, 251, 252, 256, 300, 302, 310,
318, 339, 357, 359, 360, 362, 367, 368, 369, 370, 371, 372, 373,
374, 375, 376, 377, 378, 380, 383, 384, 385, 386, 387, 389, 390,
392, 399, 405, 411, 419, 430, 455, 475, 477, 481, 483, 493, 494,
497, 503, 507, 509, 511, 526, 528, 529, 531, 535, 544, 550, 552,
555, 567, 569 and 572, wherein the numbering is relative to the
amino acid sequence of SEQ ID NO: 7. In some embodiments, the
modifications can include deletions, additions and substitutions.
The substitutions can be conservative or non-conservative
substitutions. In some embodiments, the modified polymerase
comprises an amino acid sequence that is at least 80%, 85%, 90%,
95%, 97%, 98%, 99% or 100% identical to the amino acid sequence of
SEQ ID NO: 7 and further includes any one, two, three or more amino
acid mutations selected from the group consisting of: T365G, T365F,
T365G, T365S, T365K, T365R, T365A, T365Q, T365W, T365Y, T365H,
H370G, H370T, H370S, H370K, H370R, H370A, H370Q, H370 W, H370Y,
H370F, E371G, E371H, E371T, E371S, E371K, E371R, E371A, E371Q,
E371W, E371Y, E371F, K372G, K372E, K372T, K372S, K372R, K372A,
K372Q, K372W, K372Y, K372F, K380E, K380T, K380S, K380R, K380A,
K380Q, K380W, K380Y, K380F, A481E, A481F, A481G, A481S, A481R,
A481K, A481A, A481T, A481Q, A481W, A481Y, D507H, D507G, D507E,
D507T, D507S, D507R, D507A, D507R, D507Q, D507W, D507Y, D507F,
K509H, K509G, K509D, K509R, K509E, K509T, K509S, K509R, K509A,
K509Q, K509W, K509Y and K509F, wherein the numbering is relative to
the amino acid sequence of SEQ ID NO: 7. Optionally, the modified
polymerase can further include one or more mutations reducing 3' to
5' exonuclease activity selected from the group consisting of: D9A,
E11A, E11I, T12I, H58R, N59D, D63A, Y162F, Y162C, D166A, Q377A and
S385G, wherein the numbering is relative to the amino acid sequence
of SEQ ID NO: 7. Optionally, this modified polymerase comprises the
amino acid substitution H370R.
[0421] Each the kinetic parameters of the modified polymerase,
including the various parameters described above, can be measured
with respect to a given substrate of the polymerase, including, for
example, one or more particular nucleotides. In some embodiments,
the nucleotide is a labeled nucleotide analog, for example, a
base-, sugar- or phosphate-labeled analog. The labeled nucleotide
analog can comprise one or more phosphate groups. In some
embodiments, the nucleotide analog comprises a triphosphate,
tetraphosphate, pentaphosphate, hexaphosphate, heptaphosphate,
octaphosphate, nonaphosphate or decaphosphate moieties. The labeled
nucleotide analog can comprise an organic dye attached to the omega
or terminal phosphate of the labeled nucleotide analog. In some
embodiments, the organic dye is an Alexa Fluor moiety.
[0422] Disclosed herein are modified polymerases exhibiting altered
levels of tolerance for the presence of specific labels,
particularly inorganic labels such as nanoparticles. The word
"tolerance" and its variants, as used herein with reference to a
particular polymerase, refers to the average primer extension
activity retained by the polymerase in the presence of a particular
label (e.g., dye or nanoparticle) under defined reaction
conditions, as compared to the average primer extension activity of
the polymerase in the absence of the label but under otherwise
identical reaction conditions.
[0423] In some embodiments, the modified polymerase exhibits
increased tolerance for one or more particular labels as compared
to its unmodified counterpart. Such increased tolerance can be
desirable because it allows high levels of primer extension
activity in reactions comprising labeled components, such as single
molecule sequencing reactions. The labels included in the reaction
mixture can optionally be attached to the polymerase, to the
nucleotides, and/or to any other component, of the reaction
mixture. The labels can be organic (e.g., dyes) or inorganic (e.g.,
nanoparticles). Typically, the tolerance can vary depending on the
reaction conditions, including the type(s) and concentration of any
label(s) present in the reaction mixture. The lower the decrease in
primer extension activity in the presence of the label(s), the
greater the tolerance of the polymerase for the particular
label(s).
[0424] The tolerance of a polymerase for a particular label is
typically measured by first obtaining the tolerance ratio for the
polymerase under defined reaction conditions. The tolerance ratio
is the ratio of the average primer extension activity of the
polymerase in the presence of one or more types of label under
defined reaction conditions (termed "A.sub.pol-label") and the
average primer extension activity of the polymerase in the absence
of the label but under otherwise identical reaction conditions
(termed "A.sub.pol-"). This relationship can be expressed
mathematically as follows:
Tolerance ratio=A.sub.pol-label/A.sub.pol
[0425] The tolerance is then calculated by converting the tolerance
ratio into a percentage value (%), which can be obtained by
multiplying the tolerance ratio, A.sub.pol-label/A.sub.pol, by 100.
This relationship can be represented as follows:
Tolerance (%)=(A.sub.pol,-label/A.sub.pol).times.100
[0426] For example, a polymerase that has about 90% tolerance for a
particular type of label will retain on average about 90% of its
average primer extension activity in a defined reaction mixture
including a particular concentration of label, where the average
primer extension activity of the polymerase in the absence of label
under otherwise identical reaction conditions is arbitrarily set as
100%.
[0427] In a typical embodiment, tolerance is measured using defined
reaction conditions (referred to herein as "standard tolerance
assay conditions") comprising 50 mM Tris, pH 7.5, 50 mM NaCl, 5 mM
DTT, 100 nM polymerase, 100 nM primer-template duplex, 2 mM
MnCl.sub.2 and 5 .mu.M of nucleotides, and 100 nM of label for 5
minutes at 23.degree. C. The observed primer extension activity is
measured and compared to the primer extension activity of the same
polymerase in the absence of any label but under otherwise
identical reaction conditions (control reaction), which is
arbitrarily defined as having 100% primer extension activity.
[0428] Depending on the biological application of interest,
however, the tolerance can also be determined under different,
i.e., non-standard, assay conditions, for example by measuring the
average primer extension activity of the polymerase under different
reaction conditions including higher or lower concentrations of the
label, and comparing this activity to the average primer extension
activity of the polymerase in the absence of the label but under
otherwise identical reaction conditions. In some embodiments, the
reaction conditions can optionally include exposure to excitation
radiation of defined intensity, frequency and duration.
[0429] In some embodiments, the label is a nanoparticle and the
tolerance of the polymerase for the nanoparticle is referred to as
the "nanoparticle tolerance". The nanoparticle tolerance of a
polymerase can vary with the nature of the nanoparticle label
itself.
[0430] In one exemplary and non-limiting embodiment, the
nanoparticle tolerance can be measured under standard tolerance
assay conditions as follows: a polymerase reaction mixture
comprising 50 mM Tris, pH 7.5, 50 mM NaCl, 5 mM DTT, 100 nM
polymerase, 100 nM primer-template duplex and 2 mM MnCl.sub.2 is
prepared, as well as a second aliquot of the identical reaction
mixture further comprising 100 nM of test nanoparticle. The
polymerase reaction is then initiated by the addition of 5 .mu.M of
labeled nucleotide to both mixtures, and the resulting primer
extension activity is measured after 5 minutes. All reactions are
performed at 23.degree. C. The nanoparticle tolerance ratio is
calculated by dividing the average primer extension activity
exhibited by the modified polymerase in reactions comprising 100 nM
nanoparticles (A.sub.pol,np) by the observed primer extension
activity of the polymerase in control reactions lacking
nanoparticles (A.sub.pol), as expressed in the following
equation:
Nanoparticle tolerance ratio=(A.sub.pol,np/A.sub.pol)
[0431] The nanoparticle tolerance is then calculated by converting
the nanoparticle tolerance ratio into a percentage value, by
multiplying the nanoparticle tolerance ratio,
A.sub.pol,np/A.sub.pol, by 100. This relationship can be expressed
as follows:
Nanoparticle tolerance (%)=(A.sub.pol,np/A.sub.pol).times.100
[0432] In some embodiments, the present disclosure relates to
modified polymerases having a nanoparticle tolerance
(A.sub.pol-label/A.sub.pol.times.100), of up to about 5%, 10%, 15%,
20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 80% or 90%
as measured using standard tolerance assay conditions, as described
herein. In some embodiments, the nanoparticle tolerance of the
modified polymerase is at least about 5%, 10%, 25%, 50%, 70%, 75%,
80%, 90%, 100%, 125%, 250%, 500%, 750% or 1,000% as measured using
standard tolerance assay conditions.
[0433] In some embodiments, the modified polymerase exhibits an
altered, e.g., increased or decreased, nanoparticle tolerance
(A.sub.pol,np/A.sub.pol.times.100) relative to an unmodified
counterpart. In some embodiments, the modified polymerase exhibits
a photostability (A.sub.pol,np/A.sub.pol.times.100) that is at
least about 5%, 10%, 25%, 37.5%, 50%, 75%, 100%, 110%, 125%, 150%,
200%, 250%, 500%, 750%, 1,000%, 5,000% or 10,000% of the
photostability of a reference polymerase under identical reaction
conditions. In some embodiments, the reaction conditions can
comprise standard tolerance assay conditions, as described
herein.
[0434] In some embodiments, the modified polymerase has a primer
extension activity (A.sub.pol-np) under standard tolerance assay
conditions that is at least about that is at least about 5%, 10%,
25%, 37.5%, 50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%, 500%,
750%, 1,000%, 5,000% or 10,000% of the primer extension activity of
a reference polymerase under identical reaction conditions.
[0435] In some embodiments, the reference polymerase is the
unmodified counterpart of the modified polymerase. In some
embodiments, the reference polymerase is a Phi-29 polymerase having
the amino acid sequence of SEQ ID NO: 1. In some embodiments, the
reference polymerase is a B103 polymerase having the amino acid
sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the nucleotide substrate is a natural nucleotide. In
some embodiments, the nucleotide substrate is a labeled nucleotide
analog. In some embodiments, the modified polymerase comprises the
amino acid sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other
variant of the polymerase having the amino acid sequence of SEQ ID
NO: 7. In some embodiments, the modified polymerase can be at least
80%, 85%, 97%, 98% or 99% identical to the amino acid sequence of
SEQ ID NO: 7 or SEQ ID NO: 8. In some embodiments, the modified
polymerase having altered nanoparticle tolerance comprises one or
more amino acid substitutions at positions selected from the group
consisting of: 2, 9, 12, 58, 59, 63, 129, 166, 246, 247, 339, 370,
371, 372, 373, 374, 375, 376, 377, 380, 383, 384, 385, 455, 507 and
509, or any combinations thereof.
[0436] In some embodiments the nanoparticle tolerance, expressed as
a percentage value (A.sub.pol,np/A.sub.pol.times.100) of the
modified polymerase can be about 70%, whereas the
A.sub.pol,np/A.sub.pol.times.100 value of a reference Phi-29
polymerase comprising the amino acid sequence of SEQ ID NO: 1 under
identical reaction conditions is about 60%. In some embodiments the
(A.sub.pol,np/A.sub.pol.times.100) value of the modified polymerase
can be at least about 85%, whereas the
(A.sub.pol,np/A.sub.pol.times.100) value of a reference Phi-29
polymerase comprising the amino acid sequence of SEQ ID NO: 1 is no
greater than about 55% under identical reaction conditions. In some
embodiments the (A.sub.pol,np/A.sub.pol100) value of the modified
polymerase can be about 90%, whereas the
A.sub.pol,np/A.sub.pol.times.1000 value of a reference Phi-29
polymerase comprising the amino acid sequence of SEQ ID NO: 1 under
identical reaction conditions is about 50%.
[0437] Disclosed herein are modified polymerases exhibiting altered
(e.g., increased or decreased) levels of photostability following
exposure to excitation radiation. The word "photostability" and its
variants, as used herein with reference to a particular polymerase,
refers to the average primer extension activity retained by the
polymerase following exposure to excitation radiation under defined
reaction conditions, as compared to the average primer extension
activity of the polymerase in the absence of such exposure but
under otherwise identical reaction conditions.
[0438] In some embodiments, the modified polymerase exhibits
increased photostability as compared to its unmodified counterpart,
thus increasing its utility in methods and systems involving labels
requiring excitation in order to be detectable. For example,
increased photostability can be desirable because it allows high
levels of primer extension activity in reactions involving the use
of excitation radiation, such as single molecule sequencing
reactions.
[0439] Typically, the photostability will vary depending on the
reaction conditions employed, including the intensity, wavelength
and duration of the excitation radiation. The lower the decrease in
primer extension activity following exposure to excitation
radiation, the greater the photostability of the polymerase.
[0440] The photostability of a polymerase is typically measured by
first obtaining the photostability ratio of the polymerase under
defined reaction conditions. The photostability ratio is the ratio
of the average primer extension activity of the polymerase
following exposure to excitation radiation under defined reaction
conditions (termed "A.sub.pol-R") and the average primer extension
activity of the polymerase without exposure to any excitation
radiation but under otherwise identical reaction conditions (termed
"A.sub.pol-"). This relationship can be expressed mathematically as
follows:
Photostability ratio=A.sub.pol-R/A.sub.pol
[0441] The photostability can then be calculated by converting the
photostability ratio into a percentage value (%), which can be
obtained by multiplying the ratio A.sub.pol-R/A.sub.pol by 100.
This relationship can be represented as follows:
Photostability (%)=(A.sub.pol,-R/A.sub.pol).times.100
[0442] For example, a polymerase that has about 90% photostability
will retain on average about 90% of its average primer extension
activity under defined reaction conditions (including exposure to
excitation radiation of a defined intensity, wavelength and
duration), where the average primer extension activity of the
polymerase in the absence of any exposure to excitation radiation
but under otherwise identical reaction conditions is arbitrarily
set as 100%.
[0443] In a typical embodiment, the photostability of a polymerase
is measured using defined reaction conditions (referred to herein
as "standard photostability assay conditions") comprising 50 mM
Tris, pH 7.5, 50 mM NaCl, 1 mM DTT, 2 mM MnCl.sub.2, 0.3% BSA, 200
nM His-tagged polymerase, 100 nM primed template and 100 nM
nanoparticles and further including exposure to excitation
radiation of 50 W/cm.sup.2 intensity at 405 nm wavelength and 5
minutes duration. Following such irradiation, the primer extension
reaction is initiated by adding nucleotides to a final
concentration of 5 .mu.M and primer extension is performed at
23.degree. C. for 30 seconds. The resulting primer extension
activity is measured after 30 seconds by arresting the reaction
(e.g., via addition of 10 mM EDTA). The primer extension activity
is then measured and then compared to the primer extension activity
of control sample (i.e., no exposure to excitation radiation) under
otherwise identical reaction conditions.
[0444] In one exemplary embodiment, the primer extension activity
was measured by resolving the extension products on a 8M urea, 24%
polyacrylamide, and calculating the concentration of fully extended
product relative to total concentration for all extension products.
The observed primer extension activity is compared to the primer
extension activity of the same polymerase in the absence of any
label but under otherwise identical reaction conditions (control
reaction), which is arbitrarily defined as having 100% primer
extension activity.
[0445] Depending on the biological application of interest,
however, the photostability can also be determined under different,
i.e., non-standard, assay conditions, for example by measuring the
average primer extension activity of the polymerase under different
reaction conditions including higher or lower intensities,
wavelengths and/or durations of excitation, and comparing this
activity to the average primer extension activity of the polymerase
in the absence of the label but under otherwise identical reaction
conditions. In some embodiments, the reaction conditions can
optionally include the presence of one or more labels, e.g.,
nanoparticles in the reaction mixture.
[0446] In some embodiments, the present disclosure relates to
modified polymerases having a photostability
(A.sub.pol-R/A.sub.pol.times.100) of up to about 5%, 10%, 15%, 20%,
25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 80% or 90% under
standard photostability assay conditions, as described herein. In
some embodiments, the photostability of the modified polymerase is
at least about 5%, 10%, 25%, 50%, 70%, 75%, 80%, 90%, 100%, 125%,
250%, 500%, 750% or 1,000% under standard photostability assay
conditions.
[0447] In some embodiments, the modified polymerase exhibits an
altered, e.g., increased or decreased, photostability
(A.sub.pol-R/A.sub.pol.times.100) relative to an unmodified
counterpart. In some embodiments, the modified polymerase exhibits
a photostability (A.sub.pol-R/A.sub.pol.times.100) that is at least
about 5%, 10%, 25%, 37.5%, 50%, 75%, 100%, 110%, 125%, 150%, 200%,
250%, 500%, 750%, 1,000%, 5,000% or 10,000% as high as the
photostability of a reference polymerase under identical reaction
conditions. In some embodiments, the reaction conditions can
comprise standard photostability assay conditions, as described
herein.
[0448] In some embodiments, the modified polymerase has a primer
extension activity (A.sub.pol-R) under standard photostability
assay conditions that is at least about that is at least about 5%,
10%, 25%, 37.5%, 50%, 75%, 100%, 110%, 125%, 150%, 200%, 250%,
500%, 750%, 1,000%, 5,000% or 10,000% of the primer extension
activity of a reference polymerase under identical reaction
conditions.
[0449] In some embodiments, the reference polymerase is the
unmodified counterpart of the modified polymerase. In some
embodiments, the reference polymerase is a Phi-29 polymerase having
the amino acid sequence of SEQ ID NO: 1. In some embodiments, the
reference polymerase is a B103 polymerase having the amino acid
sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the nucleotide substrate is a natural nucleotide. In
some embodiments, the nucleotide substrate is a labeled nucleotide
analog. In some embodiments, the modified polymerase comprises the
amino acid sequence of SEQ ID NO: 7, SEQ ID NO: 8, or any other
variant of the polymerase having the amino acid sequence of SEQ ID
NO: 7. In some embodiments, the modified polymerase can be at least
80%, 85%, 97%, 98% or 99% identical to the amino acid sequence of
SEQ ID NO: 7 or SEQ ID NO: 8. In some embodiments, the modified
polymerase having altered photostability comprises one or more
amino acid substitutions at positions selected from the group
consisting of: 2, 9, 12, 58, 59, 63, 129, 166, 246, 247, 339, 370,
371, 372, 373, 374, 375, 376, 377, 380, 383, 384, 385, 455, 507 and
509, or any combinations thereof.
[0450] In some embodiments, the excitation radiation comprises
light of 405 nm wavelength. The intensity of excitation radiation
can be about 10 W/cm.sup.2, 20 W/cm.sup.2 or 50 W/cm.sup.2 or any
other suitable value. In some embodiments, the duration of exposure
to excitation radiation can be less than or equal to 0.1, 0.25,
0.3, 0.4, 0.5, 0.75, 1, 2.5, 5, 10, 15, 20, 30, 45 or 60 minutes.
In some embodiments, the A.sub.pol-R/A.sub.pol value of the
modified polymerase is at least 50%, 60%, 70%, 80%, 90%, 95% or 99%
following exposure to excitation radiation at 20 W/cm.sup.2 for 5
minutes. In some embodiments, the A.sub.pol-R/A.sub.pol value of
the modified polymerase is at least 50%, 60%, 70%, 80%, 90%, 95% or
99% following exposure to excitation radiation at 50 W/cm.sup.2 for
30 seconds.
[0451] In some embodiments, the modified polymerase exhibits an
altered (e.g., increased or decreased) A.sub.pol-R/A.sub.pol value
relative to an unmodified counterpart. In some embodiments, the
modified polymerase exhibits A.sub.pol-R/A.sub.pol value that is at
least about 5%, 10%, 25%, 37.5%, 50%, 75%, 100%, 110%, 125%, 150%,
200%, 250%, 500%, 750%, 1,000%, 5,000% or 10,000% as high as the
A.sub.pol-R/A.sub.pol value of a reference polymerase under
identical reaction conditions. In some embodiments, the reference
polymerase is the unmodified counterpart of the modified
polymerase. In some embodiments, the reference polymerase is a
Phi-29 polymerase having the amino acid sequence of SEQ ID NO: 1.
In some embodiments, the reference polymerase is a B103 polymerase
having the amino acid sequence of SEQ ID NO: 6, SEQ ID NO: 7 or SEQ
ID NO: 8. In some embodiments, the nucleotide substrate is a
natural nucleotide. In some embodiments, the nucleotide substrate
is a labeled nucleotide analog. In some embodiments, the modified
polymerase comprises the amino acid sequence of SEQ ID NO: 7, SEQ
ID NO: 8, or any other variant of the polymerase having the amino
acid sequence of SEQ ID NO: 7. In some embodiments, the modified
polymerase can be at least 80%, 85%, 97%, 98% or 99% identical to
the amino acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the modified polymerase comprises one or more amino
acid substitutions at positions selected from the group consisting
of: 2, 9, 12, 58, 59, 63, 129, 166, 246, 247, 339, 370, 371, 372,
373, 374, 375, 376, 377, 380, 383, 384, 385, 455, 507 and 509, or
any combinations thereof.
[0452] Also disclosed herein are kits comprising one or more
modified polymerases of the present disclosure for use in primer
extension or single molecule sequencing reactions. For example, in
some embodiments, the kit can comprise one or more modified
polymerases and one or more nucleotides packaged in a fashion to
enable use of the polymerase to incorporate one or more nucleotides
of the kit. The modified polymerase can be a polymerase having or
comprising the amino acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8,
or a polymerase comprising an amino acid sequence that is at least
80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the amino acid
sequence of SEQ ID NO: 7 or SEQ ID NO: 8. The nucleotide can be a
labeled nucleotide analog. The label can be linked to the sugar,
base, phosphate or any other moiety of the nucleotide analog. In
some embodiments, the nucleotide is a reversible terminator.
[0453] In some embodiments, the kit can comprise a modified
polymerases according to the present disclosure linked to one or
more labels to form a labeled polymerase conjugates. Some methods
of making and using labeled polymerase conjugates are disclosed,
for example, in U.S. provisional application Nos., 61/184,770,
filed Jun. 5, 2009; 61/245,457, filed on Sep. 24, 2009; and
61/299,919, filed on Jan. 29, 2010, as well as U.S. application
Ser. No. ______ titled "Conjugates of Biomolecules to
Nanoparticles" and assigned Attorney Docket No. LT00003, filed
concurrently herewith; and U.S. application Ser. No. ______ titled
"Labeled Enzyme Compositions, Methods & Systems" and assigned
Attorney Docket No. LT00053, filed concurrently herewith. In some
embodiments, the one or more labels of the labeled polymerase
conjugate are capable of undergoing FRET with the label of the
nucleotide bound to the active site of the polymerase. Optionally,
such FRET can occur with a FRET efficiency of at least about 10% or
20%.
[0454] In some embodiments, the kit can further comprise additional
reagents, such as additional nucleotides, including labeled and
unlabeled nucleotides; divalent metal cations; nucleic acid
molecules (for example, for use as primer and/or template); buffer
solutions; salt solutions, and the like. Typically, the kit will
also comprise instructions for use of the contents in a variety of
applications such as, for example, nucleotide incorporation, primer
extension and single molecule sequencing.
[0455] Also provided herein are methods of isolating or preparing
the modified polymerases of the present disclosure. In some
embodiments, the polymerase can be a recombinant protein which is
produced by a suitable expression vector/host cell system. The
polymerases can be encoded by suitable recombinant expression
vectors carrying inserted sequences of the polymerases. The
polymerase sequence can be linked to a suitable expression vector.
The polymerase sequence can be inserted in-frame into the suitable
expression vector. The suitable expression vector can replicate in
a phage host, or a prokaryotic or eukaryotic host cell. The
suitable expression vector can replicate autonomously in the host
cell, or can be inserted into the host cell's genome and be
replicated as part of the host genome. The suitable expression
vector can carry a selectable marker that confers resistance to
drugs (e.g., kanamycin, ampicillin, tetracycline, chloramphenicol,
or the like) or requirement for nutrients. The suitable expression
vector can have one or more restriction sites for inserting the
nucleic acid molecule of interest. The suitable expression vector
can include expression control sequences for regulating
transcription and/or translation of the encoded sequence. The
expression control sequences can include: promoters (e.g.,
inducible or constitutive), enhancers, transcription terminators,
and secretion signals. The expression vector can be a plasmid,
cosmid, or phage vector. The expression vector can enter a host
cell which can replicate the vector, produce an RNA transcript of
the inserted sequence, and/or produce protein encoded by the
inserted sequence. Methods for preparing suitable recombinant
expression vectors and expressing the RNA and/or protein encoded by
the inserted sequences are well known. See, e.g., Sambrook et al.,
Molecular Cloning (1989).
[0456] As the skilled artisan will readily appreciate, the scope of
the present disclosure encompasses not only the specific amino acid
and/or nucleotide sequences disclosed herein, but also, for
example, too many related sequences encoding genes and/or peptides
with the functional properties described herein. For example,
nucleotide and amino acid sequences encoding conservative variants
of the various modified polymerases disclosed herein are also
within the scope of the present disclosure.
[0457] Also provided herein are methods of using the modified
polymerase compositions of the present disclosure.
[0458] In some embodiments, the modified polymerases of the present
disclosure can polymerize one or more nucleotides, including, for
example, labeled and unlabeled nucleotides.
[0459] In some embodiments, the disclosure relates to a method for
performing a primer extension reaction, comprising: contacting a
modified DNA polymerase as provided herein with a nucleic acid
molecule and a nucleotide under conditions where the nucleotide is
incorporated into the nucleic acid molecule by the modified DNA
polymerase. Optionally, the modified DNA polymerase comprises an
amino acid sequence that is at least 80%, 85%, 90%, 95%, 97%, 98%
or 99% identical to the amino acid sequence of SEQ ID NO: 7.
[0460] Optionally, the nucleotide is a labeled nucleotide, and the
label of the nucleotide emits a signal during incorporation of the
at least one nucleotide. Optionally, the method further comprises
detecting the signal emitted by the nucleotide label. Optionally,
the method further comprises analyzing the detected signal to
determine the identity of the incorporated nucleotide.
[0461] Optionally, the modified DNA polymerase can exhibit a
t.sub.-1 value for a labeled nucleotide that is equal to or greater
than the t.sub.-1 value of a reference Phi-29 polymerase comprising
the amino acid sequence of SEQ ID NO: 1 for the same nucleotide.
Optionally, the modified polymerase exhibits a t.sub.pol value for
a labeled nucleotide that is equal to or greater than the t.sub.pol
value of a reference Phi-29 polymerase comprising the amino acid
sequence of SEQ ID NO: 1 for the same nucleotide. Optionally, the
modified DNA polymerase exhibits a residence time for a labeled
nucleotide that is equal to or greater than the residence time of a
reference Phi-29 polymerase comprising the amino acid sequence of
SEQ ID NO: 1 for the same nucleotide. In some embodiments, the
modified DNA polymerase has a photostability of at least about 80%
under standard photostability assay conditions. In some
embodiments, the modified polymerase has a nanoparticle tolerance
of at least about 80% under standard tolerance assay
conditions.
[0462] Optionally, the nucleotide is a labeled nucleotide. In some
embodiments, the labeled nucleotide comprises a nucleotide label
linked to the base, sugar or phosphate group of the nucleotide. In
some embodiments, the labeled nucleotide is a reversible
terminator. Optionally, the modified DNA polymerase can be linked
to a label. The label can be a dye or a nanoparticle. Optionally,
the label of the modified polymerase and the nucleotide label are
capable of undergoing FRET with each other. Such FRET can
optionally occur with a FRET efficiency of at least 20%.
[0463] Disclosed herein are methods for incorporation of one or
more nucleotides onto the end of a nucleic acid molecule,
comprising: contacting a nucleic acid molecule with a modified
polymerase provided for herein and one or more nucleotides under
conditions where at least one nucleotide is incorporated by the
modified polymerase. The nucleic acid molecule can be any suitable
target nucleic acid molecule of interest. In some embodiments, the
modified polymerase can be a polymerase having or comprising the
amino acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8. In some
embodiments, the at least one nucleotide can be become incorporated
onto the 3' end of an extending nucleic acid molecule by the
polymerase. In some embodiments, the at least one nucleotide can be
a labeled nucleotide analog. The labeled nucleotide analog can
comprise a label linked to the base, sugar, phosphate or any other
portion of the nucleotide analog. In some embodiments, the
nucleotide can also comprise a blocking group that inhibits, slows
down or blocks further incorporation of nucleotides onto the end of
the nucleic acid molecule until the blocking group is removed from
the nucleotide. In some embodiments, the nucleotide comprising a
blocking group is a reversible terminator for nucleic acid
synthesis, as described further below. In some embodiments, the
blocking group can be removed from the nucleotide by chemical,
enzymatic; or photocleaving reactions.
[0464] In some embodiments, the method further includes the step of
adding one or more divalent cations to the polymerase reaction
mixture in an amount sufficient for inhibiting further
incorporation of nucleotides onto the end of the nucleic acid
molecule by the modified polymerase. In some embodiments, the
divalent cation that inhibits nucleotide incorporation is calcium.
In another embodiment, omitting, reducing, or chelating cations
that permit nucleotide incorporation (e.g, manganese and/or
magnesium) can be employed. Such methods are described, for
example, in U.S. Provisional Application 61/242,762, filed Sep. 15,
2009; and in U.S. Provisional Application No. 61/184,774, filed on
Jun. 5, 2009. In some embodiments, the polymerase can be linked to
a label, as, for example, disclosed in U.S. Provisional Application
No. 61/184,770, filed Jun. 5, 2009.
[0465] Also provided herein is a method for detecting one or more
nucleotide incorporations onto the end of a single nucleic acid
molecule, comprising: contacting a target nucleic acid molecule
with a modified polymerase provided for herein and one or more
labeled nucleotides under conditions where at least one labeled
nucleotide is incorporated by the polymerase onto the end of an
extending nucleic acid molecule and where the label of at least one
labeled nucleotide emits one or more signals indicative of
nucleotide incorporation; and detecting the one or more signals
indicative of nucleotide incorporation. In some embodiments, the
method can further include the step of analyzing the one or more
detected signals indicative of nucleotide incorporation to
determine the presence of a target nucleic acid molecule. In some
embodiments, the detecting can be performed in real or near real
time. In some embodiments, the method can further include the step
of analyzing the one or more detected signals indicative of
nucleotide incorporation to determine the identity of the target
nucleic acid molecule. In some embodiments, the method can further
include the step of analyzing the one or more detected signals
indicative of nucleotide incorporation to determine the identity of
one or more incorporated nucleotides. In some embodiments, a time
series of nucleotide incorporations can be detected and analyzed to
determine some or all of the sequence of the target nucleic acid
molecule.
[0466] Also disclosed herein is a method for determining a
nucleotide sequence of a single nucleic acid molecule, comprising:
(a) conducting a polymerase reaction comprising a modified
polymerase provided for herein and at least one labeled
nucleotides, which reaction results in the incorporation of one or
more labeled nucleotides by the polymerase and the generation of
one or more signals indicative of one or more nucleotide
incorporations; (b) detecting a time sequence of nucleotide
incorporations; and (c) determining the identity of one or more
incorporated nucleotides, thereby determining some or all of the
nucleotide sequence of a single nucleic acid molecule.
[0467] Also provided herein are methods of sequencing a nucleic
acid molecule, comprising: (a) conducting a polymerase reaction
comprising a modified polymerase and at least one labeled
nucleotide, which reaction results in the incorporation of one or
more labeled nucleotides by the polymerase and the generation of
one or more signals indicative of one or more nucleotide
incorporations; (b) detecting a time sequence of nucleotide
incorporations; and (c) determining the identity of one or more
incorporated nucleotides, thereby determining some or all of the
nucleotide sequence of a single nucleic acid molecule.
[0468] In some embodiments, the polymerase can bind a target
nucleic acid molecule, which may or may not be base-paired with a
polymerization initiation site (e.g., primer).
[0469] The polymerization initiation site is used by the polymerase
(e.g., DNA or RNA polymerase) to initiate nucleotide
polymerization. In some embodiments, the polymerization initiation
site can be a terminal 3' OH group. The 3' OH group can serve as a
substrate for the polymerase for nucleotide polymerization. The 3'
OH group can serve as a substrate for the polymerase to form a
phosphodiester bond between the terminal 3' OH group and an
incorporated nucleotide. The 3' OH group can be provided by: the
terminal end of a primer molecule; a nick or gap within a nucleic
acid molecule (e.g., oligonucleotide) which is base-paired with the
target molecule; the terminal end of a secondary structure (e.g.,
the end of a hairpin-like structure); or an origin of replication.
The polymerization initiation site can be provided by an accessory
protein (e.g., RNA polymerase or helicase/primase). The
polymerization initiation site can be provided by a terminal
protein which can be bound (covalently or non-covalently) to the
end of the target nucleic, including terminal protein (e.g., TP)
found in phage (e.g., TP from phi29 phage). Thus, the
polymerization initiation site may be at a terminal end or within a
base-paired nucleic acid molecule.
[0470] In other embodiments, the polymerization initiation site
used by some polymerases (e.g., RNA polymerase) may not include a
3'OH group.
[0471] The portion of the target molecule which is base paired with
the primer or with the oligonucleotide, or the self-primed portion
of the target molecule, can form hydrogen bonding by Watson-Crick
or Hoogstein binding to form a duplex nucleic acid structure. The
primer, oligonucleotide, and self-priming sequence may be
complementary, or partially complementary, to the nucleotide
sequence of the target molecule. The complementary base pairing can
be the standard A-T or C-G base pairing, or can be other forms of
base-pairing interactions.
[0472] The polymerization initiation site can be in a position on
the target nucleic acid molecule to permit successive nucleotide
incorporation events in a direction away from, or towards, the
solid surface.
[0473] The primer molecule can hybridize with the target nucleic
acid molecule. The sequence of the primer molecule can be
complementary or non-complementary with the sequence of the
sequence of the target molecule. The 3' terminal end of the primer
molecule can provide the polymerization initiation site.
[0474] The primers can be modified with a chemical moiety to
protect the primer from serving as a polymerization initiation site
or as a restriction enzyme recognition site. The chemical moiety
can be a natural or synthetic amino acid linked through an amide
bond to the primer.
[0475] The primer, oligonucleotide, or self-priming portion, may be
naturally-occurring, or may be produced using enzymatic or chemical
synthesis methods. The primer, oligonucleotide, or self-priming
portion may be any suitable length including 5, 10, 15, 20, 25, 30,
40, 50, 75, or 100 nucleotides or longer in length. The primer,
oligonucleotide, or self-priming portion may be linked to an energy
transfer moiety (e.g., donor or acceptor) or to a reporter moiety
(e.g., a dye) using methods well known in the art.
[0476] The primer molecule, oligonucleotide, and self-priming
portion of the target molecule, may comprise ribonucleotides,
deoxyribonucleotides, ribonucleotides, deoxyribonucleotides,
peptide nucleotides, modified phosphate-sugar backbone nucleotides
including phosphorothioate and phosphoramidate, metallonucleosides,
phosphonate nucleosides, and any variants thereof, or combinations
thereof.
[0477] In one embodiment, the primer molecule can be a recombinant
DNA molecule. The primer can be linked at the 5' or 3' end, or
internally, with at least one binding partner, such as biotin. The
biotin can be used to immobilize the primer molecule to the surface
(via an avidin-like molecule), or for attachment to a reporter
moiety. The primer can be linked to at least one energy transfer
moiety, such as a fluorescent dye or a nanoparticle, or to a
reporter moiety. The primer molecule can hybridize to the target
nucleic acid molecule. The primer molecule can be used as a capture
probe to immobilize the target molecule.
[0478] Typically, the polymerase can selectively bind to a
nucleotide. Such nucleotide binding can occur in a
template-dependent or non-template-dependent manner. Typically, the
polymerase can mediate cleavage of the bound nucleotide. Typically,
such cleavage of the nucleotide results in the formation of at
least two nucleotide cleavage products. For
polyphosphate-comprising nucleotides, such cleavage will typically
occur between the .alpha. and .beta. phosphate groups. Typically,
the polymerase can mediate incorporation of one of the nucleotide
cleavage products into a nucleic acid molecule, and release of
another nucleotide cleavage product. When used in conjunction with
polyphosphate-comprising nucleotides, the released nucleotide
cleavage product can comprise one or more phosphates (for example,
a polyphosphate chain); for nucleotides that are
non-phosphate-comprising analogs, the nucleotide cleavage product
may not comprise any phosphorus.
[0479] In some embodiments, the polymerase can mediate
incorporation of a nucleotide on to a polymerization initiation
site (e.g., terminal 3'OH of a primer).
[0480] The compositions, methods, systems and kits of the present
disclosure have particular use in single molecule sequencing
reactions. Typically, such applications comprise the performance of
a polymerase reaction using the a conjugate comprising a polymerase
linked to a label and having polymerase activity according to the
present disclosure.
[0481] In one exemplary embodiment, the temporal order of
nucleotide incorporations during the polymerase reaction is
detected and monitored in real time based on detection of FRET
signals resulting from FRET between the labeled polymerase
conjugates and the nucleotide label of an incorporating
acceptor-labeled nucleotide.
[0482] In some embodiments, the polymerase is linked to a FRET
donor and contacted with a nucleotide comprising a FRET acceptor.
In some embodiments, the donor performs FRET with the acceptor when
the polymerase and nucleotide are bought into sufficient proximity
(for example, during a productive incorporation, a non-productive
incorporation or during association of a nucleotide with the
polymerase active site), resulting in the emission of a FRET
signal. The FRET signal can optionally be detected and analyzed to
determine the occurrence of a polymerase-nucleotide
interaction.
[0483] In some embodiments, the FRET can occur prior to, during or
after productive incorporation of the nucleotide into a nucleic
acid molecule. Alternatively, the FRET can occur prior to binding
of the nucleotide to the polymerase active site, or while the
nucleotide resides within the polymerase active site, during a
non-productive incorporation.
[0484] In some embodiments, the FRET acceptor moiety can in some
embodiments be attached to, or comprise part of, the nucleotide
sugar, the nucleobase, or analogs thereof. In some embodiments, the
FRET acceptor is attached to a phosphate group of the nucleotide
that is cleaved and released upon incorporation of the underlying
nucleotide into the primer strand, for example the
.gamma.-phosphate, the .beta.-phosphate or some other terminal
phosphate of the incoming nucleotide. When this acceptor-labeled
nucleotide polyphosphate is incorporated by the labeled polymerase
conjugate into a nucleic acid molecule, the polymerase cleaves the
bond between the alpha and beta phosphate, thereby releasing a
pyrophosphate moiety comprising the acceptor that diffuses away.
Thus, in these embodiments, a signal indicative of nucleotide
incorporation is generated through FRET between the nanoparticle
and the acceptor bonded to the gamma, beta or other terminal
phosphate as each incoming nucleotide is incorporated into the
newly synthesized strand. By releasing the label upon
incorporation, successive incorporation of labeled nucleotides can
each be detected without interference from nucleotides previously
incorporated into the complementary strand. Alternatively, the
nucleotide may be labeled with a FRET acceptor moiety on an
internal phosphate, for example, the alpha phosphate, the beta
phosphate, or another internal phosphate. Although such
alpha-phosphate adducts are not cleaved and released during the
polymerization process, they can be removed and/or rendered
inoperable through appropriate treatments, e.g., chemical cleavage
or photobleaching, later in the sequencing process.
[0485] The polymerase reaction conditions can comprise any suitable
reaction conditions that permit nucleotide polymerization by
labeled polymerase conjugates of the present disclosure. In one
non-limiting example of nucleotide polymerization, the steps of
polymerization can comprise: (1) complementary base-pairing of a
target DNA molecule (e.g., a template molecule) with a primer
molecule having a terminal 3' OH (the terminal 3' OH provides the
polymerization initiation site for the polymerase); (2) binding of
the polymerase of the conjugate to the base-paired target
DNA/primer duplex to form a complex (e.g., open complex); (3)
binding of the candidate nucleotide by the polymerase of the
conjugate, which polymerase interrogates the candidate nucleotide
for complementarity with the template nucleotide on the target DNA
molecule; (4) catalysis of nucleotide polymerization by the
polymerase of the conjugate.
[0486] In one embodiment, the polymerase of the conjugate comprises
cleavage of the incorporating nucleotide by the polymerase,
accompanied by liberation of a nucleotide cleavage product. When
the nucleotide is a phosphate-comprising nucleotide, the cleavage
product can include one or more phosphate groups. In other
embodiments, where the polymerase incorporates a nucleotide analog
having substituted phosphate groups, the cleavage product may
include one or more substituted phosphate groups.
[0487] The candidate nucleotide may or may not be complementary to
the template nucleotide on the target molecule. The candidate
nucleotide may dissociate from the polymerase. If the candidate
nucleotide dissociates from the polymerase, it can be liberated; in
some embodiments, the liberated nucleotide carries intact
polyphosphate groups. When the candidate nucleotide dissociates
from the DNA polymerase, the event is known as a "non-productive
binding" event. The dissociating nucleotide may or may not be
complementary to the template nucleotide on the target
molecule.
[0488] The incorporated nucleotide may or may not be complementary
to the template nucleotide on the target. When the candidate
nucleotide binds the DNA polymerase and is incorporated, the event
is a "productive binding" event. The incorporated nucleotide may or
may not be complementary to the template nucleotide on the target
molecule.
[0489] The length of time, frequency, or duration of the binding of
the complementary candidate nucleotide to the polymerase can differ
from that of the non-complementary candidate nucleotide. This time
difference can be used to distinguish between the complementary and
non-complementary nucleotides, and/or can be used to identify the
incorporated nucleotide, and/or can be used to deduce the sequence
of the target molecule.
[0490] The signal (or change in signal) generated by the energy
transfer donor and/or acceptor can be detected before, during,
and/or after any nucleotide incorporation event.
[0491] In some embodiments, the polymerase reaction includes RNA
polymerization which does not require a 3' polymerization
initiation site. Polymerase reactions involving RNA polymerization
are well known in the art.
[0492] Productive and Non-Productive Binding
[0493] Also provided herein are energy transfer compositions and
methods for distinguishing between the productive and
non-productive binding events. The compositions and methods can
also provide base identity information during nucleotide
incorporation. The compositions include nucleotides and polymerases
each attached to a energy transfer moiety.
[0494] The compositions and methods provided herein can be used to
distinguish events such as productive and non-productive nucleotide
binding to the polymerase. In a productive binding event, the
nucleotide can bind/associate with the polymerase for a time period
which is distinguishable (e.g., longer or shorter time period),
compared to a non-productive binding event. In a non-productive
binding event, the nucleotide can bind/associate with the
polymerase and then dissociate. The donor and acceptor energy
transfer moieties produce detectable signals when they are in
proximity to each other and can be associated with productive and
non-productive binding events. Thus, the time-length difference
between signals from the productive and non-productive binding
events can provide distinction between the two types of events.
[0495] The detectable signals can be classified into true positive
and false positive signals. For example, the true positive signals
can arise from productive binding in which the nucleotide binds the
polymerase and is incorporated. The incorporated nucleotide can be
complementary to the template nucleotide. In another example, the
false positive signals can arise from different binding events,
including: non-specific binding, non-productive binding, and any
event which brings the energy transfer donor and acceptor into
sufficient proximity to induce a detectable signal.
[0496] Optionally, polymerase reactions performed using the
methods, systems, compositions and kits of the present disclosure
can be performed under any conditions which are suitable for:
forming the complex (target/polymerase or target/initiation
site/polymerase); binding the nucleotide to the polymerase;
permitting the energy transfer and reporter moieties to generate
detectable signals when the nucleotide binds the polymerase;
incorporating the nucleotide; permitting the energy transfer and
reporter moieties to generate a signal upon close proximity and/or
nucleotide incorporation; and/or detecting the signal, or change in
the signal, from the energy transfer or reporter moieties. The
suitable conditions include well known parameters for time,
temperature, pH, reagents, buffers, reagents, salts, co-factors,
nucleotides, target DNA, primer DNA, enzymes such as nucleic
acid-dependent polymerase, amounts and/or ratios of the components
in the reactions, and the like. The reagents or buffers can include
a source of monovalent ions, such as KCl, K-acetate,
NH.sub.4-acetate, K-glutamate, NH.sub.4Cl, or ammonium sulfate. The
reagents or buffers can include a source of divalent ions, such as
Mg.sup.2+ and/or Mn.sup.2+, MgCl.sub.2, or Mg-acetate. The buffer
can include Tris, Tricine, HEPES, MOPS, ACES, or MES, which can
provide a pH range of about 5.0 to about 9.5. The buffer can
include chelating agents such as EDTA and EGTA, and the like.
[0497] Reducing Photo-Damage
[0498] The suitable polymerase reaction conditions can also include
compounds which reduce photo-damage. For example, the compounds may
reduce oxygen-damage or photo-damage. Illuminating the nucleotide
binding and/or nucleotide incorporation reactions with
electromagnetic radiation at an excitation wavelength can induce
formation of reactive oxygen species from the fluorophore or other
components in the reaction. The reactive oxygen species can cause
photo-damage to the fluorophores, polymerases, or any other
component of the binding or incorporation reactions. The nucleotide
binding or nucleotide incorporation reactions can include compounds
which are capable of reducing photo-damage, including:
protocatechuate-3,4-dioxygenase, protocatechuic acid;
6-Hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic Acid (TROLOX); or
cyclooctatetraene (COT).
[0499] Other compounds for reducing photo-damage include: ascorbic
acid, astazanthin, bilirubin, biliverdin, bixin, captopril,
canthazanthin, carotene (alpha, beta, and gamma), cysteine,
beta-dimethyl cysteine, N-acetyl cysteine, diazobicyclooctane
(DABCO), dithiothreitol (DTT), ergothioneine, glucose
oxidase/catalase (GO/Cat), glutathione, glutathione peroxidase,
hydrazine (N.sub.2H.sub.4), hydroxylamine, lycopene, lutein,
polyene dialdehydes, melatonin, methionine,
mercaptopropionylglycine, 2-mercaptoethane sulfonate (MESNA),
pyridoxine1 and its derivatives, mercaptoethylamine (MEA),
.beta.-mercaptoethanol (BME), n-propyl gallate, p-phenylenediamene
(PPD), hydroquinone, sodium azide (NaN.sub.3), sodium sulfite
(Na.sub.2SO.sub.3), superoxide dismutase, tocopherols,
.alpha.-tocopheryl succinate and its analogs, and zeaxanthin.
[0500] Also provided herein are methods of using the labeled
biomolecule conjugates of the present disclosure.
[0501] For example, disclosed herein are methods for incorporation
of one or more nucleotides onto the end of a nucleic acid molecule,
comprising: contacting a conjugate including a polymerase linked to
a label with a nucleotide under conditions where the nucleotide is
incorporated into a nucleic acid molecule by the conjugate. The
nucleic acid molecule can be any suitable target nucleic acid
molecule of interest. In some embodiments, the labeled polymerase
can be a polymerase having or comprising the amino acid sequence of
SEQ ID NO: 7 or SEQ ID NO: 8. In some embodiments, the nucleotide
can be become incorporated onto the 3' end of an extending nucleic
acid molecule by the polymerase. In some embodiments, the
nucleotide can be a labeled nucleotide analog. The labeled
nucleotide analog can further comprise a label linked to the base,
sugar, phosphate or any other portion of the nucleotide analog. In
some embodiments, the nucleotide can also comprise a blocking group
that inhibits, slows down or blocks further incorporation of
nucleotides onto the end of the nucleic acid molecule until the
blocking group is removed from the nucleotide. In some embodiments,
the nucleotide comprising a blocking group is a reversible
terminator for nucleic acid synthesis, as described further below.
In some embodiments, the blocking group can be removed from the
nucleotide by chemical, enzymatic, or photocleaving reactions.
[0502] In some embodiments, the method further includes the step of
adding one or more divalent cations to the polymerase reaction
mixture in an amount sufficient for inhibiting further
incorporation of nucleotides onto the end of the nucleic acid
molecule by the labeled polymerase. In some embodiments, the
divalent cation that inhibits nucleotide incorporation is calcium.
In another embodiment, omitting, reducing, or chelating cations
that permit nucleotide incorporation (e.g, manganese and/or
magnesium) can be employed. Such methods are described, for
example, in U.S. Provisional Application 61/242,762, filed Sep. 15,
2009; and in U.S. Provisional Application No. 61/184,774, filed on
Jun. 5, 2009. In some embodiments, the polymerase can be linked to
a label, as, for example, disclosed herein and in U.S. Provisional
Application No. 61/184,770, filed Jun. 5, 2009.
[0503] Also provided herein is a method for detecting one or more
nucleotide incorporations, comprising: contacting a conjugate
including a polymerase linked to a label with a labeled nucleotide
under conditions where the labeled nucleotide is incorporated by
the conjugate into a nucleic acid molecule, and where the label of
the labeled nucleotide emits a signal indicative of such nucleotide
incorporation; and detecting the signal indicative of such
nucleotide incorporation. In some embodiments, the detecting can be
performed in real or near real time. In some embodiments, the
method can further include analyzing the detected signal indicative
of nucleotide incorporation to determine the identity of the
incorporated nucleotide. In some embodiments, the labeled
polymerase conjugate catalyzes a time series of nucleotide
incorporations, which can collectively be detected and analyzed to
determine some or all of the sequence of the target nucleic acid
molecule.
[0504] Also disclosed herein is a method for determining a
nucleotide sequence of a single nucleic acid molecule, comprising:
(a) conducting a polymerase reaction comprising a labeled
biomolecule conjugate and a labeled nucleotide under conditions
where the conjugate incorporates the labeled nucleotide into a
nucleic acid molecule and a signal indicative of such nucleotide
incorporation is generated; (b) detecting the signal indicative of
such nucleotide incorporation; and (c) analyzing the signal to
determine the identity of the incorporated nucleotide. Optionally,
a time series of nucleotide incorporation signals can be detected
and analyzed, thereby determining some or all of the nucleotide
sequence of a single nucleic acid molecule.
[0505] Also provided herein are methods of sequencing a nucleic
acid molecule, comprising: (a) performing a polymerase reaction
comprising a labeled polymerase conjugate and labeled nucleotides
under conditions resulting in a series of labeled nucleotide
incorporations by the polymerase and the generation of a signal
indicative of each nucleotide incorporation the series; (b)
detecting a time sequence of nucleotide incorporations; and (c)
determining the identity of one or more incorporated nucleotides,
thereby determining some or all of the nucleotide sequence of a
single nucleic acid molecule.
[0506] In some embodiments, the polymerase is attached to or
associated with a substrate or surface. In some embodiments, the
polymerase can be attached to or associated with a nucleic acid
molecule (termed a template), and polymerize one or more
nucleotides in a template-dependent fashion. In some embodiments,
the template can be attached to or associated with a substrate or
surface. In some embodiments, the polymerase, template, nucleotide,
substrate or surface, or some combination thereof, can also be
labeled.
[0507] In some embodiments, the methods of the present disclosure
can be performed in multiplex and/or "high-throughput" format
wherein multiple units of the labeled polymerase conjugates of the
present disclosure can each be visualized and monitored in parallel
with each other. For example, in some embodiments, multiple labeled
polymerase conjugates may be positioned, associated with, or
attached to different locations on a substrate, and a polymerase
activity of one or more of these polymerases may be detected in
isolation. In some embodiments, the polymerase or the template
nucleic acid molecule are associated with or attached to a
substrate or surface in array format. The array can be spatially
addressable.
[0508] In some embodiments, the sequencing reaction can be
performed using buffer conditions comprising 50 mM Tris buffer pH
7.5, 50 mM NaCl, 0-10 mM MgCl.sub.2, 2 mM MnCl.sub.2, 330 nM
polymerase, 100 nM primed template and 4 .mu.M labeled nucleotide
hexaphosphate. Optionally, 0.3% BSA and/or 0.05% Tween20 can be
included in the reaction mix. In some embodiments, the reaction mix
is further supplemented with 2 mM DTT and/or single stranded
binding protein (SSBP) at a concentration of 100 .mu.g/ml.
[0509] Alternatively, in some embodiments the sequencing reaction
can be performed using buffer conditions comprising 50 mM Tris pH
8.0, 50 mM NaCl and 10 mM MgCl.sub.2.
[0510] In one exemplary embodiment, a nucleic acid sequencing
system can comprise a template nucleic acid molecule attached to a
substrate, a labeled polymerase conjugate comprising a FRET donor
label linked to a polymerase, and labeled nucleotides each
comprising a nucleotide linked to one or more FRET acceptor
labels.
[0511] The template nucleic acid molecule of this sequencing system
can be attached to any suitable substrate or surface using any
suitable method in some embodiments, the template nucleic acid
molecule can comprise one or more biotin moieties, the surface can
comprise an avidin moiety, and the template nucleic acid is linked
to the surface via one or more biotin-avidin bonds. In some
embodiments, the template and surface can each comprise one or more
biotin moieties, and be linked to each other through a linkage
comprising an avidin moiety.
[0512] In some embodiments, the polymerase can be unlabeled.
Alternatively, the polymerase can be linked to one or more label to
form a labeled polymerase conjugate. In some embodiments, the label
comprises at least one energy transfer moiety. The label can be an
organic label (e.g., dye label) or an inorganic label (e.g.,
nanoparticle).
[0513] In some embodiments, the polymerase may be linked with at
least one energy transfer donor moiety. One or more energy transfer
donor moieties can be linked to the polymerase at the amino end or
carboxyl end or may be inserted at any site therebetween.
Optionally, the energy transfer donor moiety can be attached to the
polymerase in a manner which does not significantly interfere with
the nucleotide binding activity, or with the nucleotide
incorporation activity of the polymerase. In such embodiments, the
energy transfer moiety is attached to the polymerase in a manner
that does not significantly interfere with polymerase activity.
[0514] In one embodiment, a single energy transfer donor moiety can
be linked to more than one polymerase and the attachment can be at
the amino end or carboxyl end or may be inserted within the
polymerase.
[0515] In another embodiment, a single energy transfer donor moiety
can be linked to one polymerase.
[0516] In one embodiment, the energy transfer donor moiety can be a
nanoparticle (e.g., a fluorescent nanoparticle) or a fluorescent
dye. The polymerase, which can be linked to the nanoparticle or
fluorescent dye, typically retains one or more activities that are
characteristic of the polymerase, e.g., polymerase activity,
exonuclease activity, nucleotide binding, and the like.
[0517] In some embodiments, the polymerases of the present
disclosure can include one or more mutations that improve the
performance of the polymerase in the particular biological assay of
interest. The mutations can include amino acid substitutions,
insertions, or deletions.
[0518] Selecting a Polymerase
[0519] The selection of the polymerase for use in the disclosed
methods can be based on the desired polymerase behavior in the
particular biological assay of interest. For example, the
polymerase can be selected to exhibit enhanced or reduced activity
in a particular assay, or enhanced or reduced interaction with one
or more particular substrates.
[0520] For example, in some embodiments the polymerase can be
selected based on the polymerization kinetics of the polymerase
either in unconjugated form or when linked to a label (labeled
polymerase conjugate). Optionally, the label can be a nanoparticle
or fluorescent dye; in some embodiments, the label can be energy
transfer donor moiety. For example, the polymerase can be selected
on the basis of kinetic behavior relating to nucleotide binding
(e.g., association), nucleotide dissociation (intact nucleotide),
nucleotide fidelity, nucleotide incorporation (e.g., catalysis),
and/or release of the cleavage product. The selected polymerase can
be wild-type or mutant.
[0521] In one embodiment, polymerases may be selected that retain
the ability to selectively bind complementary nucleotides. In
another embodiment, the polymerases may be selected which exhibit a
modulated rate (faster or slower) of nucleotide association or
dissociation. In another embodiment, the polymerases may be
selected which exhibit a reduced rate of nucleotide incorporation
activity (e.g., catalysis) and/or a reduced rate of dissociation of
the cleavage product and/or a reduced rate of polymerase
translocation (after nucleotide incorporation). Some modified
polymerases which exhibit modified nucleotide binding and/or rates
of nucleotide incorporation, as well as methods of identifying such
polymerases, have been described. See, e.g., Rank, U.S. Published
Patent Application No. 2008/0108082; Hanzel, U.S. Published Patent
Application No. 2007/0196846; Clark, U.S. Published Patent
Application No. 2009/0176233; Bjornsen, U.S. Published Patent
Application No. 2009/0286245.
[0522] In polymerases from different classes (including
DNA-dependent polymerases), an active-site lysine can interact with
the phosphate groups of a nucleoside triphosphate molecule bound to
the active site. The lysine residue has been shown to protonate the
pyrophosphate leaving-group upon nucleotidyl transfer. Mutant
polymerases having this lysine substituted with leucine, arginine,
histidine or other amino acids, exhibit greatly reduced nucleotide
incorporation rates (Castro, et al., 2009 Nature Structural and
Molecular Biology 16:212-218). One skilled in the art can use amino
acid alignment and/or comparison of crystal structures of
polymerases as a guide to determine which lysine residue to replace
with alternative amino acids. The sequences of Phi-29 polymerase
(SEQ ID NO: 1), RB69 polymerase (SEQ ID NO: 15), an exemplary
B103-like polymerase (SEQ ID NO: 7), and Klenow fragment can be
used as the basis for selecting the amino acid residues to be
modified (for B103 polymerase, see Hendricks, et al., U.S. Ser. No.
61/242,771, filed on Sep. 15, 2009, or U.S. Ser. No. 61/293,618,
filed on Jan. 8, 2010). In one embodiment, a modified Phi-29
polymerase can include lysine at position 379 and/or 383
substituted with leucine, arginine or histidine.
[0523] In other embodiments, the polymerase can be selected based
on the combination of the polymerase and nucleotides, and the
reaction conditions, to be used for the nucleotide binding and/or
nucleotide incorporation reactions. For example, certain
polymerases in combination with nucleotides that comprise 3, 4, 5,
6, 7, 8, 9, 10 or more phosphate groups can be selected for
performing the disclosed methods. In another example, certain
polymerases in combination with nucleotides which are linked to an
energy transfer moiety can be selected for performing the
nucleotide incorporation methods.
[0524] In some embodiments, the modified polymerase can be attached
to or associated with a substrate or surface. In some embodiments,
the polymerase can be attached to or associated with a nucleic acid
molecule (termed a template), and polymerize one or more
nucleotides in a template-dependent fashion. In some embodiments,
the template can be attached to or associated with a substrate or
surface. In some embodiments, the polymerase, template, nucleotide,
substrate or surface, or some combination thereof, can also be
labeled.
[0525] In some embodiments, the methods of the present invention
can be performed in multiplex and/or "high-throughput" format
wherein multiple units of the modified polymerases of the present
disclosure can each be visualized and monitored in parallel with
each other. For example, in some embodiments, multiple modified
polymerases may be positioned, associated with, or attached to
different locations on a substrate, and a polymerase activity of
one or more of these polymerases may be detected in isolation. In
some embodiments, the polymerase or the template nucleic acid
molecule are associated with or attached to a substrate or surface
in array format. The array can be spatially addressable.
[0526] In some embodiments, the nucleic acid molecule, the modified
polymerase, or both, may be isolated within a suitable
nanostructure. i.e., a structure having at least one dimension
measuring 500 nm or less. The nanostructure can be useful in
isolating a single nucleic acid molecule or polymerase. In some
embodiments, the nanostructure can be useful in elongating the
nucleic acid molecule to permit visualization of nucleotide
synthesis along some or all of the length of the nucleic acid
molecule. In some embodiments, the nanostructure is also useful in
limiting the amount of background signal ("noise") in the system by
reducing the excitation or detection volume, and/or by reducing the
amount of labeled moieties present within the reaction chamber. In
some embodiments, the nanostructure is designed to admit only a
single polymeric molecule and elongate it as it flows through the
nanostructure. Suitable devices comprising nanostructures that may
be used to practice the inventions disclosed herein are described,
for example, in U.S. Pat. No. 6,635,163; U.S. Pat. No. 7,217,562,
U.S. Pub: No. 2004/0197843 and U.S. Pub. No. 2007/0020772. In some
embodiments, the nanostructures of the nanofluidic device will
satisfy three requirements: (1) they will have a sufficiently small
dimension to elongate and isolate macromolecules; (2) they will be
sufficient length to permit instantaneous observation of the entire
elongated macromolecule; and (3) the nanochannels or other
nanostructures will be sufficiently numerous to permit simultaneous
and parallel observation of a large population of macromolecules.
In one embodiment, the radius of the component nanostructures of
the nanofluidic device will be roughly equal to or less than the
persistence length of the target DNA. Suitable methods of detecting
nucleotide incorporations using nanostructures are disclosed, for
example, in U.S. Provisional Application Nos. 61/077,090, filed
Jun. 30, 2008; 61/089,497, filed Aug. 15, 2008; and 61/090,346,
filed Aug. 20, 2008; and International Application No.
PCT/US09/049,324, filed Jun. 30, 2009.
[0527] Typically, the polymerase reaction comprises a mixture
including a modified polymerase, a nucleic acid molecule, at least
one priming site for nucleotide polymerization, and one or more
nucleotides for the modified polymerase. In some embodiments, the
reaction can be initiated by preparing the mixture lacking one
essential component for polymerization (for example, the polymerase
or nucleotides) and then adding the withheld component to initiate
the reaction. Suitable temperatures and the addition of other
components such as divalent metal ions can be determined and
optimized based on the particular polymerase and the target nucleic
acid sequences.
[0528] In some embodiments, the polymerase reaction can be
performed using buffer conditions comprising 50 mM Tris buffer pH
7.5, 50 mM NaCl, 10 mM MgCl.sub.2, 0.5 mM MnCl.sub.2. In some
embodiments, 0.3% BSA and/or 0.05% Tween20 can be included in the
reaction mix. In some embodiments, the reaction mix is further
supplemented with 2 mM DTT and/or single stranded binding protein
(SSBP) at a concentration of 100 .mu.g/ml. Alternatively, the
polymerase reaction can be performed using buffer conditions
comprising 50 mM Tris pH 8.0, 50 mM NaCl and 10 mM MgCl.sub.2. In
some embodiments, divalent cations, such as calcium, can be added
to the polymerase reaction in an amount sufficient to block further
nucleotide incorporation. See, e.g., U.S. Provisional Application
61/242,762, filed Sep. 15, 2009.
[0529] In some embodiments, a suitable primer is included in the
nucleic acid polymerase reaction. The primer length is typically
determined by the specificity desired for binding the complementary
template as well as the stringency of the annealing and reannealing
conditions employed. The primer can be, synthetic, or produced
naturally by primases, RNA polymerases, or other oligonucleotide
synthesizing enzymes. The primer can be any suitable length
including at least 5 nucleotides, 5 to 10, 15, 20, 25, 50, 75, 100
nucleotides or longer in length. In some embodiments, the
polymerase extends the primer by a plurality of nucleotides. In
some embodiments, the primer is extended at least 50, 100, 250,
500, 1000, or at least 2000 nucleotide monomers. Alternatively, the
initiation site for nucleotide polymerization can be created
through any suitable means without requiring use of a primer. For
example, the polymer to be sequenced can comprise, or be associated
with, a polymerase priming site capable of extension via
polymerization of monomers by the polymerase. The priming site can
be generated, for example, by treatment of the polymer so as to
produce nicks or cleavage sites. Yet another option is for the
target polymer to undergo "hairpin" formation, either through
annealing to a self-complementary region within the target sequence
itself or through ligation to a self-complementary sequence,
resulting in a structure that undergoes self-priming under suitable
conditions. Alternatively, the priming can be facilitated through
the use of various accessory proteins known to facilitate priming
of DNA synthesis by a given polymerase, such as the terminal
protein of Phi-29 DNA polymerase and/or B103 DNA polymerase. See,
e.g., M. Salas, "Protein-priming of DNA replication", Ann. Rev.
Biochem. 60:39-71 (1991).
[0530] In some embodiments, the labeled nucleotide is a nucleotide
analog comprising a label linked to the base, sugar, phosphate or
any other portion of the nucleotide analog. In some embodiments,
the nucleotide can also comprise a blocking group that inhibits,
slows down or blocks further incorporation of nucleotides onto the
end of the nucleic acid molecule until the blocking group is
removed from the nucleotide. In some embodiments, the blocking
group can be removed from the nucleotide by exposure to chemical,
enzymatic, or photocleaving agents. In some embodiments, the method
further includes the step of adding one or more divalent cations to
the polymerase reaction mixture in an amount sufficient for
inhibiting further incorporation of nucleotides onto the end of the
nucleic acid molecule by the modified polymerase. Such methods are
described, for example, in U.S. Provisional Application No.
61/242,762, filed Sep. 15, 2009; and U.S. Provisional Application
No. 61/184,774, filed on Jun. 5, 2009.
[0531] In some embodiments, the methods, compositions, systems
and/or kits disclosed herein can involve the use of one or more
moieties capable of undergoing energy transfer, for example
resonance energy transfer (RET). Such energy transfer moieties can
include resonance energy transfer donors and acceptors. The energy
transfer moieties can be linked to the solid surfaces,
nanoparticles, polymerases, nucleotides, target nucleic acid
molecules, primers, and/or oligonucleotides.
[0532] In one aspect, the energy transfer moiety can be an energy
transfer donor. For example, the energy transfer donor can be a
nanoparticle or an energy transfer donor moiety (e.g., fluorescent
dye). In another aspect, the energy transfer moiety can be an
energy transfer acceptor. For example, the energy transfer acceptor
can be an energy acceptor dye. In another aspect, the energy
transfer moiety can be a quencher moiety.
[0533] In one aspect, the energy transfer pair can be linked to the
same molecule. For example, the energy transfer donor and acceptor
pair can be linked to a single polymerase, which can provide
detection of conformational changes in the polymerase. In another
aspect, the donor and acceptor can be linked to different molecules
in any combination. For example, the donor can be linked to the
polymerase, target molecule, or primer molecule, and/or the
acceptor can be linked to the nucleotide, the target molecule, or
the primer molecule.
[0534] The energy transfer donor is capable of absorbing
electromagnetic energy (e.g., light) at a first wavelength and
emitting excitation energy in response. The energy acceptor is
capable of absorbing excitation energy emitted by the donor and
fluorescing at a second wavelength in response.
[0535] The donor and acceptor moieties can interact with each other
physically or optically in a manner which produces a detectable
signal when the two moieties are in proximity with each other. A
proximity event includes two different moieties (e.g., energy
transfer donor and acceptor) approaching each other, or associating
with each other, or binding each other.
[0536] The donor and acceptor moieties can transfer energy in
various modes, including: fluorescence resonance energy transfer
(FRET) (L. Stryer 1978 Ann. Rev. Biochem. 47: 819-846; Schneider,
U.S. Pat. No. 6,982,146; Hardin, U.S. Pat. No. 7,329,492; Hanzel
U.S. published patent application No. 2007/0196846), scintillation
proximity assays (SPA) (Hart and Greenwald 1979 Molecular
Immunology 16:265-267; U.S. Pat. No. 4,658,649), luminescence
resonance energy transfer (LRET) (G. Mathis 1995 Clin. Chem.
41:1391-1397), direct quenching (Tyagi et al, 1998 Nature
Biotechnology 16:49-53), chemiluminescence energy transfer (CRET)
(Campbell and Patel 1983 Biochem. Journal 216:185-194),
bioluminescence resonance energy transfer (BRET) (Y. Xu, et al.,
1999 Proc. Natl. Acad. Sci. 96:151-156), and excimer formation (J.
R. Lakowicz 1999 "Principles of Fluorescence Spectroscopy", Kluwer
Academic/Plenum Press, New York).
[0537] In one exemplary embodiment, the energy transfer moieties
can be a FRET donor/acceptor pair. FRET is a distance-dependent
radiationless transmission of excitation energy from a first
moiety, referred to as a donor moiety, to a second moiety, referred
to as an acceptor moiety. Typically, the efficiency of FRET energy
transmission is dependent on the inverse sixth-power of the
separation distance between the donor and acceptor, r. For a
typical donor-acceptor pair, r can vary between approximately
10-100 Angstroms. FRET is useful for investigating changes in
proximity between and/or within biological molecules. In some
embodiments, FRET efficiency may depend on donor-acceptor distance
r as 1/r.sup.6 or 1/r.sup.4. The efficiency of FRET energy transfer
can sometimes be dependent on energy transfer from a point to a
plane which varies by the fourth power of distance separation (E.
Jares-Erijman, et al., 2003 Nat. Biotechnol. 21:1387). The distance
where FRET efficiency is at 50% is termed R.sub.0, also know as the
Forster distance. R.sub.0 can be unique for each donor-acceptor
combination and can range from between about 5 nm to about 10 nm. A
change in fluorescence from a donor or acceptor during a FRET event
(e.g., increase or decrease in the signal) can be an indication of
proximity between the donor and acceptor.
[0538] FRET efficiency (E) can be defined as the quantum yield of
the energy transfer transition, i.e. the fraction of energy
transfer event occurring per donor excitation event. It is a direct
measure of the fraction of photon energy absorbed by the donor
which is transferred to an acceptor, as expressed in Equation 1:
E=k.sub.ET/k.sub.f+k.sub.ET+.SIGMA.k.sub.i where k.sub.ET is the
rate of energy transfer, k.sub.f the radiative decay rate and the
k.sub.i are the rate constants of any other de-excitation
pathway.
[0539] FRET efficiency E generally depends on the inverse of the
sixth power of the distance r (nm) between the two fluorophores
(i.e., donor and acceptor pair), as expressed in Equation 2:
E=1/1+(r/R.sub.0).sup.6.
[0540] Therefore, the FRET efficiency of a donor describes the
maximum theoretical fraction of photon energy which is absorbed by
the donor (i.e., nanoparticle) and which can then be transferred to
a typical organic dye (e.g., fluoresceins, rhodamines, cyanines,
etc.).
[0541] In biological applications, FRET can provide an on-off type
signal indicating when the donor and acceptor moieties are proximal
(e.g., within R.sub.0) of each other. Additional factors affecting
FRET efficiency include the quantum yield of the donor, the
extinction coefficient of the acceptor, and the degree of spectral
overlap between the donor and acceptor. Procedures are well known
for maximizing the FRET signal and detection by selecting high
yielding donors and high absorbing acceptors with the greatest
possible spectral overlap between the two (D. W. Piston and G. J.
Kremers 2007 Trends Biochem. Sci. 32:407). Resonance energy
transfer may be either an intermolecular or intramolecular event.
Thus, the spectral properties of the energy transfer pair as a
whole, change in some measurable way if the distance and/or
orientation between the moieties are altered.
[0542] The production of signals from FRET donors and acceptors can
be sensitive to the distance between donor and acceptor moieties,
the orientation of the donor and acceptor moieties, and/or a change
in the environment of one of the moieties (Deuschle et al. 2005
Protein Science 14: 2304-2314; Smith et al. 2005 Protein Science
14:64-73). For example, a nucleotide linked with a FRET moiety
(e.g., acceptor) may produce a detectable signal when it
approaches, associates with, or binds a polymerase linked to a FRET
moiety (e.g., donor). In another example, a FRET donor and acceptor
linked to one protein can emit a FRET signal upon conformational
change of the protein. Some FRET donor/acceptor pairs exhibit
changes in absorbance or emission in response to changes in their
environment, such as changes in pH, ionic strength, ionic type
(NO.sub.2, Ca.sup.+2, Mg.sup.+2, Zn.sup.+2, Na.sup.+, Cl.sup.-,
K.sup.+), oxygen saturation, and solvation polarity.
[0543] The FRET donor and/or acceptor may be a fluorophore,
luminophore, chemiluminophore, bioluminophore, or quencher (P.
Selvin 1995 Methods Enzymol 246:300-334; C. G. dos Remedios 1995 J.
Struct. Biol. 115:175-185; P. Wu and L. Brand 1994 Anal Biochem
218:1-13).
[0544] In some embodiments, the energy transfer moieties may not
undergo FRET, but may undergo other types of energy transfer with
each other, including luminescence resonance energy transfer,
bioluminescence resonance energy transfer, chemiluminescence
resonance energy transfer, and similar types of energy transfer not
strictly following the Forster's theory, such as the
non-overlapping energy transfer when non-overlapping acceptors are
utilized (Laitala and Hemmila 2005 Anal. Chem. 77: 1483-1487).
[0545] In one embodiment, the modified polymerases as provided
herein can be linked to an energy transfer moiety, for example an
energy transfer donor moiety. In another embodiment, the nucleotide
can be linked to an energy transfer acceptor moiety. For example,
in one embodiment the nucleotide comprises a polyphosphate chain
and an energy transfer moiety linked to the terminal phosphate
group of the polyphosphate chain. A change in a fluorescent signal
can occur when the labeled nucleotide is proximal to the labeled
polymerase.
[0546] In one embodiment, when an acceptor-labeled nucleotide is
proximal to a donor-labeled modified polymerase as provided herein,
the signal emitted by the donor moiety decreases. In another
embodiment, when the acceptor-labeled nucleotide is proximal to the
donor-labeled polymerase, the signal emitted by the acceptor moiety
increases. In another embodiment, a decrease in donor signal and
increase in acceptor signal correlates with nucleotide binding to
the polymerase and/or correlates with polymerase-dependent
nucleotide incorporation.
[0547] Quenchers
[0548] In some embodiments, the energy transfer moiety can be a
FRET quencher. Typically, quenchers have an absorption spectrum
with large extinction coefficients, however the quantum yield for
quenchers is reduced, such that the quencher emits little to no
light upon excitation. Quenching can be used to reduce the
background fluorescence, thereby enhancing the signal-to-noise
ratio. In one aspect, energy transferred from the donor may be
absorbed by the quencher which emits moderated (e.g., reduced)
fluorescence. In another aspect, the acceptor can be a
non-fluorescent chromophore which absorbs the energy transferred
from the donor and emits heat (e.g., the energy acceptor is a dark
quencher).
[0549] For an example, a quencher can be used as an energy acceptor
with a nanoparticle donor in a FRET system, see I. L. Medintz, et
al., 2003 Nature Materials 2:630. One exemplary method of primer
extension using the modified polymerases of the present disclosure
involves the use of quenchers in conjunction with reporters
comprising fluorescent reporter moieties. In this strategy, certain
nucleotides in the reaction mixture are labeled with a reporter
comprising a fluorescent label, while the remaining nucleotides are
labeled with one or more quenchers. Alternatively, each of the
nucleotides in the reaction mixture is labeled with one or more
quenchers. Discrimination of the nucleotide bases is based on the
wavelength and/or intensity of light emitted from the FRET
acceptor, as well as the intensity of light emitted from the FRET
donor. If no signal is detected from the FRET acceptor, a
corresponding reduction in light emission from the FRET donor
indicates incorporation of a nucleotide labeled with a quencher.
The degree of intensity reduction may be used to distinguish
between different quenchers.
[0550] Examples of fluorescent donors and non-fluorescent acceptor
(e.g., quencher) combinations have been developed for detection of
proteolysis (Matayoshi 1990 Science 247:954-958) and nucleic acid
hybridization (L. Morrison, in: Nonisotopic DNA Probe Techniques,
ed., L. Kricka, Academic Press, San Diego, (1992) pp. 31 1-352; S.
Tyagi 1998 Nat. Biotechnol. 16:49-53; S. Tyagi 1996 Nat.
Biotechnol. 14:947-8). FRET donors, acceptors and quenchers can be
moieties which absorb electromagnetic energy (e.g., light) at about
300-900 nm, or about 350-800 nm, or about 390-800 nm.
[0551] Materials for Energy Transfer Moieties
[0552] Energy transfer donor and acceptor moieties can be made from
materials which typically fall into four general categories (see
the review in: K. E. Sapford, et al., 2006 Angew. Chem. Int. Ed.
45:4562-4588), including: (1) organic fluorescent dyes, dark
quenchers and polymers (e.g., dendrimers); (2) inorganic material
such as metals, metal chelates and semiconductors nanoparticles;
(3) biomolecules such as proteins and amino acids (e.g., green
fluorescent protein and derivatives thereof); and (4) enzymatically
catalyzed bioluminescent molecules. The material for making the
energy transfer donor and acceptor moieties can be selected from
the same or different categories.
[0553] The FRET donor and acceptor moieties which are organic
fluorescent dyes, quenchers or polymers can include traditional
dyes which emit in the UV, visible, or near-infrared region. The UV
emitting dyes include coumarin-, pyrene-, and naphthalene-related
compounds. The visible and near-infrared dyes include xanthene-,
fluorescein-, rhodol-, rhodamine-, and cyanine-related compounds.
The fluorescent dyes also includes DDAO
((7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one)),
resorufin, ALEXA FLUOR and BODIPY dyes (both Molecular Probes),
HILYTE Fluors (AnaSpec), ATTO dyes (Atto-Tec), DY dyes (Dyomics
GmbH), TAMRA (Perkin Elmer), tetramethylrhodamine (TMR), TEXAS RED,
DYLIGHT (Thermo Fisher Scientific), FAM (AnaSpec), JOE and ROX
(both Applied Biosystems), and Tokyo Green.
[0554] Additional fluorescent dyes which can be used as quenchers
includes: DNP, DABSYL, QSY (Molecular Probes), ATTO (Atto-Tec), BHQ
(Biosearch Technologies), QXL (AnaSpec), BBQ (Berry and Associates)
and CY5Q/7Q (Amersham Biosciences).
[0555] The FRET donor and acceptor moieties which comprise
inorganic materials include gold (e.g., quencher), silver, copper,
silicon, semiconductor nanoparticles, and fluorescence-emitting
metal such as a lanthanide complex, including those of Europium and
Terbium.
[0556] Suitable FRET donor/acceptor pairs include: FAM as the donor
and JOE, TAMRA, and ROX as the acceptor dyes. Other suitable pairs
include: CYA as the donor and R6G, TAMRA, and ROX as the donor
dyes. Other suitable donor/acceptor pairs include: a nanoparticle
as the donor, and ALEXA FLUORS dyes (e.g., 610, 647, 660, 680,
700). DYOMICS dyes, such as 634 and 734 can be used as energy
transfer acceptor dyes.
[0557] In some embodiments, the energy transfer moieties undergo
RET, (for example, FRET) that is characterized by the generation of
a signal, herein termed a RET or FRET signal, as the case may be.
The RET or FRET signal can be an optically detectable signal, for
example, an increase in acceptor fluorescence or a decrease in
donor fluorescence.
[0558] In some embodiments, the modified polymerase as provided
herein is linked to a FRET donor and contacted with one or more
labeled nucleotide analogs, wherein the label of the one or more
labeled nucleotides comprises a FRET acceptor. In some embodiments,
interaction of the labeled nucleotide with the labeled polymerase
(occurring, for example, in association with a productive
incorporation, a non-productive incorporation or during association
of a nucleotide with the potymerase active site) results in the
emission of a FRET signal. The FRET signal can optionally be
detected and analyzed to determine the occurrence of a
polymerase-nucleotide interaction.
[0559] Typically, the one or more signals indicative of
polymerase-nucleotide interaction are one or more FRET signals
resulting from FRET between the label of the modified polymerase
and the label of an incorporating nucleotide. The FRET can occur
prior to, during or after productive incorporation of the
nucleotide into a nucleic acid molecule. Alternatively, the FRET
can occur prior to binding of the nucleotide to the polymerase
active site, or while the nucleotide resides within the polymerase
active site, during a non-productive incorporation.
[0560] In some embodiments, the modified polymerase comprises a
FRET donor moiety and one or more nucleotides comprises a FRET
acceptor moiety. The FRET acceptor moiety can in some embodiments
be attached to, or comprise part of, the nucleotide sugar, the
nucleobase, or analogs thereof.
[0561] In some embodiments, at least one nucleotide of the
polymerase reaction is labeled with a nucleotide label. In some
embodiments, the nucleotide label is linked to the nucleotide using
a linker and/or spacer using suitable techniques. Any suitable
methods for labeling nucleotides can be employed including but not
limited to those described in U.S. Pat. Nos. 7,041,892, 7,052,839,
7,125,671 and 7,223,541; U.S. Pub. Nos. 2007/0072196 and
2008/0091005; Sood et al., 2005, J. Am. Chem. Soc. 127:2394-2395;
Arzumanov et al., 1996, J. Biol. Chem. 271:24389-24394; and Kumar
et al., 2005, Nucleosides, Nucleotides & Nucleic Acids,
24(5):401-408. Suitable labels that can be used in the disclosed
methods and linked to the polymerase or the nucleotides include any
molecule, nano-structure, or other chemical structure that capable
of being detected by a detection system, including but not limited
to fluorescent dyes.
[0562] In some embodiments, the nucleotide label is attached to a
portion of the nucleotide that is released upon incorporation of
the underlying nucleotide. For example, in some embodiments, the
nucleotide label is attached to a portion of the nucleotide that is
released upon incorporation of the underlying nucleotide, For
example, in some embodiments, the nucleotide comprises a
polyphosphate chain and the FRET acceptor is attached to a
phosphate group of the nucleotide that is cleaved and released upon
incorporation of the underlying nucleotide into the primer strand,
for example the .gamma.-phosphate, the .beta.-phosphate or some
other terminal phosphate of the incoming nucleotide. When this
acceptor-labeled nucleotide polyphosphate is incorporated by the
modified polymerase into a nucleic acid molecule, the polymerase
cleaves the bond between the alpha and beta phosphate, thereby
releasing a pyrophosphate moiety comprising the acceptor that
diffuses away. Thus, in these embodiments, a signal indicative of
nucleotide incorporation is generated through FRET between the
nanoparticle and the acceptor bonded to the gamma, beta or other
terminal phosphate as each incoming nucleotide is incorporated into
the newly synthesized strand. By cleavage of the terminal
phosphate(s) and release of the label upon incorporation of the
incoming nucleotide, the FRET signal from the label ceases after
the nucleotide is incorporated and the label diffuses away. By
releasing the label upon incorporation, successive incorporation of
labeled nucleotides can each be detected without interference from
nucleotides previously incorporated into the complementary
strand.
[0563] Alternatively, the nucleotide label can be linked to the
alpha (.alpha.) phosphate, the beta (.beta.) phosphate, another
internal phosphate, base, sugar or any other portion of the
nucleotide that typically becomes incorporated into the growing
nucleic acid molecule. Although such labels typically are typically
not cleaved and released during the incorporation process, and thus
become incorporated into the growing nucleic acid molecule, they
can optionally be removed and/or rendered inoperable via suitable
treatments, e.g., chemical cleavage, enzymatic cleavage and/or
photobleaching, later in the process. In some embodiments, the
portion of the nucleotide that remains in the extending nucleic
acid molecule after the label and/or blocking group is released or
otherwise removed is structurally similar or identical to the
portion incorporated from a natural nucleotide; alternatively, the
incorporated portion may contain structural or chemical elements
that are different from the incorporated portion of a natural
nucleotide.
[0564] In some embodiments, a signal indicative of nucleotide
incorporation is generated as each incoming nucleotide becomes
incorporated by the polymerase of the conjugate. In embodiments
where the nucleotide label is cleaved and released upon nucleotide
incorporation, successive extensions can each be detected without
interference from nucleotides previously incorporated into the
complementary strand.
[0565] In some embodiments, the nucleotide and nucleotide label are
linked using a linker. The linker can include multiple amino acid
residues (e.g., arginine) that serve as an intervening linker
between the nucleotide and the nucleotide label. For example, the
linker can comprise four arginine residues that connect a dye label
to a terminal phosphate group of the nucleotide.
[0566] In other embodiments, the label linked or attached to the
nucleotide can be a quencher. Quenchers are useful as acceptors in
FRET applications, because they produce a signal through the
reduction or quenching of fluorescence from the donor fluorophore.
For example, in a quencher-based system, illumination of the donor
fluorophore excites the donor, and if an appropriate acceptor is
not close enough to the donor, the donor fluoresces. This
fluorescence is reduced or abolished when a quencher is in
sufficient proximity to quench the donor, thereby reducing or
abolishing donor fluorescence. Thus, interaction or proximity
between a donor and quencher-acceptor can be detected by the
reduction or absence of donor fluorescence. For an example of the
use of a quencher as an acceptor with a nanoparticle donor, see,
e.g., Medintz, I. L. et al. (2003) Nat. Mater. 2:630. Examples of
quenchers include the QSY dyes available from Molecular Probes
(Eugene, Oreg.).
[0567] One exemplary method of primer extension using the modified
polymerases of the present disclosure involves the use of quenchers
in conjunction with fluorescent labels. In some embodiments,
certain nucleotides in the reaction mixture are labeled with a
fluorescent label, while the remaining nucleotides are labeled with
one or more quenchers. Alternatively, each of the nucleotides in
the reaction mixture is labeled with one or more quenchers.
Discrimination of the nucleotide bases is based on the wavelength
and/or intensity of light emitted from the FRET acceptor, as well
as the intensity of light emitted from the FRET donor. If no signal
is detected from the FRET acceptor, a corresponding reduction in
light emission from the FRET donor indicates incorporation of a
nucleotide labeled with a quencher. The degree of intensity
reduction can be used to distinguish between different
quenchers.
[0568] Typically, the label of the modified polymerase and/or the
label of the nucleotide will be selected and/or designed to
minimize any adverse effect of such labels on the progress of the
polymerization reaction as determined by speed, error rate,
fidelity, processivity and average read length of the newly
synthesized strand.
[0569] In some embodiments, the nucleotide can comprise a moiety
that alters the functional properties of the nucleotide. For
example, the moiety can interfere or impede the ability of the
nucleotide to enter the polymerase active site, become released
from the polymerase active site following incorporation of the
nucleotide onto the end of an extending nucleic acid molecule, or
become covalently linked to the end of the extending nucleic acid
molecule. In some embodiments, the moiety can affect the kinetic
properties of the nucleotide, such as, for example, modify the
K.sub.m, V.sub.max, residence time or branching ratio of the
nucleotide with one or more polymerases of the present
disclosure.
[0570] In some embodiments, the nucleotide is a labeled analog of a
naturally occurring nucleotide. The label can be an optically
detectable label. For example, the label can be a photoluminescent,
chemiluminescent, bioluminescent, fluorescent or fluorogenic
moiety. The label can be a mass tag or molecular volume tag. In
some embodiments, the label is a FRET moiety. In some embodiments,
the identity of the label correlates with the base identity of the
nucleotide. In some embodiments, the label is capable of emitting a
signal that correlates with the base identity of the nucleotide. In
some embodiments, the label of the labeled nucleotide is a
chromophore, fluorophore or luminophore. In some embodiments, the
label of the labeled nucleotide can be a fluorophore or fluorogen
selected from the group consisting of: xanthine dye, fluorescein,
cyanine, rhodamine, coumarin, acridine, Texas Red dye, BODIPY,
ALEXA (Molecular Probes/Invitrogen, Life Technologies Corp.), GFP,
and a derivative or modification of any of the foregoing. Some
examples of suitable labels are described, for example, in
International (PCT) Published Application No. WO/2008/030115;
Haugland, Molecular Probes Handbook, (Eugene, Oreg.) 6th Edition;
The Synthegen catalog (Houston, Tex.), Lakowicz, Principles of
Fluorescence Spectroscopy, 2nd Ed., Plenum Press New York (1999),
all of which are incorporated herein by reference in their
entireties.
[0571] In some embodiments, incorporation of the nucleotide into an
extending nucleic acid molecule by a polymerase can generate a
nucleic acid molecule comprising non-standard moieties, i.e.,
moieties that are not typically present in naturally occurring
nucleic acid molecules. For example, the synthesized nucleic acid
molecule may comprise one or more labels and/or include one or more
atoms, for example sulfur or boron atoms, not typically present in
naturally occurring nucleic acid molecules. In some embodiments,
the label is linked to a base, sugar or phosphate moiety of the
nucleotide via a linker.
[0572] The primer extension and/or single molecule sequencing
methods using the modified polymerases of the present disclosure
can be practiced using nucleotides. In some embodiments, the
nucleotide can comprise a moiety that facilitates purification or
detectability of the nucleotide. In some embodiments, the moiety is
a label. The label can in some embodiments be linked to a base,
sugar or phosphate moiety. In some embodiments, the nucleotide is a
nucleotide polyphosphate and the label is linked to the terminal
phosphate of the nucleotide polyphosphate.
[0573] In some embodiments the nucleotides can be linked with at
least one energy transfer moiety. The energy transfer moiety can be
an energy transfer acceptor moiety. The different types of
nucleotides (e.g., adenosine, thymidine, cytidine, guanosine, and
uridine) can be labeled with different energy transfer acceptor
moieties so that the detectable signals from each of the different
types of nucleotides can be distinguishable to permit base
identity. The nucleotides can be labeled in a way that does not
interfere with the events of polymerization. For example the
attached energy transfer acceptor moiety does not interfere with
nucleotide binding and/or does not interfere with nucleotide
incorporation and/or does not interfere with cleavage of the
phosphodiester bonds and/or does not interfere with release of the
polyphosphate product. See for example, U.S. Ser. No. 61/164,091,
Ronald Graham, filed Mar. 27, 2009. See for example U.S. Pat. Nos.
7,041,812, 7,052,839, 7,125,671, and 7,223,541; U.S. Pub. Nos.
2007/0072196 and 2008/0091005; Sood et al., 2005, J. Am. Chem. Soc.
127:2394-2395; Arzumanov et al., 1996, J. Biol. Chem.
271:24389-24394; and Kumar et al., 2005, Nucleosides, Nucleotides
& Nucleic Acids, 24(5):401-408.
[0574] In one aspect, the energy transfer acceptor moiety may be
linked to any position of the nucleotide.
[0575] For example, the energy transfer acceptor moiety can be
linked to any phosphate group (or derivatized phosphate group), the
sugar or the base. In another example, the energy transfer moiety
can be linked to any phosphate group (or derivatized phosphate
group) which is released as part of a phosphate cleavage product
upon incorporation. In yet another example, the energy transfer
acceptor moiety can be linked to the terminal phosphate group (or
derivatized phosphate group). In another aspect, the nucleotide may
be linked with an additional energy transfer acceptor moiety, so
that the nucleotide is attached with two or more energy transfer
acceptor moieties. The additional energy transfer acceptor moiety
can be the same or different as the first energy transfer acceptor
moiety. In one embodiment, the energy transfer acceptor moiety can
be a FRET acceptor moiety.
[0576] In one aspect, the nucleotide may be linked with a reporter
moiety which is not an energy transfer moiety. For example, the
reporter moiety can be a fluorophore.
[0577] In one aspect, the energy transfer acceptor moieties and/or
the reporter moiety can be attached to the nucleotide via a linear
or branched linker moiety. An intervening linker moiety can connect
the energy transfer acceptor moieties with each other and/or to the
reporter moiety, any combination of linking arrangements.
[0578] In another aspect, the nucleotides comprise a sugar moiety,
base moiety, and at least three, four, five, six, seven, eight,
nine, ten, or more phosphate groups linked to the sugar moiety by
an ester or phosphoramide linkage. The phosphates can be linked to
the 3' or 5' C of the sugar moiety. The nucleotides can be
incorporated and/or polymerized into a growing nucleic acid strand
by a naturally occurring, modified, or engineered nucleic acid
dependent polymerase.
[0579] In one aspect, different linkers can be used to operably
link the different nucleotides (e.g., A, G, C, or T/U) to the
energy transfer moieties or reporter moieties. For example,
adenosine nucleotide can be attached to one type of energy transfer
moiety using one type of linker, and guanosine nucleotide can be
linked to a different type of energy transfer moiety using a
different type of linker. In another example, adenosine nucleotide
can be attached to one type of energy transfer moiety using one
type of linker, and the other types of nucleotides can be attached
to different types of energy transfer moieties using the same type
of linker. One skilled in the art will appreciate that many
different combinations of nucleotides, energy transfer moieties,
and linkers are possible.
[0580] In one aspect, the distance between the nucleotide and the
energy transfer moiety can be altered. For example, the linker
length and/or number of phosphate groups can lengthen or shorten
the distance from the sugar moiety to the energy transfer moiety.
In another example, the distance between the nucleotide and the
energy transfer moiety can differ for each type of nucleotide
(e.g., A, G, C, or T/U).
[0581] In another aspect, the number of energy transfer moieties
which are linked to the different types of nucleotides (e.g., A, G,
C, or T/U) can be the same or different. For example: A can have
one dye, and G, C, and T have two; A can have one dye, C has two, G
has three, and T has four; A can have one dye, C and G have two,
and T has four. One skilled in the art will recognize that many
different combinations are possible.
[0582] In another aspect, the concentration of the labeled
nucleotides used to conduct the nucleotide binding or nucleotide
incorporation reactions can be about 0.0001 nM-1 .mu.M, or about
0.0001 nM-0.001 nM, or about 0.001 nM-0.01 nM, or about 0.01 nM-0.1
nM, or about 0.1 nM-1.0 nM, or about 1 nM-25 nM, or about 25 nM-50
nM, or about 50 nM-75 nM, or about 75 nM-100 nM, or about 100
nM-200 nM, or about 200 nM-500 nM, or about 500 nM-750 nM, or about
750 nM-1000 nM, or about 0.1 .mu.M-20 .mu.M, or about 20 .mu.M-50
.mu.M, or about 50 .mu.M-75 .mu.M, or about 75 .mu.M-100 .mu.M, or
about 100 .mu.M-200 .mu.M, or about 200 .mu.M-500 .mu.M, or about
500 .mu.M-750 .mu.M, or about 750 .mu.M-1000 .mu.M.
[0583] In another aspect, the concentration of the different types
of labeled nucleotides, which are used to conduct the nucleotide
binding or incorporation reaction, can be the same or different
from each other.
[0584] Sugar Moieties
[0585] The nucleotides typically comprise suitable sugar moieties,
such as carbocyclic moieties (Ferraro and Gotor 2000 Chem. Rev.
100: 4319-48), acyclic moieties (Martinez, et al., 1999 Nucleic
Acids Research 27: 1271-1274; Martinez, et al., 1997 Bioorganic
& Medicinal Chemistry Letters vol. 7: 3013-3016), and other
suitable sugar moieties (Joeng, et al., 1993 J. Med. Chem. 36:
2627-2638; Kim, et al., 1993J. Med. Chem. 36: 30-7; Eschenmosser
1999 Science 284:2118-2124.; and U.S. Pat. No. 5,558,991). The
sugar moiety may be selected from the following: ribosyl,
2'-deoxyribosyl, 3'-deoxyribosyl, 2',3'-dideoxyribosyl,
2',3'-didehydrodideoxyribosyl, 2'-alkoxyribosyl, 2'-azidoribosyl,
2'-aminoribosyl, 2'-fluororibosyl, 2'-mercaptoriboxyl,
2'-alkylthioribosyl, 3'-alkoxyribosyl, 3'-azidoribosyl,
3'-aminoribosyl, 3'-fluororibosyl, 3'-mercaptoriboxyl,
3'-alkylthioribosyl carbocyclic, acyclic and other modified sugars.
In one aspect, the 3'-position has a hydroxyl group, for
strand/chain elongation.
[0586] Base Moieties
[0587] The nucleotides can include a hetero cyclic base which
includes substituted or unsubstituted nitrogen-containing parent
heteroaromatic ring which is commonly found in nucleic acids,
including naturally-occurring, substituted, modified, or engineered
variants. The base is capable of forming Watson-Crick and/or
Hoogstein hydrogen bonds with an appropriate complementary base.
Exemplary bases include, but are not limited to, purines and
pyrimidines such as: 2-aminopurine, 2,6-diaminopurine, adenine (A),
ethenoadenine, N.sup.6-.DELTA..sup.2-isopentenyladenine (6iA),
N.sup.6-.DELTA..sup.2-isopentenyl-2-methylthioadenine (2 ms6iA),
N.sup.6-methyladenine, guanine (G), isoguanine,
N.sup.2-dimethylguanine (dmG), 7-methylguanine (7mG),
2-thiopyrimidine, 6-thioguanine (6sG), hypoxanthine and
O.sup.6-methylguanine; 7-deaza-purines such as 7-deazaadenine
(7-deaza-A) and 7-deazaguanine (7-deaza-G); pyrimidines such as
cytosine (C), 5-propynylcytosine, isocytosine, thymine (T),
4-thiothymine (4sT), 5,6-dihydrothymine, O.sup.4-methylthymine,
uracil (U), 4-thiouracil (4sU) and 5,6-dihydrouracil
(dihydrouracil; D); indoles such as nitroindole and 4-methylindole;
pyrroles such as nitropyrrole; nebularine; inosines;
hydroxymethylcytosines; 5-methycytosines; base (Y); as well as
methylated, glycosylated, and acylated base moieties; and the like.
Additional exemplary bases can be found in Fasman, 1989, in:
Practical Handbook of Biochemistry and Molecular Biology, pp.
385-394, CRC Press, Boca Raton, Fla., and the references cited
therein.
[0588] Examples of nucleotides include ribonucleotides,
deoxyribonucleotides, modified ribonucleotides, modified
deoxyribonucleotides, ribonucleotides, deoxyribonucleotides,
modified ribonucleotides, modified deoxyribonucleotides, peptide
nucleotides, modified peptide nucleotides, metallonucleosides,
phosphonate nucleosides, and modified phosphate-sugar backbone
nucleotides, and any variants of the foregoing.
[0589] Phosphate Groups
[0590] The nucleotides can optionally include phosphate groups
which can be linked to the 2', 3' and/or 5' position of the sugar
moiety. The phosphate groups include analogs, such as
phosphoramidate, phosphorothioate, phosphorodithioate, and
O-methylphosphoroamidite groups. In one embodiment, at least one of
the phosphate groups can be substituted with a fluoro and/or chloro
group. The phosphate groups can be linked to the sugar moiety by an
ester or phosphoramide linkage. Typically, the nucleotide comprises
three, four, five, six, seven, eight, nine, ten, or more phosphate
groups linked to the 5' position of the sugar moiety.
[0591] In some embodiments, the primer extension and single
molecule sequencing methods using the modified polymerases provided
herein can be practiced using any nucleotide which can be
incorporated by a polymerase, including naturally-occurring or
recombinant polymerases. In one embodiment, the nucleotides can
include a nucleoside linked to a chain of 1-10 phosphorus atoms.
The nucleoside can include a base (or base analog) linked to a
sugar (or sugar analog). The phosphorus chain can be linked to the
sugar, for example linked to the 5' position of the sugar. The
phosphorus chain can be linked to the sugar with an intervening O
or S. In one embodiment, one or more phosphorus atoms in the chain
can be part of a phosphate group having P and O. In another
embodiment, the phosphorus atoms in the chain can be linked
together with intervening O, NH, S, methylene, substituted
methylene, ethylene, substituted ethylene, CNH.sub.2, C(O),
C(CH.sub.2), CH.sub.2CH.sub.2, or C(OH)CH.sub.2R (where R can be a
4-pyridine or 1-imidazole). In one embodiment, the phosphorus atoms
in the chain can have side groups having O, BH.sub.3, or S. In the
phosphorus chain, a phosphorus atom with a side group other than O
can be a substituted phosphate group. In the phosphorus chain,
phosphorus atoms with an intervening atom other than O can be a
substituted phosphate group. Some examples of nucleotides are
described in Xu, U.S. Pat. No. 7,405,281.
[0592] In some embodiments, the nucleotide is a dye-labeled
nucleotide that comprises a polyphosphate chain and a dye moiety
linked to the terminal phosphate group. In some embodiments, the
dye-labeled nucleotide comprises a dye moiety linked to the
terminal phosphate through an alkyl linker. Optionally, the linker
comprises a 6-carbon chain and has a reactive amine group, and the
dye moiety is linked to the terminal phosphate bond though a
covalent bond formed with the amine group of the linker. In some
embodiments, the polyphosphate chain comprises 4, 5, 6, 7, 8, 9, 10
or more phosphates. One exemplary dye-labeled nucleotide that can
be used in the disclosed methods and systems has the general
structure shown in FIG. 11. This structure includes a sugar bonded
to a hexaphosphate chain at the 5' carbon position, and to a
nucleotide base (denoted as "N"). The terminal phosphate group of
the hexaphosphate is linked to a 6-carbon linker, and the other end
of the 6-carbon linker is attached to a dye moiety (denoted as
"dye"), typically through an amide bond. In some embodiments, the
dye moiety can optionally comprise any one or more of the following
dyes: rhodols; resorufins; coumarins; xanthenes; acridines;
fluoresceins; rhodamines; erythrins; cyanins; phthalaldehydes;
naphthylamines; fluorescamines; benzoxadiazoles; stilbenes;
pyrenes; indoles; borapolyazaindacenes; quinazolinones; eosin;
erythrosin; Malachite green; CY dyes (GE Biosciences), including
Cy3 (and its derivatives) and Cy5 (and its derivatives); DYOMICS
and DYLIGHT dyes (Dyomics) including DY-547, DY-630, DY-631,
DY-632, DY-633, DY-634, DY-635, DY-647, DY-649, DY-652, DY-678,
DY-680, DY-682, DY-701, DY-734, DY-752, DY-777 and DY-782; Lucifer
Yellow; CASCADE BLUE; TEXAS RED; BODIPY (boron-dipyrromethene)
(Molecular Probes) dyes including BODIPY 630/650 and BODIPY
650/670; ATTO dyes (Atto-Tec) including ATTO 390, ATTO 425, ATTO
465, ATTO 610 611X, ATTO 610 (N-succinimidyl ester), ATTO 635 (NHS
ester); ALEXA FLUORS including ALEXA FLUOR 633, ALEXA FLUOR 647,
ALEXA FLUOR 660, ALEXA FLUOR 700, ALEXA FLUOR 750, and ALEXA FLUOR
680 (Molecular Probes); DDAO
(7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one or any
derivatives thereof) (Molecular Probes); QUASAR dyes (Biosearch);
IRDYES dyes (LiCor) including IRDYE 700DX (NHS ester), IRDYE
800RS(NHS ester) and IRDYE 800CW (NHS ester); EVOBLUE dyes (Evotech
Biosystems); JODA 4 dyes (Applied Biosystems); HILYTE dyes
(AnaSpec); MR121 and MR200 dyes (Roche); Hoechst dyes 33258 and
33242 (Invitrogen); FAIR OAKS RED (Molecular Devices); SUNNYVALE
RED (Molecular Devices); LIGHT CYCLER RED (Roche); EPOCH (Glen
Research) dyes including EPOCH REDMOND RED (phosphoramidate), EPOCH
YAKIMA YELLOW (phosphoramidate), EPOCH GIG HARBOR GREEN
(phosphoramidate); Tokyo green (M. Kamiya, et al., 2005 Angew.
Chem. Int. Ed. 44:5439-5441); and CF dyes including CF 647 and
CF555 (Biotium).
[0593] In some embodiments, such dye-labeled nucleotides can be
used to assay for the nucleotide incorporation kinetics of a
particular polymerase according to the procedures described herein
(see, e.g., Example 12).
[0594] Non-Hydrolyzable Nucleotides
[0595] The nucleotide binding and nucleotide incorporation methods
can be practiced using incorporatable nucleotides and
non-hydrolyzable nucleotides. In the presence of the incorporatable
nucleotides (e.g., labeled), the non-hydrolyzable nucleotides
(e.g., non-labeled) can compete for the polymerase binding site to
permit distinction between the complementary and non-complementary
nucleotides, or for distinguishing between productive and
non-productive binding events. In the nucleotide incorporation
reaction, the presence of the non-hydrolyzable nucleotides can
alter the length of time, frequency, and/or duration of the binding
of the labeled incorporatable nucleotides.
[0596] The non-hydrolyzable nucleotides can be non-labeled or can
be linked to a reporter moiety (e.g., energy transfer moiety). The
labeled non-hydrolyzable nucleotides can be linked to a reporter
moiety at any position, such as the sugar, base, or any phosphate
(or substituted phosphate group). For example, the non-hydrolyzable
nucleotides can have the general structure:
R.sub.11--(--P)--S--B
[0597] Where B can be a base moiety, such as a hetero cyclic base
which includes substituted or unsubstituted nitrogen-containing
heteroaromatic ring. Where S can be a sugar moiety, such as a
ribosyl, riboxyl, or glucosyl group. Where n can be 1-10, or more.
Where P can be one or more substituted or unsubstituted phosphate
or phosphonate groups. Where R.sub.11, if included, can be a
reporter moiety (e.g., a fluorescent dye). In one embodiment, the
non-hydrolyzable nucleotide having multiple phosphate or
phosphonate groups, the linkage between the phosphate or
phosphonate groups can be non-hydrolyzable by the polymerase. The
non-hydrolyzable linkages include, but are not limited to, amino,
alkyl, methyl, and thio groups. Non-hydrolyzable nucleotide
tetraphosphates having alpha-thio or alpha boreno substitutions
having been described (Rank, U.S. published patent application No.
2008/0108082; and Gelfand, U.S. published patent application No.
2008/0293071).
[0598] The phosphate or phosphonate portion of the non-hydrolyzable
nucleotide can have the general structure:
##STR00001##
[0599] Where B can be a base moiety and S can be a sugar moiety.
Where any one of the R.sub.1-R.sub.7 groups can render the
nucleotide non-hydrolyzable by a polymerase. Where the sugar C5
position can be CH.sub.2, CH.sub.2O, CH.dbd., CHR, or CH.sub.2
CH.sub.2. Where the R.sub.1 group can be O, S, CH.dbd., CH(CN), or
NH. Where the R.sub.2, R.sub.3, and R.sub.4, groups can
independently be O, BH.sub.3, or SH. Where the R.sub.5 and R.sub.6
groups can independently be an amino, alkyl, methyl, thio group, or
CHF, CF.sub.2, CHBr, CCl.sub.2, O--O, or --C.ident.C--. Where the
R.sub.7 group can be oxygen, or one or more additional phosphate or
phosphonate groups, or can be a reporter moiety. Where R.sub.8 can
be SH, BH.sub.3, CH.sub.3, NH.sub.2, or a phenyl group or phenyl
ring. Where R.sub.9 can be SH. Where R.sub.10 can be CH.sub.3,
N.sub.3CH.sub.2CH.sub.2, NH.sub.2, ANS, N.sub.3, MeO, SH, Ph, F,
PhNH, PhO, or RS (where Ph can be a phenyl group or phenyl ring,
and F can be a fluorine atom or group). The substituted groups can
be in the S or R configuration.
[0600] The non-hydrolyzable nucleotides can be alpha-phosphate
modified nucleotides, alpha-beta nucleotides, beta-phosphate
modified nucleotides, beta-gamma nucleotides, gamma-phosphate
modified nucleotides, caged nucleotides, or di-nucleotides.
[0601] Many examples of non-hydrolyzable nucleotides are known
(Rienitz 1985 Nucleic Acids Research 13:5685-5695), including
commercially-available ones from Jena Bioscience (Jena,
Germany).
[0602] In some embodiments, the nucleotide comprises a releasable
label and/or a releasable blocking group that can be removed via
suitable means prior to incorporation of the next nucleotide by the
polymerase into the newly synthesized strand. The use of releasably
labeled nucleotides wherein the label can be cleaved and removed
via suitable means have been described, for example, in U.S. Pub.
Nos. US2005/0244827 and US2004/0244827, as well as U.S. Pat. Nos.
7,345,159; 6,664,079; 7,345,159; and 7,223,568.
[0603] In some embodiments, the nucleotide is a nucleotide analog
that is capable of acting as a reversible terminator of nucleic
acid synthesis. Typically, reversible terminators can be
incorporated by a polymerase onto the end of an extending nucleic
acid molecule, but then "terminate" further synthesis by blocking
further addition of nucleotides. In some embodiments, this
"termination" capability can be manipulated by adjusting the
reaction conditions and/or by suitable treatment. The ability to
terminate can result from the presence of a moiety or group,
typically named a "blocking" group, which is linked to the
nucleotide. In some embodiments, the ability of the nucleotide
analog to terminate nucleic acid synthesis can be eliminated
through physical removal, cleavage, structural modification or
disruption of the blocking group. The blocking group can be
attached to any portion of the nucleotide analog including, for
example, a base moiety, sugar moiety or phosphate moiety. The
blocking group can be attached to the nucleotide analog via a
linker. The linkage between the blocking group and the nucleotide
analog can be a photocleavable, chemically cleavable, enzymatically
cleavable, thermocleavable (i.e., cleavable upon adjustment of
temperature) or pH-sensitive linkage. In some embodiments, the
label (which is linked to the nucleotide) is the blocking
group.
[0604] In some embodiments, the reversible terminator further
comprises a label or tag that facilitates detection of nucleotide
analog. The label can be a fluorescent label. In some embodiments,
the label can also be removed via suitable treatment. In some
embodiments, the label is released from the nucleotide analog
during incorporation of the nucleotide analog into the extending
nucleic acid molecule. Alternatively, the label becomes
incorporated into the extending nucleic acid molecule and is then
removed via suitable treatment. In some embodiments, the label is
attached to the nucleotide analog via a cleavable linkage. The
cleavable linkage can be a photocleavable, chemically cleavable,
enzymatically cleavable, thermocleavable (i.e., cleavable upon
adjustment of temperature) or pH-sensitive linkage.
[0605] The removal of the blocking group can be accomplished in a
variety of ways. In some embodiments, the blocking group is
attached to the nucleotide analog via a photocleavable linkage and
can be removed from the nucleotide analog via exposure to
photocleaving radiation. In some embodiments, the linkage is a
chemically or enzymatically cleavable linkage. In some embodiments,
the linkage can be disrupted by varying reaction conditions, e.g.,
pH, temperature, concentrations of divalent cations, etc.
[0606] Non-limiting examples of suitable reversible terminators
include, inter cilia, nucleotide base-labeled nucleotide analogs
comprising one or more blocking groups attached to 3' hydroxyl
group, the base moiety or a phosphate group. For example, the
nucleotide analog can comprise an azidomethyl group linked to the
3' hydroxyl group and a fluorescent label linked to the base of the
nucleotide analog. In some embodiments, the reversible terminator
can comprise one or more blocking groups attached to the phosphate
group. In some embodiments, the nucleotide analog can comprise a
blocking group and a label. In some embodiments, both the blocking
group and the label can be linked to the base moiety, while the 3'
hydroxyl group is not modified. In some embodiments, the blocking
group can be a photocleavable group linked to the base of the
nucleotide analog. See, e.g., U.S. Publication No. 2008/0132692,
published Jun. 5, 2008. Further examples of nucleotides comprising
extension blocking groups and methods of their use in
polymerase-based applications can be found, for example, in U.S.
Pat. No. 7,078,499 issued Jul. 18, 2006; as well as in U.S.
Published Application Nos. 2004/0048300 published Mar. 11, 2004;
2008/0132692 published Jun. 5, 2008; 2009/0081686, published Mar.
26, 2009; and 2008/0131952, published Jun. 5, 2008; Tsien,
WO/1991/006678; Stemple, U.S. Pat. No. 7,270,951, Balasubramanian,
U.S. Pat. No. 7,427,673; Milton, U.S. Pat. No. 7,541,444.
[0607] In some embodiments, the nucleotide analog comprises a
cleavable label linked to the base. In some embodiments, the
blocking group and the label can be removed via the same cleavage
treatment. See, e.g., U.S. Pat. No. 7,553,949, issued Jun. 30,
2009. Alternatively, different treatments can be required to remove
the blocking group and the label. In some embodiments, the label of
the reversible terminator correlates with the base identity of the
nucleotide analog. In some embodiments, each reversible terminator
is added sequentially to the polymerase reaction; alternatively,
different kinds of reversible terminators can be present
simultaneously in the reaction mixture.
[0608] In some embodiments, the blocking group is linked to the 2'
hydroxyl group of the sugar moiety. See, e.g., U.S. Pat. No.
7,553,949, issued Jun. 30, 2009.
[0609] In some embodiments, the reversible terminator can comprise
more than one blocking group. In some embodiments, these multiple
blocking groups may function cooperatively by enhancing the
termination efficiency of the nucleotide analog. In one exemplary
embodiment, the nucleotide analog comprises a blocking group linked
to the base moiety, while another group linked to the terminal
phosphate group further suppresses the incorporation of a
nucleotide analog onto the free 3' hydroxyl group. See, e.g., U.S.
patent application Ser. No. 12/355,487, filed Jan. 16, 2009.
[0610] Typically, the modified polymerases of the present
disclosure can be used to sequence one or more nucleic acid
molecules of interest using reversible terminators. In an exemplary
method, the reversible terminator is incorporated in a
template-dependent manner onto the 3' end of an extending nucleic
acid molecule by a modified polymerase. The incorporated reversible
terminator is detected and identified; and the blocking group of
the reversible terminator is then removed. In some embodiments, the
unincorporated reversible terminators can be washed away; in some
embodiments, it is not necessary to wash or otherwise remove the
unincorporated reversible terminators prior to detection,
identification or subsequent extension of the extending nucleic
acid molecule. In some embodiments, incorporation of the reversible
terminator onto the end of a nucleic acid molecule can involve the
formation of a covalent bond between the reversible terminator and
the nucleotide moiety at the 3' end of the nucleic acid molecule.
Alternatively, incorporation of reversible terminator onto the end
of a nucleic acid molecule will not involve formation of any
covalent bond between the reversible terminator and the nucleotide
moiety at the 3' end of the nucleic acid molecule; instead, the
reversible terminator is bound in a template-dependent fashion and
positioned within the active site of the polymerase until the
blocking group is cleaved or otherwise removed, following which the
remaining portion of the reversible terminator can remain as a
portion of the extending nucleic acid molecule or alternatively
will also dissociate from the polymerase active site and diffuse
away.
[0611] "Nanoparticle" may refer to any particle with at least one
major dimension in the nanosize range. In general, nanoparticles
can be made from any suitable metal (e.g., noble metals,
semiconductors, etc.) and/or non-metal atoms. Nanoparticles can
have different shapes, each of which can have distinctive
properties including spatial distribution of the surface charge;
orientation dependence of polarization of the incident light wave;
and spatial extent of the electric field. The shapes include, but
are not limited to: spheres, rods, discs, triangles, nanorings,
nanoshells, tetrapods, nanowires, etc.
[0612] In one embodiment, the nanoparticle can be a core/shell
nanoparticle which typically comprises a core nanoparticle
surrounded by at least one shell. For example, the core/shell
nanoparticle can be surrounded by an inner and outer shell. In
another embodiment, the nanoparticle is a core nanoparticle which
has a core but no surrounding shell. The outmost surface of the
core or shell can be coated with tightly associated ligands which
are not removed by ordinary solvation.
[0613] Examples of a nanoparticle include a nanocrystal, such as a
core/shell nanocrystal, plus any associated organic ligands (which
are not removed by ordinary solvation) or other materials which may
coat the surface of the nanocrystal. In one embodiment, a
nanoparticle has at least one major dimension ranging from about 1
to about 1000 nm. In other embodiments, a nanoparticle has at least
one major dimension ranging from about 1 to about 20 nm, about 1 to
about 15 nm, about 1 to about 10 nm or about 1 to 5 nm.
[0614] In some embodiments, a nanoparticle can have a layer of
ligands on its surface which can further be cross-linked to each
other. In some embodiments, a nanoparticle can have other or
additional surface coatings which can modify the properties of the
particle, for example, increasing or decreasing solubility in water
or other solvents. Such layers on the surface are included in the
term `nanoparticle.`
[0615] In one embodiment, nanoparticle can refer to a nanocrystal
having a crystalline core, or to a core/shell nanocrystal, and may
be about 1 nm to about 100 nm in its largest dimension, about 1 nm
to about 20 nm, about 1 nm to about 15 nm, about 1 nm to about 10
nm or preferably about 5 nm to about 10 nm in its largest
dimension. Small nanoparticles are typically less than about 20 nm
in their largest dimension.
[0616] "Nanocrystal" as used herein can refer to a nanoparticle
made out of an inorganic substance that typically has an ordered
crystalline structure. It can refer to a nanocrystal having a
crystalline core (core nanocrystal) or to a core/shell
nanocrystal.
[0617] A core nanocrystal is a nanocrystal to which no shell has
been applied. Typically, it is a semiconductor nanocrystal that
includes a single semiconductor material. It can have a homogeneous
composition or its composition can vary with depth inside the
nanocrystal.
[0618] A core/shell nanocrystal is a nanocrystal that includes a
core nanocrystal and a shell disposed over the core nanocrystal.
Typically, the shell is a semiconductor shell that includes a
single semiconductor material. In some embodiments, the core and
the shell of a core/shell nanocrystal are composed of different
semiconductor materials, meaning that at least one atom type of a
binary semiconductor material of the core of a core/shell is
different from the atom types in the shell of the core/shell
nanocrystal.
[0619] The semiconductor nanocrystal core can be composed of a
semiconductor material (including binary, ternary and quaternary
mixtures thereof), from: Groups II-VI of the periodic table,
including ZnS, ZnSe, ZnTe, CdS, CdSe, CdTe, HgS, HgSe, HgTe, MgTe;
Groups III-V, including GaN, GaP, GaAs, GaSb, InN, InP, InAs, InSb,
AlAs, AlP, AlSb, AlS; and/or Group IV, including Ge, Si, Pb.
[0620] The semiconductor nanocrystal shell can be composed of
materials (including binary, ternary and quaternary mixtures
thereof) comprising: ZnO, ZnS, ZnSe, ZnTe, CdO, CdS, CdSe, CdTe,
MgS, MgSe, GaAs, GaN, GaP, GaAs, GaSb, HgO, HgS, HgSe, HgTe, InAs,
InN, InP, InSb, AlAs, AlN, AlP, or AlSb.
[0621] Many types of nanocrystals are known, and any suitable
method for making a nanocrystal core and applying a shell to the
core may be employed. Nanocrystals can have a surface layer of
ligands to protect the nanocrystal from degradation in use or
during storage.
[0622] "Quantum dot" as used herein refers to a crystalline
nanoparticle made from a material which in the bulk is a
semiconductor or insulating material, which has a tunable
photophysical property in the near ultraviolet (UV) to far infrared
(IR) range.
[0623] "Water-soluble" or "water-dispersible" is used herein to
mean the item can be soluble or suspendable in an aqueous-based
solution, such as in water or water-based solutions or buffer
solutions, including those used in biological or molecular
detection systems as known by those skilled in the art. While
water-soluble nanoparticles are not truly `dissolved` in the sense
that term is used to describe individually solvated small
molecules, they are solvated (via hydrogen, electrostatic or other
suitable physical/chemical bonding) and suspended in solvents which
are compatible with their outer surface layer, thus a nanoparticle
which is readily dispersed in water is considered water-soluble or
water-dispersible. A water-soluble nanoparticle can also be
considered hydrophilic, since its surface is compatible with water
and with water solubility.
[0624] "Hydrophobic nanoparticle" as used herein refers to a
nanoparticle which is readily dispersed in or dissolved in a
water-immiscible solvent like hexanes, toluene, and the like. Such
nanoparticles are generally not readily dispersed in water.
[0625] "Hydrophilic" as used herein refers to a surface property of
a solid, or a bulk property of a liquid, where the solid or liquid
exhibits greater miscibility or solubility in a high-dielectric
medium than it does in a lower dielectric medium. By way of
example, a material which is more soluble in methanol than in a
hydrocarbon solvent such as decane would be considered
hydrophilic.
[0626] "Coordinating solvents" as used herein refers to a solvent
such as TDPA, OP, TOP, TOPO, carboxylic acids, and amines, which
are effective to coordinate to the surface of a nanocrystal.
`Coordinating solvents` also include phosphines, phosphine oxides,
phosphonic acids, phosphinic acids, amines, and carboxylic acids,
which are often used in growth media for nanocrystals, and which
form a coating or layer on the nanocrystal surface. Coordinating
solvents can exclude hydrocarbon solvents such as hexanes, toluene,
hexadecane, octadecene and the like, which do not have heteroatoms
that provide bonding pairs of electrons to coordinate with the
nanocrystal surface. Hydrocarbon solvents which do not contain
heteroatoms such as O, S, N or P to coordinate to a nanocrystal
surface are referred to herein as non-coordinating solvents. Note
that the term `solvent` is used in its ordinary way in these terms:
it refers to a medium which supports, dissolves or disperses
materials and reactions between them, but which does not ordinarily
participate in or become modified by the reactions of the reactant
materials. However, in certain instances, the solvent can be
modified by the reaction conditions. For example, TOP may be
oxidized to TOPO, or a carboxylic acid can be reduced to an
alcohol.
[0627] As used herein, the term "population" refers to a plurality
of nanoparticles having similar physical and/or optical properties.
`Population` can refer to a solution or structure with more than
one nanoparticle at a concentration suitable for single molecule
analysis. In some embodiments, the population can be monodisperse
and can exhibit less than at least 15% rms deviation in diameter of
the nanoparticles, and spectral emissions in a narrow range of no
greater than about 75 nm full width at half max (FWHM). In the
context of a solution, suspension, gel, plastic, or colloidal
dispersion of nanoparticles, the nature of the population can be
further characterized by the number of nanoparticles present, on
average, within a particular volume of the liquid or solid, or the
concentration. In a two-dimensional format such as an array of
nanoparticles adhered to a solid substrate, the concept of
concentration is less convenient than the related measure of
particle density, or the number of individual particles per
two-dimensional area. In this case, the maximum density would
typically be that obtained by packing particles
"shoulder-to-shoulder" in an array. The actual number of particles
in this case would vary due to the size of the particles--a given
array could contain a large number of small particles or a small
number of larger particles.
[0628] As used herein, the terms "moderate to high excitation"
refers to monochromatic illumination or excitation (e.g., laser
illumination) having a high power intensity sufficiently high such
that the absorbed, photons per second for a given sample is between
about 200,000 and about 1,600,000.
[0629] In one aspect, the nanoparticle is a semiconductor
nanoparticle having size-dependent optical and electronic
properties. For example, the nanoparticle can emit a fluorescent
signal in response to excitation energy. The spectral emission of
the nanoparticle can be tunable to a desired energy by selecting
the particle size, size distribution, and/or composition of the
semiconductor nanoparticle. For example, depending on the
dimensions, the semiconductor nanoparticle can be a fluorescent
nanoparticle which emits light in the UV-visible-IR spectrum. The
shell material can have a bandgap greater than the bandgap of the
core material.
[0630] In one aspect, the nanoparticle is an energy transfer donor.
The nanoparticle can be excited by an electromagnetic source such
as a laser beam, multi-photon excitation, or electrical excitation.
The excitation wavelength can range between about 190 to about 800
nm including all values and ranges there in between. In some
embodiments, the nanoparticle can be excited by an energy source
having a wavelength of about 405 nm. In other embodiments, in
response to excitation, the nanoparticle can emit a fluorescent
signal at about 400-800 nm, or about 605 nm.
[0631] In one aspect, the nanoparticle can undergo Raman scattering
when subjected to an electromagnetic source (incident photon
source) such as a laser beam. The scattered photons have a
frequency that is different from the frequency of the incident
photons. As result, the wavelength of the scattered photons is
different than the incident photon source. In one embodiment, the
nanoparticle can be attached to a suitable tag or label to enhance
the detectability of the nanoparticle via Raman spectroscopy. The
associated tag can be fluorescent or nonfluorescent. Such
approaches can be advantageous in avoiding problems that can arise
in the context of fluorescent nanoparticles, such as photobleaching
and blinking. See, e.g., Sun et al., "Surface-Enhanced Raman
Scattering Based Nonfluorescent Probe for Multiplex DNA Detection",
Anal. Chem. 79(11):3981-3988 (2007).
[0632] In one aspect, the nanoparticle is comprised of a
multi-shell layered core which is achieved by a sequential shell
material deposition process, where one shell material is added at a
time, to provide a nanoparticle having a substantially uniform
shell of desired thickness which is substantially free of defects.
The nanoparticle can be prepared by sequential, controlled addition
of materials to build and/or applying layers of shell material to
the core. See e.g., U.S. PCT Application Ser. No. PCT/US09/61951
which is incorporated herein by reference as if set forth in
full.
[0633] In another aspect, a method is provided for making a
nanoparticle comprising a core and a layered shell, where the shell
comprises at least one inner shell layer and at least one outer
shell layer. The method comprises the steps: (a) providing a
mixture comprising a core, at least one coordinating solvent; (b)
heating the mixture to a temperature suitable for formation of an
inner shell layer; (c) adding a first inner shell precursor
alternately with a second inner shell precursor in layer additions,
to form an inner shell layer which is a desired number of layers
thick; (d) heating the mixture to a temperature suitable for
formation of an outer shell layer; and (e) adding a first outer
shell precursor alternately with a second outer shell precursor in
layer additions, to form an outer shell layer which is a desired
number of layers thick. In one embodiment, if the coordinating
solvent of (a) is not amine, the method further comprises an amine
in (a).
[0634] In one aspect, at least one coordinating solvent comprises a
trialkylphosphine, a trialkylphosphine oxide, phosphonic acid, or a
mixture of these. In another aspect, at least one coordinating
solvent comprises trioctylphosphine (TOP), trioctylphosphine oxide
(TOPO), tetradecylphosphonic acid (TDPA), or a mixture of these. In
yet another aspect, the coordinating solvent comprises a primary or
secondary amine, for example, decylamine, hexadecylamine, or
dioctylamine.
[0635] In one aspect, the nanoparticle comprises a core comprising
CdSe. In another aspect, the nanoparticle shell can comprise YZ
wherein Y is Cd or Zn, and Z is S, or Se. In one embodiment, at
least one inner shell layer comprises CdS, and the at least one
outer shell layer comprises ZnS.
[0636] In one aspect, the first inner shell precursor is
Cd(OAc).sub.2 and the second inner shell precursor is
bis(trimethylsilyl)sulfide (TMS.sub.2S). In other aspects, the
first and second inner shell precursors are added as a solution in
trioctylphosphine (TOP). In other aspects, the first outer shell
precursor is diethylzinc (Et.sub.2Zn) and the second inner shell
precursor is dimethyl zinc (TMS.sub.2S). Sometimes, the first and
second outer shell precursors are added as a solution in
trioctylphosphine (TOP).
[0637] In one aspect, the nanoparticle can have ligands which coat
the surface. The ligand coating can comprise any suitable
compound(s) which provide surface functionality (e.g., changing
physicochemical properties, permitting binding and/or other
interaction with a biomolecule, etc.). In some embodiments, the
disclosed nanoparticle has a surface ligand coating (in direct
contact with the external shell layer) that adds various
functionalities which facilitate it being water-dispersible or
soluble in aqueous solutions. There are a number of suitable
surface coatings which can be employed to permit aqueous
dispersibility of the described nanoparticle. For example, the
nanoparticle(s) disclosed herein can comprise a core/shell
nanocrystal which is coated directly or indirectly with lipids,
phospholipids, fatty acids, polynucleic acids, polyethylene glycol
(PEG), primary antibodies, secondary antibodies, antibody
fragments, protein or nucleic acid based aptamers, biotin,
streptavidin, proteins, peptides, small organic molecules (e.g.,
ligands), organic or inorganic dyes, precious or noble metal
clusters. Specific examples of ligand coatings can include, but are
not limited to, amphiphilic polymer (AMP), bidentate thiols (i.e.,
DHLA), tridentate thiols, dipeptides, functionalized
organophosphorous compounds (e.g., phosphonic acids, phosphinic
acids), etc.
[0638] Non-Blinking Nanoparticles
[0639] Provided herein are nanoparticles which exhibit modulated,
reduced, or no intermittent (e.g., continuous, non-blinking)
fluorescence.
[0640] In one aspect, the nanoparticle or populations thereof
exhibit modulated, reduced or non-detectable intermittent (e.g.,
continuous, etc.) fluorescence properties. The nanoparticles can
have a stochastic blinking profile in a timescale which is shifted
to very rapid blinking or very slow or infrequent blinking relative
to a nanoparticle previously described in the art (conventional
nanoparticles are described in the art as having on-time fractions
of <0.2 in the best of conditions examined). For example, the
nanoparticles may blink on and off on a timescale which is too
rapid to be detected under the methods employed to study this
behavior.
[0641] In one aspect the nanoparticle or populations thereof are
photostable. The nanoparticles can exhibit a reduced or no
photobleaching with long exposure to moderate to high intensity
excitation source while maintaining a consistent spectral emission
pattern.
[0642] In one aspect, the nanoparticle or populations thereof have
a consistently high quantum yield. For example, the nanoparticles
can have a quantum yield greater than: about 10%, or about 20%, or
about 30%, or about 40%, or about 50%, or about 60%, or about 70%
or about 80%.
[0643] As used herein, fluorescence (or Forster) resonance energy
transfer (FRET) is a process by which a fluorophore (the donor) in
an excited state transfers its energy to a proximal molecule (the
acceptor) by nonradiative dipole-dipole interaction (Forster, T.
"Intermolecular Energy Migration and Fluorescence", Ann. Phys.,
2:55-75, 1948; Lakowicz, J. R., Principles of Fluorescence
Spectroscopy, 2nd ed. Plenum, New York. 367-394., 1999).
[0644] FRET efficiency (E) can be defined as the quantum yield of
the energy transfer transition, i.e. the fraction of energy
transfer event occurring per donor excitation event. It is a direct
measure of the fraction of photon energy absorbed by the donor
which is transferred to an acceptor, as expressed in Equation 1:
E=k.sub.ET/k.sub.f+k.sub.ET+.SIGMA.k.sub.i where k.sub.ET is the
rate of energy transfer, k.sub.f the radiative decay rate and the
k.sub.i are the rate constants of any other de-excitation
pathway.
[0645] FRET efficiency E generally depends on the inverse of the
sixth power of the distance r (nm) between the two fluorophores
(i.e., donor and acceptor pair), as expressed in Equation 2:
E=1/1+(r/R.sub.0).sup.6.
[0646] The distance where FRET efficiency is at 50% is termed
R.sub.0, also know as the Forster distance. R.sub.0 can be unique
for each donor-acceptor combination and can range from between
about 5 nm to about 10 nm. Therefore, the FRET efficiency of a
donor (i.e., nanoparticle) describes the maximum theoretical
fraction of photon energy which is absorbed by the donor (i.e.,
nanoparticle) and which can then be transferred to a typical
organic dye (e.g., fluoresceins, rhodamines, cyanines, etc.).
[0647] In some embodiments, the disclosed nanoparticles are
relatively small (i.e., <15 nm) and thus may be particularly
well suited to be used as a donor or an acceptor in a FRET
reaction. That is, some embodiments of the disclosed nanoparticles
exhibit higher FRET efficiency than conventional nanoparticles and
thus are excellent partners (e.g., donors or acceptors) in a FRET
reaction.
[0648] "Quantum yield" as used herein refers to the emission
efficiency of a given fluorophore assessed by the number of times
which a defined event, e.g., light emission, occurs per photon
absorbed by the system. In other words, a higher quantum yield
indicates greater efficiency and thus greater brightness of the
described nanoparticle or populations thereof.
[0649] Any suitable method can be used to measure quantum yield. In
one example, quantum yield can be obtained using standard methods
such as those described in Casper et al (Casper, J. V.; Meyer, T.
J. J. Am. Chem. Soc. 1983, 105, 5583) and can be analyzed relative
to known fluorophores chosen as appropriate for maximal overlap
between standard emission and sample emission (e.g., fluorescein,
Rhodamine 6G, Rhodamine 101). Dilute solutions of the standard and
sample can be matched or nearly matched in optical density prior to
acquisition of absorbance and emission spectra for both. The
emission quantum yield (.phi..sub.em) then can be determined
according to Equation 3:
.phi. em = .phi. em ' ( i i ' ) ( A ' A ) ##EQU00005##
[0650] where A and A' are the absorbances at the excitation
wavelength for the sample and the standard respectively and I and
I' are the integrated emission intensities for the sample and
standard respectively. In this case .phi.'.sub.em can be the agreed
upon quantum yield for the standard.
[0651] Disclosed herein are fluorescent nanoparticles with superior
and robust properties which significantly expand the applications
in which nanoparticles are useful. These nanoparticles are superior
and surprisingly robust in that they are simultaneously stable,
bright, and sensitive to environmental stimuli. Moreover, the
disclosed nanoparticles have limited or no detectable blinking
(i.e., where the nanoparticle emits light non-intermittently when
subject to excitation), are highly photostable, have a consistently
high quantum yield, are small (e.g., .ltoreq.20 nm) and can act as
a donor which undergoes FRET with a suitable acceptor moiety (e.g.,
fluorescent dyes, etc.). The photostability of these nanoparticles
is reflected in their exhibiting reduced or no photobleaching
(i.e., fading) behavior when subjected to moderate to high
intensity excitation for at least about 20 minutes. Additionally,
the particles can remain substantially free from photo-induced
color shifting.
[0652] Put another way, the nanoparticles can maintain a consistent
spectral emission pattern (i.e., maintain the ability to fluoresce)
even when exposed to a large quantity of photons (i.e., moderate to
high intensity excitation) for a long period of time. This unique
combination of characteristics makes these types of nanoparticles
sensitive tools for single molecule analysis and other sensitive
high throughput applications. Moreover, these properties make the
nanoparticles particularly well suited for use as highly efficient
donor fluorophores in energy transfer reactions such as FRET
reactions (i.e., high FRET efficiency) or other reactions as well
as applications which require or are enhanced by greater response
to the environment.
[0653] Without being bound to a particular theory, blinking or
fluorescence intermittency may arise during the nanoparticle
charging process when an electron is temporarily lost to the
surrounding matrix (Auger ejection or charge tunneling) or captured
to surface-related trap states. The nanoparticle is "on" or
fluorescing when all of the electrons are intact and the particle
is "neutral" and the particle is "off" or dark when the electron is
lost and the particle is temporarily (or in some cases permanently)
charged. It is important to note that the complete suppression of
blinking may not necessarily be required and in some instances may
not be desirable. Blinking which occurs on a timescale much shorter
or much longer than the interrogation period for a particular assay
has relatively little impact on the performance of the system.
Thus, nanoparticles and nanoparticle populations having modulated
blinking properties, where blinking occurs on a very short or very
fast timescale relative to the assay interrogation periods are also
useful and fall within the scope of the present disclosure.
Localization of timescale or simply pushing timescale to one side
(e.g., to where the blinking is undetectable within the assay
system) can provide substantial benefit in application
development.
[0654] The blinking behavior of the nanoparticles described herein
can be analyzed and characterized by any suitable number of
parameters using suitable methodologies. The probability
distribution function of the "on" and "off" blinking time durations
(i.e., blinking behavior) can be determined using the form of an
inverse power law. A value, alpha (.alpha.) can be calculated,
wherein .alpha. represents an exponent in the power law. As the
percentage of the population which is non-blinking increases, the
value of .alpha..sub.on theoretically approaches zero. In
conventional nanoparticle populations previously described,
.alpha..sub.on typically ranges from about 1.5 to about 2.5, under
moderate to high excitation energy.
[0655] Most alpha calculations can use a predetermined threshold to
determine the "on" and "off" values of alpha-on and alpha-off
(i.e., .alpha..sub.on and .alpha..sub.off). Typically, an alpha
estimator which calculates the on/off threshold for each dot
individually can be employed. The data can be represented by a plot
of signal versus frequency, and typically appears as a series of
Gaussian distributions around the "off state" and one or more "on
states." A log-log plot of frequency versus time for each period of
time that the dot is "on" provides a straight line having a slope
of .alpha..sub.on. The value of alpha-off (.alpha..sub.off) can be
similarly determined.
[0656] In a specific example (the "TIRF example"), the fluorescent
intermittency measurements can be made using a Total Internal
Reflection Fluorescence (TIRF) microscope fitted with a 60.times.
oil immersion objective lens, using a dual view with a longpass
filter on the acceptor side and a bandpass filter on the donor
side. Using the TIRF setup, the nanoparticles were imaged at 30 Hz
(33 ms), typically for 5 minutes, to produce a movie showing the
time and intensity of the emitted light for each individual spot
(corresponding to a single particle) within a binned frame which
was 33 ms long; the intensity for each binned frame can be
integrated. Each data set can be manually analyzed dot-by-dot, and
aggregates and other artifacts were excluded. From the edited
results, the following parameters can be calculated: alpha-on
(".alpha..sub.on"); alpha-off (".alpha..sub.on"); the percent on;
longest on/longest off; overlap scores; and the median values for
each of these parameters.
[0657] In some aspects, provided herein is a nanoparticle or
population thereof which has an .alpha..sub.on of less than about
1.5, .alpha..sub.on of less than about 1.4, .alpha..sub.on of less
than about 1.3, .alpha..sub.on of less than about 1.2, or an
.alpha..sub.on of less than about 1.1, under moderate to high
excitation energy. In some embodiments, at least about 50%, at
least about 60%, at least about 70%, at least about 80%, at least
about 90%, at least about 95%, at least about 98%, at least about
99% or more of the population has an .alpha..sub.on of less than
about 1.5, .alpha..sub.on of less than about 1.4, .alpha..sub.on of
less than about 1.3, .alpha..sub.on of less than about 1.2, or
.alpha..sub.on of less than about 1.1 for the time observed, under
moderate to high excitation energy. The observation time can be at
least about 5 minutes, at least about 10 minutes, at least about 15
minutes, at least about 30 minutes, at least about 45 minutes, at
least about 60 minutes, at least about 90 minutes, at least about
120 minutes or more under moderate to high excitation energy.
Compositions comprising such a nanoparticle and populations thereof
also are contemplated.
[0658] In some aspects, provided herein is a nanoparticle or a
population thereof having a stochastic blinking profile which is
either undetectable or rare (e.g., no more than 1-2 events during
the interrogation period) over an observed timescale. In this case,
"undetectable" encompasses the situation in which evidence might
exist for ultra-fast blinking on a timescale which is faster than
the binning timescale (e.g., dimming and brightening from bin to
bin) but there are no "off" events persisting for longer than the
bin time. Therefore, in some embodiments, a nanoparticle or
population thereof has a stochastic blinking profile which is
undetectable for at least about 50%, at least about 60%, at least
about 70%, at least about 80%, at least about 85%, at least about
90%, at least about 95%, at least about 98%, at least about 99% or
more of the time observed, under moderate to high excitation
energy. In other embodiments, at least about 50%, at least about
60%, at least about 70%, at least about 80%, at least about 90%, at
least about 95%, at least about 98%, at least about 99% or more of
the individual nanoparticles in a population have a stochastic
blinking on a timescale which is undetectable for the time
observed, under moderate to high excitation energy. The timescale
can be at least about 5 minutes, at least about 10 minutes, at
least about 15 minutes, at least about 30 minutes, at least about
45 minutes, at least about 60 minutes, at least about 90 minutes,
at least about 120 minutes or more under moderate to high
excitation energy.
[0659] In some aspects, the longest on and longest off values can
relate to the longest period of time a nanoparticle is observed to
be in either the "on" or the "off" state. In particular, the
longest on value can be important to determining the length of time
and amount of data which may be measured in a particular assay.
[0660] Thus, the blinking characteristics of the nanoparticles
herein can also be characterized by their on-time fraction, which
represents the (total on-time)/(total experiment time). Under the
TIRF example disclosed herein, the total on time can be determined
by the total number of frames "on" multiplied by 33 ms, and the
total experiment time is 5 minutes. For example, the blinking
properties of the disclosed nanoparticles or populations thereof
can be determined under continuous irradiation conditions using a
405 nm laser with an intensity of about 1 watt per cm.sup.2 during
an experimental window of at least 5 minutes.
[0661] On-time fractions can be used to characterize the blinking
behavior of a single nanoparticle or of a population of
nanoparticles. It is important to note that the on-time fraction
for a particular nanoparticle or population of nanoparticles is a
function of the specific conditions under which the percent of
blinking or "non-blinking" nanoparticles is determined.
[0662] In some aspects, provided herein is a nanoparticle or
population thereof having an on-time fraction of at least about
0.50, at least about 0.60, at least about 0.70, at least about
0.75, at least about 0.80, at least about 0.85, at least about
0.90, at least about 0.95, at least about 0.96, at least about
0.97, at least about 0.98, or at least about 0.99 or more, under
moderate to high excitation energy. In some embodiments, a
nanoparticle or populations thereof having a percent on-time of
about 98%, about 99% (i.e., on-time fraction of about 0.99) can be
considered to be "non-blinking," under moderate to high excitation
energy. In some embodiments, at least about 50%, at least about
60%, at least about 70%, at least about 80%, at least about 90%, at
least about 95%, at least about 98%, at least about 99%, or more of
the individual nanoparticles in a population of nanoparticles can
have an on-time fraction of at least about 0.50, at least about
0.60, at least about 0.70, at least about 0.75, at least about
0.80, at least about 0.85, at least about 0.90, at least about
0.95, at least about 0.96, at least about 0.97, at least about
0.98, or at least about 0.99 or more, under moderate to high
excitation energy. The on-times of the nanoparticles are typically
for at least about 5 minutes, at least about 10 minutes, at least
about 15 minutes, at least about 20 minutes, at least about 30
minutes, at least about 45 minutes, at least about 60 minutes, at
least about 70 minutes, at least about 80 minutes, at least about
90 minutes, at least about 120 minutes under moderate to high
intensity excitation of the nanoparticle or nanoparticle
population. Under one set of conditions, continuous irradiation
with 405 nm laser with an approximate intensity of 1 watt per
cm.sup.2 was used to determine the stochastic blinking profile.
[0663] In some embodiments, nanoparticles which have a stochastic
(i.e., random) blinking profile in a timescale which shifts from
very rapid blinking or very slow/infrequent blinking (relative to a
nanoparticle previously described in the art) can be considered to
have modulated blinking properties. In some embodiments, these
nanoparticles may blink on and off on a timescale which is too
rapid to be detected under the methods employed to study this
behavior. Thus, certain nanoparticles can effectively appear to be
"always on" or to have on-time fractions of about 0.99, when in
fact they flicker on and off at a rate too fast or too slow to be
detected. Such flickering has relatively little impact on the
performance of a system, and for practical purposes such
nanoparticles can be considered to be non-blinking.
[0664] In some instances, the disclosed nanoparticles and
populations thereof are not observed to blink off under the
analysis conditions, and such particles can be assessed as "always
on" (e.g., non-blinking). The percent of usable dots which are
"always on" can be a useful way to compare nanoparticles or
populations of nanoparticles. However, a determination of "always
on" may mean that the "off" time was insufficient to provide enough
a signal gap for accurate determination and thus the value in the
regime of particles is insufficient to calculate. Even these
"non-blinking" nanoparticles may flicker on and off on a timescale
which is not detected under the conditions used to assess blinking.
For example, certain particles may blink on a timescale which is
too fast to be detected, or they may blink very rarely, and, in
some embodiments, such particles may also be considered to be
"always-on" or non-blinking, as the terms are used herein.
[0665] In one aspect, provided herein is a nanoparticle or
population thereof which demonstrate some fluctuation in
fluorescence intensity. In some embodiments, the change in
fluorescence intensity for the nanoparticle is less than about 5%,
less than about 10%, less than about 20%, or less than about 25% of
the nanoparticle or populations thereof at its greatest intensity,
under moderate to high excitation energy. In some embodiments, such
changes in fluorescence intensity of less than about 5%, less than
about 10%, less than about 20%, or less than about 25% of the
highest intensity can occur in at least about 50%, at least about
60%, at least about 70%, at least about 80%, at least about 85%, at
least about 90%, at least about 95%, at least about 98%, at least
about 99% of the nanoparticles in the population, under moderate to
high excitation energy.
[0666] In some aspects, the nanoparticles with modulated, reduced
or no intermittent (e.g., continuous, non-blinking) fluorescence
provided herein can comprise of a core and a layered gradient
shell. In some embodiments, the nanoparticle(s) disclosed herein
can be comprised of a nanocrystal core (e.g., CdSe, etc.), at least
one inner (intermediate) shell layer (e.g., CdS, etc.), and at
least one outer (external) shell layer (e.g., ZnS, etc.). In some
embodiments, the inner and/or outer shell layers are each comprised
of two or more discrete monolayers of the same material. In some
embodiments, the largest dimension of the disclosed nanoparticle(s)
is less than about 15 nm. See for example, PCT Application Serial
No. PCT US/09/61951. See also PCT/US09/061,951 and PCT/US09/061,953
both filed on Oct. 23, 2009.
[0667] As discussed previously, the disclosed nanoparticles may be
particularly well suited for use as a donor or acceptor which
undergoes FRET with a suitable complementary partner (donor or
acceptor). A "FRET capable" nanoparticle refers to a nanoparticle
which can undergo a measurable FRET energy transfer event with a
donor or an acceptor moiety. In some embodiments, a FRET capable
nanoparticle is one which has at least about 25% efficiency in a
FRET reaction.
[0668] Thus, in one aspect, a FRET capable fluorescent nanoparticle
or population thereof with modulated, reduced or non intermittent
(e.g., continuous, etc.) fluorescence is provided. In some
embodiments, the nanoparticle is the donor in a FRET reaction. In
some embodiments, the nanoparticle is the acceptor in the FRET
reaction.
[0669] In some embodiments, the FRET capable non-blinking
fluorescent nanoparticle(s) disclosed herein can comprise a core
and a layered gradient shell. In some embodiments, the FRET capable
non-blinking nanoparticle(s) disclosed herein can be comprised of a
nanocrystal core (e.g., CdSe, etc.), at least one inner
(intermediate) shell layer (e.g., CdS, etc.), and at least one
outer (external) shell layer (e.g., ZnS, etc.). In some
embodiments, the inner and/or outer shell layers are each comprised
of two or more discrete monolayers of the same material. In some
embodiments, the largest dimension of the disclosed FRET capable
nanoparticle(s) is less than about 15 nm.
[0670] In some embodiments, the nanoparticle or population thereof
has a FRET efficiency of at least about 20%, at least about 40%, at
least about 50%, at least about 60%, at least about 70%, at least
about 80%, at least about 90%, at least about 95%, at least about
98%, at least about 99%, or greater.
[0671] In some embodiments, at least about 30%, at least about 40%,
at least about 50%, at least about 60% at least about 70%, at least
about 80%, at least about 90%, at least about 95%, at least about
98%, at least about 99% or more of the individual nanoparticles in
the population have a FRET efficiency of at least about 20%, at
least about 40%, at least about 50%, at least about 60%, at least
about 70%, at least about 80%, at least about 90%, at least about
95%, at least about 98%, at least about 99% or more.
[0672] In some embodiments, the FRET efficiency of the disclosed
nanoparticle or population thereof can be maintained for at least
about the first 10%, at least about the first 20%, at least about
the first 30%, at least about the first 40%, at least about the
first 50%, at least about the first 60%, at least about the first
70%, at least about the first 80%, at least about the first 90% or
more of the total emitted photons under conditions of moderate to
high excitation.
[0673] As discussed above, the nanoparticle(s) provided herein can
be considered to be surprisingly photostable. In particular, the
nanoparticle and populations described herein can be photostable
over an extended period of time while maintaining the ability to
effectively participate in energy transfer (i.e., FRET) reactions.
The disclosed nanoparticles can be stable under high intensity
conditions involving prolonged or continuous irradiation over an
extended period of time from a moderate to high excitation
source.
[0674] Thus, in one aspect, provided herein is a non-blinking
fluorescent nanoparticle and population thereof which is
photostable.
[0675] In some embodiments, the disclosed photostable nanoparticle
and population thereof can have an emitted light or energy
intensity sustained for at least about 10 minutes and does not
decrease by more than about 20% of maximal intensity achieved
during that time. Further, these nanoparticles and populations
thereof can have a wavelength spectrum of emitted light which does
not change more than about 10% upon prolonged or continuous
exposure to an appropriate energy source (e.g. irradiation).
[0676] In one embodiment, the photostable nanoparticles disclosed
herein can remain photostable under moderate to high intensity
excitation from at least about 10 minutes to about 2 hours. In
another embodiment, the photostable nanoparticles disclosed herein
can remain photostable under moderate to high intensity excitation
from at least about 10 minutes to about 10 hours. In still another
embodiment, the photostable nanoparticles disclosed herein can
remain photostable under moderate to high from about 10 minutes to
about 48 hours. However, it should be appreciated, that these are
just example photostable times for the disclosed nanoparticles, in
practice the nanoparticles can remain photostable for longer
periods of time depending on the particular application.
[0677] It should be appreciated that nanoparticles which are
photostable over longer timescales in combination with moderate to
high excitation energy sources are well suited for more sensitive
and broad-ranging applications such as the real-time monitoring of
single molecules involving FRET. That is, the nanoparticle and
population thereof described herein can be photostable over an
extended period of time while maintaining the ability to
effectively participate in energy transfer (i.e., FRET) reactions,
which makes the subject nanoparticles particularly useful for many
applications involving the real-time monitoring of single
molecules. As such, in some embodiments the photostable
nanoparticles disclosed herein have FRET efficiencies of at least
about 20%.
[0678] In some embodiments, the disclosed nanoparticles are stable
upon prolonged or continuous irradiation (under moderate to high
excitation rate) in which they do not exhibit significant
photo-bleaching on the timescales indicated. Photobleaching can
result from the photochemical destruction of a fluorophore (and can
be characterized by the nanoparticles losing the ability to produce
a fluorescent signal) by the light exposure or excitation source
used to stimulate the fluorescence. Photobleaching can complicate
the observation of fluorescent molecules in microscopy and the
interpretation of energy transfer reactions because the signals can
be destroyed or diminished increasingly as timescales for the
experiment increase or the energy intensity increases.
[0679] Photobleaching can be assessed by measuring the intensity of
the emitted light or energy for a nanoparticle or nanoparticle
population using any suitable method. In some embodiments, the
intensity of emitted light or energy from the disclosed
nanoparticle or population thereof does not decrease by more than
about 20% (and in some embodiments, not more than about 10%) upon
prolonged or continuous irradiation (under moderate to high
excitation rate). In some embodiments, the intensity of emitted
light from the disclosed nanoparticle or population thereof does
not decrease by more than about 20%, about 15%, about 10%, about 5%
or less upon irradiation from about 10 minutes, about 20 minutes,
about 30 minutes, about 45 minutes, about 60 minutes, about 90
minutes, about 2 hours, about 3 hours to about 4 hours, under
moderate to high excitation energy.
[0680] In some embodiments, the photostable nanoparticles provided
herein further demonstrate enhanced stability in which they exhibit
a reduction in or absence of spectral shifting during prolonged
excitation. In the conventional nanoparticles previously described
in the art, increased exposure to an excitation source--whether via
increase time or power--results in a spectral shift of the
wavelength emission wavelength profile of a nanoparticle and
populations thereof from a longer wavelength to an increasingly
shorter wavelength. Such spectral shifting of emission wavelength
represents a significant limitation as precise resolution of
emission spectra is required for applications which require rapid
detection, multi-color analysis, and the like. Shifting of any
significance then requires that the wavelength emissions used in an
assay be sufficiently separated to permit resolution, thus reducing
the number of colors available as well as increasing signal to
noise ratio to an unacceptable level as the initial spectral
profile cannot be relied upon once spectral shifting begins. Such
shifting may require shortened observation times or use of
fluorophores with widely separated emission spectra. The
nanoparticles provided herein have little to no spectral shift,
particularly over extended periods of excitation.
[0681] Wavelength emission spectra can be assessed by any suitable
method. For example, spectral characteristics of nanoparticles can
generally be monitored using any suitable light-measuring or
light-accumulating instrumentation. Examples of such
instrumentation are CCD (charge-coupled device) cameras, video
devices, CIT imaging, digital cameras mounted on a fluorescent
microscope, photomultipliers, fluorometers and luminometers,
microscopes of various configurations, and even the human eye. The
emission can be monitored continuously or at one or more discrete
time points. The photostability and sensitivity of nanoparticles
allow recording of changes in electrical potential over extended
periods of time.
[0682] Thus, in some embodiments, the photostable nanoparticle and
population thereof has a wavelength spectrum of emitted light which
does not change more than about 10% upon prolonged or continuous
exposure to an appropriate energy source (e.g. irradiation) over
about 4 minutes to about 10 minutes, under moderate to high
excitation energy. In some embodiments, the wavelength emission
spectra does not change more than about 5%, more than about 10%,
more than about 20% over 10 minutes, about 20 minutes, about 30
minutes, about 45 minutes, about 60 minutes, about 90 minutes,
about 2 hours, about 3 hours to about 4 hours.
[0683] It should be appreciated that there can be various other
objective indicia of nanoparticle photostability. For example, a
nanoparticle can be classified as photostable when the
nanoparticle, under moderate to high excitation, emits about
1,000,000 to about 100,000,000 photons or more preferably about
100,000,001 to about 100,000,000,000 photons or even more
preferably more than about 100,000,000,000 photons before becoming
non-emissive (i.e., bleached).
[0684] A nanoparticle with modulated, reduced or no fluorescent
intermittency (e.g., continuous, non-blinking, etc.); reduced or
absent spectral shifting; low to no photobleaching; high quantum
yield; and sufficient FRET efficiency can be of any suitable size.
Typically, it is sized to provide fluorescence in the UV-visible
portion of the electromagnetic spectrum as this range is convenient
for use in monitoring biological and biochemical events in relevant
media. The disclosed nanoparticle and population thereof can have
any combination of the properties described herein.
[0685] Thus, in some embodiments the nanoparticle or population
thereof has modulated or no blinking, are photostable (e.g.,
limited or no photobleaching, limited or no spectral shift), has
high quantum yield, have high FRET efficiency, has a diameter of
less than about 15 nm, is spherical or substantially spherical
shape, or any combination of all these properties as described
herein.
[0686] Likewise, in some embodiments, at least about 50%, at least
about 60%, at least about 70%, at least about 80%, at leak about
90%, at least about 95%, at least about 98%, at least about 99%, or
more of the individual nanoparticles in a population of
nanoparticles have modulated or no blinking, are photostable (e.g.,
limited or no photobleaching, limited or no spectral shift), have
high quantum yield, have high FRET efficiency, have diameters of
less than about 15 nm, are spherical or substantially spherical
shape, or any combination of or all of these properties as
described herein.
[0687] In one aspect, the FRET capable, non-blinking and/or
photostable nanoparticle or population thereof provided herein has
a maximum diameter of less than about 20 nm. In some embodiments,
the nanoparticle(s) can be less than about 15 nm, less than about
10 nm, less than about 8 nm, less than about 6 nm, less than about
5 nm, less than about 4 nm, less than about 3 nm or less in its
largest diameter when measuring the core/shell structure. Any
suitable method may be used to determine the diameter of the
nanoparticle(s). The nanoparticle(s) provided herein can be grown
to the desired size using any of the methods disclosed herein. In
some embodiments, at least about 50%, at least about 60%, at least
about 70%, at least about 80%, at least about 90%, at least about
95%, at least about 98%, at least about 99%, or more of the
individual members of a population of nanoparticles have maximum
diameters (when measuring the core, core/shell or core/shell/ligand
structure) which are less than about 20 nm, less than about 15 nm,
less than about 10 nm, less than about 8 nm, less than about 6 nm,
less than about 5 nm, less than about 4 nm, less than about 3 nm or
less.
[0688] The FRET capable, non-blinking and/or photostable
nanoparticle(s) provided herein and populations thereof can be
spherical or substantially spherical. In some embodiments, a
substantially spherical nanoparticle can be one where any two
radius measurements do not differ by more than about 10%, about 8%,
about 5%, about 3% or less. In some embodiments, at least about
50%, at least about 60%, at least about 70%, at least about 80%, at
least about 90%, at least about 95%, at least about 98%, at least
about 99%, or more of the individual members of a population of
nanoparticles are spherical or substantially spherical.
[0689] Nanoparticles can be synthesized in shapes of different
complexity such as spheres, rods, discs, triangles, nanorings,
nanoshells, tetrapods, nanowires and so on. Each of these
geometries can have distinctive properties: spatial distribution of
the surface charge, orientation dependence of polarization of the
incident light wave, and spatial extent of the electric field. In
some embodiments, the nanoparticles are substantially spherical or
spheroidal.
[0690] For embodiments where the nanoparticle is not spherical or
spheroidal, e.g. rod-shaped, it may be from about 1 to about 15 nm,
from about 1 nm to about 10 nm, or 1 nm to about 5 nm in its
smallest dimension. In some such embodiments, the nanoparticles may
have a smallest dimension of about 0.5 nm, about 1 nm, about 2 nm,
about 3 nm, about 4 nm, about 5 nm, about 6 nm, about 7 nm, about 8
nm, about 9 nm, about 10 nm, about 11 nm, about 12 nm, about 13 nm,
about 14 nm, about 15 nm, about 16 nm, about 17 nm, about 18 nm,
about 19 nm, about 20 nm, about 25 nm, about 30 nm, about 35 nm,
about 40 nm, about 45 nm, about 50 nm and ranges between any two of
these values.
[0691] The single-color preparation of the nanoparticles disclosed
herein can have individual nanoparticles which are of substantially
identical size and shape. Thus, in some embodiments, the size and
shape between the individual nanoparticles in a population of
nanoparticles vary by no more than about 20%, no more than about
15%, no more than about 10%, no more than about 8%, no more than
about 6%, no more than about 5%, no more than about 4%, no more
than about 3% or less in at least one measured dimension. In some
embodiments, disclosed herein is a population of nanoparticles,
where at least about 60%, at least about 70%, at least about 80%,
at least about 90%, at least about 95%, and ideally about 100% of
the particles are of the same size. Size deviation can be measured
as root mean square ("rms") of the diameter, with the population
having less than about 30% rms, preferably less than about 20% rms,
more preferably less than about 10% rms. Size deviation can be less
than about 10% rms, less than about 9% rms, less than about 8% rms,
less than about 7% rms, less than about 6% rms, less than about 5%
rms, less than about 3% rms, or ranges between any two of these
values. Such a collection of particles is sometimes referred to as
being a "monodisperse" population.
[0692] The color (emitted light) of a nanoparticle can be "tuned"
by varying the size and composition of the particle. Nanoparticles
as disclosed herein can absorb a wide spectrum of wavelengths, and
emit a relatively narrow wavelength of light. The excitation and
emission wavelengths are typically different, and non-overlapping.
The nanoparticles of a monodisperse population may be characterized
in that they produce a fluorescence emission having a relatively
narrow wavelength band. Examples of emission widths include less
than about 200 nm, less than about 175 nm, less than about 150 nm,
less than about 125 nm, less than about 100 nm, less than about 75
nm, less than about 60 nm, less than about 50 nm, less than about
40 nm, less than about 30 nm, less than about 20 nm, and less than
about 10 nm. In some embodiments, the width of emission is less
than about 60 nm full width at half maximum (FWHM), or less than
about 50 nm FWHM, and sometimes less than about 40 nm FWHM, less
than about 30 nm FWHM or less than about 20 nm FWHM. In some
embodiments, the emitted light preferably has a symmetrical
emission of wavelengths.
[0693] The emission maxima of the disclosed nanoparticle and
population thereof can generally be at any wavelength from about
200 nm to about 2,000 nm. Examples of emission maxima include about
200 nm, about 400 nm, about 600 nm, about 800 nm, about 1,000 nm,
about 1,200 nm, about 1,400 nm, about 1,600 nm, about 1,800 nm,
about 2,000 nm, and ranges between any two of these values.
[0694] As discussed previously, the disclosed nanoparticle or
populations thereof can comprise a core and a layered shell,
wherein the shell includes at least one inner (intermediate) shell
layer comprising a first shell material and at least one outer
(external) shell layer comprising a second shell material, and
wherein the layered shell is substantially uniform in coverage
around the core and is substantially free of defects.
[0695] Thus, in one aspect, the nanoparticle or population thereof
comprises a core (M.sup.1Y) and a layered shell, wherein the shell
comprises m inner shell monolayers comprising a first shell
material (M.sup.1X).sub.m and n outer shell monolayers comprising a
second shell material (M.sup.2X).sub.n, wherein M can be a metal
atom and X can be a non-metal atom, each of m and n is
independently an integer from 1 to 10, and the layered shell is
substantially uniform in coverage around the core and is
substantially free of defects. In specific embodiments, the sum of
m+n is 3-20, or 5-14, or 6-12, or 7-10.
[0696] In certain embodiments, the disclosed nanoparticles can
further comprise one or more additional shell layers between the at
least one inner shell layer and the at least one outer shell
layer.
[0697] In some embodiments, the nanoparticle core and population
thereof can have a first bandgap energy and the first shell
material can have a second bandgap energy, wherein the second
bandgap energy can be greater than the first bandgap energy.
[0698] In a further aspect, provided herein is a nanoparticle or
population thereof comprising a core and a layered shell, wherein
the shell comprises sequential monolayers comprising an alloyed
multi-component shell material of the form
M.sup.1.sub.xM.sup.2.sub.yX, where M.sup.1 and M.sup.2 can be metal
atoms and X can be a non metal atom, where the composition becomes
successively enriched in M.sup.2 as the monolayers of shell
material are deposited, where x and y represent the ratio of
M.sup.1 and M.sup.2 in the shell material, and wherein the
monolayered shell is substantially uniform in coverage around the
core and is substantially free of defects. In some embodiments, the
layered shell sometimes has about 3-20 monolayers of shell
material, sometimes about 5-14 monolayers of shell material,
sometimes about 6-12 monolayers of shell material, or sometimes
about 7-10 monolayers of shell material.
[0699] In one aspect, provided herein is a nanoparticle or
population thereof comprising a core and a layered shell having a
gradient potential, wherein the shell comprises at least one inner
shell layer and at least one outer shell layer, and wherein the
layered shell is substantially uniform in coverage around the core
and is substantially free of defects.
[0700] The layered shell may be engineered such that the sequential
monolayers are selected to provide a gradient potential from the
nanoparticle core to the outer surface of the nanoparticle shell.
The steepness of the potential gradient may vary depending on the
nature of the shell materials selected for each monolayer or group
of monolayers. For example, a nanoparticle comprising several
sequential monolayers of the same shell material may reduce the
potential through a series of steps, while a more continuous
gradient may be achievable through the use of sequential monolayers
of a multi-component alloyed shell material. In some embodiments,
both single component and multi-component shell materials may be
applied as different monolayers of a multi-layer shell on a
nanoparticle.
[0701] The nanoparticles can be synthesized as disclosed to the
desired size by sequential, controlled addition of materials to
build and/or apply monolayers of shell material to the core. This
is in contrast to conventional methods of adding shells where
materials (e.g., diethylzinc and bis(trimethylsilyl)sulfide) are
added together. Sequential addition permits the formation of thick
(e.g., >2 nm) relatively uniform individual shells (e.g.,
uniform size and depth) on a core. The layer additions generally
require the addition of an appropriate amount of the shell
precursors to form a single monolayer, based on the starting size
of the underlying core. This means that as each monolayer of shell
material is added, a new "core" size must be determined by taking
the previous "core" size and adding to it the thickness of
just-added shell monolayer. This leads to a slightly larger volume
of the following shell material needing to be added for each
subsequent monolayer of shell material being added.
[0702] Each monolayer of shell material can be independently
selected, and may be made up of a single component, or may comprise
a multi-component (e.g., alloyed, etc.) shell material. In some
embodiments, it is suitable to apply one or more sequential
monolayers of a first shell material, followed by one or more
sequential monolayers of a second shell material. This approach
allows the deposition of at least one inner shell layer of a
material having a bandgap and lattice size compatible with the
core, followed by the deposition of at least one outer shell layer
of a material having a bandgap and lattice size compatible with the
inner shell layer. In some embodiments, multiple sequential
monolayers of a single shell material can be applied to provide a
uniform shell of a desired number of monolayers of a single shell
material; in these embodiments, the first and second shell
materials are the same. In other embodiments, sequential monolayers
of an alloyed shell material are applied, where the ratio of the
components varies such that the composition becomes successively
enriched in one component of the multi-component mixture as the
successive monolayers of shell material are deposited.
[0703] In some embodiments, the layered shell can be about 3-20
monolayers of shell material thick, sometimes about 5-14 monolayers
of shell material thick, sometimes about 6-12 monolayers of shell
material thick or sometimes about 7-10 monolayers of shell material
thick. In some embodiments, at least one inner shell layer can be
comprised of about 3-5 monolayers, sometimes about 3-7 monolayers,
of the first shell material. In other embodiments, at least one
outer shell layer can be comprised of about 3-5 monolayers,
sometimes about 3-7 monolayers, of the second shell material. In
some embodiments, the inner shell layer can be at least 3
monolayers thick; in other embodiments, the outer shell layer can
be at least 3 monolayers thick. The individual monolayers can be
formed by the controlled, sequential addition of the layer
materials methods described herein. The monolayers may not always
be completely distinct as they may, in some embodiments, be a
latticing between the surfaces of contacting monolayers.
[0704] In certain embodiments, provided herein are nanoparticles
having a thick, uniform, layered shell, as described herein,
wherein the core comprises CdSe, the at least one inner shell layer
comprises CdS, and the at least one outer shell layer comprises
ZnS. In a particular embodiment, provided herein is a nanoparticle
or population thereof having a CdSe core and a layered shell
comprising 4CdS+3.5ZnS layers. In some embodiments, provided herein
is a nanoparticle which consists essentially of
CdSe/4CdS-3,5ZnS.
[0705] Also disclosed herein are methods of making a nanoparticle
and population thereof with modulated, reduced or no fluorescence
intermittency or "blinking". These nanoparticles can be small,
photostable, bright, highly FRET efficient or some combination
thereof. These nanoparticles can have a multi-shell layered core
achieved by a sequential shell material deposition process, whereby
one shell material is added at a time, to provide a nanoparticle
having a substantially uniform shell of desired thickness which is
substantially free of defects.
[0706] In one aspect, provided herein is a method for making a
nanoparticle or population thereof with modulated, reduced or no
fluorescence intermittency, comprising: providing a mixture
comprising a core and at least one coordinating solvent; adding a
first inner shell precursor alternately with a second inner shell
precursor in layer additions, to form an inner shell layer which is
a desired number of layers thick; and adding a first outer shell
precursor alternately with a second outer shell precursor in layer
additions, to form an outer shell layer which is a desired number
of layers thick. If the coordinating solvent of is not amine, the
method further comprises an amine in.
[0707] In some embodiments, the mixture can be heated to a
temperature which is suitable for shell formation before and/or
after every sequential addition of a shell precursor. In some
embodiments, the shell is substantially uniform in coverage around
the core and is substantially free of defects. In some embodiments,
the resulting nanoparticles have a diameter of less than about 15
nm. In other embodiments, the nanoparticles have a diameter of
between about 6 nm to about 10 nm. The nanoparticles made by this
method can have quantum yields greater than about 80%. The
nanoparticle made by this method can have on-time fractions (i.e.,
ratio of the time which nanoparticle emission is turned "on" when
the nanoparticle is excited) of greater than about 0.80 (under
moderate to high excitation energy).
[0708] In another aspect, provided herein is a method for making a
FRET capable nanoparticle and populations thereof with modulated,
reduced or no fluorescence intermittency, comprising: (a) providing
a mixture comprising a plurality of nanocrystal cores and at least
one coordinating solvent; (b) adding a first intermediate shell
precursor alternately with a second intermediate shell precursor in
layer additions to form an intermediate shell layer on each of the
plurality of nanocrystal cores, wherein the intermediate shell
layer is comprised of more than one monolayer; (c) adding a first
external shell precursor alternately with a second external shell
precursor in layer additions to form an external shell layer on
each of the plurality of nanocrystal cores, wherein the external
shell layer is disposed on top of the intermediate shell layer and
is comprised of more than one monolayer; (d) adding an aqueous
solution comprising a hydrophilic ligand; and (e) maintaining the
mixture under conditions which cause the plurality of nanocrystals
to migrate into an aqueous phase. If the coordinating solvent is
not an amine, at least one amine can be included in step (a). In
some embodiments, the resulting population of FRET capable
non-blinking nanoparticles has a .alpha..sub.on value which is less
than about 1.4. In other embodiments, the resulting population of
FRET capable non-blinking nanoparticles has an on-time fraction of
least about 0.8 (under moderate to high excitation energy). In some
embodiments, the resulting population of FRET capable non-blinking
nanoparticles has diameters which are less than about 15 nm. In
some embodiments, the resulting population of FRET capable
non-blinking nanoparticles has a FRET efficiency of at least 20%.
In some embodiments, the resulting population of FRET capable
non-blinking nanoparticles has a quantum yield of at least about
40%.
[0709] In some embodiments, the methods disclosed above utilize a
one step or a two step ligand exchange process to replace the
hydrophobic ligands on the nanoparticles with hydrophilic ligands
to cause the plurality of nanocrystals to migrate into the aqueous
phase. See PCT Application Serial No. PCT/US09/53018 and
PCT/US09/59456 which are expressly incorporated herein by reference
as if set forth in full.
[0710] In another aspect, provided herein is a method for making a
FRET capable nanoparticle and populations thereof with modulated,
reduced or no fluorescence intermittency, comprising: providing a
mixture comprising a plurality of nanocrystal cores, functionalized
organophosphorous-based hydrophilic ligands and at least one
coordinating solvent; adding a first intermediate shell precursor
alternately with a second intermediate shell precursor in layer
additions to form an intermediate shell layer on each of the
plurality of nanocrystal cores; and adding a first external shell
precursor alternately with a second external shell precursor in
layer additions to form an external shell layer on each of the
plurality of nanocrystal cores. In some embodiments, the resulting
population of FRET capable non-blinking nanoparticles has an
.alpha..sub.on value which is less than about 1.4. In other
embodiments, the resulting population of FRET capable non-blinking
nanoparticles has an on-time fraction of least about 0.8. In some
embodiments, the resulting population of FRET capable non-blinking
nanoparticles has diameters which are less than about 15 nm. In
some embodiments, the resulting population of FRET capable
non-blinking nanoparticles has a FRET efficiency of at least 20%.
In some embodiments, the resulting population of FRET capable
non-blinking nanoparticles has a quantum yield of at least about
40%.
[0711] In some embodiments, the functionalized
organophosphorous-based hydrophilic ligands are multi-functional
surface ligands which include a phosphonate/phosphinate nanocrystal
binding center, a linker, and a functional group, which imparts
functionality on the nanocrystal. As used herein the term
"functional group" may refer to a group which affects reactivity,
solubility, or both reactivity and solubility when present on a
multi-functional surface ligand. Embodiments can include a wide
variety of functional groups which can impart various types of
functionality on the nanocrystal including hydrophilicity,
water-solubility, or dispersibility and/or reactivity, and the
functionality may generally not include only hydrophobicity or only
solubility in organic solvents without increasing reactivity. For
example, a functional group which is generally hydrophobic but
which increases reactivity such as an alkene or alkyne and certain
esters and ethers can be encompassed by embodiments, whereas alkyl
groups, which do not generally impart reactivity but increase
hydrophobicity may be excluded.
[0712] In certain embodiments, the FRET capable and non-blinking
nanoparticles produced by the disclosed methods may be coated with
ligands which impart water solubility and/or reactivity on the
nanoparticle obviating the need for ligand replacement. Without
wishing to be bound by theory, eliminating ligand replacement may
provide more consistent thermodynamic properties, which may lead to
reduction in variability of coating and less loss of quantum yield,
among other improvements in the properties of nanoparticles
produced by the methods embodied herein. Eliminating ligand
replacement may also allow for the production of nanoparticles
having a wide variety of functional groups associated with the
coating. In particular, while ligand replacement is generally
limited to production of nanoparticles having amine and/or
carboxylic acid functional groups, in various embodiments, the
skilled artisan may choose among numerous functional groups when
preparing the multi-functional ligands and may, therefore, generate
nanoparticles which provide improved water-solubility or
water-dispersity and/or support improved crosslinking and/or
improved reactivity with cargo molecules. See PCT Application
Serial No. PCT/US09/59117 which is expressly incorporated herein by
reference as if set forth in full.
[0713] In another aspect, provided herein is a method of making a
nanoparticle or population thereof comprising a core and a layered
gradient shell, wherein the shell comprises an multi-component
(e.g., alloy, etc.) shell material of the form
M.sup.1.sub.xM.sup.2.sub.yX, where x and y represent the ratio of
M.sup.1 and M.sup.2 in the shell material. The method comprising:
(a) providing a mixture comprising a core, at least one
coordinating solvent; (b) heating said mixture to a temperature
suitable for formation of the shell layer; and (c) adding a first
inner shell precursor comprising M.sup.1.sub.x and M.sup.2.sub.y
alternately with a second inner shell precursor comprising X in
layer additions, wherein the ratio of y to x gradually increases in
sequential layer additions, such that the shell layers becomes
successively enriched in M.sup.2, to form a layered gradient shell
which is a desired number of monolayers thick. If the coordinating
solvent is not an amine, at least one amine can be included in step
(a).
[0714] In one embodiment, the method described above provides a
nanoparticle having a layered gradient shell, wherein the core
comprises CdSe and the shell comprises sequential layers of
Cd.sub.xZn.sub.yS, where the ratio of y to x increases gradually
from the innermost shell layer to the outermost shell layer, to
provide a layered gradient shell with a finely graded potential. In
some such embodiments, the outermost shell layer is essentially
pure ZnS. In some embodiments, the percent of Zn in the gradient
shell varies from less than about 10% at the innermost shell layer
to greater than about 80% at the outermost shell layer.
[0715] Typically, the heating steps in the disclosed methods are
conducted at a temperature within the range of about
150-350.degree. C., more preferably within the range of about
200-300.degree. C. In some embodiments, the temperature suitable
for formation of at least one inner shell layer is about
215.degree. C. In some embodiments, the temperature suitable for
formation of at least one outer shell layer is about 245.degree. C.
It is understood that the above ranges are merely exemplary and are
not intended to be limiting in any manner as the actual temperature
ranges may vary, dependent upon the relative stability of the
precursors, ligands, and solvents. Higher or lower temperatures may
be appropriate for a particular reaction. The determination of
suitable time and temperature conditions for providing
nanoparticles is within the level of skill in the art using routine
experimentation.
[0716] It can be advantageous to conduct the nanoparticle-forming
reactions described herein with the exclusion of oxygen and
moisture. In some embodiments the reactions are conducted in an
inert atmosphere, such as in a dry box. The solvents and reagents
are also typically rigorously purified to remove moisture and
oxygen and other impurities, and are generally handled and
transferred using methods and apparatus designed to minimize
exposure to moisture and/or oxygen. In addition, the mixing and
heating steps can be conducted in a vessel which is evacuated and
filled and/or flushed with an inert gas such as nitrogen. The
filling can be periodic or the filling can occur, followed by
continuous flushing for a set period of time.
[0717] In some embodiments, the at least one coordinating solvent
comprises a trialkylphosphine, a trialkylphosphine oxide, a
phosphonic acid, or a mixture of these. Sometimes, the at least one
coordinating solvent comprises TOP, TOPO, TDPA, OPA or a mixture of
these. The solvent for these reactions often comprises a primary or
secondary amine, for example, decylamine, hexadecylamine, or
dioctylamine. In some embodiments, the amine is decylamine. In some
embodiments, the first inner shell precursor is Cd(OAc).sub.2 and
the second inner shell precursor is bis(trimethylsilyl)sulfide
(TMS.sub.2S). Sometimes, the first and second inner shell
precursors are added as a solution in TOP. In some embodiments, the
first outer shell precursor is Et.sub.2Zn and the second inner
shell precursor is TMS.sub.2S. Sometimes, the first and second
outer shell precursors are added as a solution in TOP.
[0718] In certain embodiments, the disclosed nanoparticles may be
prepared using the method described herein to build a layered
CdS--ZnS shell on a CdSe quantum size core. The shells for these
materials can have varying numbers of layers of CdS and ZnS.
Prototypical materials containing a CdSe core and approximately 4
monolayers CdS and 3.5 monolayers of ZnS (the final 0.5 monolayer
is essentially pure Zn), or a CdSe core and 9 monolayers CdS and
3.5 monolayers of ZnS were prepared as described in the
examples.
[0719] In some embodiments, for either the inner or outer layer, or
both, less than a full layer of the appropriate first shell
precursor can be added alternately with less than a full layer of
the appropriate second shell precursor, so the total amount of the
first and second shell precursor required is added in two or more
portions. Sometimes, the portion is about 0.25 monolayers of shell
material, so that the 4 portions of 0.25 monolayer of first shell
precursor are added alternately with 4 portions of 0.25 monolayer
of second shell precursor; sometimes the portion is about 0.5
monolayers of shell material, and sometimes about 0.75 monolayers
of shell material.
[0720] Examples of compounds useful as the first precursor can
include, but are not limited to: organometallic compounds such as
alkyl metal species, salts such as metal halides, metal acetates,
metal carboxylates, metal phosphonates, metal phosphinates, metal
oxides, or other salts. In some embodiments, the first precursor
provides a neutral species in solution. For example, alkyl metal
species such as diethylzinc (Et.sub.2Zn) or dimethyl cadmium are
typically considered to be a source of neutral zinc atoms
(Zn.sup.0) in solution. In other embodiments, the first precursor
provides an ionic species (i.e., a metal cation) in solution. For
example, zinc chloride (ZnCl.sub.2) and other zinc halides, zinc
acetate (Zn(OAc).sub.2) and zinc carboxylates are typically
considered to be sources of Zn.sup.2+ cations in solution.
[0721] By way of example only, suitable first precursors providing
neutral metal species include dialkyl metal sources, such as
dimethyl cadmium (Me.sub.2Cd), diethyl zinc (Et.sub.2Zn), and the
like. Suitable first precursors providing metal cations in solution
include, e.g., cadmium salts, such as cadmium acetate
(Cd(OAc).sub.2), cadmium nitrate (Cd(NO.sub.3).sub.2), cadmium
oxide (CdO), and other cadmium salts; and zinc salts such as zinc
chloride (ZnCl.sub.2), zinc acetate (Zn(OAc).sub.2), zinc oleate
(Zn(oleate).sub.2), zinc chloro(oleate), zinc undecylenate, zinc
salicylate, and other zinc salts. In some embodiments, the first
precursor is salt of Cd or Zn. In some embodiments, it is a halide,
acetate, carboxylate, or oxide salt of Cd or Zn. In other
embodiments, the first precursor is a salt of the form
M(O.sub.2CR)X, wherein M is Cd or Zn; X is a halide or O.sub.2CR;
and R is a C4-C24 alkyl group which is optionally unsaturated.
Other suitable forms of Groups 2, 12, 13 and 14 elements useful as
first precursors are known in the art.
[0722] Precursors useful as the "second" precursor in the disclosed
methods include compounds containing elements from Group 16 of the
Periodic Table of the Elements (e.g., S, Se, Te, and the like),
compounds containing elements from Group 15 of the Periodic Table
of the Elements (N, P, As, Sb, and the like), and compounds
containing elements from Group 14 of the Periodic Table of the
Elements (Ge, Si, and the like). Many forms of the precursors can
be used in the disclosed methods. It will be understood that in
some embodiments, the second precursor will provide a neutral
species in solution, while in other embodiments the second
precursor will provide an ionic species in solution.
[0723] When the first precursor comprises a metal cation, the
second precursor can provide an uncharged (i.e., neutral) non-metal
atom in solution. In frequent embodiments, when the first precursor
comprises a metal cation, the second precursor contributes a
neutral chalcogen atom, most commonly S.sup.0, Se.sup.0 or
Te.sup.0.
[0724] Suitable second precursors for providing a neutral chalcogen
atom include, for example, elemental sulfur (often as a solution in
an amine, e.g., decylamine, oleylamine, or dioctylamine, or an
alkene, such as octadecene), and tri-alkylphosphine adducts of S,
Se and Te. Such trialkylphosphine adducts are sometimes described
herein as R3P=X, wherein X is S, Se or Te, and each R is
independently H, or a C1-C24 hydrocarbon group which can be
straight-chain, branched, cyclic, or a combination of these, and
which can be unsaturated. Exemplary second precursors of this type
include tri-n (butylphosphine)selenide (TBP=Se),
tri-n-(octylphosphine)selenide (TOP=Se), and the corresponding
sulfur and tellurium reagents, TBP=S, TOP=S, TBP=Te and TOP=Te.
These reagents are frequently formed by combining a desired
element, such as Se, S, or Te with an appropriate coordinating
solvent, e.g., TOP or TBP. Precursors which provide anionic species
under the reaction conditions are typically used with a first
precursor which provides a neutral metal atom, such as alkylmetal
compounds and others described above or known in the art.
[0725] In some embodiments, the second precursor provides a
negatively charged non-metal ion in solution (e.g., S-2, Se-2 or
Te-2). Examples of suitable second precursors providing an ionic
species include silyl compounds such as bis(trimethylsilyl)selenide
((TMS).sub.2Se), bis(trimethylsilyl)sulfide ((TMS).sub.2S) and
bis(trimethylsilyl)telluride ((TMS).sub.2Te). Also included are
hydrogenated compounds such as H2Se, H2S, H2Te; and metal salts
such as NaHSe, NaSH or NaHTe. In this situation, an oxidant can be
used to oxidize a neutral metal species to a cationic species which
can react with the anionic precursor in a `matched` reaction, or an
oxidant can be used increase the oxidation state of the anionic
precursor to provide a neutral species which can undergo a
`matched` reaction with a neutral metal species.
[0726] Other exemplary organic precursors are described in U.S.
Pat. Nos. 6,207,229 and 6,322,901 to Bawendi et al., and synthesis
methods using weak acids as precursor materials are disclosed by Qu
et al., (2001), Nano Lett., 1(6):333-337, the disclosures of each
of which are incorporated herein by reference in their
entirety.
[0727] Both the first and the second precursors can be combined
with an appropriate solvent to form a solution for use in the
disclosed methods. The solvent or solvent mixture used to form a
first precursor solution may be the same or different from that
used to form a second precursor solution. Typical coordinating
solvents include alkyl phosphines, alkyl phosphine oxides, alkyl
phosphonic acids, alkyl phosphinic acids, or carboxylic acid
containing solvents, or mixtures of these.
[0728] Suitable reaction solvents include, by way of illustration
and not limitation, hydrocarbons, amines, alkyl phosphines, alkyl
phosphine oxides, carboxylic acids, ethers, furans, phosphoacids,
pyridines and mixtures thereof. The solvent may actually comprise a
mixture of solvents, often referred to in the art as a "solvent
system". In some embodiments, the solvent comprises at least one
coordinating solvent. In some embodiments, the solvent system
comprises a secondary amine and a trialkyl phosphine (e.g., TBP or
TOP) or a trialkylphosphine oxide (e.g., TOPO). If the coordinating
solvent is not an amine, an amine can be included.
[0729] A coordinating solvent might be a mixture of an essentially
non-coordinating solvent such as an alkane and a ligand as defined
below.
[0730] Suitable hydrocarbons include alkanes, alkenes and aromatic
hydrocarbons from 10 to about 30 carbon atoms; examples include
octadecene and squalane. The hydrocarbon may comprise a mixture of
alkane, alkene and aromatic moieties, such as alkylbenzenes (e.g.,
mesitylene).
[0731] Suitable amines include, but are not limited to,
monoalkylamines, dialkylamines, and trialkylamines, for example
dioctylamine, oleylamine, decylamine, dodecylamine,
hexyldecylamine, and so forth. Alkyl groups for these amines
typically contain about 6-24 carbon atoms per alkyl, and can
include an unsaturated carbon-carbon bond, and each amine typically
has a total number of carbon atoms in all of its alkyl groups
combined of about 10-30 carbon atoms.
[0732] Exemplary alkyl phosphines include, but are not limited to,
the trialkyl phosphines, tri-n-butylphosphine (TBP),
tri-n-octylphosphine (TOP), and so forth. Alkyl groups for these
phosphines contain about 6-24 carbon atoms per alkyl, and can
contain an unsaturated carbon-carbon bond, and each phosphine has a
total number of carbon atoms in all of its alkyl groups combined of
about 10-30 carbon atoms.
[0733] Suitable alkyl phosphine oxides include, but are not limited
to, the trialkyl phosphine oxide, tri-n-octylphosphine oxide
(TOPO), and so forth. Alkyl groups for these phosphine oxides
contain about 6-24 carbon atoms per alkyl, and can contain an
unsaturated carbon-carbon bond, and each phosphine oxide has a
total number of carbon atoms in all of its alkyl groups combined of
about 10-30 carbon atoms.
[0734] Exemplary fatty acids include, but are not limited to,
stearic, oleic, palmitic, myristic and lauric acids, as well as
other carboxylic acids of the formula R--COOH, wherein R is a
C6-C24 hydrocarbon group and can contain an unsaturated
carbon-carbon bond. It will be appreciated that the rate of
nanocrystal growth generally increases as the length of the fatty
acid chain decreases.
[0735] Exemplary ethers and furans include, but are not limited to,
tetrahydrofuran and its methylated forms, glymes, and so forth.
[0736] Suitable phosphonic and phosphinic acids include, but are
not limited to hexylphosphonic acid (HPA), tetradecylphosphonic
acid (TDPA), and octylphosphinic acid (OPA), and are frequently
used in combination with an alkyl phosphine oxide such as TOPO.
Suitable phosphonic and phosphinic acids are of the formula
RPO.sub.3H.sub.2 or R.sub.2PO2H, wherein each R is independently a
C6-C24 hydrocarbon group and can contain an unsaturated
carbon-carbon bond.
[0737] Exemplary pyridines include, but are not limited to,
pyridine, alkylated pyridines, nicotinic acid, and so forth.
[0738] Suitable alkenes include, e.g., octadecene and other C4-C24
hydrocarbons which are unsaturated.
[0739] Nanoparticle core or shell precursors can be represented as
a M-source and an X-donor. The M-source can be an M-containing
salt, such as a halide, carboxylate, phosphonate, carbonate,
hydroxide, or diketonate, or a mixed salt thereof (e.g., a halo
carboxylate salt, such as Cd(halo)(oleate)), of a metal, M, in
which M can be, e.g., Cd, Zn, Mg, Hg, Al, Ga, In, or Tl. In the
X-donor, X can be, e.g., O, S, Se, Te, N, P, As, or Sb. The mixture
can include an amine, such as a primary amine (e.g., a C8-C20 alkyl
amine). The X donor can include, for example, a phosphine
chalcogenide, a bis(trialkylsilyl)chalcogenide, a dioxygen species,
an ammonium salt, or a tris(trialkylsilyl)phosphine, or the
like.
[0740] The M-source and the X donor can be combined by contacting a
metal, M, or an M-containing salt, and a reducing agent to form an
M-containing precursor. The reducing agent can include an alkyl
phosphine, a 1,2-diol or an aldehyde, such as a C.sub.6-C.sub.20
alkyl diol or a C.sub.6-C.sub.20 aldehyde.
[0741] Suitable M-containing salts include, for example, cadmium
acetylacetonate, cadmium iodide, cadmium bromide, cadmium chloride,
cadmium hydroxide, cadmium carbonate, cadmium acetate, cadmium
oxide, zinc acetylacetonate, zinc iodide, zinc bromide, zinc
chloride, zinc hydroxide, zinc carbonate, zinc acetate, zinc oxide,
magnesium acetylacetonate, magnesium iodide, magnesium bromide,
magnesium chloride, magnesium hydroxide, magnesium carbonate,
magnesium acetate, magnesium oxide, mercury acetylacetonate,
mercury iodide, mercury bromide, mercury chloride, mercury
hydroxide, mercury carbonate, mercury acetate, aluminum
acetylacetonate, aluminum iodide, aluminum bromide, aluminum
chloride, aluminum hydroxide, aluminum carbonate, aluminum acetate,
gallium acetylacetonate, gallium iodide, gallium bromide, gallium
chloride, gallium hydroxide, gallium carbonate, gallium acetate,
indium acetylacetonate, indium iodide, indium bromide, indium
chloride, indium hydroxide, indium carbonate, indium acetate,
thallium acetylacetonate, thallium iodide, thallium bromide,
thallium chloride, thallium hydroxide, thallium carbonate, or
thallium acetate. Suitable M-containing salts also include, for
example, carboxylate salts, such as oleate, stearate, myristate,
and palmitate salts, mixed halo carboxylate salts, such as
M(halo)(oleate) salts, as well as phosphonate salts.
[0742] Alkyl is a branched or unbranched saturated hydrocarbon
group of 1 to 100 carbon atoms, preferably 1 to 30 carbon atoms,
such as methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl,
t-butyl, octyl, decyl, tetradecyl, hexadecyl, eicosyl, tetracosyl
and the like, as well as cycloalkyl groups such as cyclopentyl,
cyclohexyl and the like. Optionally, an alkyl can contain 1 to 6
linkages selected from the group consisting of --O--, --S--, -M-
and --NR-- where R is hydrogen, or C1-C8 alkyl or lower
alkenyl.
[0743] The X donor is a compound capable of reacting with the
M-containing salt to form a material with the general formula MX.
The X donor is generally a chalcogenide donor or a phosphine donor,
such as a phosphine chalcogenide, a bis(silyl) chalcogenide,
dioxygen, an ammonium salt, or a tris(trialkylsilyl) phosphine.
Suitable X donors include dioxygen, elemental sulfur,
bis(trimethylsilyl) selenide ((TMS).sub.2Se), trialkyl phosphine
selenides such as (tri-n-octylphosphine) selenide (TOPSe) or
(tri-n-butylphosphine) selenide (TBPSe), trialkyl phosphine
tellurides such as (tri-n-octylphosphine) telluride (TOPTe) or
hexapropylphosphorustriamide telluride (HPPTTe),
bis(trimethylsilyl)telluride ((TMS).sub.2Te), sulfur,
bis(trimethylsilyl)sulfide ((TMS).sub.2S), a trialkyl phosphine
sulfide such as (tri-n-octylphosphine) sulfide (TOPS),
tris(dimethylamino) arsine, an ammonium salt such as an ammonium
halide (e.g., NH.sub.4Cl), tris(trimethylsilyl) phosphide
((TMS).sub.3P), tris(trimethylsilyl) arsenide ((TMS).sub.3As), or
tris(trimethylsilyl) antimonide ((TMS).sub.3Sb). In certain
embodiments, the M donor and the X donor can be moieties within the
same molecule.
[0744] Ligand Exchange Processes for Coating Nanoparticles
[0745] Provided herein are ligand exchange processes that permit
efficient conversion of a conventional hydrophobic nanoparticle or
population thereof into a water-dispersible and functionalized
nanoparticle or population of nanoparticles. It also permits
preparation of small nanoparticles which are highly stable and
bright enough to be useful in biochemical and biological assays.
The resulting nanoparticles can also be linked to a target molecule
or cell or enzyme (e.g., polymerase) of interest.
[0746] Typically, the nanoparticle used for this process is a
core/shell nanocrystal which is coated with a hydrophobic ligand
such as tetradecylphosphonic acid (TDPA), trioctylphosphine oxide
(TOPO), trioctyl phosphine (TOP), octylphosphonic acid (OPA), and
the like, or a mixture of such ligands; these hydrophobic ligands
typically have at least one long-chain alkyl group, i.e. an alkyl
group having at least 8 carbons, or for the phosphine/phosphine
oxide ligands, this hydrophobic character may be provided by two or
three alkyl chains on a single ligand molecule having a total of at
least 10 carbon atoms. Therefore, in some embodiments, the surface
of the core/shell nanocrystal or population thereof can be coated
with varying quantities of TDPA hydrophobic ligands prior to
replacement with hydrophilic ligand(s). For example, TDPA can
represent at least about 10%, at least about 20%, at least about
30%, at least about 40%, at least about 50%, at least about 80%, at
least about 95%, at least about 98%, at least about 99% or more of
the total surface ligands coating the core/shell nanoparticles.
Moreover, certain hydrophobic ligands show an unexpected and
apparent ease of replacement with the hydrophilic ligand. For
example, nanoparticles with OPA on the surface have been observed
to transfer into aqueous buffer more readily and more completely
than the same type of core-shell with TDPA on the surface.
Therefore, in some embodiments, the surface of the core/shell
nanocrystal or populations thereof can be coated with varying
quantities of OPA hydrophobic ligands prior to replacement with
hydrophilic ligand(s). For example, OPA can represent at least
about 10%, at least about 20%, at least about 30%, at least about
40%, at least about 50%, at least about 80%, at least about 95%, at
least about 98%, at least about 99% or more of the total surface
ligands coating the core/shell nanocrystal.
[0747] In one aspect, provided herein is a "one-step" ligand
exchange process to apply various types of ligands to the surface
of a nanoparticle, by substituting a desired hydrophilic ligand for
a conventional hydrophobic ligand like TOPO, TOP, TDPA, OPA, and
the like. The process steps, comprising: providing a nanocrystal
coated with a surface layer comprising a hydrophobic ligand, and
dissolved or dispersed in a non-aqueous solvent, contacting the
nanocrystal dispersion with a phase transfer agent and an aqueous
solution comprising a hydrophilic ligand, to form a biphasic
mixture having an aqueous phase and a non-aqueous phase and
maintaining the mixture under conditions that cause the nanocrystal
to migrate from the non-aqueous solvent into the aqueous phase. See
PCT Application Serial No. PCT/US09/53018 which is expressly
incorporated herein by reference as if set forth in full.
[0748] The `one-step` ligand exchange process described herein
utilizes phase transfer catalysts which are particularly effective,
and provide faster exchange reactions. Butanol has been utilized as
a phase transfer catalyst for this type of exchange reaction;
however, the reaction takes several days typically, and requires
heating to about 70.degree. C. The time for this reaction exposes
the nanoparticles to these reaction conditions for a long period of
time, which may contribute to some reduction in its ultimate
stability. The embodiments disclosed herein provide more efficient
conditions which achieve ligand exchange more rapidly, thus better
protecting the nanoparticles. As a result of accelerating the
exchange reaction and allowing use of milder conditions, these
phase transfer catalysts produce higher quality nanoparticles.
[0749] The phase transfer agent for this process can be a crown
ether, a PEG, a trialkylsulfonium, a tetralkylphosphonium, and an
alkylammonium salt, or a mixture of these. In some embodiments, the
phase transfer agent is 18-crown-6, 15-crown-5, or 12-crown-4. In
some embodiments, the phase transfer agent is a PEG, which can have
a molecular weight from about 500 to about 5000. In some
embodiments, the phase transfer agent is a trialkylsulfonium,
tetralkylphosphonium, or alkylammonium (including
monoalkylammonium, dialkylammonium, trialkylammonium and
tetralkylammonium) salt.
[0750] Tetralkylammonium salts are sometimes preferred as phase
transfer agents. Examples of suitable tetralkylammonium salts
include triethylbenzyl ammonium, tetrabutylammonium,
tetraoctylammonium, and other such quaternary salts. Other
tetralkylammonium salts, where each alkyl group is a C1-C12 alkyl
or arylalkyl group, can also be used. Typically, counting all of
the carbons on the alkyl groups of a trialkylsulfonium,
tetralkylphosphonium, and alkylammonium salt, the phase transfer
agent will contain a total of at least 2 carbons, at least 10
carbons and preferably at least 12 carbon atoms. Each of the
trialkylsulfonium, tetralkylphosphonium, and alkylammonium salts
has a counterion associated with it; suitable counterions include
halides, preferably chloride or fluoride; sulfate, nitrate,
perchlorate, and sulfonates such as mesylate, tosylate, or
triflate; mixtures of such counterions can also be used. The
counterion can also be a buffer or base, such as borate, hydroxide
or carbonate; thus, for example, tetrabutylammonium hydroxide can
be used to provide the phase transfer catalyst and a base. Specific
phase transfer salts for use in these methods include
tetrabutylammonium chloride (or bromide) and tetraoctylammonium
bromide (or chloride).
[0751] Suitable hydrophilic ligands are organic molecules which
provide at least one binding group to associate tightly with the
surface of a nanocrystal. The hydrophilic ligand typically is an
organic moiety having a molecular weight between about 100 and
1500, and contains enough polar functional groups to be water
soluble. Some examples of suitable hydrophilic ligands include
small peptide having 2-10 amino acid residues (preferably including
at least one histidine or cysteine residue), mono- or polydentate
thiol containing compounds.
[0752] Following ligand exchange, the surface layer can optionally
be crosslinked.
[0753] In another aspect, provided herein is a "two-step" ligand
exchange process to apply various types of ligands to the surface
of a nanoparticle, by substituting a desired hydrophilic ligand for
a conventional hydrophobic ligand like TOPO, TOP, TDPA, OPA, and
the like. The process involves the removal of phosphonate or
phosphinate ligands from the surface of a nanoparticle or
nanocrystal by treatment with sulfonate reagents, particularly
silylsulfonate derivatives of weak bases or other poorly
coordinating groups.
[0754] The process steps, comprising: providing a nanocrystal whose
surface comprises a phosphonate ligand, contacting the nanocrystal
with a sulfonate reagent in an organic solvent, contacting the
sulfonate ligand coated nanocrystal with a functionalized organic
molecule (i.e., hydrophilic ligand) comprising at least one
nanocrystal surface attachment group, contacting the nanocrystal
dispersion with an aqueous solution to form a biphasic mixture
having an aqueous phase and a non-aqueous phase, and maintaining
the biphasic mixture under conditions which cause the nanocrystal
to migrate from the non-aqueous phase into the aqueous phase. See
PCT Application Serial No. PCT/US09/59456 which is expressly
incorporated herein by reference as if set forth in full.
[0755] The result of this removal of phosphonate ligands is
replacement of the phosphonates with the weakly coordinating
groups. One example is the use of silyl sulfonates, such as
trimethylsilyl triflate, to form a sulfonate-coated nanoparticle.
Triflate is a conventional/common name for a
trifluoromethanesulfonyloxy group, CF.sub.3SO.sub.2O--.
[0756] The same type of replacement process can also occur on
nanoparticles having phosphinic acid ligands of the formula
R.sub.2P(.dbd.O)--OH or on nanoparticles having carboxylic acid
ligands of the formula RC(.dbd.O)--OH, which could be incorporated
on the surface of a nanocrystal by known methods; R can be a
C.sub.1-C.sub.24 hydrocarbon group in these phosphinates, and the
two R groups can be the same or different. Thus, it is understood
that when phosphonate-containing nanocrystals are described herein,
phosphinate-containing nanocrystals can be used instead, with
similar results.
[0757] This process provides a mild and selective method for
removing phosphonate, phosphinate, and carboxylate ligands from the
surface of a nanocrystal. As a result, it provides a way for a user
to remove these groups and replace them, without removing other
ligands which are not displaced or affected by the
silylsulfonate.
[0758] The sulfonate ligands can comprise an alkyl or aryl moiety
linked to --SO.sub.3X, where X can represent whatever the sulfonate
group is attached to. For example, where the sulfonate ligand is a
sulfonate anion (i.e., triflate), X would represent a nanocrystal,
or the surface of a nanocrystal. Some of the sulfonate embodiments
disclosed herein can also be described with reference to feature
`A` of Formula I, as set forth below.
##STR00002##
[0759] wherein R.sup.1, R.sup.2, R.sup.3 and A are each,
independently, C.sub.1-C.sub.10 alkyl or C.sub.5-C.sub.10 aryl; and
each alkyl and aryl is optionally substituted.
[0760] The alkyl groups for Formula I compounds are independently
selected, and can be straight chain, branched, cyclic, or
combinations of these, and optionally can include a C1-C4 alkoxy
group as a substituent. Typically, the alkyl groups are lower
alkyls, e.g., C1-C4 alkyl groups which are linear or branched.
Methyl is one suitable example.
[0761] The aryl group for the compounds of Formula I can be phenyl,
naphthyl or a heteroaryl having up to 10 ring members, and can be
monocyclic or bicyclic, and optionally contain up to two
heteroatoms selected from N, O and S as ring members in each ring.
(It will be understood by those skilled in the art that the
5-membered aryl is a heteroaryl ring.) Phenyl is a preferred aryl
group; and an aryl group is typically only present if the other
organic groups on the silicon other than the sulfonate are lower
alkyls, and preferably they are each Me.
[0762] Examples of silylsulfonate ligands can include, but are not
limited to: (trimethylsilyl)triflate, (triethylsilyl)triflate,
(t-butyldimethylsilyl)triflate, (phenyldimethylsily)triflate,
trimethylsilyl fluoromethanesulfonate, trimethylsilyl
methanesulfonate, trimethylsilyl nitrophenylsulfonate,
trimethylsilyl trifluoroethylsulfonate, trimethylsilyl
phenylsulfonate, trimethylsilyl toluenesulfonate, diisopropylsilyl
bis(trifluoromethanesulfonate), tertbutyldimethylsilyl
trifluoromethanesulfonate, triisopropylsilyl
trifluoromethanesulfonate and trimethylsilyl chlorosulfonate.
[0763] Examples of other sulfonate ligands can include, but are not
limited to: trifluoromethanesulfonate (triflate),
fluoromethanesulfonate, methanesulfonate (mesylate),
nitrophenylsulfonate (nosylate), trifluorethylsulfonate,
phenylsulfonate (besylate) and toluenesulfonate (tosylate).
[0764] Some suitable examples of the hydrophilic ligand are
disclosed, for example, in Naasani, U.S. Pat. Nos. 6,955,855;
7,198,847; 7,205,048; 7,214,428; and 7,368,086. Suitable
hydrophilic ligands also include imidazole containing compounds
such as peptides, particularly dipeptides, having at least one
histidine residue, and peptides, particularly dipeptides, having at
least one cysteine residue. Specific ligands of interest for this
purpose can include carnosine (which contains beta-alanine and
histidine); His-Leu; Gly-His; His-Lys; His-Glu; His-Ala; His-His;
His-Cys; Cys-His; His-Ile; His-Val; and other dipeptides where His
or Cys is paired with any of the common alpha-amino acids; and
tripeptides, such as Gly-His-Gly, His-Gly-His, and the like. The
chiral centers in these amino acids can be the natural
L-configuration, or they can be of the D-configuration or a mixture
of L and D. Thus a dipeptide having two chiral centers such as
His-Leu can be of the L,L-configuration, or it can be L,D- or D,L;
or it can be a mixture of diastereomers.
[0765] Furthermore, suitable hydrophilic ligands can also include
mono- or polydentate thiol containing compounds, for example:
monodentate thiols such as mercaptoacetic acid, bidentate thiols
such as dihydrolipoic acid (DHLA), tridentate thiols such as
compounds of Formula II-VII as shown below, and the like.
##STR00003##
[0766] In compounds of Formula II-VII, R.sup.1, R.sup.2, R.sup.3
can independently be H, halo, hydroxyl,
(--(C.dbd.O)--C.sub.1-C.sub.22, --(C.dbd.O)CF.sub.3,) alkanoyl,
C.sub.1-C.sub.22 alkyl, C.sub.1-C.sub.22 heteroalkyl,
((CO)OC.sub.1-C.sub.22) alkylcarbonato, alkylthio
(C.sub.1-C.sub.22) or (--(CO)NH(C.sub.1-C.sub.20) or
--(CO)N(C.sub.1-C.sub.20).sub.2) alkylcarbamoyl. In some
embodiments, R.sup.1, R.sup.2, and R.sup.3 are different. In other
embodiments, R.sup.1, R.sup.2, and R.sup.3 are the same.
[0767] In compounds of Formula II-VII, R.sup.4, and R.sup.5 can
independently be H, C.sub.1-C.sub.20 alkyl, C.sub.6-C.sub.18 aryl,
C.sub.1-C.sub.22 heteroalkyl or C.sub.1-C.sub.22 heteroaryl. In
some embodiments, R.sup.4 and R.sup.5 are different. In other
embodiments, R.sup.4 and R.sup.5 are the same.
[0768] In compounds of Formula II-VII, R.sup.6 can be H or a
polyethylene glycol based moiety of Formula VIII:
##STR00004##
[0769] In certain embodiments of Formula VII, R.sup.7 can be
--NH.sub.2, --N.sub.3, --NHBoc, --NHFmoc, --NHCbz, --COOH,
--COOt-Bu, --COOMe, iodoaryl, hydroxyl, alkyne, boronic acid,
allylic alcohol carbonate, --NHBiotin, --(CO)NHNHBoc,
--(CO)NHNHFmoc or --OMe. In some embodiments, n can be an integer
from 1 to 100.
[0770] In still further embodiments, the tridentate thiol ligands
can be a compound of Formula IX, X, XI, XII, XIII, XIV, XV, XVI,
XVII, XVIII, XIX, XX, XXI, XXII, XXIII or XXIV:
##STR00005## ##STR00006## ##STR00007##
[0771] Functionalized TDPA Ligands on Nanoparticles
[0772] Provided herein are methods for preparing water-soluble
semi-conducting, insulating, or metallic nanoparticles including
the steps of admixing one or more nanocrystal precursors and one or
more multi-functional surface ligands with a solvent to form a
solution and heating the solution to a suitable temperature, and in
certain embodiments, methods may include the steps of admixing
nanocrystal cores, one or more nanocrystal precursors, and one or
more multi-functional surface ligands with a solvent to form a
solution and heating the solution to a suitable temperature. In
such embodiments, the one or more multi-functional surface ligands
may at least include a nanocrystal binding center, a linker, and a
functional group, which imparts functionality on the nanocrystal.
As used herein the term "functional group" may refer to a group
which affects reactivity, solubility, or both reactivity and
solubility when present on a multi-functional surface ligand.
Embodiments can include a wide variety of functional groups which
can impart various types of functionality on the nanocrystal
including hydrophilicity, water-solubility, or dispersibility
and/or reactivity, and the functionality may generally not include
only hydrophobicity or only solubility in organic solvents without
increasing reactivity. For example, a functional group which is
generally hydrophobic but which increases reactivity such as an
alkene or alkyne and certain esters and ethers can be encompassed
by embodiments, whereas alkyl groups, which do not generally impart
reactivity but increase hydrophobicity may be excluded.
[0773] In certain embodiments, the nanoparticles produced by the
methods of such embodiments may be coated with ligands which impart
water solubility and/or reactivity on the nanoparticle obviating
the need for ligand replacement. Without wishing to be bound by
theory, eliminating ligand replacement may provide more consistent
thermodynamic properties, which may lead to reduction in
variability of coating and less loss of quantum yield, among other
improvements in the properties of nanoparticles produced by the
methods embodied herein. Eliminating ligand replacement may also
allow for the production of nanoparticles having a wide variety of
functional groups associated with the coating. In particular, while
ligand replacement is generally limited to production of
nanoparticles having amine and/or carboxylic acid functional
groups, in various embodiments, the skilled artisan may choose
among numerous functional groups when preparing the
multi-functional ligands and may, therefore, generate nanoparticles
which provide improved water-solubility or water-dispersity and/or
support improved crosslinking and/or improved reactivity with cargo
molecules. See for example PCT Application Serial No.
PCT/US09/59117 filed Sep. 30, 2009 which are expressly incorporated
herein by reference as if set forth in full.
[0774] In some embodiments, the one or more signals indicative of
nucleotide incorporation can be detected to permit visualization of
polymerase activity. In some embodiments, such visualization
happens in real time or near real time. In some embodiments, the
signal can be an optically detectable signal. In some embodiments,
the optically detectable signal can be a fluorescent signal or a
nonfluorescent signal.
[0775] In some embodiments, one or more labels must be excited
before they can be visualized. In some embodiments, illumination of
the reaction site permits observation of the signals, e.g., FRET
signals, which indicate the nucleotide incorporation event. In some
embodiments, the optical system comprises at least two elements,
namely an excitation source and a detector. The excitation source
generates and transmits incident radiation used to excite the
reactants contained in the array. Depending on the intended
application, the source of the incident light can be a laser, laser
diode, a light-emitting diode (LED), a ultra-violet light bulb,
and/or a white light source. Where desired, more than one source
can be employed simultaneously. The use of multiple sources is
particularly desirable in applications that employ multiple
different reagent compounds having differing excitation spectra,
consequently allowing detection of more than one fluorescent signal
to track the interactions of more than one or one type of molecules
simultaneously.
[0776] The one or more signals indicative of nucleotide
incorporation can be detected and analyzed using any suitable
methods and related devices. Typically, the optical system will
achieve these functions by generating and transmitting an incident
wavelength to the polynucleotides isolated within nanostructures,
and collecting and analyzing the emissions from the reactants.
[0777] In some embodiments, detection is simplified by placing one
or few polymerase and nucleic acid molecules in a sufficiently
small volume such that background signal from non-incorporated
nucleotides is minimized. This can be done, for example, by
isolating, confining or immobilizing a single polymerase, or a
single template nucleic acid molecule, in an optical confinement
such as a zero-mode waveguide. In some embodiments, the polymerase
and/or template nucleic acid molecule can be placed within a
nanochannel. In some embodiments, the nanochannel can be structured
to permit isolation and/or elongation of individual nucleic acid
molecules.
[0778] Exemplary labeling and detection strategies for use with one
or more of the modified polymerases disclosed herein include, but
are not limited to, those disclosed in U.S. Pat. Nos. 6,423,551 and
6,864,626; U.S. Published Application Nos. 2005/0003464,
2006/0176479, 2006/0177495, 2007/0109536, 2007/0111350,
2007/0116868, 2007/0250274 and 2008/08825. A wide variety of
detectors are available in the art. Representative detectors
include but are not limited to optical readers, high-efficiency
photon detection systems, photodiodes (e.g. avalanche photo diodes
(APD); APD arrays, etc.), cameras, charge couple devices (CCD),
electron-multiplying charge-coupled device (EMCCD), intensified
charge coupled device (ICCD), photomultiplier tubes (PMT), a
multi-anode PMT, and a confocal microscope equipped with any of the
foregoing detectors. Where desired, the subject arrays can contain
various alignment aides or keys to facilitate a proper spatial
placement of each spatially addressable array location and the
excitation sources, the photon detectors, or the optical
transmission element as described below.
[0779] In some embodiments, the detection system comprises:
excitation illumination, optical transmission elements, detectors,
and/or computers. In some embodiments, the detection system can
comprise excitation illumination which can excite the energy
transfer or reporter moieties which produce a signal. The
excitation illumination can be electromagnetic energy, such as
radio waves, infrared, visible light, ultraviolet light, X-rays or
gamma rays. The source of the electromagnetic radiation can be a
laser, which possesses properties of mono-chromaticity,
directionality, coherence, polarization, and/or intensity. The
laser can produce a continuous output beam (e.g., continuous wave
laser) or produce pulses of light (e.g., Q-switching or
mode-locking). The laser can be used in a one-photon or
multi-photon excitation mode. The laser can produce a focused laser
beam. The wavelength of the electromagnetic radiation can be
between about 325-840 nm, or between about 325-752 nm, or between
about 330-752 nm, or between about 405-752 nm.
[0780] In some embodiments, the detection system comprises suitable
optical transmission elements that are capable of transmitting
light from one location to another with the desired refractive
indices and geometries. The optical transmission elements transmit
the excitation illumination and/or the emitted energy in an
unaltered or altered form. The optical transmission elements
include: lens, optical fibers, polarization filters (e.g., dichroic
filters), diffraction gratings (e.g., etched diffraction grating),
arrayed waveguide gratings (AWG), optical switches, mirrors,
dichroic mirrors, dichroic beam splitter, lenses (e.g., microlens
and nanolens), collimators, filters, prisms, optical attenuators,
wavelength filters (low-pass, band-pass, or high-pass),
wave-plates, and delay lines, or any combination thereof.
[0781] In some embodiments, spectral detection can also be combined
and/or replaced by other detection methods capable of
discriminating between chemically similar or different labels in
parallel, including, but not limited to, polarization, lifetime,
Raman, intensity, ratiometric, time-resolved anisotropy,
fluorescence recovery after photobleaching (FRAP) and parallel
multi-color imaging. See, for example, Lakowitz, supra. In the
latter technique, use of an image splitter (such as, for example, a
dichroic mirror, filter, grating, prism, etc.) to separate the
spectral components characteristic of each label allows the same
detector, typically a CCD, to collect the images in parallel.
[0782] In some embodiments, multiple cameras or detectors can be
used to view the sample through optical elements (such as, for
example, dichroic mirrors, filters, gratings, prisms, etc.) of
different wavelength specificity. Other suitable methods to
distinguish emission events include, but are not limited to,
correlation/anti-correlation analysis, fluorescent lifetime
measurements, anisotropy, time-resolved methods and polarization
detection.
[0783] Suitable imaging methodologies that can be implemented for
detection of emissions include, but are not limited to, confocal
laser scanning microscopy, Total Internal Reflection (TIR), Total
Internal Reflection Fluorescence (TIRF), near-field scanning
microscopy, far-field confocal microscopy, wide-field
epi-illumination, light scattering, dark field microscopy,
photoconversion, wide field fluorescence, single and/or
multi-photon excitation, spectral wavelength discrimination,
evanescent wave illumination, scanning two-photon, scanning wide
field two-photon, Nipkow spinning disc, multi-foci multi-photon,
and/or other forms of microscopy.
[0784] In some embodiments, the detection system can include one or
more optical transmission elements that serve to collect and/or
direct the incident wavelength to the reactant array; to transmit
and/or direct the signals emitted from the reactants to the photon
detector; and/or to select and modify the optical properties of the
incident wavelengths or the emitted wavelengths from the reactants.
Illustrative examples of suitable optical transmission elements and
optical detection systems include but are not limited to
diffraction gratings, arrayed wave guide gratings (AWG), optic
fibers, optical switches, mirrors, lenses (including microlens and
nanolens), collimators. Other examples include optical attenuators,
polarization filters (e.g., dichroic filters), wavelength filters
(low-pass, band-pass, or high-pass), wave-plates, and delay lines.
Examples of a suitable sequencing and detection systems that may be
used according to the present disclosure include, for example, U.S.
Provisional Application Nos. 61/077,090, filed Jun. 30, 2008;
61/089,497, filed Aug. 15, 2008; 61/090,346, filed Aug. 20, 2008;
and 61/164,324, filed Mar. 27, 2009.
[0785] All of the compositions and methods disclosed and claimed
herein can be made and executed without undue experimentation in
light of the present disclosure. While the compositions and methods
of this invention may have been described in terms of specific
examples or preferred embodiments, these examples and embodiments
are in no way intended to limit the scope of the claims, and it
will be apparent to those of skill in the art that variations may
be applied to the compositions and/or methods and in the steps or
in the sequence of steps of the methods described herein without
departing from the concept, spirit and scope of the invention. More
specifically, it will be apparent that certain agents which are
both chemically and physiologically related may be substituted for
the agents described herein while the same or similar results would
be achieved. All such similar substitutes and modifications
apparent to those skilled in the art are deemed to be within the
spirit, scope and concept of the invention as defined by the
appended claims.
EXAMPLES
Example 1
Production of a Polynucleotide Encoding an Exemplary Modified
Polymerase
[0786] This example illustrates the production of a polynucleotide
encoding an exemplary modified polymerase comprising the amino acid
sequence of SEQ ID NO: 7. A nucleotide sequence encoding a B103
polymerase having the amino acid sequence of SEQ ID NO: 6 was
synthesized and cloned into a suitable expression vector. The
recombinant expression construct was transformed into a suitable
bacterial strain, and transformants were picked and screened for
expression of the recombinant protein. The mutations F383L and
D384N were introduced via site-directed mutagenesis according to
standard methods, thereby generating a nucleotide sequence encoding
a modified polymerase comprising the amino acid sequence of SEQ ID
NO: 7 cloned into the expression vector pTTQ. FIG. 2 provides an
exemplary depiction of this expression vector comprising an open
reading frame comprising the amino acid sequence of SEQ ID NO: 7
(referred to in FIG. 2 as "B104").
Example 2
Purification of an Exemplary Modified Polymerase
[0787] To obtain a purified preparation of the modified polymerase
protein, a highly expressing clone was selected and cultured to a
cell density of 0.5 OD at 37.degree. C. The culture was shifted to
18.degree. C. At OD 0.6, expression of the recombinant protein was
induced by the addition of IPTG to a final concentration of 0.5 or
1 mM, and the culture was grown for an additional 18 hours. Cells
were harvested by differential centrifugation. The yield was
approximately 5 g cells/liter. The cell pellets were frozen at
-80.degree. C. until processed. Unless otherwise indicated, all
subsequent steps were performed on ice or at 4.degree. C. To purify
the modified polymerase, cell pellets were resuspended in 5-10 ml
lysis buffer (50 mM Tris pH 7.5, 50 mM glucose, 0.1 mM EDTA pH 8.0,
0.05% Tween-20, 1 mM DTT) per gram of cell paste. The cells were
lysed under high pressure using a Microfluidizer, M110
(Microfluidics Corp, Boston, Mass.). Streptomycin sulfate (50%
solution in 50 mM Tris pH 7.5) was added to the lysate to a final
concentration of 2% while stirring on ice. The lysate was stirred
for 30 minutes. The cell debris was pelleted by centrifugation at
10,000 rpm in a SLC1500 rotor for 30 minutes. The pellets were
discarded. A 10% solution of polyethyleneimine (pH 7.5) was added
to the lysate, drop wise, to a final concentration of 0.2% while
stirring on ice. The lysate continued stirring for 30 minutes and
then centrifuged as described previously. The supernatant was
returned to the ice bath. Solid ammonium sulfate was added to the
stirring supernatant to a final concentration of 65% ammonium
sulfate saturation (43 grams/100 mls lysate). The sample was
stirred for an additional one hour. The precipitated proteins were
collected by centrifugation in an SS34 rotor for 30 minutes at
15,000 rpm. The supernatant was discarded. The precipitated protein
pellets were stored at -20.degree. C.
[0788] The pellets were also subjected to affinity purification
using a His-TRAP FF (GE Healthcare). One 5 ml His-TRAP FF column
was equilibrated in HIS Buffer A (25 mM Hepes pH 7.5, 500 mM NaCl,
1 mM DTT) and 5% His Buffer B (25 mM Hepes pH 7.5, 500 mM NaCl, 1
mM DTT, 500 mM imidazole pH 7.5) on an AKTA 10S (GE Healthcare).
The ammonium sulfate pellets were resuspended in resuspension
buffer (25 mM Hepes pH 7.5, 500 mM NaCl, 1 mM DTT, 25 mM
imidazole). Each sample was filtered with a 1 .mu.M filter
(Acrodisc) and then applied to the His-TRAP column with a P960
pump. The sample was eluted from the column with a 12-70 column
volume gradient of His Buffer B ranging from 5% to 100%. 1.8 ml
fractions were collected. An aliquot of each fraction was subjected
to SDS PAGE to determine which fractions contained the purest
expressed protein (SDS PAGE: 10% NuPage, MES).
[0789] The protein-containing fractions were pooled and diluted
using HIS Buffer A to a conductivity of 17 millisiemens/cm. The
diluted solution was then subjected to affinity purification using
a Heparin column. A Poros HE50 column (10 mm.times.100 mm; 7.8 mls,
Applied Biosystems) was equilibrated in HE Buffer A (25 mM Hepes pH
7.5, 1 mM DTT, 0.05% Tween 20) containing 10% HE Buffer B (25 mM
Hepes pH 7.5, 1M NaCl, 1 mM DTT, 0.05% Tween 20) on the AKTA 10S.
Fractions from the His-trap column containing the purest protein as
judged by SDS PAGE, were pooled and diluted with HE Buffer A to
.about.12-20 mS/cm. The sample (-250 ml) was loaded onto the HE
column at 10 mls a minute with the P960 pump. The proteins were
eluted from the column with a 20 column volume gradient from 10% to
100% HE Buffer B at flow rate of 8 ml/min (156 ml) and 4 ml
fractions were collected. An aliquot of each fraction was subjected
to SDS PAGE to determine the fractions that contained the purest
fraction of the expressed protein (SDS PAGE: 10% NuPage, MES).
[0790] The purest protein samples (as determined by SDS PAGE) were
pooled and dialyzed overnight against Storage Buffer (10 mM Tris pH
7.5, 100 mM NaCl, 0.1 mM EDTA, 1 mM DTT, 50% glycerol). The
concentration of the dialysates was then determined by UV
spectroscopy. The dialyzed protein was diluted 1:10 or 1:20 in
buffer containing 10 mM Tris pH 7.5, 0.1 mM EDTA, 100 mM NaCl; 25%
glycerol. A UV wavelength scan from 220 nm to 320 nm was performed
using a DU780 spectrometer (Beckman). The protein concentration was
determined from the average of three readings at 280 nM. The molar
extinction coefficient as determined by the Vector NTI package
(Invitrogen, Life Technologies) is 98,130 M.sup.-1 cm.sup.-1 and
the predicted molecular weight was 67,717.
Example 3
Characterization of Extension Activity and Nucleotide Incorporation
Activity of Exemplary Reference and Modified Polymerases
[0791] The fractional extension activity of an exemplary modified
polymerase having the amino acid of SEQ ID NO: 8 (referred to as
"B104(exo-)" in FIG. 3) was measured and compared to the fractional
extension activities of two different exemplary reference
polymerases, including an RB69 reference polymerase comprising the
amino acid sequence SEQ ID NO: 15 and a His-tagged Phi-29 reference
polymerase comprising the amino acid sequence of SEQ ID NO: 20
(referred to herein as "HP1 polymerase"). All polymerases were
prepared according to the method of Example 1. Both modified and
reference polymerases were evaluated and compared in an assay to
measure the fractional extension activity of each polymerase, i.e.,
the fraction of nucleic acid templates that are extended by at
least one nucleotide in a polymerase reaction. In this assay, the
fractional extension activity of a polymerase is defined as the
fraction (measured as a percentage fraction) of nucleic acid
templates that are extended by at least one nucleotide by the test
or reference polymerase under the following reaction conditions: 50
mM Tris, pH 7.0, 50 mM NaCl, 1 mM MnCl.sub.2, 1 .mu.M dNTP, 330 nM
enzyme, 100 nM primer-template duplex and 0.5% BSA, wherein the
extension is performed at room temperature for 10 seconds.
[0792] The primer-template duplex was formed by annealing the
following polynucleotides:
TABLE-US-00020 (SEQ ID NO: 21) 5'-GGTACTAAGCGGCCGCATG-3'
("TOP")
[0793] This primer comprises a fluorescein moiety linked to the 5'
terminal nucleotide.
TABLE-US-00021 (SEQ ID NO: 22) 3'-CCATGATTCGCCGGCGTACTTTTTTT-5'
("BOT T6T") (SEQ ID NO: 23) 3'-CCATGATTCGCCGGCGTACAAAAAAA-5' ("BOT
A6A") (SEQ ID NO: 24) 3'-CCATGATTCGCCGGCGTACCCCCCCC-5' ("BOT C6C")
(SEQ ID NO: 25) 3'-CCATGATTCGCCGGCGTACGGGGGGG-5' ("BOT G6G")
[0794] Annealing of the primer of SEQ ID NO: 21 with any of the
templates of SEQ ID NOS: 22-25 results in formation of a
non-extendible duplex comprising a 7-nucleotide overhang.
[0795] The polymerase reaction products were resolved using PAGE
electrophoresis. The extended products were visualized by scanning
the gel with a Bio-Rad Imager for fluorescence emissions at 488 nm.
The results are depicted in FIG. 3. As shown in FIG. 3, the
fractional extension activity (as measured by both intensity and
length of products, as well as by reduced intensity of starting
material) of a modified polymerase comprising the amino acid
sequence of SEQ ID NO: 8 was observed to be higher than the
fractional extension activity of the reference RB69 polymerase
comprising the amino acid sequence of SEQ ID NO: 15 and of the
reference His-tagged Phi-29 polymerase comprising the amino acid
sequence of SEQ ID NO: 20.
Example 4
Characterization of Exonuclease Activity of Exemplary Reference and
Modified Polymerases
[0796] An assay comparing the endogenous exonuclease activity of a
reference polymerase, T7 DNA polymerase, with the exonuclease
activity of a polymerase comprising the amino acid of SEQ ID NO: 7,
was performed. Exonuclease activity was measured by incubating 2, 4
or 10 of each enzyme sample with 7.5 .mu.L Invitrogen Low Mass
ladder, (10068-013) in a 504 reaction containing 10 mM Tris, pH
7.5, 50 mM NaCl and 10 mM MgCl.sub.2 for 16 hours at 37.degree. C.
in an ABI 9700 PCR machine. The samples were resolved via
electrophoresis on a 1.2% E-Gel (Life Technologies). The extent of
exonuclease activity was estimated by visually assessing the
disappearance of the bands of the Low Mass ladder, as compared to
negative control reactions, to which water ("W") or enzyme storage
buffer ("SB") was added instead of purified polymerase). T7 DNA
polymerase served as the reference polymerase (positive control,
indicated as "+control" in FIG. 4. The amount of protein added to
each reaction is indicated at the top of each well. (2, 4, 10 .mu.g
protein, or water ("W") or storage buffer ("SB") for negative
control lanes) As shown in FIG. 4, both the reference and modified
polymerases exhibited comparable levels of exonuclease
activity.
[0797] To determine if the product contained single-strand DNase
(ssDNase) activity that could result from contaminating
polypeptides, the enzyme was tested with AMBION DNase Alert
according to manufacturer's instructions (AM1970, Applied
Biosystems). The fluorescently labeled DNase Alert substrate
(suspended in TE) (10 .mu.L), the supplied 10.times. buffer, and
increasing concentrations of the test enzyme were combined in a
final volume of 100 .mu.L. The samples were read in a Molecular
Devices Plate reader at 485/590 excitation/emission for 60 min at
37.degree. C. No detectable fluorescence was recorded. DNase I
served as a positive control. No ssDNase activity was observed in
either control or sample reactions (results not shown). Exemplary
results are depicted in FIG. 4.
Example 5
Characterization of Nanoparticle Tolerance of Exemplary Reference
and Modified Polymerases
[0798] The nanoparticle tolerance of exemplary modified and
reference polymerases was measured and compared. The nucleotide
incorporation activity of an exemplary modified polymerase
comprising the amino acid sequence of SEQ ID NO: 19 and further
comprising the amino acid substitution D175A was measured both in
the absence and presence of equimolar amounts of a test
nanoparticle. The results were compared to those of an exemplary
reference Phi-29 polymerase comprising the amino acid sequence of
SEQ ID NO: 20.
[0799] Primer extension activity was measured using an assay
wherein free pyrophosphate released as a result of extension of a
primer:template duplex is detected as a fluorescent product.
Reaction conditions included 50 mM Tris, pH 7.5, 50 mM NaCl, 5 mM
DTT, 100 nM polymerase, 100 nM hairpin-template, and 2 mM
MnCl.sub.2 at 23.degree. C., either with or without 100 nM of
nanoparticle added to the mixture. Individual reactions were set up
in microtiter plate wells and initiated by the addition of 2 .mu.l
of 100 .mu.M terminally-labeled nucleotide. The resulting
fluorescence emissions were monitored as a function of time using a
plate reader (Molecular Devices, SpectraMax M5). Reactions without
nucleotides were also monitored as negative controls. Reactions
were monitored for 20 minutes or until the samples reached
saturation.
[0800] Exemplary results are depicted in FIG. 5, which provides a
graph of relative fluorescence observed in each sample (RFU,
arbitrary units, Y axis) against time (seconds, X axis). The
various fluorescence traces depicted in FIG. 5 are as follows:
solid circles and solid squares (two curves along X axis):
fluorescence traces of negative control reactions lacking
polymerase and including or not including nanoparticles; open
diamonds: reaction including a reference Phi-29 polymerase
comprising the amino acid sequence of SEQ ID NO: 1 and further
comprising the amino acid substitution N62D (.PHI.29(exo-)) and
including nanoparticles; open squares and open circles: modified
polymerase comprising the amino acid sequence of SEQ ID NO: 19,
including and not including nanoparticles, respectively. Primer
extension activity was measured as the average slope of the curve
obtained by plotting fluorescence (RFU) vs. time (seconds, X axis)
between the zero time point and at 5 minutes. The primer extension
activity in the presence and absence of dots was computed.
Nanoparticle tolerance is determined as the percentage of primer
extension activity, measured in the presence of test nanoparticle,
relative to the amount of primer extension activity observed in the
absence of the test nanoparticle. These slope values for each
fluorescence trace are depicted below the graph in FIG. 5.
[0801] According to the results of FIG. 5, the modified polymerase
of SEQ ID NO: 19 exhibits approximately 10% loss in primer
extension activity in the presence of equimolar amounts of the test
nanoparticle (i.e., 90% nanoparticle tolerance under these defined
reaction conditions), as compared to a 50% loss in primer extension
activity exhibited by the reference Phi-29 polymerase under
identical test conditions (i.e., 50% nanoparticle tolerance
exhibited by the Phi-29 polymerase under these defined reaction
conditions).
Example 6
Characterization of Photostability of Exemplary Reference and
Modified Polymerases
[0802] The photostability of an exemplary reference polymerase
comprising a His-tagged version of Phi-29 polymerase ("HP1; see,
e.g., U.S. Provisional Application No. 61/184,770, filed Jun. 5,
2009 for disclosure of HP1 sequence and purification) comprising
the amino acid sequence of SEQ ID NO: 20, and an exemplary modified
polymerase comprising the amino acid sequence of SEQ ID NO: 19 and
further comprising the amino acid substitution D175A were
characterized by measuring the amount of primer extension observed
in each sample prior to and following exposure to excitation
radiation at 405 nm. Reactions (100 .mu.L) containing 50 mM Tris,
pH 7.5, 50 mM NaCl, 1 mM DTT, 2 mM MnCl.sub.2, 0.3% BSA, 10-200 nM
polymerase and 100 nM nanoparticles (or premade
polymerase-nanoparticle conjugates; see, e.g., U.S. Provisional
Application No. 61/184,770 filed Jun. 5, 2009), and 100 nM
5'-[.sup.32P]-labeled templates or 5'-TAMRA-labeled templates were
prepared with and without the Oxygen Scavenging System (OSS). The
OSS consists of 0.1 mg/ml Glucose Oxidase (Sigma, Catalog
#G3660-1CAP), 2 units/.mu.l Katalase (Fluka, Catalog #02071), 2 mM
Trolox, and 0.5% glucose (added just prior to illuminations with
405 laser). Aliquots (4 .mu.L) were added to a quartz cuvette
having a path length of 1.5 mm and a height of 15 mm (Hellma,
105.252-QS) and illuminated with a 405 nm laser for a specified
time and at specified power levels. After illumination, samples
were removed and placed on ice until extensions were performed at
23.degree. C. The extensions were performed by addition of 5 .mu.M
nucleotide hexaphosphates comprising a hexaphosphate moiety linked
to the 3' carbon of the sugar moiety, and further comprising a
6-carbon linker attached to the terminal phosphate but without any
fluorescent label. Extensions were performed for 30 seconds
followed by termination with loading buffer (90% formamide, 10 mM
EDTA). Samples were resolved on denaturing polyacrylamide gels (8M
urea, 20% polyacrylamide) and exposed to phosphorimager screen.
Representative results are provided in FIG. 6A. Polymerase activity
was quantified as the % of extended primer (as compared to the
total starting amount of primer), as measured by densitometric
analysis. Phototoxicity is quantified by measuring the percent
decrease in polymerase activity that occurs when samples are
illuminated compared to non-illuminated samples. The photostability
is quantified by subtracting the observed photosensitivity from
100.
[0803] FIG. 6B shows the % activity retained (Y axis) after 30
seconds of exposure to radiation of various intensities (X axis,
W/cm.sup.2). As shown in FIG. 6B, the modified polymerase
comprising the amino acid sequence of SEQ ID NO: 19 and the amino
acid substitution D175A (solid diamonds) retained 80-90% activity
following exposure at 50 W/cm2, whereas the reference Phi-29
polymerase comprising the amino acid sequence of HP1 (solid
squares) retained less than 40% activity.
Example 7
Characterization of t.sub.-1 Values of Exemplary Reference and
Modified Polymerases
[0804] In this example, the t.sub.-1 values of an exemplary
modified polymerase comprising the amino acid of SEQ ID NO: 8 and
an exemplary reference polymerase comprising the amino acid
sequence of SEQ ID NO: 20 were measured and compared. These kinetic
parameters were evaluated using an assay system wherein mixtures
comprising a test polymerase and a primer:template duplex were
mixed in a stopped-flow assay with nucleotides. To measure
t.sub.-1, the primer used to form the primer:template duplex was a
non-extendible primer including a dideoxynucleotide at its 3' end,
and the template was a synthetic DNA template comprising a donor
Alexa Fluor 546 moiety at its 5' end. This primer-template duplex
was preincubated with a test polymerase and a terminally-labeled
nucleoside hexaphosphate or tetraphosphate (".omega.dN4P" or
".omega.dN6P", respectively) to form an EDNA.omega.dN4P or
EDNA.omega.dN6P ternary complex. These terminally-labeled
nucleotides comprise terminal-phosphate-labeled nucleotides having
an alkyl linker with a functional amine group attached to the dye.
The ternary complex was mixed with unlabeled nucleotides in a
stopped-flow experiment, and the resulting fluorescence was
monitored as described below. Unless noted otherwise, all
concentrations refer to the initial concentrations prior to mixing.
All experiments were carried out in 50 mM Tris pH 7.5, 50 mM NaCl,
4 mM DTT, 2 mM MnCl.sub.2 and 0.2% BSA ("extension buffer") using
an Applied Photophysics SX20 stopped-flow spectrometer (Applied
Photophysics, London, U.K.).
[0805] To prepare the primer:template duplex, 20 .mu.M of primer
and 20 .mu.M of template were mixed in solution. The solution was
heated to 90.degree. C. for 5 minutes and then cooled stepwise in a
thermocycler to 4.degree. C. at a rate of 1.degree. C. every 18
seconds. Five different primer:template duplexes were prepared,
each comprising a different template sequence as described
below.
[0806] The nucleotide sequence of the primer was as follows:
TABLE-US-00022 (SEQ ID NO: 26) 5'-GCC TCG CAG CCG TCC AAC CAA
CTC.sup.ddC-3'
[0807] where .sup.ddC indicates a dideoxycytosine triphosphate
moiety. This sequence is referred to as "dd-Top-25-mer".
[0808] Four different templates were tested in separate assays. The
nucleotide sequence of the first template was as follows:
TABLE-US-00023 (SEQ ID NO: 27) AF546-5'-CAG TAA CGG AGT TGG TTG GAC
GGC TGC GAG GC-3'
[0809] where AF546 indicates an Alexa Fluor 546 moiety. This
sequence is referred to as "dd-Template C-32-mer".
[0810] The nucleotide sequence of the second template was as
follows:
TABLE-US-00024 (SEQ ID NO: 28) AF546-5'-CAG TAA GGG AGT TGG TTG GAC
GGC TGC GAG GC-3'
[0811] where AF546 indicates an Alexa Fluor 546 moiety. This
sequence is referred to as "dd-Template G-32-mer".
[0812] The nucleotide sequence of the third template was as
follows:
TABLE-US-00025 (SEQ ID NO: 29) AF546-5'-CAG TAA AGG AGT TGG TTG GAC
GGC TGC GAG GC-3'
[0813] where AF546 indicates an Alexa Fluor 546 moiety. This
sequence is referred to as "dd-Template A-32-mer".
[0814] The nucleotide sequence of the fourth template was as
follows:
TABLE-US-00026 (SEQ ID NO: 30) AF546-5'-CAG TAA TGG AGT TGG TTG GAC
GGC TGC GAG GC-3'
[0815] where AF546 indicates an Alexa Fluor 546 moiety. This
sequence is referred to as "dd-Template T-32-mer".
[0816] Annealing of the primer of SEQ ID NO: 25 with any of the
templates of SEQ ID NOS: 26-30 results in formation of a
non-extendible duplex comprising a 7-nucleotide overhang.
[0817] Preincubated mixtures comprising 200 nM of a primer:templex
duplex, 660 nM of test polymerase, and 14 .mu.M of .omega.dN4P were
prepared and then mixed with a solution comprising the unlabeled
cognate nucleotide (50 .mu.M) in a stopped-flow apparatus. The
fluorescence at both 546 nm and 647 nm was monitored following
mixing. The averaged stopped-flow fluorescence traces were fitted
with a single exponential function having the form of Equation (1)
to extrapolate the t.sub.-1 value of the test polymerase. Using the
above procedure, the estimated t.sub.-1 values of an exemplary
modified polymerase comprising the amino acid sequence of SEQ ID
NO: 8 and an exemplary reference polymerase comprising the amino
acid sequence of SEQ ID NO: 1 were determined to be comparable
(data not shown).
Example 8
Characterization of t.sub.pol Values of Exemplary Reference and
Modified Polymerases
[0818] In this example, the t.sub.pol values of an exemplary
modified polymerase comprising the amino acid of SEQ ID NO: 8 and
was measured and compared to the t.sub.pol value of an exemplary
reference polymerase comprising the amino acid sequence of SEQ ID
NO: 20. These kinetic parameters were evaluated using a
stopped-flow assay wherein a mixture comprising an extendible
dye-labeled primer:template duplex and test polymerase was mixed
with a solution comprising terminally-labeled nucleotide
tetraphosphates or terminally-labeled nucleotide hexaphosphates.
These terminally-labeled nucleotides comprise
terminal-phosphate-labeled nucleotides having an alkyl linker with
a functional amine group attached to the dye. The fluorescence of
the resulting mixture was monitored over time. Unless noted
otherwise, all concentrations refer to the initial concentrations
prior to mixing. All experiments were carried out in 50 mM Tris pH
7.5, 50 mM NaCl, 4 mM DTT, 2 mM MnCl.sub.2 and 0.2% BSA ("extension
buffer") using an Applied Photophysics SX20 stopped-flow
spectrometer (Applied Photophysics, London, U.K.).
[0819] The primer-template duplex comprised an extendible primer
annealed to a synthetic DNA template comprising a donor Alexa Fluor
546 moiety at its 5' end. To prepare the primer:template duplex, 20
.mu.M of primer and 20 .mu.M of template were mixed in solution.
The solution was heated to 90.degree. C. for 5 minutes and then
cooled stepwise in a thermocycler to 4.degree. C. at a rate of
1.degree. C. every 18 seconds.
[0820] The nucleotide sequence of the primer was as follows:
TABLE-US-00027 (SEQ ID NO: 31) 5'-GTT GCA AAG GAG CGG GCG-3'
[0821] Four different templates were prepared and tested in
separate assays. The nucleotide sequence of the first template was
as follows:
TABLE-US-00028 (SEQ ID NO: 32) AF546-5'-CGT TCC CCG CCC GCT CCT TTG
CAA C-3'
[0822] where AF546 indicates an Alexa Fluor 546 moiety.
[0823] The nucleotide sequence of the second template was as
follows:
TABLE-US-00029 (SEQ ID NO: 33) AF546-5'-CGT TCC GCG CCC GCT CCT TTG
CAA C-3'
[0824] where AF546 indicates an Alexa Fluor 546 moiety.
[0825] The nucleotide sequence of the third template was as
follows:
TABLE-US-00030 (SEQ ID NO: 34) AF546-5'-CGT TCC ACG CCC GCT CCT TTG
CAA C-3'
[0826] where AF546 indicates an Alexa Fluor 546 moiety.
[0827] The nucleotide sequence of the fourth template was as
follows:
TABLE-US-00031 (SEQ ID NO: 35) AF546-5'-CGT TCC TCG CCC GCT CCT TTG
CAA C-3'
[0828] where AF546 indicates an Alexa Fluor 546 moiety.
[0829] Annealing of the primer of SEQ ID NO: 25 with any of the
templates of SEQ ID NOS: 26-29 results in formation of an
extendible duplex comprising a 7-nucleotide overhang.
[0830] Each primer-template duplex (200 nM) was preincubated with
test polymerase (660 nM) and to form an EDNA binary complex. This
binary complex was mixed with the cognate omega-labeled nucleoside
tetraphosphate (.omega.dN4P; 14 .mu.M) in a stopped-flow
experiment, and the fluorescence at both 546 nm and 647 nm was
monitored following mixing. The averaged stopped-flow fluorescence
traces were fitted with the double exponential function of Equation
(2) to extrapolate the t.sub.pol value of the test polymerase:
[0831] Using the above procedure, the estimated t.sub.pol values of
an exemplary modified polymerase comprising the amino acid sequence
of SEQ ID NO: 8 and an exemplary reference polymerase comprising
the amino acid sequence of SEQ ID NO: 1 were determined to be
comparable (data not shown).
Example 9
Kinetics of Nucleotide Incorporation by Reference and Modified
Polymerases with Different Nucleotide Compounds
[0832] In this example, the kinetics of nucleotide incorporation by
exemplary reference and modified polymerases were analyzed and
compared in a stopped-flow nucleotide incorporation reaction
comprising the test polymerase of interest, labeled nucleotide
polyphosphates and an extendible primer:template duplex labeled
with ALEXA FLUOR 546 ("AF546"). The AF546-labeled primer-template
duplex was preincubated with the test polymerase, and then mixed in
a stopped-flow assay with terminally-labeled nucleotides comprising
a dye label attached to the terminal phosphate group using
identical reaction conditions as used for t.sub.pol measurements in
the preceding Example (Example 8, above).
[0833] In one study, the primer:template duplex was formed using a
primer having SEQ ID NO: 31 and a template having SEQ ID NO: 32.
Three separate assays were conducted, each using a mutant Phi-29
polymerase and any single one of the following three different
terminally labeled nucleotides: AF647dG3P, AF647dG4P, AF647dG6P.
These nucleotides comprise an ALEXA FLUOR dye ("AF647") on the
terminal phosphate, but differ from each other in the number of
phosphates included in the polyphosphate chain. The resulting
fluorescence time traces are depicted in FIG. 7 (Panel A: Reaction
comprising AF647dG3P; Panel B: Reaction comprising AF647dG4P; Panel
C: Reaction comprising AF647dG6P).
[0834] In another study, the fluorescence time traces observed
using two different Phi-29 mutant polymerases were obtained and
compared. The results are depicted in FIG. 8.
[0835] As illustrated by both FIG. 7 and FIG. 8, different
polymerase-nucleotide combinations result in different time traces
of fluorescence emission. By testing various polymerase-nucleotide
combinations, it is possible to select combinations that exhibit
optimal nucleotide binding affinities and binding speeds, as well
as optimal amplitudes of fluorescence change during the nucleotide
incorporation reaction so as to optimize the detectability of the
reaction progress.
Example 10
Real-Time Single Molecule Sequencing Reaction Using an Exemplary
Modified Polymerase and Labeled Nucleotides
[0836] A exemplary modified polymerase comprising the amino acid
sequence of SEQ ID NO: 8 was used in a nucleotide incorporation
reaction comprising donor-labeled template and acceptor-labeled
nucleotides. A graphical depiction of this nucleotide incorporation
reaction system, showing the immobilized donor-labeled template,
test polymerase and acceptor-labeled nucleotides, is provided in
FIG. 9.
[0837] Preparing PEG-Biotin Surfaces:
[0838] Glass coverslips surfaces were plasma cleaned and treated
with a mixture of poly-ethyleneglycol (PEG) and biotin-PEG to
produce a low density biotin surface with a PEG coating to prevent
non-specific background of proteins and macromolecules.
[0839] Fluidic Chamber Assembly:
[0840] Fluidic cassettes were assembled with glass coverslips to
create fluidic chambers capable of containing approximately 2 .mu.l
of fluid.
[0841] Attaching Biotinylated DNA to Low Density Peg-Biotin
Surfaces:
[0842] Streptavidin protein was diluted to 200 pM in Incubation
Buffer (50 mM NaCl; 50 mM Tris-Cl pH=7.5; 0.5% BSA was optionally
added in some experiments). Diluted streptavidin was flowed into
fluidic chamber and streptavidin was incubated for 10-15 minutes.
Chambers were washed 1.times. with 1 ml Incubation Buffer.
Biotinylated-DNA templates were diluted to 10 pM in Incubation
Buffer and allowed to bind for 10-15 minutes. Surfaces were washed
1.times. with 1 ml Incubation Buffer.
[0843] The primer sequence was as follows:
TABLE-US-00032 (SEQ ID NO: 36) 5'-GCCTCGCAGCCGTCCAACCAA CTCC
-3'
[0844] The template sequence was as follows:
TABLE-US-00033 (SEQ ID NO: 37) Cy3-5'-TGCCACCGGAGTTGGT
TGGACGGCTGCGAGG C-3'-Biotin
[0845] The extension sequence for a duplex formed between this
primer and template in the presence of guanine- and
thymine-comprising nucleotides is GGTGG.
[0846] A reaction mix of 100 uL was prepared comprising 200 nM
dye-labeled guanine nucleotide hexaphosphates, which included the
dye AF647 attached to the omega-phosphate group (AF647-w-dG6P); 200
nM unlabeled thymine nucleotide tetraphosphates (dT4P); and 200 nM
of test polymerase in extension buffer (50 mM ACES, pH 6.5; 50 mM
NaCl) supplemented with 0.4% Glucose, 0.1 mg/mL Glucose Oxidase,
2000 unit/mL Katalase, 2 mM Trolox and 2 mM MnCl.sub.2
[0847] This reaction mixture was injected into the fluidic chamber
comprising immobilized biotinylated duplex and the surface was
imaged by exciting the fluorescence donor at a power density of
about 100W/cm.sup.2 at 532 nm. Images were recorded using an
Olympus microscope outfitted with a TIRF objective lens
(100.times.; 1.45 NA). Emissions were imaged on a CCD camera.
Images were collected at a frame rate of approximately 30
ms/frame.
[0848] To convert the observed fluorescence emissions detected
during the nucleotide incorporation reaction into nucleotide
sequence information, the raw data comprising a movie of observed
emissions was first processed by using a Hidden Markov Model
(HMM)-based algorithm to detect and identify FRET events. The
subsequent detected FRET events were filtered and filtered
sequences were aligned. Each of these two steps, FRET event
detection and sequence analysis, are described in more detail
below. The HMM-based algorithm was used to analyze the data.
[0849] 1) Detection of FRET Events
[0850] The analysis underlying FRET event detection is designed to
process spatially correlated movie(s) comprising real time sequence
fluorescence emission data, and extract time-series of interest
from those data. A movie typically contains one or more channels
where each channel represents the same spatial location at
different wavelengths. The analysis chain begins with the
submission of one or more movies to the analysis machine via a
comprehensive user interface. The user interface requires the user
to input various parameters which describe the movie(s) (e.g.
channel regions, dye emission properties). Once this data is
submitted the movie(s) are then processed by the image analysis
software where a sliding window of N frames propagates through the
movie calculating a temporal local average of the frames within the
window. At each position of the window in the movie, the local
average image is then further processed and enhanced using well
known image processing algorithms and a record of the maximum
projection of all the local average images is recorded to produce a
global image of the movie. This global image is the input into a
spot identification algorithm which produces a set of spots
identified by a unique spot identification, its x and y location
and its corresponding channel. Each set of spots for a given
channel is then registered to the set of spots in every other
channel. In this way a set of spot tuples is constructed. If a
detected spot in one channel does not have a corresponding detected
spot in another channel, then the position of the undetected spot
using the transformation between the two channels and the location
of the detected spot is inferred. Once a complete set of spot
tuples is constructed the movie is iterated over and at each frame
the amplitude of each spot is calculated and appended to the
appropriate time-series.
[0851] The collection of time-series from a spot tuple consists of
time-series from donor and corresponding acceptor channels. This
collection is called a Vector Time-Series (VTS). The FRET detection
process starts with a data segmentation step using a Markov Chain
Monte-Carlo (MCMC) algorithm. Each segment of VTS is modeled by a
multivariate Gaussian model, with each of the channel modeled by a
mean and a standard deviation. This model establishes a baseline
for each channel, from which quantities such as "Donor Down" and
"Acceptor Up" can be calculated. A Hidden Markov Model (HMM) was
used to model the observed data. The underlying states consist of a
null state, a blink state and a number of FRET states (one for each
acceptor channel). Each state has its emission probability, which
reflects the state's corresponding physical concept. FRET states
are characterized by significant "donor down" and "acceptor up"
signals. Blink state is characterized by significant "donor down"
with no "acceptor up". Null state is characterized by no "donor
down" and no "acceptor up". Given the observed VTS signal, the
emission matrix, and a state transition probability matrix, the
most probable state path can be computed using the Viterbi
algorithm. This state path assigns each of the frames to a state.
Temporally neighboring FRET frames are grouped into FRET events.
For each of the detected FRET events, a list of event features are
calculated, including event duration, signal average, signal to
noise ratio, FRET efficiency, probability of event, color calling
and other features. This list of events and corresponding features
are stored in a file.
[0852] The final stage of the automated analysis generates a report
summarizing the results in the form of a web page containing
summary image, statistics of the spots and FRET detection, together
with line intensity plots and base call plots. See for example,
Watkins et al., "Detection of Intensity Change Points in
Time-Resolved Single-Molecule Measurements" J. Phys. Chem. B.,
109(1):617-628 (2005).
[0853] Using the above process, the movie data obtained from the
sequencing reactions was analyzed to detect and identify FRET
events according to the process described above. The FRET events
were then processed to identify sequences as described below.
[0854] Sequence Analysis
[0855] Beginning with the set of detected Forster resonance energy
transfer (FRET) events, a data overview was constructed in the form
of a color image interpreted as a sequencing plot. To generate the
plot, the original FRET event data was pre-processed using a set of
filters constructed by a priori knowledge of the sequence. For each
reaction site (each molecule) an ordered sequence of FRET events
was constructed. The base call letters for each FRET event (e.g.
"A", "C", "G" or "T") were concatenated to form a sequence ASCII
string. The order of letters in the string reflects the temporal
relationship of the events. Given that the expected sequence was
known a priori, a regular expression was then constructed which
represented the full or partial expected sequence or sequence
pattern. Matching against the regular expression (expected
sequence) was then computed for each sequence in the set and the
start and stop indices of the match were recorded. A color plot
image was then constructed where each row corresponds to a sequence
in the set. The plot image was padded to accommodate sequences of
different lengths. A color map of 2*N+1 colors was constructed,
where N denotes the number of possible base calls in each sequence
(N=2 for the plot of this Example). N colors were assigned to the
base characters which fell within the pattern, N colors were
assigned to the base characters which did not fall within the
pattern (muted color), and finally a color was assigned to the
padding (background) of the image. The rows of the image were then
sorted according to the number of base calls in the first part of
the sequence pattern. The rows of the image were also aligned such
that the start of the expected sequence is in the same column for
all rows of the plot.
[0856] One representative output using the reaction conditions
described above is depicted in FIG. 10.
Example 11
Detecting Nucleotide Incorporation with Labeled Biomolecule
Conjugates Comprising a Modified B103 Polymerase Linked to a
Fluorescent Dye Label
[0857] In this Example, a modified B103 polymerase comprising the
amino acid sequence of SEQ ID NO: 42, below, was prepared,
biotinylated and labeled as outlined below. This modified B103
polymerase comprises the amino acid sequence of SEQ ID NO: 8 and
further includes the mutation H370R as well as a biotinylation site
and His tag fused to the N-terminus of the protein. The dye-labeled
polymerase conjugate was then used to study nucleotide
incorporations in single molecule format.
[0858] Preparation of Biotinylated Polymerase
[0859] The construct HB B104 (H370R)_pAN6 was transformed and
expressed in CVB101 (for in vivo biotinylation) cells. The cells
were grown at 30.degree. C. to OD 0.6 and induced with 0.5 mM IPTG.
Upon induction 200 uM D-Biotin was added and cultures were moved to
18.degree. C. shaker and grown 0/N and harvested the following
morning. Cell pellets were resuspended in Buffer B and sonicated to
lyse. PEI (0.3%) was added to cell resuspension and incubated on
ice for 30 min. Cell resuspension was centrifuged to remove cell
debris and DNA. Ammonium sulfate was added to cell lysate at final
concentration of 55%. Lysate was centrifuged and pellets containing
HB B104 (H370R) were resuspended in Buffer, loaded onto EMD-sulfate
column and eluted with linear gradient 10-100% BufferB. Fractions
containing HB B104 (H370R) were pooled and loaded onto a His Trap
column, eluted with linear gradient from 5-100% Buffer C. Peak
fractions were pooled and loaded onto a Heparin column, eluted with
a linear gradient from 10-100% B. Fractions were then quantitated
and analyzed for polymerase activity.
[0860] Buffer compositions were as follows:
[0861] Buffer A: 30 mM Tris pH 7.5, 100 mM NaCl, 2 mM DTT, 0.1 mM
EDTA, 8% glycerol
[0862] Buffer B: 30 mM Tris pH 7.5, 1 M NaCl, 2 mM DTT, 0.1 mM
EDTA, 8% glycerol
[0863] Buffer C: 30 mM Tris pH 7.5, 100 mM NaCl, 2 mM DTT, 0.5M
Imidazole, 8% glycerol
[0864] Preparing NHS-Ester Surfaces:
[0865] Glass coverslips surfaces were plasma cleaned and treated
with a mixture of poly-ethyleneglycol (PEG) and NHS-ester to
produce a low density NHS-ester surface with a PEG coating to
prevent non-specific background of proteins and macromolecules.
[0866] Fluidic Chamber Assembly:
[0867] Fluidic cassettes were assembled with glass coverslips to
create fluidic chambers capable of carrying approximately 2 .mu.l
of fluid.
[0868] Attaching Amine Terminated Hairpin DNA to Low Density
NHS-Ester Surfaces:
Target DNA hairpin sequence:
TABLE-US-00034 (SEQ ID NOS 38 and 49, respectively, in order of
appearance) 5'-TTTTTTTTACCCCCGGGTGACAGGTTXTTCCTGTCACCC-3'
where "X" is an amine group.
[0869] The target DNA was diluted to 500 nM in 1 M NaHCO.sub.3. The
diluted target molecules were flowed into the fluidic chamber and
incubated for 1 hour. Chambers were washed 1.times. with 1 ml
deactivating buffer (ethanolamine). Surfaces were washed 1.times.
with 1 ml incubation buffer (50 mM Tris-C1, pH=7.5; 50 mM NaCl;
0.3% BSA).
[0870] SA-Polymerase Conjugate Preparation:
[0871] Streptavidin was labeled with Cy3. Streptavidin-Cy3 was
mixed with biotinylated mutant B103 polymerase (b-B103-exo minus)
comprising the amino acid sequence of SEQ ID NO: 42 at a 1:1 ratio
of SA-protein: b-B103-exo minus in 1.times.PBS to produce
conjugates comprising biotinylated mutant B103polymerase linked to
dye.
[0872] Briefly, 500 .mu.l of a 3.4 .mu.M solution of Cy3
streptavidin (Invitrogen, SA1010) was mixed with 25 .mu.l of 200
.mu.M biotin-B104 H370R. Twenty five microliters of 5M NaCl were
added to the mixture and it was left at 4 deg C. for 1 hour. To
remove any free, unconjugated labeled streptavidin, the mixture was
diluted with an equal volume of phosphate buffer saline buffer
(PBS) and loaded onto a 1 ml HisTrap cartridge (GE Healthcare).
Following the loading, the cartridge was washed with PBS until the
initially colored eluate from the cartridge became completely
colorless. Finally, the bound Cy3 streptavidin-biotin B104 H370R
conjugate was eluted off the cartridge with a solution of 500 mM
imidazole in PBS buffer containing 200 mM additional NaCl. To the
eluted material was added 50 mM biocytin to a final concentration
of 5 mM, and the mixture was dialyzed overnight against a solution
containing 50% glycerol, 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM
DTT.
[0873] SA-Cy3-b-B103 Binding to Templates:
[0874] The conjugates were diluted to 1 nM in binding buffer (50 mM
Tris-Cl; pH=7.5; 0.3% BSA; 100 mM NaCl). The conjugates were flowed
into the fluidic chamber which were previously loaded with DNA
templates on the surface. Surfaces were incubated for 5 minutes
with conjugates. Surfaces were washed with 1.times.1 ml incubation
buffer.
[0875] Fluorescence Imaging:
[0876] The microscope body was purchased from Olympus and was
outfitted with a TIRF objective lens (100.times.; 1.45 NA). The
excitation light passes through an excitation filter (EX
FT--543/22), and dichroic mirror (DM--532) and the sample was
epi-illuminated (Coherent) using TIR at typically 100 W/cm.sup.2.
Upon excitation, the resulting epifluorescence emission passed
through an emission filter (EM FT--540LP) and the resulting
emission was split into three paths (tri-view) using 2 dichroic
mirrors and the appropriate bandpass filters for the dye sets of
choice. Using this filter combination, we were able to spectrally
resolve 1 donor dye and 3 acceptor dyes in 3 detection
channels.
[0877] In separate experiments, 1 donor dye and 4 different
acceptor dyes could be resolved in 4 detection channels. The
optical detection scheme was as follows: DC1=635, F1 640LP;
DC2=675, F2=688/31; DC3=705, F3=700 LP. The donor dye used in this
case was CY3 and the 4 acceptor dyes are as follows DY634, AF647,
AF676, AF700
[0878] The emissions resulting in each experiment were imaged on a
CCD camera. Images were collected at a frame rate of approximately
20 ms.
[0879] Three-Color Nucleotide Incorporation Reaction:
[0880] Hexa-phosphate dye-labeled nucleotides were diluted to 200
nM in extension buffer (50 mM MOPS pH=7.1; 75 mM potassium acetate
(pH=7.0); 0.3% BSA; 1 mM MnCl.sub.2; 300 nM procatuate dioxygenase;
4 mM 3,4 dihydroxyl benzoic acid; 1 mM 2-nitrobenzoic acid; 400
.mu.M1,2 phenylenediamine; 100 .mu.M ferrocene monocarboxylic acid;
0.02% cyclooctratetraene; 6 mM TROLOX). Nucleotide mix was flowed
into channel with conjugate bound to DNA template and images are
recorded for approximately 2 minutes at approximately 20 ms frame
rates. In this example, the synthesized strand is expected to have
the following sequence: (G).sub.5T(A).sub.8 (SEQ ID NO: 50).
Terminal phosphate-labeled nucleotides and 125 nM cold dC6P were
used for the nucleotide incorporation reaction. The labeled
nucleotides included 125 nM 647-dT6P, 125 nM 676-dG6P, 125 nM
700-dA6P. The spectral signatures for the ALEXA FLUOR-676 G signal,
AF-647 T signal, and AF-700 A signal were identified that resulted
from fluorescence resonance energy transfer (FRET) from the Cy3
donor molecule, and corresponded to the correct insertion sequence
pattern.
[0881] Analysis of Three-Color Sequencing Results
[0882] Resulting pattern sequencing data was processed using an
alignment algorithm. The alignment algorithm found 100 molecules in
the field of view, which demonstrated completion of the full
14-nucleotide sequence ((G).sub.5T(A).sub.8, which represented
approximately 20% of the total single molecule donor population.
The consensus sequence was determined using an HMM alignment
algorithm (e.g., see Example 14). By plotting the accuracy
definition (measured as a percentage value) against the HMM score
(X axis), a linear relationship was detected (data not shown).
Various measurements of accuracy can be devised that can be
suitable for such analysis. In one exemplary experiment, the
accuracy was estimated according to the following equation:
.alpha. ( T , A ) = .beta. - .delta. - .eta. + .lamda. 2 .lamda.
##EQU00006##
[0883] The measurement of accuracy in the above equation is
intended to provide some measure of similarity between some given
template, T, and some alignment, A, of an observed sequence O. It
should be noted that alphabet of T, A, and O are identical. The
length of T is denoted by .lamda., the number of deletions in the
alignment A by .delta., the number of insertions in the alignment
by .eta., and the number of matches in the alignment by .beta..
Equation (1) is normalized by .lamda. such that a an accuracy of 1
indicates a total agreement, and an accuracy of 0 indicates no
agreement between T and A. The above definition of accuracy is
provided as an example only and is in no way intended to limit the
disclosure to any particular theory or definition of accuracy;
alternative definitions of accuracy are also possible and it may be
suitable to use such alternative definitions in some contexts.
[0884] The accuracy in this system using an HMM alignment threshold
of 0 was estimated to be approximately 80% (data not shown).
[0885] Four-Color Nucleotide Incorporation Reaction:
[0886] Oligonucleotides
[0887] 401 Template Molecule:
TABLE-US-00035 (SEQ ID NO: 39) TTTTTCCCCGACGATGCCTCCCC g ACA Cgg
Agg TTC TAT CAT CgT CAT CgT CAT CgT CAT Cg-Biotin TEG-T-3
[0888] Primer for 401 Template:
TABLE-US-00036 (SEQ ID NO: 40) 5' TGA TAG AAC CTC CGT GTC 3'
[0889] In this example, the synthesized strand is expected to have
the following sequence: GGGGAGGCATCGTCGGGAAAA (SEQ ID NO: 41)
[0890] Nucleotide Incorporation Reaction:
[0891] Hexa-phosphate dye-labeled nucleotides were diluted to 200
nM in extension buffer (50 mM MOPS pH=7.1; 75 mM potassium acetate
(pH=7.0); 0.3% BSA; 1 mM MnCl.sub.2; 300 nM procatuate dioxygenase;
4 mM 3,4 dihydroxyl benzoic acid; 1 mM 2-nitrobenzoic acid; 400
.mu.M 1,2 phenylenediamine; 100 .mu.M ferrocene monocarboxylic
acid; 0.02% cyclooctratetraene; 6 mM TROLOX). Nucleotide mix was
flowed into channel with SA-Cy3-b-B103 bound to DNA template and
images are recorded for approximately 2 minutes at approximately 20
ms frame rates.
[0892] The terminal phosphate-labeled nucleotides used for the
nucleotide incorporation reaction included 125 nM DY634-dA6P, 125
nM 647-dT6P, 125 nM 676-dG6P, 125 nM 700-dC6P. The spectral
signatures for the DY-634 A signal, and the ALEXA FLUOR G, T and C
signals (AF-676 G signal, AF-647 T signal, and AF-700 C signal)
were identified that resulted from fluorescence resonance energy
transfer (FRET) from the Cy3 donor molecule, and corresponded to
the correct insertion sequence pattern. 4-color sequence alignment
was obtained by visual inspection.
[0893] The observed FRET event durations for various SA-Cy3-b-B103
conjugates, the event count distributions, and the observed
extension speeds of various SA-Cy3-b-B103 conjugates were
calculated.
[0894] The amino acid sequence of the modified B103 polymerase
comprising the mutation H370R and a biotinylation site and His tag
fused to its N-terminus was as follows:
TABLE-US-00037 (SEQ ID NO: 42) 10 20 30 40 50 60 MSHHHHHHSM
SGLNDIFEAQ KIEWHEGAPG ARGSKHMPRK MFSCDFETTT KLDDCRVWAY 70 80 90 100
110 120 GYMEIGNLDN YKIGNSLDEF MQWVMEIQAD LYFHNLKFDG AFIVNWLEHH
GFKWSNEGLP 130 140 150 160 170 180 NTYNTIISKM GQWYMIDICF GYKGKRKLHT
VIYDSLKKLP FPVKKIAKDF QLPLLKGDID 190 200 210 220 230 240 YHAERPVGHE
ITPEEYEYIK NAIEIIARAL DIQFKQGLDR MTAGSDSLKG FKDILSTKKF 250 260 270
280 290 300 NKVFPKLSLP MDKEIRRAYR GGFTWLNDKY KEKEIGEGMV FDVNSLYPSQ
MYSRPLPYGA 310 320 330 340 350 360 PIVFQGKYEK DEQYPLYIQR IRFEFELKEG
YIPTIQIKKN PFFKGNEYLK NSGAEPVELY 370 380 390 400 410 420 LTNVDLELIQ
EHYEMYNVEY IDGFKFREKT GLFKEFIDKW TYVKTREKGA KKQLAKLMLN 430 440 450
460 470 480 SLYGKFASNP DVTGKVPYLK EDGSLGFRVG DEEYKDPVYT PMGVFITAWA
RFTTITAAQA 490 500 510 520 530 540 CYDRIIYCDT DSIHLTGTEV PEIIKDIVDP
KKLGYWAHES TFKRAKYLRQ KTYIQDIYAK 550 560 570 580 590 600 EVDGKLIECS
PDEATTTKFS VKCAGMTDTI KKKVTFDNFR VGFSSTGKPK PVQVNGGVVL VDSVFTIK
Example 12
Measurement of t.sub.-1 and Values of Modified Phi-29 and B103
Polymerases
[0895] In this example, the t.sub.-1 and t.sub.pol values of a
Phi-29 polymerase comprising the amino acid sequence of SEQ ID NO:
1 and a modified B103 polymerase comprising the amino acid sequence
of SEQ ID NO: 8 (referred to as "mB103 in the table below) and
further including amino acid substitutions at various positions
were measured using a stopped-flow procedure. The stopped-flow
techniques for measuring t.sub.pol (1/k.sub.pol) followed the
techniques described by M P Roettger (2008 Biochemistry
47:9718-9727; M. Bakhtina 2009 Biochemistry 48:3197-320).
[0896] Stopped-Flow Measurements of t.sub.pol
Template C Sequence:
TABLE-US-00038 [0897] (SEQ ID NO: 44)
5'-CGTTAACCGCCCGCTCCTTTGCAAC-3'
Primer Sequence:
TABLE-US-00039 [0898] (SEQ ID NO: 45) 5'-GTTGCAAAGGAGCGGGCG-3'
[0899] The template sequence (SEQ ID NO: 44) further included an
Alexa Fluor 546 dye moiety bonded to the 5' position of the
template.
[0900] The kinetics of nucleotide incorporation by each polymerase
was measured in an Applied Photophysics SX20 stopped-flow
spectrometer by monitoring changes in fluorescence from the
dye-labeled primer-template duplex complexed to enzyme, following
the mixing of the enzyme-DNA complex with dye-labeled nucleotides.
These dye-labeled nucleotides comprise terminal-phosphate-labeled
nucleotides having an alkyl linker with a functional amine group
attached to the dye, and have the general structure shown in FIG.
11. This structure includes a sugar bonded to a hexaphosphate chain
at the 5' carbon position, and to a nucleotide base (denoted as
"N"). The terminal phosphate group of the hexaphosphate is linked
to a 6-carbon linker, and the other end of the 6-carbon linker is
attached to a dye moiety (denoted as "dye"), typically through an
amide bond. In this example, the particular dye-labeled nucleotide
added was a labeled nucleotide hexaphosphate comprising a guanine
base at the N (base) position and an Alexa Fluor 647 (AF647) at the
dye position, and is referred to herein as "AF647-C6-dG6P".
[0901] The primer and template were annealed to form a dye-labeled
primer-template duplex using standard methods. This duplex was
preincubated with polymerase. The mixture included 330 nM
recombinant DNA polymerase, 100 nM template/primer duplex in buffer
("reaction buffer") comprising 50 mM Tris-HCl, pH 7.5, 50 mM NaCl,
4 mM DTT, 0.2% BSA, and 2 mM MnCl.sub.2. The dye-labeled nucleotide
AF647-C6-dG6P was then added to a final concentration of 7 .mu.M,
and the resulting fluorescence was monitored over time.
[0902] The averaged (5 traces) stopped-flow fluorescence traces
(>1.5 ms) were fitted with a double exponential equation (1) to
extrapolate the rates of the nucleotide binding and product
release,
Fluorescence=A.sub.1*e.sup.-k1*1+A.sub.2*e.sup.-kpol*1+C (equation
1)
where A.sub.1 and A.sub.2 represent corresponding fluorescence
amplitudes, C is an offset constant, and k1 and kpol are the
observed rate constants for the fast and slow phases of the
fluorescence transition, respectively.
[0903] Stopped-Flow Measurements of t.sub.-1
[0904] The stopped-flow techniques for measuring t.sub.-1
(1/k.sub.-1) followed the techniques described by M. Bakhtina (2009
Biochemistry 48:3197-3208).
Template C Sequence:
TABLE-US-00040 [0905] (SEQ ID NO: 46) 5'-CAGTAACGG AGT TGG TTG GAC
GGC TGC GAG GC-3'
Dideoxy-Primer Sequence:
TABLE-US-00041 [0906] (SEQ ID NO: 47) 5'-CCC TCG CAG CCG TCC AAC
CAA CTC ddC-3'
[0907] The rate of the nucleotide dissociation (k.sub.-1) from the
ternary complex of [enzymeDNAnucleotide] was measured in an Applied
Photophysics SX20 stopped-flow spectrometer by monitoring changes
in fluorescence from in fluorescence from a duplex Alexa fluor 546
dye-labeled-DNA template following the mixing of the
[enzymeDNAlabeled nucleotide] ternary complex with 50 .mu.M cognate
non-labeled deoxynucleoside triphosphate in a buffer containing 50
mM Tris-HCl (pH 7.5), 50 mM NaCl, 4 mM DTT, 0.2% BSA, and 2 mM
MnCl.sub.2.
[0908] The ternary complexes were prepared using: 330 nM
polymerase, 100 nM template/primer duplex, and 7 .mu.M terminal
phosphate-labeled nucleotides (AF647-C6-dG6P).
[0909] The averaged stopped-flow fluorescence traces (>1.5 msec)
were fitted with a single exponential equation (2) to extrapolate
the rate of the nucleotide dissociation (k.sub.-1) from the
[enzymeDNAnucleotide] ternary complex.
Fluorescence=A.sub.1*e.sup.-k-1*1+C (equation 2)
where A.sub.1 represents the corresponding fluorescence amplitude,
C is an offset constant, and k.sub.-1 and the observed rate
constants for the fluorescence transition.
[0910] Some representative results of, the stopped flow data are
shown in the table below.
TABLE-US-00042 TABLE Summary of t.sub.pol and t.sub.-1 measurements
for various exemplary modified Phi-29 and B103 polymerases Protein
t.sub.pol t.sub.-1 mB103 (SEQ ID: 8) 14 16 mB103 + H370R 17 43
mB103 + H370Y 15 12 mB103 + E371R 11 17 mB103 + E371Y 11 7 K372R 14
12 K380R 783 17 mB103 + D507G 11 13 mB103 + D507H 7 16 mB103 +
K509Y 10 20 Phi-29 (exo-) 11 27 Phi-29 (exo-) + T373R 15 81 Phi-29
(exo-) + T373Y 14 45
Example 13
Measurement of Primer Extension Activity of a Sample Polymerase
Using a Fluorescein-Labeled Oligonucleotide
[0911] This example provides an exemplary assay for primer
extension activity in a sample. Primer extension activity is
quantified by monitoring the fluorescence intensity change over
time during extension of a fluorescein-labeled hairpin
oligonucleotide, comprising the following nucleotide sequence,
known as "oligo 221" (SEQ ID NO: 43). The fluorescence intensity
correlates with the level of primer extension activity in the
sample.
TABLE-US-00043 (SEQ ID NO: 43) (5'-TTTTTTTGCAGGTGACAGGTTTTTCCTGTCA-
CC(fluorescein-T)GC-3').
[0912] The extension reactions are performed in 1.times. extension
buffer (50 mM Tris buffer pH 7.5, 50 mM NaCl, 10 mM MgCl.sub.2 and
0.5 mM MnCl.sub.2). To reaction wells that contain 100 .mu.L of 150
nM of a fluorescein-labeled hairpin oligonucleotide, oligo221 (SEQ
ID NO: 43, above) and 10 nM of polymerase (or conjugated
polymerase) in extension buffer, 2 .mu.L of 1 mM dATP (final
concentration: 20 .mu.M) is added to initiate the enzymatic
reaction and the fluorescence intensity in each well is recorded at
525 nm fluorescence with 490 nm excitation for every 20 seconds for
the next 10 minutes. Control reaction wells include the same
components without any addition of dATP. The fluorescence intensity
at 525 nm (as measured in arbitrary fluorescence units, RFU, y
axis) is plotted against time (seconds, X axis) for each sample, as
well as the control wells (no nucleotide). The fluorescence time
course data from each well is used to calculate the primer
extension activity of each sample using the following
equations:
Activity ( base / sec / enz ) = .DELTA. RFU sample _per _sec
.DELTA. RFU max _per _nMsubs .times. 1 50 nM .times. 7 ( base )
##EQU00007## and ##EQU00007.2## .DELTA. RFU max _per _nMsubs = RFU
max - RFU min substr_conc . ( nM ) ##EQU00007.3##
[0913] Where: RFU.sub.max is the average maximal RFU in the
reference polymerase reaction wells; RFU.sub.min is the average
minimal RFU in the reference polymerase control wells; Substr_conc.
(nM) is the oligo 221 concentration in assay, which is 150 nM;
and:
.DELTA. RFU sample _per _sec = RFU t - RFU 0 t ( sec )
##EQU00008##
[0914] Where: t (sec) is the time period where the fluorescence
intensity increases in the reference enzyme reaction well linearly
from the start; RFU.sub.1 is the average RFU of the reference
enzyme extension wells at t second point; and RFU.sub.0 is the
average RFU of the reference enzyme extension wells at the start
point.
Example 14
Preparation of Core-Shell Nanoparticle CdSe/4CdS-3.5ZnS
Core Synthesis
[0915] Cores are prepared using standard methods, such as those
described in U.S. Pat. No. 6,815,064, the only change being that
the growth is halted at 535 nm emission. These cores were
precipitated and cleaned in the standard methods and resuspended
into hexane for use in the shell reaction.
[0916] Shell Synthesis:
[0917] A 1:1 (w:v) mixture of tri-n-octylphosphine oxide (TOPO) and
tri-n-octylphosphine (TOP) was introduced into a flask.
Tetradecylphosphonic acid (TDPA) was added to the flask in an
amount suitable to fully passivate the final material, as can be
calculated from the reaction scale and the expected final
nanoparticle size. The contents of the flask were heated to
125.degree. C. under vacuum and then the flask was refilled with
N.sub.2 and cooled.
[0918] Inside the glovebox, a solution of a suitable cadmium
precursor (such as dimethylcadmium or cadmium acetate) in TOP was
prepared in a quantity sufficient to produce a desired thickness of
shell, as can be calculated by one of ordinary skill in the art.
When a zinc shell was also desired, a solution of a suitable zinc
precursor (such as diethylzinc or zinc stearate) was prepared in
TOP in a quantity sufficient to produce the desired shell
thickness. Separately, a solution of trimethylsilylsulfide
[(TMS).sub.2S] in TOP was prepared in a quantity sufficient to
produce the desired shell thickness. Each of these solutions was
taken up in separate syringes and removed from the glove box.
[0919] Of the previously prepared core/hexane solution, 17 mL (at
an optical density of 21.5 at the band edge) was added to the
reaction flask and the hexane was removed by vacuum; the flask was
then refilled with N.sub.2. The flask was heated to the desired
synthesis temperature, typically about 200 to about 250.degree. C.
During this heat-up, 17 mL of decylamine was added.
[0920] The cadmium and sulfur precursor solutions were then added
alternately in layer additions, which were based upon the starting
size of the underlying cores. So this means that as each layer of
shell material was added, a new "core" size was determined by
taking the previous "core" size and adding to it the thickness of
just-added shell material. This leads to a slightly larger volume
of the following shell material needing to be added for each
subsequent layer of shell material.
[0921] After a desired thickness of CdS shell material was added,
the cadmium precursor solution was replaced with the zinc precursor
solution. Zinc and sulfur solutions were then added alternately in
layer additions until a desired thickness of ZnS was added. A final
layer of the zinc solution was added at the end, the reaction flask
was cooled, and the product was isolated by conventional
precipitation methods.
Example 15
Exchange Process Using Dipeptide Ligands and Butanol as a
Cosolvent
[0922] Core/shell nanocrystals (quantum dots) were prepared by
standard methods, and were washed with acetic acid/toluene several
times, and suspended in hexanes. 10 nmol of core/shell nanocrystals
were suspended in 40 mL hexane. This was mixed with 10 mL of a 300
mM solution of carnosine and 10 mL of 1 M sodium carbonate solution
n-Butanol (14 mL) was added, and the vessel was flushed with argon.
The mixture was mixed vigorously overnight at room temperature. The
mixture was then heated and allowed to cool to room temperature.
The aqueous phase was then removed and filtered through a 0.2/0.8
micron syringe filter.
[0923] Excess carnosine was removed by dialyzing against 3.5 L of
25 mM NaCl for one hour. The solution was concentrated to 1 mL
using a 10K MWCO (10,000 molecular weight cut-off) Amicon
centricon. A solution was then prepared with 568 mg of His-Leu
dipeptide plus 212 mg of Gly-His dipeptide in 9 mL sodium carbonate
solution, and this solution was combined with the aqueous solution
of quantum dots. This mixture was stirred overnight at room
temperature. The mixture of water-soluble quantum dots was then
dialyzed against 3.5 L of 25 mM NaCl for one hour.
[0924] To crosslink the peptide ligands (clarify)A solution of 0.5
mM 4-aminobenzophenone in ethanol was then added to the aqueous
quantum dots mixture, and the mixture was irradiated at 365 nm for
4 hours to effect reaction of the aminobenzophenone with the
surface molecules on the quantum dots. To this, 5 mmol of THP
(tris(hydroxymethyl)phosphine) was added, and the mixture was
stirred at RT overnight, to induce crosslinking. Another 5 mmol of
THP was added, and again the mixture was stirred overnight at RT.
Another 5 mmol of THP was added the next day, along with 300
micromoles of PEG1000-COOH. This was mixed overnight at room
temperature, then another 5 mmol of THP was added along with 30
mmol of glycine, and the mixture was stirred overnight at RT.
[0925] The material was purified by dialysis using the 10K MWCO
Amicon centricon, and was washed with 50 mM borate buffer (pH 9).
The final material was dispersed into 50 mM borate buffer to a
final concentration of 2.5 micromolar for storage.
Example 16
Exchange Process Using Trithiol Ligands
[0926] A solution of hydrophobic phosphonate-coated quantum dots in
organic solvent (e.g. toluene, chloroform, etc) with a
concentration of between about 0.1 and 10 micromolar quantum dots
was prepared. Approximately 1000 to 1000000 equivalents of a
suitable trithiol ligand was added, optionally as a solution in a
suitable organic solvent (e.g. acetone, methanol, etc). The
reaction mixture was stirred for 1-48 hours and then the solution
was basicified by addition of an organic base (e.g.
tetramethylammonium hydroxide, tetrabutylammonium hydroxide, etc).
After a shorter second stirring period, water or aqueous buffer was
used to extract the dots with hydrophilic ligands. The aqueous
solution was washed with additional organic solvent (e.g. toluene,
chloroform, etc) and purified by filtration.
Example 17
Two-Step Ligand Exchange: Process for Exchanging Phosphonate
Ligands with Sulfonate (Tritlate) Ligands
[0927] A nanoparticle comprising a core/shell nanocrystal having
TDPA ligands on its surface is dissolved in dichloromethane, and
excess TMS triflate is added to it. After 1-2 hours at room
temperature, analysis indicates that the TDPA ligands have been
removed, and the nanoparticle remains dispersed in the solvent. It
is dialyzed against dichloromethane using a 10K MWCO (10,000
molecular-weight cut-off) dialysis membrane to remove excess TMS
triflate and the TMS-TDPA produced by the reaction of TMS triflate
with the TDPA ligands. This produces a solution/suspension of
nanoparticles comprising triflate ligands on the surface of
nanocrystals. These triflate-containing nanoparticles are soluble
in many organic solvents, but may not be readily soluble in
hexanes, depending upon the complement of ligands present.
[0928] Two-Step Process for Exchanging Sulfonate (Triflate) Ligands
with PEG Conjugated Dithiol (DHLA) Ligands Using n-Butanol as an
Intermediate Ligand and DMF as a Co-Solvent
[0929] The triflate-containing nanoparticle solution, described
above, can be contacted with excess n-butanol in acetonitrile,
using DMF as a co-solvent, to provide an intermediate nanoparticle
believed to comprise butanol ligands in place of the triflates
which were on the nanoparticle. This intermediate nanoparticle can
be isolated from the medium, or it can be further modified without
isolation. This intermediate nanoparticle is contacted with an
excess of a dihydrolipoic acid-PEG conjugate of this formula:
##STR00008##
[0930] where n is 1-100.
[0931] The product is a water-soluble, stable nanoparticle. It can
be collected by extraction into a pH 9 buffer, and isolated by
conventional methods, including dialysis with a 10K MWCO dialysis
filter, or by size exclusion (gel filtration) chromatography.
[0932] Two-Step Process for Exchanging Sulfonate (Triflate) Ligands
with Nucleophilic Reactanct Group Containing Ligands Using
n-Butanol as an Intermediate Ligand and DMF as a Co-Solvent
[0933] The triflate-containing nanoparticle solution from can be
contacted with excess n-butanol in acetonitrile, using DMF as a
co-solvent, to provide an intermediate nanoparticle believed to
comprise butanol ligands in place of the triflates which were on
the nanoparticle. This intermediate nanoparticle can be isolated
from the medium, or it can be further modified without isolation.
To further modify it, it is treated with a new ligand containing at
least one nucleophilic reactant group: suitable ligands include
HS--CH.sub.2--CH.sub.2-PEG; aminomethyl phosphonic acid;
dihydrolipoic acid; omega-thio-alkanoic acids, and
carboxymethylphosphonic acid. The mixture is then treated with
TMEDA (tetramethylethylene diamine), and monitored until triflate
is displaced, then the nanocrystal product is extracted into pH 9
buffer and purified by conventional methods.
[0934] Process for Exchanging Sulfonate (Triflate) Ligands with
Carboxylate Functionalized Dithiol (DHLA) Ligands
[0935] The triflate-containing nanoparticle is contacted with neat
dihydrolipoic acid (DHLA) for an hour at room temperature, and is
then dispersed into pH 9 buffer and isolated by conventional
methods. This provides a nanoparticle having carboxylate groups to
provide water solubility, and having two thiol groups binding the
carboxylate to the nanocrystal surface. The product is water
soluble and stable in aqueous buffer. It provides good colloidal
stability, and a moderate quantum yield. This composition
containing DHLA as a ligand contains free carboxyl groups which can
be used to attach other groups such as a PEG moiety, optionally
linked to a functional group or a biomolecule. The same reaction
can be performed to replace triflate groups on a nanoparticle with
thioglycolic acid (HS--CH.sub.2--COOH) ligands. This provides a
highly stabilized nanoparticle which produces a high quantum yield,
but has lower colloidal stability than the product having DHLA on
its surface.
[0936] Process for Exchanging Sulfonate (Triflate) Ligands with
Amine Ligands
[0937] The triflate-containing nanoparticle is dispersed in
dichloromethane plus hexanes, and an alkylamine is added. Suitable
alkylamines are preferably primary amines, and include, e.g.,
H.sub.2N--(CH.sub.2).sub.r-PEG (r=2-10), p-aminomethylbenzoic acid,
and lysine ethyl ester. After an hour at room temperature, the
exchange process is completed, and the nanoparticle product can be
isolated by conventional methods.
[0938] Process for Pre-Treating Phosphonate Coated Nanocrystals
with Toluene Acetic Acid to Remove Impurities Prior to Exchanging
with Sulfonate (Triflate) Ligands
[0939] TDPA-covered nanocrystals were synthesized which emitted
light at 605 nm and had shells of CdS and of ZnS. These when
treated with 200,000 equivalents of TMS triflate in hexanes did not
produce a precipitate. This was attributed to excess TDPA-derived
impurities in the nanocrystals. This was alleviated by dissolving
the nanocrystals in toluene-acetic acid and precipitating them with
methanol, to remove TDPA salts or related by-products. The
resultant TDPA nanocrystals behaved as described above,
demonstrating that impurities were causing the nanocrystals to
behave differently when made with excess TDPA present, and that
those impurities can be removed by precipitation under conditions
better suited to dissolving TDPA-related impurities.
[0940] Process for Exchanging Activated (Sulfonate Coated)
Nanocrystals with Dithiol
[0941] (DHLA) Ligands Using Butanol, DMF or Isopropyl Alcohol as
Dispersants
[0942] Three different methods of depositing the DHLA ligands were
employed, each of which was considerably more rapid than the
classic approach using non-activated dots. In the first approach,
the activated dot powder was dispersed in butanol and stirred with
DHLA, then precipitated with hexane and collected in aqueous
buffer. In the second approach, the activated dot powder was
dispersed in dimethylformamide (DMF) and stirred with DHLA, then
precipitated with toluene and collected in aqueous buffer. In the
third approach, the activated dot powder was stirred as a slurry in
neat DHLA, then dispersed in isopropyl alcohol, precipitated with
hexane, and collected in aqueous buffer and purified with a
filtration membrane.
[0943] These three samples, plus a sample derived from
non-activated dots were diluted to 60 nM for a colloidal stability
challenge, wherein the absorbance is monitored over the course of
days to watch for precipitation. Samples 1 (butanol-mediated), 2
(DMF-mediated), and 4 (classic) all precipitated on day 3 or 4 of
the stability challenge, but sample 3 (neat DHLA) lasted twice as
long, coming out of solution on day 7. HPLC measurements indicated
that the DHLA-coated particles produced from activated dots showed
even less aggregation than the classic DHLA particles made by the
displacement of TOPO or pyridine ligands from nanocrystals. Thus
the invention provided rapid reactions leading to improved
colloidal stability and comparable or lower aggregation levels than
conventional ligand replacement methods of putting DHLA on a
nanocrystal. Similar treatment with other thiol ligands like
mercaptoundecanoic acid (MUA) or the PEGylated thiol also provided
water-dispersible nanocrystals. Reacting triflate-coated
nanoparticles with MUA or PEG-thiol gave particles which were
readily dispersible in water, indicating that ligand exchange had
occurred. The observed quantum yield was over 70% in each case.
[0944] Process for Exchanging Activated (Sulfonate Coated)
Nanocrystals with Hydrophilic Phosphonate Ligands
[0945] Triflate-coated dots were dispersed in butanol and then
stirred with phosphonoacetic acid. Triethylamine was added to form
the triethylammonium salt of both the phosphonate and carboxylate
functionalities, and then pH 9 aqueous borate buffer was added to
extract the hydrophilic particles. The result was a bright orange
aqueous dispersion of quantum dots, with no remaining color
observed in the butanol layer. The particles were purified by
centrifugal filtration and the quantum yield was measured to be
72%. Multiple batches of particles were prepared and remained in
solution through room temperature storage for at least eight weeks.
The same method can be successfully employed with DHLA, MUA, and
PEGylated thiol ligands.
[0946] Process for Exchanging Activated (Sulfonate Coated)
Nanocrystals with a Variety of Hydrophilic Phosphonate Ligands Via
Biphasic Exchange
[0947] Using a biphasic exchange method, dispersing the quantum
dots in organic solvents such as chloroform and the exchangeable
ligands in aqueous solution, quantum dots were made water soluble
and stable after ligand exchange with
N,N-Bis(phosphonomethyl)glycine (1) or phosphonoacetic acid (2). In
a typical bi-phasic ligand exchange experiment, 1 nmol of quantum
dots were dispersed in 1 mL of chloroform and placed in a vial with
2 mL of 300 mM phosphonic acid in basic buffer and the mixture was
rapidly stirred at room temperature for 2 days. Quantum yields as
high as 53% were achieved; however the quantum yields achieved were
dependent on core-shell batch employed, probably as a result of
variable amounts of long-chain alkyl phosphonates remaining on the
nanocrystal surface post-ligand exchange. This demonstrated that
complete removal of TDPA from nanocrystals is important for
successful modification of the surface. Though the dots were
rendered water stable by the above phosphonate-containing ligands,
they were not successfully modified with PEG2000-diamine using
standard EDC condensation chemistry.
##STR00009##
[0948] Nanocrystals coated with compounds 1, 2, or 3 were readily
prepared by this method, as well as nanocrystals having a mixture
of compounds I and 2, or 1 and 3, or 2 and 3. In each case, the
nanocrystals were stable, bright and water-soluble. Using mixed
ligands, it was found that PEGylation (with PEG2000-diamine using
standard EDC condensation chemistry) could be achieved with these
phosphonate-containing ligands to produce highly stable, bright,
water soluble nanoparticles. These nanoparticles can be further
stabilized by at least partially cross-linking the ligands using a
diamine such as putrescine, cadaverine, 1,2-diaminoethane,
bis(hexamethylene)triamine, PAMAM dendrimer, and cystamine.
[0949] Two-Step Ligand Exchange Process with Tridentate Thiol
Ligands
[0950] Triflate exchange step was performed following the procedure
described above. Next, the triflate nanoparticles were dispersed in
organic solvent (e.g. toluene, chloroform, etc) with a
concentration of between about 0.1 and 10 micromolar quantum dots.
Approximately 1000 to 1000000 equivalents of a suitable tridentate
thiol ligand was added, optionally as a solution in a suitable
organic solvent (e.g. acetone, methanol, etc). The reaction mixture
was stirred for 1-48 hours and then the solution was basicified by
addition of an organic base (e.g. tetramethylammonium hydroxide,
tetrabutylammonium hydroxide, etc). After a shorter second stirring
period, water or aqueous buffer was used to extract the dots with
hydrophilic ligands. The aqueous solution was washed with
additional organic solvent (e.g. toluene, chloroform, etc) and
purified by filtration.
Example 18
Functionalized Ligands on Nanoparticles
General Core Reaction Procedure
[0951] Into a 25 mL 3 neck flask with 14/20 joints, 1.575 g of
>99% tri-n-octylphosphine oxide (TOPO) was weighed. To this,
1-1000 micromoles of a bi-functional phosphonate ligand was added.
A stir bar was added to this flask. The flask was connected to an
inert atmosphere manifold and evacuated thoroughly, then refilled
with nitrogen. A solution of a suitable cadmium salt in
tri-n-octylphosphine (TOP) was prepared with a concentration of 0.5
mol Cd per kg solution. A desired amount of cadmium as required for
growth of nanoparticles of a desired size was extracted from this
solution, diluted with 0.9 mL of additional TOP, and added to the
flask. The flask was stirred and heated to .about.200-350.degree.
C. under nitrogen flow. A 1 molar solution of selenium in TOP was
prepared and a desired amount as required for growth of
nanoparticles of a desired size was added to the solution,
optionally with addition of a reaction promoter to achieve desired
levels of particle nucleation. One minute after the reaction was
initiated by adding these final reagents, a 20 microliter sample
was removed from the reaction, mixed with 5 mL of hexane, and an
emission spectrum was collected. This aliquot removal and
measurement process was repeated after 2, 3, 4, 5, 6, 7, 8, 10, 12,
and 14 minutes. After 14 minutes, the reaction was rapidly cooled
and the products were isolated by methods understood in the
art.
[0952] Control Core Reaction with Tetradecylphosphonic Acid
[TDPA]
##STR00010##
[0953] The core reaction using TDPA as the phosphonate ligand was
demonstrated as a control reaction. This reaction proceeded with an
initial emission reading at 1 minute of .about.490 nm and
progressing to a final emission reading of .about.544 nm at 14
minutes. The full width at half maximum intensity (FWHM) never got
above 28 nm. The final "growth solution" of the cores was
yellow/light orange in appearance by eye. The aliquoted samples of
this reaction remained dispersed and clear solutions in hexane.
[0954] Core Reaction with 11-methoxy-11-oxo-undecylphosphonic
acid
##STR00011##
[0955] The reaction using 11-methoxy-11-oxo-undecylphosphonic acid
as the phosphonate ligand proceeded with an initial emission
reading at 1 minute was .about.560 nm; this was redder than the
final emission of the control reaction. The final emission of this
reaction was .about.610 nm. The FWHM of this reaction started at
.about.35 nm and steadily got more broad throughout the reaction
for a final FWHM of .about.50 nm.
[0956] The aliquoted samples were not soluble in hexane, and became
almost instantly flocculated and settled to the bottom of the vials
within minutes.
[0957] Core Reaction with 6-ethoxy-6-oxohexylphosphonic acid
##STR00012##
[0958] The core reaction using 6-ethoxy-6-oxohexylphosphonic acid
as the phosphonate ligand had an initial emission reading at 1
minute of .about.560 nm and a final emission reading of .about.606
nm. The FWHM of this reaction started out at 1 minute at .about.43
nm and narrowed to a final FWHM of .about.40.5 nm.
[0959] The solubility of the aliquoted samples was observed. The
hexane samples were immediately cloudy, however the flocculation
did not settle to the bottom of the vials. Six of the aliquoted
samples were centrifuged and the resulting clear, colorless
supernatants were discarded. The pellets were soluble in toluene,
dichloromethane (CH.sub.2Cl.sub.2), dimethylformamide (DMF), and
methanol (MeOH). The pellets were not soluble in water, 50 mM
borate buffer at pH=8.3 or hexane.
[0960] Particles synthesized in the presence of TDPA are soluble in
hexane, toluene, CH.sub.2Cl.sub.2, DMF and hexane. The
6-ethoxy-6-oxohexylphosphonic acid itself is not soluble in hexane,
and neither were the resulting particles from this reaction,
suggesting that the ligand was indeed coating the nanoparticles--a
suggestion which was confirmed with infrared and NMR spectroscopy
indicating the expected ester functionality. Using a solvent system
of toluene as the solubilizing solvent and hexane as a
precipitating solvent, a pellet can be formed along with a clear,
colorless supernatant. The resulting pellet can be re-solubilized
in toluene. This resulting toluene solution allowed an absorbance
spectrum of these cores to be obtained.
[0961] These data suggest that quantum confined nanoparticles have
been formed with 6-ethoxy-6-oxohexylphosphonic acid on the particle
surface. The resulting core particles were taken further into a
shell reaction.
[0962] Shell Reaction Procedure Using 6-ethoxy-6-oxohexylphosphonic
acid
[0963] Core Precipitation
[0964] Three (3) mL of growth solution cores using
6-ethoxy-6-oxohexylphosphonic acid ligand (prepared according to
the procedure of Example 17) was solubilized into 3 mL toluene in a
250 mL conical bottom centrifuge tube. A total of 135 mL of hexane
was added to precipitate the cores. The tube was centrifuged at
3000 RPM for 5 min. The resulting clear, colorless supernatant was
discarded and the pellet was dispersed into 3 mL of toluene.
[0965] Shell Reaction
[0966] Into a 25 mL 3 neck flask with 14/20 joints, 1.4 g of TOPO
was weighed. To this, 1-1000 mg of 6-ethoxy-6-oxohexylphosphonic
acid was added. A stir bar and 1.4 mL of TOP were added to the
flask. The flask was connected to an inert atmosphere manifold and
evacuated thoroughly, then refilled with nitrogen. 2.6 mL of the
toluene solution of cores was added to the flask and the flask was
warmed and evacuated to remove the toluene, then refilled with
nitrogen. Approximately 1 mL of a suitably high-boiling amine was
added to the flask and the flask was heated to 200-350.degree. C.
Solutions of suitable cadmium and zinc precursors in TOP were
prepared with a concentration of 0.5 mol metal ion per kg of
solution. A solution of 10% trimethylsilylsulfide in TOP by weight
was prepared as well. The metal and sulfur precursor solutions were
added slowly over the course of several hours to minimize
additional nanoparticle nucleation. Sufficient shell precursors
were added to grow a shell of a desired thickness, as can be
calculated by one of ordinary skill in the art. When the desired
shell thickness was reached, the reaction was cooled and the
core/shell nanoparticles were isolated by conventional means.
Aliquots taken during the reaction permitted monitoring of the
progress of the shell reaction. It was observed that the emission
maximum after heating but before addition of shell precursors was
very similar to that of the initial cores (.about.600 nm),
suggesting that the bi-functional phosphonate was sufficiently
strongly coordinated to the nanoparticle surface to minimize
Ostwald ripening. A red-shift during shell precursor addition of
.about.50 nm was typical of a shell as deposited in a reaction
employing TDPA, suggesting that the shell formed as expected. In
addition, the nanoparticle solution became much more intensely
emissive, as would be expected of successful deposition of an
insulating shell. Infrared and NMR spectroscopy confirmed that the
functionalized phosphonates were present on the nanoparticles.
Sequence CWU 1
1
501575PRTBacillus sp.Phage Phi-29 1Met Lys His Met Pro Arg Lys Met
Tyr Ser Cys Asp Phe Glu Thr Thr1 5 10 15Thr Lys Val Glu Asp Cys Arg
Val Trp Ala Tyr Gly Tyr Met Asn Ile 20 25 30Glu Asp His Ser Glu Tyr
Lys Ile Gly Asn Ser Leu Asp Glu Phe Met 35 40 45Ala Trp Val Leu Lys
Val Gln Ala Asp Leu Tyr Phe His Asn Leu Lys 50 55 60Phe Asp Gly Ala
Phe Ile Ile Asn Trp Leu Glu Arg Asn Gly Phe Lys65 70 75 80Trp Ser
Ala Asp Gly Leu Pro Asn Thr Tyr Asn Thr Ile Ile Ser Arg 85 90 95Met
Gly Gln Trp Tyr Met Ile Asp Ile Cys Leu Gly Tyr Lys Gly Lys 100 105
110Arg Lys Ile His Thr Val Ile Tyr Asp Ser Leu Lys Lys Leu Pro Phe
115 120 125Pro Val Lys Lys Ile Ala Lys Asp Phe Lys Leu Thr Val Leu
Lys Gly 130 135 140Asp Ile Asp Tyr His Lys Glu Arg Pro Val Gly Tyr
Lys Ile Thr Pro145 150 155 160Glu Glu Tyr Ala Tyr Ile Lys Asn Asp
Ile Gln Ile Ile Ala Glu Ala 165 170 175Leu Leu Ile Gln Phe Lys Gln
Gly Leu Asp Arg Met Thr Ala Gly Ser 180 185 190Asp Ser Leu Lys Gly
Phe Lys Asp Ile Ile Thr Thr Lys Lys Phe Lys 195 200 205Lys Val Phe
Pro Thr Leu Ser Leu Gly Leu Asp Lys Glu Val Arg Tyr 210 215 220Ala
Tyr Arg Gly Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys Glu Lys225 230
235 240Glu Ile Gly Glu Gly Met Val Phe Asp Val Asn Ser Leu Tyr Pro
Ala 245 250 255Gln Met Tyr Ser Arg Leu Leu Pro Tyr Gly Glu Pro Ile
Val Phe Glu 260 265 270Gly Lys Tyr Val Trp Asp Glu Asp Tyr Pro Leu
His Ile Gln His Ile 275 280 285Arg Cys Glu Phe Glu Leu Lys Glu Gly
Tyr Ile Pro Thr Ile Gln Ile 290 295 300Lys Arg Ser Arg Phe Tyr Lys
Gly Asn Glu Tyr Leu Lys Ser Ser Gly305 310 315 320Gly Glu Ile Ala
Asp Leu Trp Leu Ser Asn Val Asp Leu Glu Leu Met 325 330 335Lys Glu
His Tyr Asp Leu Tyr Asn Val Glu Tyr Ile Ser Gly Leu Lys 340 345
350Phe Lys Ala Thr Thr Gly Leu Phe Lys Asp Phe Ile Asp Lys Trp Thr
355 360 365Tyr Ile Lys Thr Thr Ser Glu Gly Ala Ile Lys Gln Leu Ala
Lys Leu 370 375 380Met Leu Asn Ser Leu Tyr Gly Lys Phe Ala Ser Asn
Pro Asp Val Thr385 390 395 400Gly Lys Val Pro Tyr Leu Lys Glu Asn
Gly Ala Leu Gly Phe Arg Leu 405 410 415Gly Glu Glu Glu Thr Lys Asp
Pro Val Tyr Thr Pro Met Gly Val Phe 420 425 430Ile Thr Ala Trp Ala
Arg Tyr Thr Thr Ile Thr Ala Ala Gln Ala Cys 435 440 445Tyr Asp Arg
Ile Ile Tyr Cys Asp Thr Asp Ser Ile His Leu Thr Gly 450 455 460Thr
Glu Ile Pro Asp Val Ile Lys Asp Ile Val Asp Pro Lys Lys Leu465 470
475 480Gly Tyr Trp Ala His Glu Ser Thr Phe Lys Arg Ala Lys Tyr Leu
Arg 485 490 495Gln Lys Thr Tyr Ile Gln Asp Ile Tyr Met Lys Glu Val
Asp Gly Lys 500 505 510Leu Val Glu Gly Ser Pro Asp Asp Tyr Thr Asp
Ile Lys Phe Ser Val 515 520 525Lys Cys Ala Gly Met Thr Asp Lys Ile
Lys Lys Glu Val Thr Phe Glu 530 535 540Asn Phe Lys Val Gly Phe Ser
Arg Lys Met Lys Pro Lys Pro Val Gln545 550 555 560Val Pro Gly Gly
Val Val Leu Val Asp Asp Thr Phe Thr Ile Lys 565 570
57526PRTArtificial SequenceDescription of Artificial Sequence
Synthetic consensus sequence 2Asp Xaa Ser Leu Tyr Pro1
537PRTArtificial SequenceDescription of Artificial Sequence
Synthetic consensus sequence 3Lys Xaa Asn Ser Xaa Tyr Gly1
546PRTArtificial SequenceDescription of Artificial Sequence
Synthetic consensus sequence 4Tyr Gly Asp Thr Asp Ser1
553PRTArtificial SequenceDescription of Artificial Sequence
Synthetic consensus sequence 5Lys Xaa Tyr16572PRTBacillus sp.Phage
Phi-29 6Met Pro Arg Lys Met Phe Ser Cys Asp Phe Glu Thr Thr Thr Lys
Leu1 5 10 15Asp Asp Cys Arg Val Trp Ala Tyr Gly Tyr Met Glu Ile Gly
Asn Leu 20 25 30Asp Asn Tyr Lys Ile Gly Asn Ser Leu Asp Glu Phe Met
Gln Trp Val 35 40 45Met Glu Ile Gln Ala Asp Leu Tyr Phe His Asn Leu
Lys Phe Asp Gly 50 55 60Ala Phe Ile Val Asn Trp Leu Glu His His Gly
Phe Lys Trp Ser Asn65 70 75 80Glu Gly Leu Pro Asn Thr Tyr Asn Thr
Ile Ile Ser Lys Met Gly Gln 85 90 95Trp Tyr Met Ile Asp Ile Cys Phe
Gly Tyr Lys Gly Lys Arg Lys Leu 100 105 110His Thr Val Ile Tyr Asp
Ser Leu Lys Lys Leu Pro Phe Pro Val Lys 115 120 125Lys Ile Ala Lys
Asp Phe Gln Leu Pro Leu Leu Lys Gly Asp Ile Asp 130 135 140Tyr His
Ala Glu Arg Pro Val Gly His Glu Ile Thr Pro Glu Glu Tyr145 150 155
160Glu Tyr Ile Lys Asn Asp Ile Glu Ile Ile Ala Arg Ala Leu Asp Ile
165 170 175Gln Phe Lys Gln Gly Leu Asp Arg Met Thr Ala Gly Ser Asp
Ser Leu 180 185 190Lys Gly Phe Lys Asp Ile Leu Ser Thr Lys Lys Phe
Asn Lys Val Phe 195 200 205Pro Lys Leu Ser Leu Pro Met Asp Lys Glu
Ile Arg Arg Ala Tyr Arg 210 215 220Gly Gly Phe Thr Trp Leu Asn Asp
Lys Tyr Lys Glu Lys Glu Ile Gly225 230 235 240Glu Gly Met Val Phe
Asp Val Asn Ser Leu Tyr Pro Ser Gln Met Tyr 245 250 255Ser Arg Pro
Leu Pro Tyr Gly Ala Pro Ile Val Phe Gln Gly Lys Tyr 260 265 270Glu
Lys Asp Glu Gln Tyr Pro Leu Tyr Ile Gln Arg Ile Arg Phe Glu 275 280
285Phe Glu Leu Lys Glu Gly Tyr Ile Pro Thr Ile Gln Ile Lys Lys Asn
290 295 300Pro Phe Phe Lys Gly Asn Glu Tyr Leu Lys Asn Ser Gly Ala
Glu Pro305 310 315 320Val Glu Leu Tyr Leu Thr Asn Val Asp Leu Glu
Leu Ile Gln Glu His 325 330 335Tyr Glu Met Tyr Asn Val Glu Tyr Ile
Asp Gly Phe Lys Phe Arg Glu 340 345 350Lys Thr Gly Leu Phe Lys Glu
Phe Ile Asp Lys Trp Thr Tyr Val Lys 355 360 365Thr His Glu Lys Gly
Ala Lys Lys Gln Leu Ala Lys Leu Met Phe Asp 370 375 380Ser Leu Tyr
Gly Lys Phe Ala Ser Asn Pro Asp Val Thr Gly Lys Val385 390 395
400Pro Tyr Leu Lys Glu Asp Gly Ser Leu Gly Phe Arg Val Gly Asp Glu
405 410 415Glu Tyr Lys Asp Pro Val Tyr Thr Pro Met Gly Val Phe Ile
Thr Ala 420 425 430Trp Ala Arg Phe Thr Thr Ile Thr Ala Ala Gln Ala
Cys Tyr Asp Arg 435 440 445Ile Ile Tyr Cys Asp Thr Asp Ser Ile His
Leu Thr Gly Thr Glu Val 450 455 460Pro Glu Ile Ile Lys Asp Ile Val
Asp Pro Lys Lys Leu Gly Tyr Trp465 470 475 480Ala His Glu Ser Thr
Phe Lys Arg Ala Lys Tyr Leu Arg Gln Lys Thr 485 490 495Tyr Ile Gln
Asp Ile Tyr Ala Lys Glu Val Asp Gly Lys Leu Ile Glu 500 505 510Cys
Ser Pro Asp Glu Ala Thr Thr Thr Lys Phe Ser Val Lys Cys Ala 515 520
525Gly Met Thr Asp Thr Ile Lys Lys Lys Val Thr Phe Asp Asn Phe Arg
530 535 540Val Gly Phe Ser Ser Thr Gly Lys Pro Lys Pro Val Gln Val
Asn Gly545 550 555 560Gly Val Val Leu Val Asp Ser Val Phe Thr Ile
Lys 565 5707572PRTArtificial SequenceDescription of Artificial
Sequence Synthetic polypeptide 7Met Pro Arg Lys Met Phe Ser Cys Asp
Phe Glu Thr Thr Thr Lys Leu1 5 10 15Asp Asp Cys Arg Val Trp Ala Tyr
Gly Tyr Met Glu Ile Gly Asn Leu 20 25 30Asp Asn Tyr Lys Ile Gly Asn
Ser Leu Asp Glu Phe Met Gln Trp Val 35 40 45Met Glu Ile Gln Ala Asp
Leu Tyr Phe His Asn Leu Lys Phe Asp Gly 50 55 60Ala Phe Ile Val Asn
Trp Leu Glu His His Gly Phe Lys Trp Ser Asn65 70 75 80Glu Gly Leu
Pro Asn Thr Tyr Asn Thr Ile Ile Ser Lys Met Gly Gln 85 90 95Trp Tyr
Met Ile Asp Ile Cys Phe Gly Tyr Lys Gly Lys Arg Lys Leu 100 105
110His Thr Val Ile Tyr Asp Ser Leu Lys Lys Leu Pro Phe Pro Val Lys
115 120 125Lys Ile Ala Lys Asp Phe Gln Leu Pro Leu Leu Lys Gly Asp
Ile Asp 130 135 140Tyr His Ala Glu Arg Pro Val Gly His Glu Ile Thr
Pro Glu Glu Tyr145 150 155 160Glu Tyr Ile Lys Asn Asp Ile Glu Ile
Ile Ala Arg Ala Leu Asp Ile 165 170 175Gln Phe Lys Gln Gly Leu Asp
Arg Met Thr Ala Gly Ser Asp Ser Leu 180 185 190Lys Gly Phe Lys Asp
Ile Leu Ser Thr Lys Lys Phe Asn Lys Val Phe 195 200 205Pro Lys Leu
Ser Leu Pro Met Asp Lys Glu Ile Arg Arg Ala Tyr Arg 210 215 220Gly
Gly Phe Thr Trp Leu Asn Asp Lys Tyr Lys Glu Lys Glu Ile Gly225 230
235 240Glu Gly Met Val Phe Asp Val Asn Ser Leu Tyr Pro Ser Gln Met
Tyr 245 250 255Ser Arg Pro Leu Pro Tyr Gly Ala Pro Ile Val Phe Gln
Gly Lys Tyr 260 265 270Glu Lys Asp Glu Gln Tyr Pro Leu Tyr Ile Gln
Arg Ile Arg Phe Glu 275 280 285Phe Glu Leu Lys Glu Gly Tyr Ile Pro
Thr Ile Gln Ile Lys Lys Asn 290 295 300Pro Phe Phe Lys Gly Asn Glu
Tyr Leu Lys Asn Ser Gly Ala Glu Pro305 310 315 320Val Glu Leu Tyr
Leu Thr Asn Val Asp Leu Glu Leu Ile Gln Glu His 325 330 335Tyr Glu
Met Tyr Asn Val Glu Tyr Ile Asp Gly Phe Lys Phe Arg Glu 340 345
350Lys Thr Gly Leu Phe Lys Glu Phe Ile Asp Lys Trp Thr Tyr Val Lys
355 360 365Thr His Glu Lys Gly Ala Lys Lys Gln Leu Ala Lys Leu Met
Leu Asn 370 375 380Ser Leu Tyr Gly Lys Phe Ala Ser Asn Pro Asp Val
Thr Gly Lys Val385 390 395 400Pro Tyr Leu Lys Glu Asp Gly Ser Leu
Gly Phe Arg Val Gly Asp Glu 405 410 415Glu Tyr Lys Asp Pro Val Tyr
Thr Pro Met Gly Val Phe Ile Thr Ala 420 425 430Trp Ala Arg Phe Thr
Thr Ile Thr Ala Ala Gln Ala Cys Tyr Asp Arg 435 440 445Ile Ile Tyr
Cys Asp Thr Asp Ser Ile His Leu Thr Gly Thr Glu Val 450 455 460Pro
Glu Ile Ile Lys Asp Ile Val Asp Pro Lys Lys Leu Gly Tyr Trp465 470
475 480Ala His Glu Ser Thr Phe Lys Arg Ala Lys Tyr Leu Arg Gln Lys
Thr 485 490 495Tyr Ile Gln Asp Ile Tyr Ala Lys Glu Val Asp Gly Lys
Leu Ile Glu 500 505 510Cys Ser Pro Asp Glu Ala Thr Thr Thr Lys Phe
Ser Val Lys Cys Ala 515 520 525Gly Met Thr Asp Thr Ile Lys Lys Lys
Val Thr Phe Asp Asn Phe Arg 530 535 540Val Gly Phe Ser Ser Thr Gly
Lys Pro Lys Pro Val Gln Val Asn Gly545 550 555 560Gly Val Val Leu
Val Asp Ser Val Phe Thr Ile Lys 565 5708572PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
8Met Pro Arg Lys Met Phe Ser Cys Asp Phe Glu Thr Thr Thr Lys Leu1 5
10 15Asp Asp Cys Arg Val Trp Ala Tyr Gly Tyr Met Glu Ile Gly Asn
Leu 20 25 30Asp Asn Tyr Lys Ile Gly Asn Ser Leu Asp Glu Phe Met Gln
Trp Val 35 40 45Met Glu Ile Gln Ala Asp Leu Tyr Phe His Asn Leu Lys
Phe Asp Gly 50 55 60Ala Phe Ile Val Asn Trp Leu Glu His His Gly Phe
Lys Trp Ser Asn65 70 75 80Glu Gly Leu Pro Asn Thr Tyr Asn Thr Ile
Ile Ser Lys Met Gly Gln 85 90 95Trp Tyr Met Ile Asp Ile Cys Phe Gly
Tyr Lys Gly Lys Arg Lys Leu 100 105 110His Thr Val Ile Tyr Asp Ser
Leu Lys Lys Leu Pro Phe Pro Val Lys 115 120 125Lys Ile Ala Lys Asp
Phe Gln Leu Pro Leu Leu Lys Gly Asp Ile Asp 130 135 140Tyr His Ala
Glu Arg Pro Val Gly His Glu Ile Thr Pro Glu Glu Tyr145 150 155
160Glu Tyr Ile Lys Asn Ala Ile Glu Ile Ile Ala Arg Ala Leu Asp Ile
165 170 175Gln Phe Lys Gln Gly Leu Asp Arg Met Thr Ala Gly Ser Asp
Ser Leu 180 185 190Lys Gly Phe Lys Asp Ile Leu Ser Thr Lys Lys Phe
Asn Lys Val Phe 195 200 205Pro Lys Leu Ser Leu Pro Met Asp Lys Glu
Ile Arg Arg Ala Tyr Arg 210 215 220Gly Gly Phe Thr Trp Leu Asn Asp
Lys Tyr Lys Glu Lys Glu Ile Gly225 230 235 240Glu Gly Met Val Phe
Asp Val Asn Ser Leu Tyr Pro Ser Gln Met Tyr 245 250 255Ser Arg Pro
Leu Pro Tyr Gly Ala Pro Ile Val Phe Gln Gly Lys Tyr 260 265 270Glu
Lys Asp Glu Gln Tyr Pro Leu Tyr Ile Gln Arg Ile Arg Phe Glu 275 280
285Phe Glu Leu Lys Glu Gly Tyr Ile Pro Thr Ile Gln Ile Lys Lys Asn
290 295 300Pro Phe Phe Lys Gly Asn Glu Tyr Leu Lys Asn Ser Gly Ala
Glu Pro305 310 315 320Val Glu Leu Tyr Leu Thr Asn Val Asp Leu Glu
Leu Ile Gln Glu His 325 330 335Tyr Glu Met Tyr Asn Val Glu Tyr Ile
Asp Gly Phe Lys Phe Arg Glu 340 345 350Lys Thr Gly Leu Phe Lys Glu
Phe Ile Asp Lys Trp Thr Tyr Val Lys 355 360 365Thr His Glu Lys Gly
Ala Lys Lys Gln Leu Ala Lys Leu Met Leu Asn 370 375 380Ser Leu Tyr
Gly Lys Phe Ala Ser Asn Pro Asp Val Thr Gly Lys Val385 390 395
400Pro Tyr Leu Lys Glu Asp Gly Ser Leu Gly Phe Arg Val Gly Asp Glu
405 410 415Glu Tyr Lys Asp Pro Val Tyr Thr Pro Met Gly Val Phe Ile
Thr Ala 420 425 430Trp Ala Arg Phe Thr Thr Ile Thr Ala Ala Gln Ala
Cys Tyr Asp Arg 435 440 445Ile Ile Tyr Cys Asp Thr Asp Ser Ile His
Leu Thr Gly Thr Glu Val 450 455 460Pro Glu Ile Ile Lys Asp Ile Val
Asp Pro Lys Lys Leu Gly Tyr Trp465 470 475 480Ala His Glu Ser Thr
Phe Lys Arg Ala Lys Tyr Leu Arg Gln Lys Thr 485 490 495Tyr Ile Gln
Asp Ile Tyr Ala Lys Glu Val Asp Gly Lys Leu Ile Glu 500 505 510Cys
Ser Pro Asp Glu Ala Thr Thr Thr Lys Phe Ser Val Lys Cys Ala 515 520
525Gly Met Thr Asp Thr Ile Lys Lys Lys Val Thr Phe Asp Asn Phe Arg
530 535 540Val Gly Phe Ser Ser Thr Gly Lys Pro Lys Pro Val Gln Val
Asn Gly545 550 555 560Gly Val Val Leu Val Asp Ser Val Phe Thr Ile
Lys 565 57091719DNAArtificial SequenceDescription of Artificial
Sequence Synthetic polynucleotide 9atgcctcgca aaatgtttag ctgcgatttt
gaaaccacca ccaaactgga tgattgtcgt 60gtttgggcct atggctatat ggaaattggc
aacctggata attataaaat cggcaatagc 120ctggatgaat ttatgcagtg
ggttatggaa attcaggccg atctgtattt tcataacctg 180aaatttgatg
gtgcctttat tgtgaattgg ctggaacatc atggctttaa atggtctaat
240gaaggcctgc cgaataccta taacaccatc attagcaaaa tgggccagtg
gtatatgatt 300gatatttgct ttggctataa aggcaaacgt aaactgcata
ccgtgattta tgatagcctg 360aaaaaactgc cgtttccggt gaaaaaaatc
gccaaagatt tccaattacc tttactgaag 420ggtgatattg attatcatgc
agaacgtccg gttggtcatg aaattacacc ggaagaatat 480gaatacatca
agaatgatat tgaaattatt gcccgtgccc tggatattca gtttaaacag
540ggtctggatc gtatgaccgc aggtagcgat tctctgaaag gctttaaaga
tattctgagc 600accaaaaaat ttaacaaagt gtttccgaaa ctgagcctgc
cgatggataa agaaattcgt 660cgtgcctatc gtggtggttt tacctggctg
aatgataaat ataaagaaaa agaaattggc 720gaaggcatgg tttttgatgt
taatagcctg tatccgagcc agatgtatag ccgtccgctg 780ccgtatggtg
caccgattgt gtttcagggc aaatatgaaa aagatgaaca gtatccgctg
840tatattcagc gcatccgctt tgaatttgaa ctgaaagaag gctatatccc
gaccatccag 900attaaaaaaa atccgttttt taaaggcaac gaatatctga
aaaatagcgg tgcagaaccg 960gttgaactgt atctgaccaa tgtggatctg
gaactgatcc aggaacatta tgaaatgtac 1020aacgtggaat atattgatgg
ttttaaattt cgcgaaaaaa ccggtctgtt taaagagttc 1080attgataaat
ggacctatgt gaaaacccat gaaaaaggtg caaaaaaaca gctggccaaa
1140ctgatgttga attccctgta tggcaaattt gcaagcaatc cggatgttac
cggtaaagtt 1200ccgtatctga aagaagatgg tagcctgggt tttcgtgttg
gtgatgaaga atataaagat 1260ccggtttata ccccgatggg tgtttttatt
accgcatggg cacgttttac caccattacc 1320gcagcacagg catgttatga
ccgcattatt tattgcgata ccgatagcat tcatctgacc 1380ggcaccgaag
ttccggaaat tattaaagat attgttgatc cgaaaaaact gggttattgg
1440gcacatgaaa gcacctttaa acgtgcaaaa tatctgcgcc agaaaaccta
tattcaggat 1500atttatgcca aagaagtgga cggtaaactg attgaatgtt
ctccggatga agcaaccacc 1560acaaaattta gcgttaaatg cgcaggtatg
accgatacca ttaaaaaaaa agtgaccttt 1620gataactttc gtgtgggttt
tagcagcacc ggtaaaccga aaccggttca ggttaatggt 1680ggtgttgttc
tggttgatag cgtgtttacc attaaataa 1719101716DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
10atgcctagaa aaatgtttag ttgtgacttt gagacgacta caaagttaga cgattgtcgt
60gtatgggcat atggctatat ggaaatcggt aatctcgaca actacaagat tggaaatagc
120ttagatgaat tcatgcagtg ggttatggaa attcaagctg atttatattt
ccacaatcta 180aaatttgacg gtgctttcat tgtaaactgg ttagagcatc
atggttttaa gtggtcaaac 240gaagggttac cgaatactta taacacaata
atatcaaaaa tgggtcaatg gtatatgatt 300gacatatgtt tcggctataa
gggaaaacgg aaattacata cagtgatata cgacagctta 360aagaaattgc
cgttcccagt aaagaaaata gcgaaagatt ttcaattacc gttattgaag
420ggtgacattg attaccacgc tgaacgtcct gttggacatg agataacacc
cgaagaatac 480gagtatatta agaacgacat agaaattatc gcacgtgcac
ttgacattca atttaaacag 540ggtttagacc gaatgacagc tgggagcgat
agccttaaag ggtttaagga catacttagc 600accaagaaat ttaacaaggt
gtttcctaag cttagcctac caatggataa agaaataagg 660cgagcttatc
gtggtggctt cacatggtta aacgataaat acaaagaaaa agagattggt
720gaaggtatgg tgtttgacgt taacagccta taccccagtc agatgtattc
ccgaccactc 780ccgtacggag cgccaatcgt attccaagga aagtatgaga
aagatgagca atatccgctc 840tatatacagc gtatcagatt tgagtttgaa
ttgaaagagg gctatatacc cacaattcag 900attaagaaaa atcccttttt
taagggtaat gagtatctta aaaacagtgg cgctgagcct 960gttgaactat
atcttactaa tgtagattta gaattaatac aggaacacta cgaaatgtat
1020aacgttgagt atattgacgg atttaaattc cgtgaaaaga ctggattatt
caaagagttt 1080attgataaat ggacatatgt aaaaactcat gaaaagggag
ctaagaaaca attggctaag 1140ctaatgttga atagtctcta tggtaaattt
gcaagtaacc ctgacgttac aggtaaagtc 1200ccttatttaa aagaagatgg
gagccttggt ttccgtgttg gtgatgagga atataaagac 1260cctgtttata
cacctatggg tgtgtttata acggcatggg ctagatttac aactataaca
1320gcggcacaag cgtgttacga tagaattata tattgtgaca ctgatagtat
acatttaaca 1380ggtacagaag taccagaaat aataaaggat attgttgatc
caaaaaagtt agggtactgg 1440gcgcatgaaa gcacatttaa gagagcaaaa
tatttacgtc agaaaacgta tattcaagac 1500atatatgcga aagaggttga
cggtaaattg atagagtgtt cacctgatga agctacgaca 1560actaaattca
gtgtgaaatg tgccggaatg actgacacta tcaaaaagaa agtcacattt
1620gataacttta gagttggttt cagtagcacg ggtaaaccta aaccagttca
agttaatggc 1680ggggtagtgt tggttgatag tgtgtttacg attaaa
1716111719DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 11atgcctcgca aaatgtttag ctgcgatttt
gaaaccacca ccaaactgga tgattgtcgt 60gtttgggcct atggctatat ggaaattggc
aacctggata attataaaat cggcaatagc 120ctggatgaat ttatgcagtg
ggttatggaa attcaggccg atctgtattt tcataacctg 180aaatttgatg
gtgcctttat tgtgaattgg ctggaacatc atggctttaa atggtctaat
240gaaggcctgc cgaataccta taacaccatc attagcaaaa tgggccagtg
gtatatgatt 300gatatttgct ttggctataa aggcaaacgt aaactgcata
ccgtgattta tgatagcctg 360aaaaaactgc cgtttccggt gaaaaaaatc
gccaaagatt tccaattacc tttactgaag 420ggtgatattg attatcatgc
agaacgtccg gttggtcatg aaattacacc ggaagaatat 480gaatacatca
agaatgctat tgaaattatt gcccgtgccc tggatattca gtttaaacag
540ggtctggatc gtatgaccgc aggtagcgat tctctgaaag gctttaaaga
tattctgagc 600accaaaaaat ttaacaaagt gtttccgaaa ctgagcctgc
cgatggataa agaaattcgt 660cgtgcctatc gtggtggttt tacctggctg
aatgataaat ataaagaaaa agaaattggc 720gaaggcatgg tttttgatgt
taatagcctg tatccgagcc agatgtatag ccgtccgctg 780ccgtatggtg
caccgattgt gtttcagggc aaatatgaaa aagatgaaca gtatccgctg
840tatattcagc gcatccgctt tgaatttgaa ctgaaagaag gctatatccc
gaccatccag 900attaaaaaaa atccgttttt taaaggcaac gaatatctga
aaaatagcgg tgcagaaccg 960gttgaactgt atctgaccaa tgtggatctg
gaactgatcc aggaacatta tgaaatgtac 1020aacgtggaat atattgatgg
ttttaaattt cgcgaaaaaa ccggtctgtt taaagagttc 1080attgataaat
ggacctatgt gaaaacccat gaaaaaggtg caaaaaaaca gctggccaaa
1140ctgatgttga attccctgta tggcaaattt gcaagcaatc cggatgttac
cggtaaagtt 1200ccgtatctga aagaagatgg tagcctgggt tttcgtgttg
gtgatgaaga atataaagat 1260ccggtttata ccccgatggg tgtttttatt
accgcatggg cacgttttac caccattacc 1320gcagcacagg catgttatga
ccgcattatt tattgcgata ccgatagcat tcatctgacc 1380ggcaccgaag
ttccggaaat tattaaagat attgttgatc cgaaaaaact gggttattgg
1440gcacatgaaa gcacctttaa acgtgcaaaa tatctgcgcc agaaaaccta
tattcaggat 1500atttatgcca aagaagtgga cggtaaactg attgaatgtt
ctccggatga agcaaccacc 1560acaaaattta gcgttaaatg cgcaggtatg
accgatacca ttaaaaaaaa agtgaccttt 1620gataactttc gtgtgggttt
tagcagcacc ggtaaaccga aaccggttca ggttaatggt 1680ggtgttgttc
tggttgatag cgtgtttacc attaaataa 1719121716DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
12atgcctagaa aaatgtttag ttgtgacttt gagacgacta caaagttaga cgattgtcgt
60gtatgggcat atggctatat ggaaatcggt aatctcgaca actacaagat tggaaatagc
120ttagatgaat tcatgcagtg ggttatggaa attcaagctg atttatattt
ccacaatcta 180aaatttgacg gtgctttcat tgtaaactgg ttagagcatc
atggttttaa gtggtcaaac 240gaagggttac cgaatactta taacacaata
atatcaaaaa tgggtcaatg gtatatgatt 300gacatatgtt tcggctataa
gggaaaacgg aaattacata cagtgatata cgacagctta 360aagaaattgc
cgttcccagt aaagaaaata gcgaaagatt ttcaattacc gttattgaag
420ggtgacattg attaccacgc tgaacgtcct gttggacatg agataacacc
cgaagaatac 480gagtatatta agaacgccat agaaattatc gcacgtgcac
ttgacattca atttaaacag 540ggtttagacc gaatgacagc tgggagcgat
agccttaaag ggtttaagga catacttagc 600accaagaaat ttaacaaggt
gtttcctaag cttagcctac caatggataa agaaataagg 660cgagcttatc
gtggtggctt cacatggtta aacgataaat acaaagaaaa agagattggt
720gaaggtatgg tgtttgacgt taacagccta taccccagtc agatgtattc
ccgaccactc 780ccgtacggag cgccaatcgt attccaagga aagtatgaga
aagatgagca atatccgctc 840tatatacagc gtatcagatt tgagtttgaa
ttgaaagagg gctatatacc cacaattcag 900attaagaaaa atcccttttt
taagggtaat gagtatctta aaaacagtgg cgctgagcct 960gttgaactat
atcttactaa tgtagattta gaattaatac aggaacacta cgaaatgtat
1020aacgttgagt atattgacgg atttaaattc cgtgaaaaga ctggattatt
caaagagttt 1080attgataaat ggacatatgt aaaaactcat gaaaagggag
ctaagaaaca attggctaag 1140ctaatgttga atagtctcta tggtaaattt
gcaagtaacc ctgacgttac aggtaaagtc 1200ccttatttaa aagaagatgg
gagccttggt ttccgtgttg gtgatgagga atataaagac 1260cctgtttata
cacctatggg tgtgtttata acggcatggg ctagatttac aactataaca
1320gcggcacaag cgtgttacga tagaattata tattgtgaca ctgatagtat
acatttaaca 1380ggtacagaag taccagaaat aataaaggat attgttgatc
caaaaaagtt agggtactgg 1440gcgcatgaaa gcacatttaa gagagcaaaa
tatttacgtc agaaaacgta tattcaagac 1500atatatgcga aagaggttga
cggtaaattg atagagtgtt cacctgatga agctacgaca 1560actaaattca
gtgtgaaatg tgccggaatg actgacacta tcaaaaagaa agtcacattt
1620gataacttta gagttggttt cagtagcacg ggtaaaccta aaccagttca
agttaatggc 1680ggggtagtgt tggttgatag tgtgtttacg attaaa
171613572PRTBacillus sp.Phage M2Y 13Met Ser Arg Lys Met Phe Ser Cys
Asp Phe Glu Thr Thr Thr Lys Leu1 5 10 15Asp Asp Cys Arg Val Trp Ala
Tyr Gly Tyr Met Glu Ile Gly Asn Leu 20 25 30Asp Asn Tyr Lys Ile Gly
Asn Ser Leu Asp Glu Phe Met Gln Trp Val 35 40 45Met Glu Ile Gln Ala
Asp Leu Tyr Phe His Asn Leu Lys Phe Asp Gly 50 55 60Ala Phe Ile Val
Asn Trp Leu Glu Gln His Gly Phe Lys Trp Ser Asn65 70 75 80Glu Gly
Leu Pro Asn Thr Tyr Asn Thr Ile Ile Ser Lys Met Gly Gln 85 90 95Trp
Tyr Met Ile Asp Ile Cys Phe Gly Tyr Lys Gly Lys Arg Lys Leu 100 105
110His Thr Val Ile Tyr Asp Ser Leu Lys Lys Leu Pro Phe Pro Val Lys
115 120 125Lys Ile Ala Lys Asp Phe Gln Leu Pro Leu Leu Lys Gly Asp
Ile Asp 130 135 140Tyr His Thr Glu Arg Pro Val Gly His Glu Ile Thr
Pro Glu Glu Tyr145 150 155 160Glu Tyr Ile Lys Asn Asp Ile Glu Ile
Ile Ala Arg Ala Leu Asp Ile 165 170 175Gln Phe Lys Gln Gly Leu Asp
Arg Met Thr Ala Gly Ser Asp Ser Leu 180 185 190Lys Gly Phe Lys Asp
Ile Leu Ser Thr Lys Lys Phe Asn Lys Val Phe 195 200 205Pro Lys Leu
Ser Leu Pro Met Asp Lys Glu Ile Arg Lys Ala Tyr Arg 210 215 220Gly
Gly Phe Thr Trp Leu Asn Asp Lys Tyr Lys Glu Lys Glu Ile Gly225 230
235 240Glu Gly Met Val Phe Asp Val Asn Ser Leu Tyr Pro Ser Gln Met
Tyr 245 250 255Ser Arg Pro Leu Pro Tyr Gly Ala Pro Ile Val Phe Gln
Gly Lys Tyr 260 265 270Glu Lys Asp Glu Gln Tyr Pro Leu Tyr Ile Gln
Arg Ile Arg Phe Glu 275 280 285Phe Glu Leu Lys Glu Gly Tyr Ile Pro
Thr Ile Gln Ile Lys Lys Asn 290 295 300Pro Phe Phe Lys Gly Asn Glu
Tyr Leu Lys Asn Ser Gly Val Glu Pro305 310 315 320Val Glu Leu Tyr
Leu Thr Asn Val Asp Leu Glu Leu Ile Gln Glu His 325 330 335Tyr Glu
Leu Tyr Asn Val Glu Tyr Ile Asp Gly Phe Lys Phe Arg Glu 340 345
350Lys Thr Gly Leu Phe Lys Asp Phe Ile Asp Lys Trp Thr Tyr Val Lys
355 360 365Thr His Glu Glu Gly Ala Lys Lys Gln Leu Ala Lys Leu Met
Leu Asn 370 375 380Ser Leu Tyr Gly Lys Phe Ala Ser Asn Pro Asp Val
Thr Gly Lys Val385 390 395 400Pro Tyr Leu Lys Asp Asp Gly Ser Leu
Gly Phe Arg Val Gly Asp Glu 405 410 415Glu Tyr Lys Asp Pro Val Tyr
Thr Pro Met Gly Val Phe Ile Thr Ala 420 425 430Trp Ala Arg Phe Thr
Thr Ile Thr Ala Ala Gln Ala Cys Tyr Asp Arg 435 440 445Ile Ile Tyr
Cys Asp Thr Asp Ser Ile His Leu Thr Gly Thr Glu Val 450 455 460Pro
Glu Ile Ile Lys Asp Ile Val Asp Pro Lys Lys Leu Gly Tyr Trp465 470
475 480Ala His Glu Ser Thr Phe Lys Arg Ala Lys Tyr Leu Arg Gln Lys
Thr 485 490 495Tyr Ile Gln Asp Ile Tyr Val Lys Glu Val Asp Gly Lys
Leu Lys Glu 500 505 510Cys Ser Pro Asp Glu Ala Thr Thr Thr Lys Phe
Ser Val Lys Cys Ala 515 520 525Gly Met Thr Asp Thr Ile Lys Lys Lys
Val Thr Phe Asp Asn Phe Ala 530 535 540Val Gly Phe Ser Ser Met Gly
Lys Pro Lys Pro Val Gln Val Asn Gly545 550 555 560Gly Val Val Leu
Val Asp Ser Val Phe Thr Ile Lys 565 57014572PRTBacillus sp.Phage Nf
14Met Ser Arg Lys Met Phe Ser Cys Asp Phe Glu Thr Thr Thr Lys Leu1
5 10 15Asp Asp Cys Arg Val Trp Ala Tyr Gly Tyr Met Glu Ile Gly Asn
Leu 20 25 30Asp Asn Tyr Lys Ile Gly Asn Ser Leu Asp Glu Phe Met Gln
Trp Val 35 40 45Met Glu Ile Gln Ala Asp Leu Tyr Phe His Asn Leu Lys
Phe Asp Gly 50 55 60Ala Phe Ile Val Asn Trp Leu Glu Gln His Gly Phe
Lys Trp Ser Asn65 70 75 80Glu Gly Leu Pro Asn Thr Tyr Asn Thr Ile
Ile Ser Lys Met Gly Gln 85 90 95Trp Tyr Met Ile Asp Ile Cys Phe Gly
Tyr Arg Gly Lys Arg Lys Leu 100 105 110His Thr Val Ile Tyr Asp Ser
Leu Lys Lys Leu Pro Phe Pro Val Lys 115 120 125Lys Ile Ala Lys Asp
Phe Gln Leu Pro Leu Leu Lys Gly Asp Ile Asp 130 135 140Tyr His Thr
Glu Arg Pro Val Gly His Glu Ile Thr Pro Glu Glu Tyr145 150 155
160Glu Tyr Ile Lys Asn Asp Ile Glu Ile Ile Ala Arg Ala Leu Asp Ile
165 170 175Gln Phe Lys Gln Gly Leu Asp Arg Met Thr Ala Gly Ser Asp
Ser Leu 180 185 190Lys Gly Phe Lys Asp Ile Leu Ser Thr Lys Lys Phe
Asn Lys Val Phe 195 200 205Pro Lys Leu Ser Leu Pro Met Asp Lys Glu
Ile Arg Lys Ala Tyr Arg 210 215 220Gly Gly Phe Thr Trp Leu Asn Asp
Lys Tyr Lys Glu Lys Glu Ile Gly225 230 235 240Glu Gly Met Val Phe
Asp Val Asn Ser Leu Tyr Pro Ser Gln Met Tyr 245 250 255Ser Arg Pro
Leu Pro Tyr Gly Ala Pro Ile Val Phe Gln Gly Lys Tyr 260 265 270Glu
Lys Asp Glu Gln Tyr Pro Leu Tyr Ile Gln Arg Ile Arg Phe Glu 275 280
285Phe Glu Leu Lys Glu Gly Tyr Ile Pro Thr Ile Gln Ile Lys Lys Asn
290 295 300Pro Phe Phe Lys Gly Asn Glu Tyr Leu Lys Asn Ser Gly Val
Glu Pro305 310 315 320Val Glu Leu Tyr Leu Thr Asn Val Asp Leu Glu
Leu Ile Gln Glu His 325 330 335Tyr Glu Leu Tyr Asn Val Glu Tyr Ile
Asp Gly Phe Lys Phe Arg Glu 340 345 350Lys Thr Gly Leu Phe Lys Asp
Phe Ile Asp Lys Trp Thr Tyr Val Lys 355 360 365Thr His Glu Glu Gly
Ala Lys Lys Gln Leu Ala Lys Leu Met Leu Asn 370 375 380Ser Leu Tyr
Gly Lys Phe Ala Ser Asn Pro Asp Val Thr Gly Lys Val385 390 395
400Pro Tyr Leu Lys Asp Asp Gly Ser Leu Gly Phe Arg Val Gly Asp Glu
405 410 415Glu Tyr Lys Asp Pro Val Tyr Thr Pro Met Gly Val Phe Ile
Thr Ala 420 425 430Trp Ala Arg Phe Thr Thr Ile Thr Ala Ala Gln Ala
Cys Tyr Asp Arg 435 440 445Ile Ile Tyr Cys Asp Thr Asp Ser Ile His
Leu Thr Gly Thr Glu Val 450 455 460Pro Glu Ile Ile Lys Asp Ile Val
Asp Pro Lys Lys Leu Gly Tyr Trp465 470 475 480Ala His Glu Ser Thr
Phe Lys Arg Ala Lys Tyr Leu Arg Gln Lys Thr 485 490 495Tyr Ile Gln
Asp Ile Tyr Val Lys Glu Val Asp Gly Lys Leu Lys Glu 500 505 510Cys
Ser Pro Asp Glu Ala Thr Thr Thr Lys Phe Ser Val Lys Cys Ala 515 520
525Gly Met Thr Asp Thr Ile Lys Lys Lys Val Thr Phe Asp Asn Phe Ala
530 535 540Val Gly Phe Ser Ser Met Gly Lys Pro Lys Pro Val Gln Val
Asn Gly545 550 555 560Gly Val Val Leu Val Asp Ser Val Phe Thr Ile
Lys 565 57015903PRTUnknownDescription of Unknown Enterobacteria
phage RB69 15Met Lys Glu Phe Tyr Leu Thr Val Glu Gln Ile Gly Asp
Ser Ile Phe1 5 10 15Glu Arg Tyr Ile Asp Ser Asn Gly Arg Glu Arg Thr
Arg Glu Val Glu 20 25 30Tyr Lys Pro Ser Leu Phe Ala His Cys Pro Glu
Ser Gln Ala Thr Lys 35 40 45Tyr Phe Asp Ile Tyr Gly Lys Pro Cys Thr
Arg Lys Leu Phe Ala Asn 50 55 60Met Arg Asp Ala Ser Gln Trp Ile Lys
Arg Met Glu Asp Ile Gly Leu65 70 75 80Glu Ala Leu Gly Met Asp Asp
Phe Lys Leu Ala Tyr Leu Ser Asp Thr 85 90 95Tyr Asn Tyr Glu Ile Lys
Tyr Asp His Thr Lys Ile Arg Val Ala Asn 100 105 110Phe Asp Ile Glu
Val Thr Ser Pro Asp Gly Phe Pro Glu Pro Ser Gln 115 120 125Ala Lys
His Pro Ile Asp Ala Ile Thr His Tyr Asp Ser Ile Asp Asp 130 135
140Arg Phe Tyr Val Phe Asp Leu Leu Asn Ser Pro Tyr Gly Asn Val
Glu145 150 155 160Glu Trp Ser Ile Glu Ile Ala Ala Lys Leu Gln Glu
Gln Gly Gly Asp 165 170 175Glu Val Pro Ser Glu Ile Ile Asp Lys Ile
Ile Tyr Met Pro Phe Asp 180 185
190Asn Glu Lys Glu Leu Leu Met Glu Tyr Leu Asn Phe Trp Gln Gln Lys
195 200 205Thr Pro Val Ile Leu Thr Gly Trp Asn Val Glu Ser Phe Asp
Ile Pro 210 215 220Tyr Val Tyr Asn Arg Ile Lys Asn Ile Phe Gly Glu
Ser Thr Ala Lys225 230 235 240Arg Leu Ser Pro His Arg Lys Thr Arg
Val Lys Val Ile Glu Asn Met 245 250 255Tyr Gly Ser Arg Glu Ile Ile
Thr Leu Phe Gly Ile Ser Val Leu Asp 260 265 270Tyr Ile Asp Leu Tyr
Lys Lys Phe Ser Phe Thr Asn Gln Pro Ser Tyr 275 280 285Ser Leu Asp
Tyr Ile Ser Glu Phe Glu Leu Asn Val Gly Lys Leu Lys 290 295 300Tyr
Asp Gly Pro Ile Ser Lys Leu Arg Glu Ser Asn His Gln Arg Tyr305 310
315 320Ile Ser Tyr Asn Ile Ile Asp Val Tyr Arg Val Leu Gln Ile Asp
Ala 325 330 335Lys Arg Gln Phe Ile Asn Leu Ser Leu Asp Met Gly Tyr
Tyr Ala Lys 340 345 350Ile Gln Ile Gln Ser Val Phe Ser Pro Ile Lys
Thr Trp Asp Ala Ile 355 360 365Ile Phe Asn Ser Leu Lys Glu Gln Asn
Lys Val Ile Pro Gln Gly Arg 370 375 380Ser His Pro Val Gln Pro Tyr
Pro Gly Ala Phe Val Lys Glu Pro Ile385 390 395 400Pro Asn Arg Tyr
Lys Tyr Val Met Ser Phe Asp Leu Thr Ser Leu Tyr 405 410 415Pro Ser
Ile Ile Arg Gln Val Asn Ile Ser Pro Glu Thr Ile Ala Gly 420 425
430Thr Phe Lys Val Ala Pro Leu His Asp Tyr Ile Asn Ala Val Ala Glu
435 440 445Arg Pro Ser Asp Val Tyr Ser Cys Ser Pro Asn Gly Met Met
Tyr Tyr 450 455 460Lys Asp Arg Asp Gly Val Val Pro Thr Glu Ile Thr
Lys Val Phe Asn465 470 475 480Gln Arg Lys Glu His Lys Gly Tyr Met
Leu Ala Ala Gln Arg Asn Gly 485 490 495Glu Ile Ile Lys Glu Ala Leu
His Asn Pro Asn Leu Ser Val Asp Glu 500 505 510Pro Leu Asp Val Asp
Tyr Arg Phe Asp Phe Ser Asp Glu Ile Lys Glu 515 520 525Lys Ile Lys
Lys Leu Ser Ala Lys Ser Leu Asn Glu Met Leu Phe Arg 530 535 540Ala
Gln Arg Thr Glu Val Ala Gly Met Thr Ala Gln Ile Asn Arg Lys545 550
555 560Leu Leu Ile Asn Ser Leu Tyr Gly Ala Leu Gly Asn Val Trp Phe
Arg 565 570 575Tyr Tyr Asp Leu Arg Asn Ala Thr Ala Ile Thr Thr Phe
Gly Gln Met 580 585 590Ala Leu Gln Trp Ile Glu Arg Lys Val Asn Glu
Tyr Leu Asn Glu Val 595 600 605Cys Gly Thr Glu Gly Glu Ala Phe Val
Leu Tyr Gly Asp Thr Asp Ser 610 615 620Ile Tyr Val Ser Ala Asp Lys
Ile Ile Asp Lys Val Gly Glu Ser Lys625 630 635 640Phe Arg Asp Thr
Asn His Trp Val Asp Phe Leu Asp Lys Phe Ala Arg 645 650 655Glu Arg
Met Glu Pro Ala Ile Asp Arg Gly Phe Arg Glu Met Cys Glu 660 665
670Tyr Met Asn Asn Lys Gln His Leu Met Phe Met Asp Arg Glu Ala Ile
675 680 685Ala Gly Pro Pro Leu Gly Ser Lys Gly Ile Gly Gly Phe Trp
Thr Gly 690 695 700Lys Lys Arg Tyr Ala Leu Asn Val Trp Asp Met Glu
Gly Thr Arg Tyr705 710 715 720Ala Glu Pro Lys Leu Lys Ile Met Gly
Leu Glu Thr Gln Lys Ser Ser 725 730 735Thr Pro Lys Ala Val Gln Lys
Ala Leu Lys Glu Cys Ile Arg Arg Met 740 745 750Leu Gln Glu Gly Glu
Glu Ser Leu Gln Glu Tyr Phe Lys Glu Phe Glu 755 760 765Lys Glu Phe
Arg Gln Leu Asn Tyr Ile Ser Ile Ala Ser Val Ser Ser 770 775 780Ala
Asn Asn Ile Ala Lys Tyr Asp Val Gly Gly Phe Pro Gly Pro Lys785 790
795 800Cys Pro Phe His Ile Arg Gly Ile Leu Thr Tyr Asn Arg Ala Ile
Lys 805 810 815Gly Asn Ile Asp Ala Pro Gln Val Val Glu Gly Glu Lys
Val Tyr Val 820 825 830Leu Pro Leu Arg Glu Gly Asn Pro Phe Gly Asp
Lys Cys Ile Ala Trp 835 840 845Pro Ser Gly Thr Glu Ile Thr Asp Leu
Ile Lys Asp Asp Val Leu His 850 855 860Trp Met Asp Tyr Thr Val Leu
Leu Glu Lys Thr Phe Ile Lys Pro Leu865 870 875 880Glu Gly Phe Thr
Ser Ala Ala Lys Leu Asp Tyr Glu Lys Lys Ala Ser 885 890 895Leu Phe
Asp Met Phe Asp Phe 9001616PRTArtificial SequenceDescription of
Artificial Sequence Synthetic peptide 16Leu Leu Gly Ala Ala Ala Lys
Gly Ala Ala Ala Lys Gly Ser Ala Ala1 5 10 151719PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 17Leu
Leu Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser Ala Ala Ala Gly1 5 10
15Ser Ala Ala18597PRTArtificial SequenceDescription of Artificial
Sequence Synthetic polypeptide 18Met Asn His Leu Val His His His
His His His Ile Glu Gly Arg His1 5 10 15Met Glu Leu Gly Thr Leu Glu
Gly Ser Met Pro Arg Lys Met Phe Ser 20 25 30Cys Asp Phe Glu Thr Thr
Thr Lys Leu Asp Asp Cys Arg Val Trp Ala 35 40 45Tyr Gly Tyr Met Glu
Ile Gly Asn Leu Asp Asn Tyr Lys Ile Gly Asn 50 55 60Ser Leu Asp Glu
Phe Met Gln Trp Val Met Glu Ile Gln Ala Asp Leu65 70 75 80Tyr Phe
His Asn Leu Lys Phe Asp Gly Ala Phe Ile Val Asn Trp Leu 85 90 95Glu
His His Gly Phe Lys Trp Ser Asn Glu Gly Leu Pro Asn Thr Tyr 100 105
110Asn Thr Ile Ile Ser Lys Met Gly Gln Trp Tyr Met Ile Asp Ile Cys
115 120 125Phe Gly Tyr Lys Gly Lys Arg Lys Leu His Thr Val Ile Tyr
Asp Ser 130 135 140Leu Lys Lys Leu Pro Phe Pro Val Lys Lys Ile Ala
Lys Asp Phe Gln145 150 155 160Leu Pro Leu Leu Lys Gly Asp Ile Asp
Tyr His Ala Glu Arg Pro Val 165 170 175Gly His Glu Ile Thr Pro Glu
Glu Tyr Glu Tyr Ile Lys Asn Asp Ile 180 185 190Glu Ile Ile Ala Arg
Ala Leu Asp Ile Gln Phe Lys Gln Gly Leu Asp 195 200 205Arg Met Thr
Ala Gly Ser Asp Ser Leu Lys Gly Phe Lys Asp Ile Leu 210 215 220Ser
Thr Lys Lys Phe Asn Lys Val Phe Pro Lys Leu Ser Leu Pro Met225 230
235 240Asp Lys Glu Ile Arg Arg Ala Tyr Arg Gly Gly Phe Thr Trp Leu
Asn 245 250 255Asp Lys Tyr Lys Glu Lys Glu Ile Gly Glu Gly Met Val
Phe Asp Val 260 265 270Asn Ser Leu Tyr Pro Ser Gln Met Tyr Ser Arg
Pro Leu Pro Tyr Gly 275 280 285Ala Pro Ile Val Phe Gln Gly Lys Tyr
Glu Lys Asp Glu Gln Tyr Pro 290 295 300Leu Tyr Ile Gln Arg Ile Arg
Phe Glu Phe Glu Leu Lys Glu Gly Tyr305 310 315 320Ile Pro Thr Ile
Gln Ile Lys Lys Asn Pro Phe Phe Lys Gly Asn Glu 325 330 335Tyr Leu
Lys Asn Ser Gly Ala Glu Pro Val Glu Leu Tyr Leu Thr Asn 340 345
350Val Asp Leu Glu Leu Ile Gln Glu His Tyr Glu Met Tyr Asn Val Glu
355 360 365Tyr Ile Asp Gly Phe Lys Phe Arg Glu Lys Thr Gly Leu Phe
Lys Glu 370 375 380Phe Ile Asp Lys Trp Thr Tyr Val Lys Thr His Glu
Lys Gly Ala Lys385 390 395 400Lys Gln Leu Ala Lys Leu Met Leu Asn
Ser Leu Tyr Gly Lys Phe Ala 405 410 415Ser Asn Pro Asp Val Thr Gly
Lys Val Pro Tyr Leu Lys Glu Asp Gly 420 425 430Ser Leu Gly Phe Arg
Val Gly Asp Glu Glu Tyr Lys Asp Pro Val Tyr 435 440 445Thr Pro Met
Gly Val Phe Ile Thr Ala Trp Ala Arg Phe Thr Thr Ile 450 455 460Thr
Ala Ala Gln Ala Cys Tyr Asp Arg Ile Ile Tyr Cys Asp Thr Asp465 470
475 480Ser Ile His Leu Thr Gly Thr Glu Val Pro Glu Ile Ile Lys Asp
Ile 485 490 495Val Asp Pro Lys Lys Leu Gly Tyr Trp Ala His Glu Ser
Thr Phe Lys 500 505 510Arg Ala Lys Tyr Leu Arg Gln Lys Thr Tyr Ile
Gln Asp Ile Tyr Ala 515 520 525Lys Glu Val Asp Gly Lys Leu Ile Glu
Cys Ser Pro Asp Glu Ala Thr 530 535 540Thr Thr Lys Phe Ser Val Lys
Cys Ala Gly Met Thr Asp Thr Ile Lys545 550 555 560Lys Lys Val Thr
Phe Asp Asn Phe Arg Val Gly Phe Ser Ser Thr Gly 565 570 575Lys Pro
Lys Pro Val Gln Val Asn Gly Gly Val Val Leu Val Asp Ser 580 585
590Val Phe Thr Ile Lys 59519581PRTArtificial SequenceDescription of
Artificial Sequence Synthetic polypeptide 19Met His His His His His
His Lys His Met Pro Arg Lys Met Phe Ser1 5 10 15Cys Asp Phe Glu Thr
Thr Thr Lys Leu Asp Asp Cys Arg Val Trp Ala 20 25 30Tyr Gly Tyr Met
Glu Ile Gly Asn Leu Asp Asn Tyr Lys Ile Gly Asn 35 40 45Ser Leu Asp
Glu Phe Met Gln Trp Val Met Glu Ile Gln Ala Asp Leu 50 55 60Tyr Phe
His Asn Leu Lys Phe Asp Gly Ala Phe Ile Val Asn Trp Leu65 70 75
80Glu His His Gly Phe Lys Trp Ser Asn Glu Gly Leu Pro Asn Thr Tyr
85 90 95Asn Thr Ile Ile Ser Lys Met Gly Gln Trp Tyr Met Ile Asp Ile
Cys 100 105 110Phe Gly Tyr Lys Gly Lys Arg Lys Leu His Thr Val Ile
Tyr Asp Ser 115 120 125Leu Lys Lys Leu Pro Phe Pro Val Lys Lys Ile
Ala Lys Asp Phe Gln 130 135 140Leu Pro Leu Leu Lys Gly Asp Ile Asp
Tyr His Ala Glu Arg Pro Val145 150 155 160Gly His Glu Ile Thr Pro
Glu Glu Tyr Glu Tyr Ile Lys Asn Asp Ile 165 170 175Glu Ile Ile Ala
Arg Ala Leu Asp Ile Gln Phe Lys Gln Gly Leu Asp 180 185 190Arg Met
Thr Ala Gly Ser Asp Ser Leu Lys Gly Phe Lys Asp Ile Leu 195 200
205Ser Thr Lys Lys Phe Asn Lys Val Phe Pro Lys Leu Ser Leu Pro Met
210 215 220Asp Lys Glu Ile Arg Arg Ala Tyr Arg Gly Gly Phe Thr Trp
Leu Asn225 230 235 240Asp Lys Tyr Lys Glu Lys Glu Ile Gly Glu Gly
Met Val Phe Asp Val 245 250 255Asn Ser Leu Tyr Pro Ser Gln Met Tyr
Ser Arg Pro Leu Pro Tyr Gly 260 265 270Ala Pro Ile Val Phe Gln Gly
Lys Tyr Glu Lys Asp Glu Gln Tyr Pro 275 280 285Leu Tyr Ile Gln Arg
Ile Arg Phe Glu Phe Glu Leu Lys Glu Gly Tyr 290 295 300Ile Pro Thr
Ile Gln Ile Lys Lys Asn Pro Phe Phe Lys Gly Asn Glu305 310 315
320Tyr Leu Lys Asn Ser Gly Ala Glu Pro Val Glu Leu Tyr Leu Thr Asn
325 330 335Val Asp Leu Glu Leu Ile Gln Glu His Tyr Glu Met Tyr Asn
Val Glu 340 345 350Tyr Ile Asp Gly Phe Lys Phe Arg Glu Lys Thr Gly
Leu Phe Lys Glu 355 360 365Phe Ile Asp Lys Trp Thr Tyr Val Lys Thr
His Glu Lys Gly Ala Lys 370 375 380Lys Gln Leu Ala Lys Leu Met Leu
Asn Ser Leu Tyr Gly Lys Phe Ala385 390 395 400Ser Asn Pro Asp Val
Thr Gly Lys Val Pro Tyr Leu Lys Glu Asp Gly 405 410 415Ser Leu Gly
Phe Arg Val Gly Asp Glu Glu Tyr Lys Asp Pro Val Tyr 420 425 430Thr
Pro Met Gly Val Phe Ile Thr Ala Trp Ala Arg Phe Thr Thr Ile 435 440
445Thr Ala Ala Gln Ala Cys Tyr Asp Arg Ile Ile Tyr Cys Asp Thr Asp
450 455 460Ser Ile His Leu Thr Gly Thr Glu Val Pro Glu Ile Ile Lys
Asp Ile465 470 475 480Val Asp Pro Lys Lys Leu Gly Tyr Trp Ala His
Glu Ser Thr Phe Lys 485 490 495Arg Ala Lys Tyr Leu Arg Gln Lys Thr
Tyr Ile Gln Asp Ile Tyr Ala 500 505 510Lys Glu Val Asp Gly Lys Leu
Ile Glu Cys Ser Pro Asp Glu Ala Thr 515 520 525Thr Thr Lys Phe Ser
Val Lys Cys Ala Gly Met Thr Asp Thr Ile Lys 530 535 540Lys Lys Val
Thr Phe Asp Asn Phe Arg Val Gly Phe Ser Ser Thr Gly545 550 555
560Lys Pro Lys Pro Val Gln Val Asn Gly Gly Val Val Leu Val Asp Ser
565 570 575Val Phe Thr Ile Lys 58020600PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
20Met Asn His Leu Val His His His His His His Ile Glu Gly Arg His1
5 10 15Met Glu Leu Gly Thr Leu Glu Gly Ser Met Lys His Met Pro Arg
Lys 20 25 30Met Tyr Ser Cys Ala Phe Glu Thr Thr Thr Lys Val Glu Asp
Cys Arg 35 40 45Val Trp Ala Tyr Gly Tyr Met Asn Ile Glu Asp His Ser
Glu Tyr Lys 50 55 60Ile Gly Asn Ser Leu Asp Glu Phe Met Ala Trp Val
Leu Lys Val Gln65 70 75 80Ala Asp Leu Tyr Phe His Asn Leu Lys Phe
Ala Gly Ala Phe Ile Ile 85 90 95Asn Trp Leu Glu Arg Asn Gly Phe Lys
Trp Ser Ala Asp Gly Leu Pro 100 105 110Asn Thr Tyr Asn Thr Ile Ile
Ser Arg Met Gly Gln Trp Tyr Met Ile 115 120 125Asp Ile Cys Leu Gly
Tyr Lys Gly Lys Arg Lys Ile His Thr Val Ile 130 135 140Tyr Asp Ser
Leu Lys Lys Leu Pro Phe Pro Val Lys Lys Ile Ala Lys145 150 155
160Asp Phe Lys Leu Thr Val Leu Lys Gly Asp Ile Asp Tyr His Lys Glu
165 170 175Arg Pro Val Gly Tyr Lys Ile Thr Pro Glu Glu Tyr Ala Tyr
Ile Lys 180 185 190Asn Asp Ile Gln Ile Ile Ala Glu Ala Leu Leu Ile
Gln Phe Lys Gln 195 200 205Gly Leu Asp Arg Met Thr Ala Gly Ser Asp
Ser Leu Lys Gly Phe Lys 210 215 220Asp Ile Ile Thr Thr Lys Lys Phe
Lys Lys Val Phe Pro Thr Leu Ser225 230 235 240Leu Gly Leu Asp Lys
Glu Val Arg Tyr Ala Tyr Arg Gly Gly Phe Thr 245 250 255Trp Leu Asn
Asp Arg Phe Lys Glu Lys Glu Ile Gly Glu Gly Met Val 260 265 270Phe
Asp Val Asn Ser Leu Tyr Pro Ala Gln Met Tyr Ser Arg Leu Leu 275 280
285Pro Tyr Gly Glu Pro Ile Val Phe Glu Gly Lys Tyr Val Trp Asp Glu
290 295 300Asp Tyr Pro Leu His Ile Gln His Ile Arg Cys Glu Phe Glu
Leu Lys305 310 315 320Glu Gly Tyr Ile Pro Thr Ile Gln Ile Lys Arg
Ser Arg Phe Tyr Lys 325 330 335Gly Asn Glu Tyr Leu Lys Ser Ser Gly
Gly Glu Ile Ala Asp Leu Trp 340 345 350Leu Ser Asn Val Asp Leu Glu
Leu Met Lys Glu His Tyr Asp Leu Tyr 355 360 365Asn Val Glu Tyr Ile
Ser Gly Leu Lys Phe Lys Ala Thr Thr Gly Leu 370 375 380Phe Lys Asp
Phe Ile Asp Lys Trp Thr Tyr Ile Lys Thr Thr Ser Glu385 390 395
400Gly Ala Ile Lys Gln Leu Ala Lys Leu Met Leu Asn Ser Leu Tyr Gly
405 410 415Lys Phe Ala Ser Asn Pro Asp Val Thr Gly Lys Val Pro Tyr
Leu Lys 420 425 430Glu Asn Gly Ala Leu Gly Phe Arg Leu Gly Glu Glu
Glu Thr Lys Asp 435 440 445Pro Val Tyr Thr Pro Met Gly Val Phe Ile
Thr Ala Trp Ala Arg Tyr 450 455 460Thr Thr Ile Thr Ala Ala Gln Ala
Cys Tyr Asp Arg Ile Ile Tyr Cys465 470 475 480Asp Thr Asp Ser Ile
His Leu Thr Gly Thr Glu Ile Pro Asp Val Ile
485 490 495Lys Asp Ile Val Asp Pro Lys Lys Leu Gly Tyr Trp Ala His
Glu Ser 500 505 510Thr Phe Lys Arg Ala Lys Tyr Leu Arg Gln Lys Thr
Tyr Ile Gln Asp 515 520 525Ile Tyr Met Lys Glu Val Asp Gly Lys Leu
Val Glu Gly Ser Pro Asp 530 535 540Asp Tyr Thr Asp Ile Lys Phe Ser
Val Lys Cys Ala Gly Met Thr Asp545 550 555 560Lys Ile Lys Lys Glu
Val Thr Phe Glu Asn Phe Lys Val Gly Phe Ser 565 570 575Arg Lys Met
Lys Pro Lys Pro Val Gln Val Pro Gly Gly Val Val Leu 580 585 590Val
Asp Asp Thr Phe Thr Ile Lys 595 6002119DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
21ggtactaagc ggccgcatg 192226DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 22tttttttcat
gcggccgctt agtacc 262326DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 23aaaaaaacat
gcggccgctt agtacc 262426DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 24ccccccccat
gcggccgctt agtacc 262526DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 25gggggggcat
gcggccgctt agtacc 262625DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 26gcctcgcagc cgtccaacca actcc
252732DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 27cagtaacgga gttggttgga cggctgcgag gc
322832DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 28cagtaaggga gttggttgga cggctgcgag gc
322932DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 29cagtaaagga gttggttgga cggctgcgag gc
323032DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 30cagtaatgga gttggttgga cggctgcgag gc
323118DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 31gttgcaaagg agcgggcg 183225DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 32cgttccccgc ccgctccttt gcaac 253325DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 33cgttccgcgc ccgctccttt gcaac 253425DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 34cgttccacgc ccgctccttt gcaac 253525DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 35cgttcctcgc ccgctccttt gcaac 253625DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
36gcctcgcagc cgtccaacca actcc 253732DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 37tgccaccgga gttggttgga cggctgcgag gc
323826DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 38ttttttttac ccccgggtga caggtt
263962DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 39tttttccccg acgatgcctc cccgacacgg
aggttctatc atcgtcatcg tcatcgtcat 60cg 624018DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
40tgatagaacc tccgtgtc 184121DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 41ggggaggcat
cgtcgggaaa a 2142608PRTArtificial SequenceDescription of Artificial
Sequence Synthetic polypeptide 42Met Ser His His His His His His
Ser Met Ser Gly Leu Asn Asp Ile1 5 10 15Phe Glu Ala Gln Lys Ile Glu
Trp His Glu Gly Ala Pro Gly Ala Arg 20 25 30Gly Ser Lys His Met Pro
Arg Lys Met Phe Ser Cys Asp Phe Glu Thr 35 40 45Thr Thr Lys Leu Asp
Asp Cys Arg Val Trp Ala Tyr Gly Tyr Met Glu 50 55 60Ile Gly Asn Leu
Asp Asn Tyr Lys Ile Gly Asn Ser Leu Asp Glu Phe65 70 75 80Met Gln
Trp Val Met Glu Ile Gln Ala Asp Leu Tyr Phe His Asn Leu 85 90 95Lys
Phe Asp Gly Ala Phe Ile Val Asn Trp Leu Glu His His Gly Phe 100 105
110Lys Trp Ser Asn Glu Gly Leu Pro Asn Thr Tyr Asn Thr Ile Ile Ser
115 120 125Lys Met Gly Gln Trp Tyr Met Ile Asp Ile Cys Phe Gly Tyr
Lys Gly 130 135 140Lys Arg Lys Leu His Thr Val Ile Tyr Asp Ser Leu
Lys Lys Leu Pro145 150 155 160Phe Pro Val Lys Lys Ile Ala Lys Asp
Phe Gln Leu Pro Leu Leu Lys 165 170 175Gly Asp Ile Asp Tyr His Ala
Glu Arg Pro Val Gly His Glu Ile Thr 180 185 190Pro Glu Glu Tyr Glu
Tyr Ile Lys Asn Ala Ile Glu Ile Ile Ala Arg 195 200 205Ala Leu Asp
Ile Gln Phe Lys Gln Gly Leu Asp Arg Met Thr Ala Gly 210 215 220Ser
Asp Ser Leu Lys Gly Phe Lys Asp Ile Leu Ser Thr Lys Lys Phe225 230
235 240Asn Lys Val Phe Pro Lys Leu Ser Leu Pro Met Asp Lys Glu Ile
Arg 245 250 255Arg Ala Tyr Arg Gly Gly Phe Thr Trp Leu Asn Asp Lys
Tyr Lys Glu 260 265 270Lys Glu Ile Gly Glu Gly Met Val Phe Asp Val
Asn Ser Leu Tyr Pro 275 280 285Ser Gln Met Tyr Ser Arg Pro Leu Pro
Tyr Gly Ala Pro Ile Val Phe 290 295 300Gln Gly Lys Tyr Glu Lys Asp
Glu Gln Tyr Pro Leu Tyr Ile Gln Arg305 310 315 320Ile Arg Phe Glu
Phe Glu Leu Lys Glu Gly Tyr Ile Pro Thr Ile Gln 325 330 335Ile Lys
Lys Asn Pro Phe Phe Lys Gly Asn Glu Tyr Leu Lys Asn Ser 340 345
350Gly Ala Glu Pro Val Glu Leu Tyr Leu Thr Asn Val Asp Leu Glu Leu
355 360 365Ile Gln Glu His Tyr Glu Met Tyr Asn Val Glu Tyr Ile Asp
Gly Phe 370 375 380Lys Phe Arg Glu Lys Thr Gly Leu Phe Lys Glu Phe
Ile Asp Lys Trp385 390 395 400Thr Tyr Val Lys Thr Arg Glu Lys Gly
Ala Lys Lys Gln Leu Ala Lys 405 410 415Leu Met Leu Asn Ser Leu Tyr
Gly Lys Phe Ala Ser Asn Pro Asp Val 420 425 430Thr Gly Lys Val Pro
Tyr Leu Lys Glu Asp Gly Ser Leu Gly Phe Arg 435 440 445Val Gly Asp
Glu Glu Tyr Lys Asp Pro Val Tyr Thr Pro Met Gly Val 450 455 460Phe
Ile Thr Ala Trp Ala Arg Phe Thr Thr Ile Thr Ala Ala Gln Ala465 470
475 480Cys Tyr Asp Arg Ile Ile Tyr Cys Asp Thr Asp Ser Ile His Leu
Thr 485 490 495Gly Thr Glu Val Pro Glu Ile Ile Lys Asp Ile Val Asp
Pro Lys Lys 500 505 510Leu Gly Tyr Trp Ala His Glu Ser Thr Phe Lys
Arg Ala Lys Tyr Leu 515 520 525Arg Gln Lys Thr Tyr Ile Gln Asp Ile
Tyr Ala Lys Glu Val Asp Gly 530 535 540Lys Leu Ile Glu Cys Ser Pro
Asp Glu Ala Thr Thr Thr Lys Phe Ser545 550 555 560Val Lys Cys Ala
Gly Met Thr Asp Thr Ile Lys Lys Lys Val Thr Phe 565 570 575Asp Asn
Phe Arg Val Gly Phe Ser Ser Thr Gly Lys Pro Lys Pro Val 580 585
590Gln Val Asn Gly Gly Val Val Leu Val Asp Ser Val Phe Thr Ile Lys
595 600 6054336DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 43tttttttgca ggtgacaggt
ttttcctgtc acctgc 364425DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 44cgttaaccgc
ccgctccttt gcaac 254518DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 45gttgcaaagg agcgggcg
184632DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 46cagtaacgga gttggttgga cggctgcgag gc
324725DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 47gcctcgcagc cgtccaacca actcc 25486PRTArtificial
SequenceDescription of Artificial Sequence Synthetic 6xHis tag
48His His His His His His1 54912DNAArtificial SequenceDescription
of Artificial Sequence Synthetic oligonucleotide 49ttcctgtcac cc
125014DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 50gggggtaaaa aaaa 14
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