U.S. patent number RE47,476 [Application Number 15/879,240] was granted by the patent office on 2019-07-02 for recombinant polymerases with increased phototolerance.
This patent grant is currently assigned to Pacific Biosciences of California, Inc.. The grantee listed for this patent is Pacific Biosciences of California, Inc.. Invention is credited to Arek Bibillo, Satwik Kamtekar, Walter Lee, Erik Miller, Insil Park.
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United States Patent |
RE47,476 |
Kamtekar , et al. |
July 2, 2019 |
Recombinant polymerases with increased phototolerance
Abstract
Provided are compositions comprising recombinant DNA polymerases
that include amino acid substitutions, insertions, deletions,
and/or exogenous features that confer modified properties upon the
polymerase for enhanced single molecule sequencing. Such properties
include increased resistance to photodamage, and can also include
enhanced metal ion coordination, reduced exonuclease activity,
reduced reaction rates at one or more steps of the polymerase
kinetic cycle, decreased branching fraction, altered cofactor
selectivity, increased yield, increased thermostability, increased
accuracy, increased speed, increased readlength, and the like. Also
provided are nucleic acids which encode the polymerases with the
aforementioned phenotypes, as well as methods of using such
polymerases to make a DNA or to sequence a DNA template.
Inventors: |
Kamtekar; Satwik (Mountain
View, CA), Bibillo; Arek (Cupertino, CA), Lee; Walter
(Campbell, CA), Miller; Erik (Berkeley, CA), Park;
Insil (Fremont, CA) |
Applicant: |
Name |
City |
State |
Country |
Type |
Pacific Biosciences of California, Inc. |
Menlo Park |
CA |
US |
|
|
Assignee: |
Pacific Biosciences of California,
Inc. (Menlo Park, CA)
|
Family
ID: |
48982539 |
Appl.
No.: |
15/879,240 |
Filed: |
January 24, 2018 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
Issue Date |
|
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14533571 |
Nov 5, 2014 |
9296999 |
|
|
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13756113 |
Jan 31, 2013 |
8906660 |
|
|
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61593569 |
Feb 1, 2012 |
|
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Reissue of: |
15049512 |
Feb 22, 2016 |
9476035 |
Oct 25, 2016 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q
1/6869 (20130101); C12Y 207/07007 (20130101); C12Y
207/07007 (20130101); C12Q 1/6869 (20130101); C12P
19/34 (20130101); C12P 19/34 (20130101); C12N
9/1252 (20130101); C12N 9/1252 (20130101); Y02P
20/52 (20151101); Y02P 20/52 (20151101) |
Current International
Class: |
C12N
9/12 (20060101); C12Q 1/6869 (20180101); C12P
19/34 (20060101); C12Q 1/68 (20180101) |
References Cited
[Referenced By]
U.S. Patent Documents
Foreign Patent Documents
Other References
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Bacillus subtilis phage PZA, a close relative of phi 29. Gene 38:
45-56, 1985. cited by examiner .
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polymerase: conserved segments within protein-priming DNA
polymerases and DNA polymerase I Eschiricia coli. Gene 84: 247-255,
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DNA polymerase active site. Mutational analysis of conserved motif
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.
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.
Augustin et al. (2001) "Progress towards single-molecule
sequencing: enzymatic synthesis of nucleotide-specifically labeled
DNA" J. Biotechnol. 86:289-301. cited by applicant .
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with substrate: The mechanism of translocation in B-family
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revised nomenclature" J Biol Chem. 276(47): 43487-90. cited by
applicant .
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amplification performance by fusion of DNA binding motifs", PNAS,
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molecules," Science 323:133-138. cited by applicant .
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recognition in an archaeon DNA polymerase," Nucleic Acids Research
27(12):2545-2553. cited by applicant .
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Incorporation by Vent DNA Polymerase," J. Biol. Chem. 279(12):
11834-11842. cited by applicant .
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nucleotides by DNA polymerases. I. Chemical synthesis of various
reporter group-labeled 2'-deoxyribonucleoside-5'-triphosphates,"
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applicant .
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polymerase of bacteriophage .PHI.29" Mol. Cell 16(4): 609-618).
cited by applicant .
Kamtekar et al. (2006) "The phi29 DNA polymerase:protein-primer
structure suggests a model for the initiation to elongation
transition," EMBO J. 25(6):1335-1343. cited by applicant .
Korlach et al. (2010) "Real-Time DNA Sequencing from Single
Polymerase Molecules," Methods in Enzymology vol. 472, Chapter 20,
pp. 431-455. cited by applicant .
Korlach et al. (2008) "Long, processive enzymatic DNA synthesis
using 100% dye-labeled terminal phosphate-linked nucleotides,"
Nucleosides, Nucleotides and Nucleic Acids 27:1072-1083. cited by
applicant .
Korlach et al. (2008) "Selective aluminum passivation for targeted
immobilization of single DNA polymerase molecules in zero-mode
waveguide nanostructures," PNAS, 105(4): 1176-1181. cited by
applicant .
Levene et al. (2003) "Zero-mode waveguides for single-molecule
analysis at high concentrations" Science 299:682-686. cited by
applicant .
Meijer et al. (2001) ".PHI.29 Family of Phages" Microbiology and
Molecular Biology Reviews, 65(2):261-287. cited by applicant .
Mendez et al.(l994) "Primer-terminus stabilization at the phi 29
DNA polymerase active site. Mutational analysis of conserved motif
TXZGR" J Biol Chem. Nov. 25;269(47):30030-30038. cited by applicant
.
Patel et al. (1991) "Pre-steady-state kinetic analysis of
processive DNA replication including complete characterization of
an exonuclease-deficient mutant" Biochemistry 30(2):511-525. cited
by applicant .
Pinard et al. (2006) "Assessment of Whole genome
amplification-induced bias through high-throughput, massively
parallel whole genome sequencing" BMC Genomics 7:216. cited by
applicant .
Ried et al. (1992) "Simultaneous Visualization of seven different
DNA probes by in situ hybridization using combinatorial
fluorescence and digital imaging microscopy," PNAS, 89:1388-1392.
cited by applicant .
Silander and Saarela (2008) "Whole Genome Amplification with Phi29
DNA Polymerase to Enable Genetic or Genomic Analysis of Samples of
Low DNA Yield" Methods in Molecular Biology 439:1-18. cited by
applicant .
Steitz (1999) "DNA polymerases: structural diversity and common
mechanisms" J Biol Chem 274(25):17395-17398. cited by applicant
.
Tonon et al. (2000) "Spectral karyotyping combined with
locus-specific FISH simultaneously defines genes and chromosomes
involved in chromosomal translocations" Genes Chromosom. Cancer
27:418-423. cited by applicant .
Truniger et al. (2005) "Involvement of the "linker" region between
the exonuclease and polymerization domains of phi29 DNA polymerase
in DNA and TP binding" Gene, 348:89-99. cited by applicant .
Tsai and Johnson (2006) "A new paradigm for DNA polymerase
specificity," Biochemistry 45(32):9675-9687. cited by applicant
.
Yu et al. (1994) "Cyanine dye dUTP analogs for enzymatic labeling
of DNA probes," Nucleic Acids Res. 22(15):3226-3232. cited by
applicant .
Zhu and Waggoner (1997) "Molecular mechanism controlling the
incorporation of fluorescent nucleotides into DNA by PCR"
Cytometry, 28:206-211. cited by applicant .
Zhu et al. (1994) "Directly labeled DNA probes using fluorescent
nucleotides with different length linkers" Nucleic Acids Res.,
22(16):3418-3422. cited by applicant.
|
Primary Examiner: Campbell; Bruce R
Attorney, Agent or Firm: Elrod-Erickson; Monicia
Parent Case Text
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation of U.S. patent application Ser.
No. 14/533,571 filed Nov. 5, 2014, which is a continuation of U.S.
patent application Ser. No. 13/756,113 filed Jan. 31, 2013, which
claims the benefit of Provisional U.S. Patent Application No.
61/593,569, filed Feb. 1, 2012. Each of these applications is
incorporated herein by reference in its entirety for all purposes.
Claims
What is claimed is:
1. A composition comprising a .phi.29-type (phi29-type) recombinant
DNA polymerase, which recombinant polymerase comprises an amino
acid sequence that is at least 80% identical to SEQ ID NO:1, and
which recombinant polymerase comprises one or more mutation
selected from the group consisting of .[.an amino acid substitution
at position S194, an amino acid substitution at position Y439,.].
an amino acid substitution at position T441, an amino acid
substitution at position A447, an amino acid substitution at
position S527, L142R substitution, .[.a D510Q substitution,.].
.Iadd.an S194A substitution, an S194T substitution, a Y439E
substitution, a Y439A substitution, a Y439K substitution,
.Iaddend.and a D523H substitution, wherein identification of
positions is relative to SEQ ID NO:1, and wherein said polymerase
exhibits polymerase activity.
2. The composition of claim 1, wherein the recombinant polymerase
comprises one or more mutation selected from the group consisting
of a T441I substitution, a T441L substitution, and an S527K
substitution, wherein identification of positions is relative to
SEQ ID NO:1.
3. The composition of claim 1, wherein the recombinant polymerase
comprises one or more mutation selected from the group consisting
of .[.an S194A substitution, an S194T substitution, a Y439E
substitution, a Y439A substitution, a Y439K substitution,.]. a
T441G substitution, a T441V substitution, a T441N substitution, a
T441A substitution, an A447L substitution, an A447E substitution,
an S527E substitution, and an S527N substitution, wherein
identification of positions is relative to SEQ ID NO:1.
4. The composition of claim 1, wherein the recombinant polymerase
comprises one or more mutation or combination of mutations selected
from the group consisting of an amino acid substitution at position
253, an amino acid substitution at position 375, an amino acid
substitution at position 484, an amino acid substitution at
position 512, an amino acid substitution at position 510, an amino
acid substitution at position 148, an amino acid substitution at
position 224, an amino acid substitution at position 239, an amino
acid substitution at position 250, an amino acid substitution at
position 437, an amino acid substitution at position 235, an amino
acid substitution at position 515, an amino acid substitution at
position 141, an amino acid substitution at position 142, an amino
acid substitution at position 504, an amino acid substitution at
position 508, an amino acid substitution at position 513, an amino
acid substitution at position 523, an amino acid substitution at
position 536, an amino acid substitution at position 539, an amino
acid substitution at position 205, an amino acid substitution at
position 472, an amino acid substitution at position 437 and an
amino acid substitution at position 253, an amino acid substitution
at position 508 and an amino acid substitution at position 510, an
A437G substitution and an L253H substitution, an A437G substitution
and an L253C substitution, a V250A substitution and an L253H
substitution, an A437G substitution, a D235E substitution, an E515Q
substitution, an E515P substitution, an E515K substitution, a V250A
substitution, a V250I substitution, a Y148I substitution, a Y224K
substitution, an E239G substitution, a V141K substitution, an L142K
substitution, an E508K substitution, an E508K substitution and a
D510S substitution, a K536Q substitution, a K539Q substitution, a
K205E substitution, a K205D substitution, a K205A substitution, a
K472A substitution, an E375Y substitution, a K512Y substitution, an
A484E substitution, an L253A substitution, an L253C substitution,
an L253S substitution, an L253H substitution, and a D510K
substitution, wherein identification of positions is relative to
SEQ ID NO:1.
5. The composition of claim 1, wherein the recombinant polymerase
comprises E375Y, A484E, and K512Y substitutions, wherein
identification of positions is relative to SEQ ID NO:1.
6. The composition of claim 1, where the recombinant polymerase
comprises an amino acid sequence that is at least 90% identical to
SEQ ID NO:1.
7. .[.The composition of claim 1,.]. .Iadd.A composition comprising
a .phi.29-type (phi29-type) recombinant DNA polymerase, which
recombinant polymerase comprises an amino acid sequence that is at
least 80% identical to SEQ ID NO:1, and which recombinant
polymerase comprises one or more mutation selected from the group
consisting of an amino acid substitution at position S194, an amino
acid substitution at position Y439, an amino acid substitution at
position T441, an amino acid substitution at position A447, an
amino acid substitution at position S527, an L142R substitution,
and a D523H substitution, wherein identification of positions is
relative to SEQ ID NO:1, and wherein said polymerase exhibits
polymerase activity, .Iaddend.wherein the recombinant polymerase
comprises one or more exogenous features at the C-terminal and/or
N-terminal region of the polymerase.
8. The composition of claim 7, wherein the recombinant polymerase
comprises a biotin ligase recognition sequence and a polyhistidine
tag.
9. The composition of claim 7, wherein the C-terminal region of the
recombinant polymerase comprises a His10 tag.
10. .[.The composition of claim 1,.]. .Iadd.A composition
.Iaddend.comprising a phosphate-labeled nucleotide analog .Iadd.
and a .phi.29-type (phi29-type) recombinant DNA polymerase, which
recombinant polymerase comprises an amino acid sequence that is at
least 80% identical to SEQ ID NO:1, and which recombinant
polymerase comprises one or more mutation selected from the group
consisting of an amino acid substitution at position S194, an amino
acid substitution at position Y439, an amino acid substitution at
position T441, an amino acid substitution at position A447, an
amino acid substitution at position S527, an L142R substitution,
and a D523H substitution, wherein identification of positions is
relative to SEQ ID NO:1, and wherein said polymerase exhibits
polymerase activity.Iaddend..
11. The composition of claim 10, wherein the nucleotide analog
comprises a fluorophore.
12. The composition of claim .[.1.]. .Iadd.10.Iaddend., comprising
.[.a phosphate-labeled nucleotide analog and.]. a DNA template,
wherein the recombinant polymerase incorporates the nucleotide
analog into a copy nucleic acid in response to the DNA
template.
13. .[.The composition of claim 1,.]. .Iadd.A composition
comprising a .phi.29-type (phi29-type) recombinant DNA polymerase,
which recombinant polymerase comprises an amino acid sequence that
is at least 80% identical to SEQ ID NO:1, and which recombinant
polymerase comprises one or more mutation selected from the group
consisting of an amino acid substitution at position S194, an amino
acid substitution at position Y439, an amino acid substitution at
position T441, an amino acid substitution at position A447, an
amino acid substitution at position S527, an L142R substitution,
and a D523H substitution, wherein identification of positions is
relative to SEQ ID NO:1, and wherein said polymerase exhibits
polymerase activity, .Iaddend.wherein the composition is present in
a DNA sequencing system.
14. The composition of claim 13, wherein the sequencing system
comprises a zero-mode waveguide.
15. The composition of claim 14, wherein the recombinant polymerase
is immobilized on a surface of the zero-mode waveguide in an active
form.
16. A method of sequencing a DNA template, the method comprising:
a) providing a reaction mixture comprising: the DNA template, a
replication initiating moiety that complexes with or is integral to
the template, .[.the recombinant polymerase of claim 1,.]. .Iadd.a
.phi.29-type (phi29-type) recombinant DNA polymerase, which
recombinant polymerase comprises an amino acid sequence that is at
least 80% identical to SEQ ID NO:1, and which recombinant
polymerase comprises one or more mutation selected from the group
consisting of an amino acid substitution at position S194, an amino
acid substitution at position Y439, an amino acid substitution at
position T441, an amino acid substitution at position A447, an
amino acid substitution at position S527, an L142R substitution,
and a D523H substitution, wherein identification of positions is
relative to SEQ ID NO:1, and wherein said polymerase exhibits
polymerase activity, .Iaddend.wherein the polymerase is capable of
replicating at least a portion of the template using the moiety in
a template-dependent polymerization reaction, and one or more
nucleotides and/or nucleotide analogs; b) subjecting the reaction
mixture to a polymerization reaction in which the modified
recombinant polymerase replicates at least a portion of the
template in a template-dependent manner, whereby the one or more
nucleotides and/or nucleotide analogs are incorporated into the
resulting DNA; and c) identifying a time sequence of incorporation
of the one or more nucleotides and/or nucleotide analogs into the
resulting DNA.
17. The method of claim 16, wherein the subjecting and identifying
steps are performed in a zero mode waveguide.
18. A method of making a DNA, the method comprising: (a) providing
a reaction mixture comprising: a template, a replication initiating
moiety that complexes with or is integral to the template, the
recombinant polymerase of claim 1, which polymerase is capable of
replicating at least a portion of the template using the moiety in
a template-dependent polymerase reaction, and one or more
nucleotides and/or nucleotide analogs; and (b) reacting the mixture
such that the polymerase replicates at least a portion of the
template in a template-dependent manner, whereby the one or more
nucleotides and/or nucleotide analogs are incorporated into the
resulting DNA.
19. The method of claim 18, wherein the mixture is reacted in a
zero mode waveguide.
20. The method of claim 18, the method comprising detecting
incorporation of at least one of the nucleotides and/or nucleotide
analogs.
Description
INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED BY U.S.P.T.O.
eFS-WEB
The instant application contains a Sequence Listing which is being
submitted in computer readable form via the United States Patent
and Trademark Office eFS-WEB system and which is hereby
incorporated by reference in its entirety for all purposes. The txt
file submitted herewith contains a 233 KB file
(01013803_2016-05-09_SequenceListing.txt).
FIELD OF THE INVENTION
The invention relates to modified DNA polymerases for single
molecule sequencing. The polymerases include modified recombinant
polymerases that display a reduced susceptibility to photodamage.
The invention also relates to methods for amplifying nucleic acids
and to methods for determining the sequence of nucleic acid
molecules using such polymerases.
BACKGROUND OF THE INVENTION
DNA polymerases replicate the genomes of living organisms. In
addition to this central role in biology, DNA polymerases are also
ubiquitous tools of biotechnology. They are widely used, e.g., for
reverse transcription, amplification, labeling, and sequencing, all
central technologies for a variety of applications such as nucleic
acid sequencing, nucleic acid amplification, cloning, protein
engineering, diagnostics, molecular medicine, and many other
technologies.
Because of the importance of DNA polymerases, they have been
extensively studied. This study has focused, e.g., on phylogenetic
relationships among polymerases, structure of polymerases,
structure-function features of polymerases, and the role of
polymerases in DNA replication and other basic biological
processes, as well as ways of using DNA polymerases in
biotechnology. For a review of polymerases, see, e.g., Hubscher et
al. (2002) "Eukaryotic DNA Polymerases" Annual Review of
Biochemistry Vol. 71: 133-163, Alba (2001) "Protein Family Review:
Replicative DNA Polymerases" Genome Biology 2(1): reviews
3002.1-3002.4, Steitz (1999) "DNA polymerases: structural diversity
and common mechanisms" J Biol Chem 274:17395-17398, and Burgers et
al. (2001) "Eukaryotic DNA polymerases: proposal for a revised
nomenclature" J Biol Chem. 276(47): 43487-90. Crystal structures
have been solved for many polymerases, which often share a similar
architecture. The basic mechanisms of action for many polymerases
have been determined.
A fundamental application of DNA technology involves various
labeling strategies for labeling a DNA that is produced by a DNA
polymerase. This is useful in DNA sequencing, microarray
technology, SNP detection, cloning, PCR analysis, and many other
applications. Labeling is often performed in various post-synthesis
hybridization or chemical labeling schemes, but DNA polymerases
have also been used to directly incorporate various labeled
nucleotides in a variety of applications, e.g., via nick
translation, reverse transcription, random priming, amplification,
the polymerase chain reaction, etc. See, e.g., Giller et al. (2003)
"Incorporation of reporter molecule-labeled nucleotides by DNA
polymerases. I. Chemical synthesis of various reporter
group-labeled 2'-deoxyribonucleoside-5'-triphosphates" Nucleic
Acids Res. 31(10):2630-2635, Augustin et al. (2001) "Progress
towards single-molecule sequencing: enzymatic synthesis of
nucleotide-specifically labeled DNA" J. Biotechnol. 86:289-301,
Tonon et al. (2000) "Spectral karyotyping combined with
locus-specific FISH simultaneously defines genes and chromosomes
involved in chromosomal translocations" Genes Chromosom. Cancer
27:418-423, Zhu and Waggoner (1997) "Molecular mechanism
controlling the incorporation of fluorescent nucleotides into DNA
by PCR" Cytometry, 28:206-211, Yu et al. (1994) "Cyanine dye dUTP
analogs for enzymatic labeling of DNA probes" Nucleic Acids Res.
22:3226-3232, Zhu et al. (1994) "Directly labeled DNA probes using
fluorescent nucleotides with different length linkers" Nucleic
Acids Res. 22:3418-3422, and Reid et al. (1992) "Simultaneous
visualization of seven different DNA probes by in situ
hybridization using combinatorial fluorescence and digital imaging
microscopy" Proc. Natl Acad. Sci. USA, 89:1388-1392.
DNA polymerase mutants have been identified that have a variety of
useful properties, including altered nucleotide analog
incorporation abilities relative to wild-type counterpart enzymes.
For example, Vent.sup.A488L DNA polymerase can incorporate certain
non-standard nucleotides with a higher efficiency than native Vent
DNA polymerase. See Gardner et al. (2004) "Comparative Kinetics of
Nucleotide Analog Incorporation by Vent DNA Polymerase" J. Biol.
Chem. 279(12):11834-11842 and Gardner and Jack "Determinants of
nucleotide sugar recognition in an archaeon DNA polymerase" Nucleic
Acids Research 27(12):2545-2553. The altered residue in this
mutant, A488, is predicted to be facing away from the nucleotide
binding site of the enzyme. The pattern of relaxed specificity at
this position roughly correlates with the size of the substituted
amino acid side chain and affects incorporation by the enzyme of a
variety of modified nucleotide sugars.
Additional modified polymerases, e.g., modified polymerases that
display improved properties useful for single molecule sequencing
(SMS) and other polymerase applications (e.g., DNA amplification,
sequencing, labeling, detection, cloning, etc.), are desirable. The
present invention provides new recombinant DNA polymerases with
desirable properties, including increased resistance to
photodamage. Other exemplary properties include exonuclease
deficiency, altered cofactor selectivity, increased yield,
increased thermostability, increased accuracy, increased speed,
increased readlength, and the like. Also included are methods of
making and using such polymerases, as well as many other features
that will become apparent upon a complete review of the
following.
SUMMARY OF THE INVENTION
Modified DNA polymerases can find use in such applications as,
e.g., single-molecule sequencing (SMS), geno-typing analyses such
as SNP genotyping using single-base extension methods, sample
preparation, and real-time monitoring of amplification, e.g.,
RT-PCR. Among other aspects, the invention provides compositions
comprising recombinant polymerases that comprise mutations which
confer properties which can be particularly desirable for these
applications. These properties can, e.g., increase enzyme (and
therefore assay) robustness, facilitate readout accuracy, or
otherwise improve polymerase performance. Also provided by the
invention are methods of generating such modified polymerases and
methods in which such polymerases can be used to, e.g., sequence a
DNA template and/or make a DNA.
One general class of embodiments provides a composition comprising
a recombinant .PHI.29-type DNA polymerase, which recombinant
polymerase comprises one or more mutation selected from the group
consisting of an amino acid substitution at position 131, an amino
acid substitution at position 132, a K135Q substitution, a K135S
substitution, an H149D substitution, a Q183F substitution, a G197D
substitution, a G197E substitution, an I201E substitution, a K206E
substitution, an A437N substitution, and a D510S substitution,
wherein identification of positions is relative to wild-type
.PHI.29 polymerase (SEQ ID NO:1). Exemplary mutations at positions
131 and 132 include, e.g., K131E, K131Q, and K132Q. Optionally, the
recombinant polymerase is more resistant to photodamage than is a
wild-type polymerase or a parental polymerase lacking the one or
more mutations.
The polymerase can also include mutations at additional positions.
For example, the polymerase can include one or more mutation or
combination of mutations selected from the group consisting of an
amino acid substitution at position 253, an amino acid substitution
at position 375, an amino acid substitution at position 484, an
amino acid substitution at position 512, an amino acid substitution
at position 510, an amino acid substitution at position 148, an
amino acid substitution at position 224, an amino acid substitution
at position 239, an amino acid substitution at position 250, an
amino acid substitution at position 437, an amino acid substitution
at position 235, an amino acid substitution at position 515, an
amino acid substitution at position 141, an amino acid substitution
at position 142, an amino acid substitution at position 504, an
amino acid substitution at position 508, an amino acid substitution
at position 513, an amino acid substitution at position 523, an
amino acid substitution at position 536, an amino acid substitution
at position 539, an amino acid substitution at position 205, an
amino acid substitution at position 472, an amino acid substitution
at position 437 and an amino acid substitution at position 253, and
an amino acid substitution at position 508 and an amino acid
substitution at position 510, wherein identification of positions
is relative to SEQ ID NO:1.
The polymerase optionally includes one or more mutation or
combination of mutations selected from the group consisting of
A437G and L253H, A437G and L253C, V250A and L253H, A437G, D235E,
E515Q, E515P, E515K, V250A, V250I, Y148I, Y224K, E239G, V141K,
L142K, E508K, E508K and D510S, K536Q, K539Q, K205E, K205D, K205A,
K472A, E375Y, K512Y, A484E, L253A, L253C, L253S, L253H, and D510K,
wherein identification of positions is relative to SEQ ID NO:1. In
one class of embodiments, the recombinant polymerase comprises
E375Y, A484E, and K512Y substitutions, wherein identification of
positions is relative to SEQ ID NO:1.
Optionally, the polymerase comprises mutations at two or more,
three or more, four or more, five or more, or even six or more of
the indicated positions. Exemplary combinations of mutations
include K131E, Y148I, Y224K, E239G, V250I, L253A, E375Y, A437G,
A484E, D510K, K512Y, and E515Q; K135Q, Y148I, Y224K, E239G, V250I,
L253A, E375Y, A437G, A484E, D510K, K512Y, and E515Q; K131E, Y148I,
Y224K, D235E, E239G, V250A, L253H, E375Y, A437G, A484E, D510K,
K512Y, and E515Q; Y148I, Y224K, E239G, L253S, E375Y, A437G, A484E,
D510K, K512Y, and E515Q; Y148I, Q183F, D235E, E239G, L253H, E375Y,
A437G, A484E, D510K, K512Y, and E515Q; Y148I, Y224K, E239G, V250I,
L253H, E375Y, A437G, A484E, D510K, and K512Y; Y148I, Y224K, E239G,
V250I, L253A, E375Y, A437G, A484E, D510K, K512Y, and E515Q; K131E,
Y148I, Y224K, D235E, E239G, L253H, E375Y, A437G, A484E, D510K,
K512Y, and E515Q; Y148I, Y224K, D235E, E239G, L253H, E375Y, A437G,
A484E, D510K, K512Y, and E515Q; Y148I, Y224K, E239G, V250I, L253A,
E375Y, A437G, A484E, D510K, and K512Y; Y148I, Y224K, E239G, V250I,
L253A, E375Y, A437G, A484E, D510K, and K512Y; K131E, Y148I, Y224K,
E239G, V250I, L253A, E375Y, A484E, D510K, and K512Y; K135Q, Y148I,
Y224K, E239G, V250I, L253A, E375Y, A484E, D510K, and K512Y; Y148I,
Y224K, E239G, L253H, E375Y, A437G, A484E, D510K, and K512Y; K131E,
K135Q, V141K, L142K, Y148I, Y224K, E239G, V250I, L253A, E375Y,
A437G, A484E, E508K, D510K, K512Y, E515Q, and K536Q; K131E, Y148I,
Y224K, E239G, V250I, L253A, E375Y, A437G, A484E, E508K, D510K,
K512Y, and E515Q; and K131Q, Y148I, Y224K, E239G, V250I, L253A,
E375Y, A484E, D510K, and K512Y; wherein identification of positions
is relative to SEQ ID NO:1.
Additional exemplary mutations and combinations are described
herein or can be formed from those disclosed herein, and
polymerases including such combinations are also features of the
invention.
The recombinant polymerase can be a modified recombinant .PHI.29
polymerase. Thus, in one class of embodiments, the recombinant
polymerase is at least 70% identical to wild-type .PHI.29
polymerase (SEQ ID NO:1), for example, at least 80%, at least 85%,
at least 90%, at least 95%, at least 98%, or even at least 99%
identical to wild-type .PHI.29 polymerase (SEQ ID NO:1). As another
example, the recombinant polymerase can be a modified recombinant
M2Y polymerase. Thus, in one class of embodiments, the recombinant
polymerase is at least 70% identical to wild-type M2Y polymerase
(SEQ ID NO:2), for example, at least 80%, at least 85%, at least
90%, at least 95%, at least 98%, or even at least 99% identical to
wild-type M2Y polymerase (SEQ ID NO:2). In other exemplary
embodiments, the recombinant polymerase is a recombinant B103,
GA-1, PZA, .PHI.15, BS32, Nf, G1, Cp-1, PRD1, PZE, SF5, Cp-5, Cp-7,
PR4, PR5, PR722, or L17 polymerase.
The recombinant polymerase optionally comprises one or more
exogenous features, e.g., at the C-terminal and/or N-terminal
region of the polymerase, for example, a polyhistidine tag (e.g., a
His10 tag) or a biotin ligase recognition sequence. As a few
examples, the polymerase can include a C-terminal polyhistidine
tag, a C-terminal polyhistidine tag and biotin ligase recognition
sequence, or an N-terminal polyhistidine tag and biotin ligase
recognition sequence and a C-terminal polyhistidine tag.
A related general class of embodiments provides a composition
comprising a recombinant DNA polymerase, which recombinant
polymerase comprises an amino acid sequence selected from the group
consisting of SEQ ID NOs:27-46 or a conservative or substantially
identical variant thereof.
A composition comprising a recombinant polymerase of the invention
can also include a nucleotide analog, e.g., a phosphate-labeled
nucleotide analog. The analog optionally comprises a fluorophore.
The analog can comprise three phosphate groups, or it can comprise
four or more phosphate groups, e.g., 4-7 phosphate groups (that is,
the analog can be a tetraphosphate, pentaphosphate, hexaphosphate,
or heptaphosphate analog). In one class of embodiments, the
composition includes a nucleotide analog (e.g., a phosphate-labeled
nucleotide analog) and a DNA template, and the polymerase
incorporates the nucleotide analog into a copy nucleic acid in
response to the DNA template. The composition can be present in a
DNA sequencing system, e.g., a zero-mode waveguide (ZMW). The
recombinant polymerase can be immobilized on a surface, for
example, on a surface of a zero-mode waveguide, preferably in an
active form.
In one aspect, the invention provides methods of sequencing a DNA
template. In the methods, a reaction mixture that includes the DNA
template, a replication initiating moiety that complexes with or is
integral to the template, one or more nucleotides and/or nucleotide
analogs, and a recombinant polymerase of the invention (e.g., a
recombinant .PHI.29-type DNA polymerase) is provided. The
polymerase is capable of replicating at least a portion of the
template using the moiety in a template-dependent polymerization
reaction. The reaction mixture is subjected to a polymerization
reaction in which the recombinant polymerase replicates at least a
portion of the template in a template-dependent manner, whereby the
one or more nucleotides and/or nucleotide analogs are incorporated
into the resulting DNA. A time sequence of incorporation of the one
or more nucleotides and/or nucleotide analogs into the resulting
DNA is identified.
The nucleotide analogs used in the methods can comprise a first
analog and a second analog (and optionally third, fourth, etc.
analogs), each of which comprise different fluorescent labels. The
different fluorescent labels can optionally be distinguished from
one another during the step in which a time sequence of
incorporation is identified. Optionally, subjecting the reaction
mixture to a polymerization reaction and identifying a time
sequence of incorporation are performed in a zero mode waveguide.
Essentially all of the features noted for the compositions herein
apply to these methods as well, as relevant.
In a related aspect, the invention provides methods of making a
DNA. In the methods, a reaction mixture is provided that includes a
template, a replication initiating moiety that complexes with or is
integral to the template, one or more nucleotides and/or nucleotide
analogs, and a recombinant polymerase of the invention (e.g., a
recombinant .PHI.29-type DNA polymerase). The polymerase is capable
of replicating at least a portion of the template using the moiety
in a template-dependent polymerase reaction. The mixture is reacted
such that the polymerase replicates at least a portion of the
template in a template-dependent manner, whereby the one or more
nucleotides and/or nucleotide analogs are incorporated into the
resulting DNA. The reaction mixture is optionally reacted in a zero
mode waveguide. The methods optionally include detecting
incorporation of at least one of the nucleotides and/or nucleotide
analogs. Essentially all of the features noted for the compositions
herein apply to these methods as well, as relevant.
In one aspect, the invention provides methods of making a
recombinant polymerase. In the methods, a parental polymerase
(e.g., a wild-type or other .PHI.29-type polymerase) is mutated at
one or more of the positions described herein (e.g., one or more of
positions K131, K132, K135, V141, L142, Y148, H149, Q183, G197,
1201, K205, K206, Y224, D235, E239, V250, L253, E375, A437, K472,
A484, I504, E508, D510, K512, L513, E515, D523, K536, and K539,
where identification of positions is relative to SEQ ID NO:1).
Optionally, one or more property of the recombinant polymerase
(e.g., resistance to photodamage) is assessed and compared to that
for the parental polymerase.
BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 presents an alignment between the amino acid sequences of
wild-type M2Y polymerase (SEQ ID NO:2) and wild-type .PHI.29
polymerase (SEQ ID NO:1).
FIG. 2 depicts the structure of A488dA4P.
FIGS. 3A-3B schematically illustrate an exemplary single molecule
sequencing by incorporation process in which the compositions of
the invention provide particular advantages.
FIG. 4 presents a fluorescence time trace for a ZMW, showing pulses
representing incorporation of different nucleotide analogs. The
inset schematically illustrates the catalytic cycle for
polymerase-mediated extension; the box indicates the portion of the
catalytic cycle that corresponds to the pulse when sequencing is
performed with phosphate-labeled nucleotide analogs.
FIG. 5 depicts the electrostatic surface of .PHI.29 polymerase with
a bound phosphate-labeled hexaphosphate analog.
FIG. 6 depicts the location of exemplary residues that can be
mutated to reduce positive surface charge of .PHI.29 polymerase
without loss of sequence performance.
FIG. 7 provides exemplary polymerase mutations and combinations
thereof in accordance with the invention. Positions of the
mutations are identified relative to a wild-type .PHI.29 DNA
polymerase (SEQ ID NO:1) where the name of the polymerase includes
"Phi29" or relative to a wild-type M2Y polymerase (SEQ ID NO:2)
where the name of the polymerase includes "M2."
FIG. 8 shows a view in the vicinity of residues 253 and 437 of a
recombinant .PHI.29 polymerase including D12A, D66A, Y224K, E239G,
L253H, E375Y, A437G, A484E, D510K, and K512Y substitutions.
Schematic figures are not necessarily to scale.
DEFINITIONS
Unless defined otherwise, all technical and scientific terms used
herein have the same meaning as commonly understood by one of
ordinary skill in the art to which the invention pertains. The
following definitions supplement those in the art and are directed
to the current application and are not to be imputed to any related
or unrelated case, e.g., to any commonly owned patent or
application. Although any methods and materials similar or
equivalent to those described herein can be used in the practice
for testing of the present invention, the preferred materials and
methods are described herein. Accordingly, the terminology used
herein is for the purpose of describing particular embodiments
only, and is not intended to be limiting.
As used in this specification and the appended claims, the singular
forms "a," "an" and "the" include plural referents unless the
context clearly dictates otherwise. Thus, for example, reference to
"a protein" includes a plurality of proteins; reference to "a cell"
includes mixtures of cells, and the like.
The term "about" as used herein indicates the value of a given
quantity varies by +/-10% of the value, or optionally+/-5% of the
value, or in some embodiments, by +/-1% of the value so
described.
The term "nucleic acid" or "polynucleotide" encompasses any
physical string of monomer units that can be corresponded to a
string of nucleotides, including a polymer of nucleotides (e.g., a
typical DNA or RNA polymer), PNAs, modified oligonucleotides (e.g.,
oligonucleotides comprising nucleotides that are not typical to
biological RNA or DNA, such as 2'-O-methylated oligonucleotides),
and the like. A nucleic acid can be e.g., single-stranded or
double-stranded. Unless otherwise indicated, a particular nucleic
acid sequence of this invention encompasses complementary
sequences, in addition to the sequence explicitly indicated.
A "polypeptide" is a polymer comprising two or more amino acid
residues (e.g., a peptide or a protein). The polymer can
additionally comprise non-amino acid elements such as labels,
quenchers, blocking groups, or the like and can optionally comprise
modifications such as glycosylation, biotinylation, or the like.
The amino acid residues of the polypeptide can be natural or
non-natural and can be unsubstituted, unmodified, substituted or
modified.
An "amino acid sequence" is a polymer of amino acid residues (a
protein, polypeptide, etc.) or a character string representing an
amino acid polymer, depending on context.
A "polynucleotide sequence" or "nucleotide sequence" is a polymer
of nucleotides (an oligonucleotide, a DNA, a nucleic acid, etc.) or
a character string representing a nucleotide polymer, depending on
context. From any specified polynucleotide sequence, either the
given nucleic acid or the complementary polynucleotide sequence
(e.g., the complementary nucleic acid) can be determined.
Numbering of a given amino acid or nucleotide polymer "corresponds
to numbering of" or is "relative to" a selected amino acid polymer
or nucleic acid when the position of any given polymer component
(amino acid residue, incorporated nucleotide, etc.) is designated
by reference to the same residue position in the selected amino
acid or nucleotide polymer, rather than by the actual position of
the component in the given polymer. Similarly, identification of a
given position within a given amino acid or nucleotide polymer is
"relative to" a selected amino acid or nucleotide polymer when the
position of any given polymer component (amino acid residue,
incorporated nucleotide, etc.) is designated by reference to the
residue name and position in the selected amino acid or nucleotide
polymer, rather than by the actual name and position of the
component in the given polymer. Correspondence of positions is
typically determined by aligning the relevant amino acid or
polynucleotide sequences. For example, residue K221 of wild-type
M2Y polymerase (SEQ ID NO:2) is identified as position Y224
relative to wild-type .PHI.29 polymerase (SEQ ID NO:1); see, e.g.,
the alignment shown in FIG. 1. Similarly, residue L138 of wild-type
M2Y polymerase (SEQ ID NO:2) is identified as position V141
relative to wild-type .PHI.29 polymerase (SEQ ID NO:1), and an
L138K substitution in the M2Y polymerase is thus identified as a
V141K substitution relative to SEQ ID NO:1. Amino acid positions
herein are generally identified relative to SEQ ID NO:1 unless
explicitly indicated otherwise.
The term "recombinant" indicates that the material (e.g., a nucleic
acid or a protein) has been artificially or synthetically
(non-naturally) altered by human intervention. The alteration can
be performed on the material within, or removed from, its natural
environment or state. For example, a "recombinant nucleic acid" is
one that is made by recombining nucleic acids, e.g., during
cloning, DNA shuffling or other procedures, or by chemical or other
mutagenesis; a "recombinant polypeptide" or "recombinant protein"
is, e.g., a polypeptide or protein which is produced by expression
of a recombinant nucleic acid.
A ".PHI.29-type DNA polymerase" (or "phi29-type DNA polymerase") is
a DNA polymerase from the .PHI.29 phage or from one of the related
phages that, like .PHI.29, contain a terminal protein used in the
initiation of DNA replication. .PHI.29-type DNA polymerases are
homologous to the .PHI.29 DNA polymerase (e.g., as listed in SEQ ID
NO:1); examples include the B103, GA-1, PZA, .PHI.15, BS32, M2Y
(also known as M2), Nf, G1, Cp-1, PRD1, PZE, SF5, Cp-5, Cp-7, PR4,
PR5, PR722, L17, and AV-1 DNA polymerases, as well as chimeras
thereof. A modified recombinant .PHI.29-type DNA polymerase
includes one or more mutations relative to naturally-occurring
wild-type .PHI.29-type DNA polymerases, for example, one or more
mutations that increase phototolerance, alter interaction with
and/or incorporation of nucleotide analogs, and/or alter another
polymerase property, and may include additional alterations or
modifications over the wild-type .PHI.29-type DNA polymerase, such
as one or more deletions, insertions, and/or fusions of additional
peptide or protein sequences (e.g., for immobilizing the polymerase
on a surface or otherwise tagging the polymerase enzyme).
A variety of additional terms are defined or otherwise
characterized herein.
DETAILED DESCRIPTION
One aspect of the invention is generally directed to compositions
comprising a recombinant polymerase, e.g., a recombinant
.PHI.29-type DNA polymerase, that includes one or more mutations
(e.g., amino acid substitutions, deletions, or insertions) as
compared to a reference polymerase, e.g., a wild-type .PHI.29-type
polymerase. Depending on the particular mutation or combination of
mutations, the polymerase exhibits one or more properties that find
use in, e.g., single molecule sequencing applications or nucleic
acid amplification. Exemplary properties exhibited by various
polymerases of the invention include increased resistance to
photodamage, a reduction in the rate of one or more steps of the
polymerase kinetic cycle (resulting from, e.g., enhanced
interaction of the polymerase with nucleotide analog, enhanced
metal coordination, etc.), increased closed complex stability, an
altered branching fraction, reduced or eliminated exonuclease
activity, altered cofactor selectivity, and increased processivity,
yield, thermostability, accuracy, speed, and/or readlength, as well
as other features that will become apparent upon a complete review
of the present disclosure. The polymerases can include one or more
exogenous or heterologous features, e.g., at the N- and/or
C-terminal regions of the polymerase. Such features find use not
only for purification of the recombinant polymerase and/or
immobilization of the polymerase to a substrate, but can also alter
one or more properties of the polymerase.
Among other aspects, the present invention provides new polymerases
that incorporate nucleotide analogs, such as dye labeled phosphate
labeled analogs, into a growing template copy during DNA
amplification. These polymerases are modified such that they have
one or more desirable properties, for example, increased resistance
to photodamage, decreased branching fraction formation when
incorporating the relevant analogs, improved DNA-polymerase
stability or processivity, reduced exonuclease activity, increased
thermostability and/or yield, altered cofactor selectivity,
improved accuracy, speed, and/or readlength, and/or altered kinetic
properties as compared to corresponding wild-type or other parental
polymerases (e.g., polymerases from which modified recombinant
polymerases of the invention were derived, e.g., by mutation). The
polymerases of the invention can also include any of the additional
features for improved specificity, improved processivity, improved
retention time, improved surface stability, affinity tagging,
and/or the like noted herein.
These new polymerases are particularly well suited to DNA
amplification and/or sequencing applications, particularly
sequencing protocols that include detection in real time of the
incorporation of labeled analogs into DNA amplicons, since the
increased phototolerance can prolong useful life of the polymerase
under assay conditions and the altered rates, reduced or eliminated
exonuclease activity, decreased branch fraction, improved complex
stability, altered metal cofactor selectivity, or the like can
facilitate discrimination of nucleotide incorporation events from
non-incorporation events such as transient binding of a mismatched
nucleotide in the active site of the complex, improve processivity,
and/or facilitate detection of incorporation events.
Polymerases of the invention include, for example, a recombinant
.PHI.29-type DNA polymerase that comprises a mutation at one or
more positions selected from the group consisting of Q99, K131,
K132, K135, V141, L142, Y148, H149, Q183, G197, 1201, K205, K206,
Y224, D235, E239, V250, L253, C290, R306, R308, K311, E375, A437,
T441, C455, K472, A484, I504, E508, D510, K512, L513, E515, D523,
K536, and K539, where identification of positions is relative to
wild-type .PHI.29 polymerase (SEQ ID NO:1). Optionally, the
polymerase comprises mutations at two or more, three or more, four
or more, five or more, or even six or more of these positions. For
example, the polymerase can include a mutation at position E375, a
mutation at position K512, and a mutation at one or more positions
selected from the group consisting of Q99, K131, K132, K135, V141,
L142, Y148, H149, Q183, G197, 1201, K205, K206, Y224, D235, E239,
V250, C290, R306, R308, K311, A437, T441, C455, K472, I504, E508,
L513, E515, D523, K536, and K539 (where identification of positions
is relative to SEQ ID NO:1), and can optionally also include a
mutation at one or more additional positions, e.g., as described
herein. Similarly, for example, the polymerase can comprise
mutations at positions 375, 512, and 253, positions 375, 512, and
484, positions 253 and 484, positions 375, 512, 253, and 484, or
positions 375, 512, 253, 484, and 510, and a mutation at one or
more positions selected from the group consisting of Q99, K131,
K132, K135, V141, L142, Y148, H149, Q183, G197, 1201, K205, K206,
Y224, D235, E239, V250, C290, R306, R308, K311, A437, T441, C455,
K472, I504, E508, L513, E515, D523, K536, and K539 (where
identification of positions is relative to SEQ ID NO:1). A number
of exemplary substitutions at these (and other) positions are
described herein.
As a few examples, a mutation at E375 can comprise an amino acid
substitution selected from the group consisting of E375Y, E375F,
E375R, E375Q, E375H, E375L, E375A, E375K, E375S, E375T, E375C,
E375G, and E375N; a mutation at position K512 can comprise an amino
acid substitution selected from the group consisting of K512Y,
K512F, K512I, K512M, K512C, K512E, K512G, K512H, K512N, K512Q,
K512R, K512V, and K512H; a mutation at position L253 can comprise
an amino acid substitution selected from the group consisting of
L253A, L253H, L253S, and L253C; a mutation at position A484 can
comprise an A484E substitution; and/or a mutation at position D510
can comprise a D510K or D510S substitution. Other exemplary
substitutions include, e.g., Q99W, K131E, K131Q, K135Q, K135S,
V141K, L142K, Y148I, H149D, Q183F, G197D, G197E, I201E, K205E,
K205D, K205A, K206E, Y224K, D235E, E239G, V250A, V250I, C290F,
R306Q, R308L, K311E, A437G, T441I, C455A, K472A, E508K, E515Q,
E515P, E515K, and K536Q; additional substitutions are described
herein.
The polymerase mutations and mutational strategies noted herein can
be combined with each other and with essentially any other
available mutations and mutational strategies to confer additional
improvements in, e.g., nucleotide analog specificity, enzyme
processivity, improved retention time of labeled nucleotides in
polymerase-DNA-nucleotide complexes, phototolerance, and the like.
For example, the mutations and mutational strategies herein can be
combined with those taught in, e.g., WO 2007/076057 POLYMERASES FOR
NUCLEOTIDE ANALOGUE INCORPORATION by Hanzel et al., WO 2008/051530
POLYMERASE ENZYMES AND REAGENTS FOR ENHANCED NUCLEIC ACID
SEQUENCING by Rank et al., U.S. patent application publication
2010-0075332 ENGINEERING POLYMERASES AND REACTION CONDITIONS FOR
MODIFIED INCORPORATION PROPERTIES by Pranav Patel et al., U.S.
patent application publication 2010-0093555 ENZYMES RESISTANT TO
PHOTODAMAGE by Keith Bjornson et al., U.S. patent application
publication 2010-0112645 GENERATION OF MODIFIED POLYMERASES FOR
IMPROVED ACCURACY IN SINGLE MOLECULE SEQUENCING by Sonya Clark et
al., U.S. patent application publication 2011-0189659 GENERATION OF
MODIFIED POLYMERASES FOR IMPROVED ACCURACY IN SINGLE MOLECULE
SEQUENCING by Sonya Clark et al., and U.S. patent application
publication 2012-0034602 RECOMBINANT POLYMERASES FOR IMPROVED
SINGLE MOLECULE SEQUENCING. This combination of
mutations/mutational strategies can be used to impart several
simultaneous improvements to a polymerase (e.g., increased
phototolerance, decreased branch fraction formation, improved
specificity, improved processivity, altered rates, improved
retention time, improved stability of the closed complex, tolerance
for a particular metal cofactor, etc.). In addition, polymerases
can be further modified for application-specific reasons, such as
to improve activity of the enzyme when bound to a surface, as
taught, e.g., in WO 2007/075987 ACTIVE SURFACE COUPLED POLYMERASES
by Hanzel et al. and WO 2007/075873 PROTEIN ENGINEERING STRATEGIES
TO OPTIMIZE ACTIVITY OF SURFACE ATTACHED PROTEINS by Hanzel et al.,
or to include purification or handling tags as is taught in the
cited references and as is common in the art. Similarly, the
modified polymerases described herein can be employed in
combination with other strategies to improve polymerase
performance, for example, reaction conditions for controlling
polymerase rate constants such as taught in U.S. patent application
publication U.S. 2009-0286245 entitled "Two slow-step polymerase
enzyme systems and methods."
Also taught are approaches for modifying polymerases to enhance one
or more properties exhibited by the polymerases or to confer an
additional property not provided by a starting combination of
mutations. For example, provided below are approaches for
structure-based design of polymerases with increased resistance to
photodamage (increased phototolerance).
DNA Polymerases
DNA polymerases that can be modified to have increased
phototolerance and/or other desirable properties as described
herein are generally available. DNA polymerases are sometimes
classified into six main groups based upon various phylogenetic
relationships, e.g., with E. coli Pol I (class A), E. coli Pol II
(class B), E. coli Pol III (class C), Euryarchaeotic Pol II (class
D), human Pol beta (class X), and E. coli UmuC/DinB and eukaryotic
RAD30/xeroderma pigmentosum variant (class Y). For a review of
recent nomenclature, see, e.g., Burgers et al. (2001) "Eukaryotic
DNA polymerases: proposal for a revised nomenclature" J Biol Chem.
276(47):43487-90. For a review of polymerases, see, e.g., Hubscher
et al. (2002) "Eukaryotic DNA Polymerases" Annual Review of
Biochemistry Vol. 71: 133-163; Alba (2001) "Protein Family Review:
Replicative DNA Polymerases" Genome Biology 2(1):reviews
3002.1-3002.4; and Steitz (1999) "DNA polymerases: structural
diversity and common mechanisms" J Biol Chem 274:17395-17398. The
basic mechanisms of action for many polymerases have been
determined. The sequences of literally hundreds of polymerases are
publicly available, and the crystal structures for many of these
have been determined or can be inferred based upon similarity to
solved crystal structures for homologous polymerases. For example,
the crystal structure of .PHI.29, a preferred type of parental
enzyme to be modified according to the invention, is available.
Many such polymerases that are suitable for modification are
available, e.g., for use in sequencing, labeling, and amplification
technologies. For example, human DNA Polymerase Beta is available
from R&D systems. DNA polymerase I is available from Epicenter,
GE Health Care, Invitrogen, New England Biolabs, Promega, Roche
Applied Science, Sigma Aldrich, and many others. The Klenow
fragment of DNA Polymerase I is available in both recombinant and
protease digested versions, from, e.g., Ambion, Chimerx, eEnzyme
LLC, GE Health Care, Invitrogen, New England Biolabs, Promega,
Roche Applied Science, Sigma Aldrich and many others. .PHI.29 DNA
polymerase is available from e.g., Epicentre. Poly A polymerase,
reverse transcriptase, Sequenase, SP6 DNA polymerase, T4 DNA
polymerase, T7 DNA polymerase, and a variety of thermostable DNA
polymerases (Taq, hot start, titanium Taq, etc.) are available from
a variety of these and other sources. Recent commercial DNA
polymerases include Phusion.TM. High-Fidelity DNA Polymerase,
available from New England Biolabs; GoTaq.RTM. Flexi DNA
Polymerase, available from Promega; RepliPHI.TM. .PHI.29 DNA
Polymerase, available from Epicentre Biotechnologies; PfuUltra.TM.
Hotstart DNA Polymerase, available from Stratagene; KOD HiFi DNA
Polymerase, available from Novagen; and many others.
Biocompare(dot)com provides comparisons of many different
commercially available polymerases.
DNA polymerases that are preferred substrates for mutation to
increase phototolerance, reduce reaction rates, reduce or eliminate
exonuclease activity, decrease branching fraction, improve closed
complex stability, alter metal cofactor selectivity, and/or alter
one or more other property described herein include Taq
polymerases, exonuclease deficient Taq polymerases, E. coli DNA
Polymerase 1, Klenow fragment, reverse transcriptases, .PHI.29
related polymerases including wild type .PHI.29 polymerase and
derivatives of such polymerases such as exonuclease deficient
forms, T7 DNA polymerase, T5 DNA polymerase, RB69 polymerase,
etc.
In one aspect, the polymerase that is modified is a .PHI.29-type
DNA polymerase. For example, the modified recombinant DNA
polymerase can be homologous to a wild-type or exonuclease
deficient .PHI.29 DNA polymerase, e.g., as described in U.S. Pat.
Nos. 5,001,050, 5,198,543, or 5,576,204. Alternately, the modified
recombinant DNA polymerase can be homologous to another
.PHI.29-type DNA polymerase, such as B103, GA-1, PZA, .PHI.15,
BS32, M2Y (also known as M2), Nf, G1, Cp-1, PRD1, PZE, SF5, Cp-5,
Cp-7, PR4, PR5, PR722, L17, AV-1, .PHI.21, or the like. For
nomenclature, see also, Meijer et al. (2001) ".PHI.29 Family of
Phages" Microbiology and Molecular Biology Reviews, 65(2):261-287.
See, e.g., SEQ ID NO:1 for the amino acid sequence of wild-type
.PHI.29 polymerase, SEQ ID NO:2 for the amino acid sequence of
wild-type M2Y polymerase, SEQ ID NO:3 for the amino acid sequence
of wild-type B103 polymerase, SEQ ID NO:4 for the amino acid
sequence of wild-type GA-1 polymerase, SEQ ID NO:5 for the amino
acid sequence of wild-type AV-1 polymerase, and SEQ ID NO:6 for the
amino acid sequence of wild-type CP-1 polymerase.
In addition to wild-type polymerases, chimeric polymerases made
from a mosaic of different sources can be used. For example,
.PHI.29-type polymerases made by taking sequences from more than
one parental polymerase into account can be used as a starting
point for mutation to produce the polymerases of the invention.
Chimeras can be produced, e.g., using consideration of similarity
regions between the polymerases to define consensus sequences that
are used in the chimera, or using gene shuffling technologies in
which multiple .PHI.29-related polymerases are randomly or
semi-randomly shuffled via available gene shuffling techniques
(e.g., via "family gene shuffling"; see Crameri et al. (1998) "DNA
shuffling of a family of genes from diverse species accelerates
directed evolution" Nature 391:288-291; Clackson et al. (1991)
"Making antibody fragments using phage display libraries" Nature
352:624-628; Gibbs et al. (2001) "Degenerate oligonucleotide gene
shuffling (DOGS): a method for enhancing the frequency of
recombination with family shuffling" Gene 271:13-20; and Hiraga and
Arnold (2003) "General method for sequence-independent
site-directed chimeragenesis: J. Mol. Biol. 330:287-296). In these
methods, the recombination points can be predetermined such that
the gene fragments assemble in the correct order. However, the
combinations, e.g., chimeras, can be formed at random. For example,
using methods described in Clarkson et al., five gene chimeras,
e.g., comprising segments of a Phi29 polymerase, a PZA polymerase,
a M2 polymerase, a B103 polymerase, and a GA-1 polymerase, can be
generated. Appropriate mutations to increase phototolerance and/or
alter another desirable property as described herein can be
introduced into the chimeras.
Available DNA polymerase enzymes have also been modified in any of
a variety of ways, e.g., to reduce or eliminate exonuclease
activities (many native DNA polymerases have a proof-reading
exonuclease function that interferes with, e.g., sequencing
applications), to simplify production by making protease digested
enzyme fragments such as the Klenow fragment recombinant, etc. As
noted, polymerases have also been modified to confer improvements
in specificity, processivity, and retention time of labeled
nucleotides in polymerase-DNA-nucleotide complexes (e.g., WO
2007/076057 POLYMERASES FOR NUCLEOTIDE ANALOGUE INCORPORATION by
Hanzel et al. and WO 2008/051530 POLYMERASE ENZYMES AND REAGENTS
FOR ENHANCED NUCLEIC ACID SEQUENCING by Rank et al.), to alter
branching fraction and translocation (e.g., U.S. patent application
publication 2010-0075332 by Pranav Patel et al. entitled
"ENGINEERING POLYMERASES AND REACTION CONDITIONS FOR MODIFIED
INCORPORATION PROPERTIES"), to increase photostability (e.g., U.S.
patent application publication 2010-0093555 ENZYMES RESISTANT TO
PHOTODAMAGE by Keith Bjornson et al.), to slow one or more
catalytic steps during the polymerase kinetic cycle, increase
closed complex stability, decrease branching fraction, alter
cofactor selectivity, and increase yield, thermostability,
accuracy, speed, and readlength (e.g., U.S. patent application
publication 2010-0112645 GENERATION OF MODIFIED POLYMERASES FOR
IMPROVED ACCURACY IN SINGLE MOLECULE SEQUENCING by Sonya Clark et
al., U.S. patent application publication 2011-0189659 GENERATION OF
MODIFIED POLYMERASES FOR IMPROVED ACCURACY IN SINGLE MOLECULE
SEQUENCING by Sonya Clark et al., and U.S. patent application
publication 2012-0034602 RECOMBINANT POLYMERASES FOR IMPROVED
SINGLE MOLECULE SEQUENCING), and to improve surface-immobilized
enzyme activities (e.g., WO 2007/075987 ACTIVE SURFACE COUPLED
POLYMERASES by Hanzel et al. and WO 2007/075873 PROTEIN ENGINEERING
STRATEGIES TO OPTIMIZE ACTIVITY OF SURFACE ATTACHED PROTEINS by
Hanzel et al.). Any of these available polymerases can be modified
in accordance with the invention.
Nucleotide Analogs
As discussed, various polymerases of the invention can incorporate
one or more nucleotide analogs into a growing oligonucleotide
chain. Upon incorporation, the analog can leave a residue that is
the same as or different than a natural nucleotide in the growing
oligonucleotide (the polymerase can incorporate any non-standard
moiety of the analog, or can cleave it off during incorporation
into the oligonucleotide). A "nucleotide analog" herein is a
compound, that, in a particular application, functions in a manner
similar or analogous to a naturally occurring nucleoside
triphosphate (a "nucleotide"), and does not otherwise denote any
particular structure. A nucleotide analog is an analog other than a
standard naturally occurring nucleotide, i.e., other than A, G, C,
T, or U, though upon incorporation into the oligonucleotide, the
resulting residue in the oligonucleotide can be the same as (or
different from) an A, G, C, T, or U residue.
In one useful aspect of the invention, nucleotide analogs can also
be modified to achieve any of the improved properties desired. For
example, various linkers or other substituents can be incorporated
into analogs that have the effect of reducing branching fraction,
improving processivity, or altering rates. Modifications to the
analogs can include extending the phosphate chains, e.g., to
include a tetra-, penta-, hexa- or heptaphosphate group, and/or
adding chemical linkers to extend the distance between the
nucleotide base and the dye molecule, e.g., a fluorescent dye
molecule. Substitution of one or more non-bridging oxygen in the
polyphosphate, for example with S or BH.sub.3, can change the
polymerase reaction kinetics, e.g., to achieve a system having two
slow steps as described hereinbelow. Optionally, one or more, two
or more, three or more, or four or more non-bridging oxygen atoms
in the polyphosphate group of the analog has an S substituted for
an O. While not being bound by theory, it is believed that the
properties of the nucleotide, such as the metal chelation
properties, electronegativity, or steric properties, can be altered
by substitution of the non-bridging oxygen(s).
Many nucleotide analogs are available and can be incorporated by
the polymerases of the invention. These include analog structures
with core similarity to naturally occurring nucleotides, such as
those that comprise one or more substituent on a phosphate, sugar,
or base moiety of the nucleoside or nucleotide relative to a
naturally occurring nucleoside or nucleotide. In one embodiment,
the nucleotide analog includes three phosphate containing groups;
for example, the analog can be a labeled nucleoside triphosphate
analog and/or an .alpha.-thiophosphate nucleotide analog having
three phosphate groups. In one embodiment, a nucleotide analog can
include one or more extra phosphate containing groups, relative to
a nucleoside triphosphate. For example, a variety of nucleotide
analogs that comprise, e.g., from 4-6 or more phosphates are
described in detail in U.S. patent application publication
2007-0072196, incorporated herein by reference in its entirety for
all purposes. Other exemplary useful analogs, including
tetraphosphate and pentaphosphate analogs, are described in U.S.
Pat. No. 7,041,812, incorporated herein by reference in its
entirety for all purposes.
For example, the analog can include a labeled compound of the
formula:
##STR00001## wherein B is a nucleobase (and optionally includes a
label); S is selected from a sugar moiety, an acyclic moiety or a
carbocyclic moiety (and optionally includes a label); L is an
optional detectable label; R.sub.1 is selected from O and S;
R.sub.2, R.sub.3 and R.sub.4 are independently selected from O, NH,
S, methylene, substituted methylene, C(O), C(CH.sub.2), CNH.sub.2,
CH.sub.2CH.sub.2, C(OH)CH.sub.2R where R is 4-pyridine or
1-imidazole, provided that R.sub.4 may additionally be selected
from
##STR00002## and
##STR00003## R.sub.5, R.sub.6, R.sub.7, R.sub.8, R.sub.11 and
R.sub.13 are, when present, each independently selected from O,
BH.sub.3, and S; and R.sub.9, R.sub.10 and R.sub.12 are
independently selected from O, NH, S, methylene, substituted
methylene, CNH.sub.2, CH.sub.2CH.sub.2, and C(OH)CH.sub.2R where R
is 4-pyridine or 1-imidazole. In some cases, phosphonate analogs
may be employed as the analogs, e.g., where one of R.sub.2,
R.sub.3, R.sub.4, R.sub.9, R.sub.10 or R.sub.12 are not O, e.g.,
they are methyl etc. See, e.g., U.S. patent application publication
2007-0072196, previously incorporated herein by reference in its
entirety for all purposes.
The base moiety incorporated into the analog is generally selected
from any of the natural or non-natural nucleobases or nucleobase
analogs, including, e.g., purine or pyrimidine bases that are
routinely found in nucleic acids and available nucleic acid
analogs, including adenine, thymine, guanine, cytidine, uracil, and
in some cases, inosine. As noted, the base optionally includes a
label moiety. For convenience, nucleotides and nucleotide analogs
are generally referred to based upon their relative analogy to
naturally occurring nucleotides. As such, an analog that operates,
functionally, like adenosine triphosphate may be generally referred
to herein by the shorthand letter A. Likewise, the standard
abbreviations of T, G, C, U and I may be used in referring to
analogs of naturally occurring nucleosides and nucleotides
typically abbreviated in the same fashion. In some cases, a base
may function in a more universal fashion, e.g., functioning like
any of the purine bases in being able to hybridize with any
pyrimidine base, or vice versa. The base moieties used in the
present invention may include the conventional bases described
herein or they may include such bases substituted at one or more
side groups, or other fluorescent bases or base analogs, such as
1,N6 ethenoadenosine or pyrrolo C, in which an additional ring
structure renders the B group neither a purine nor a pyrimidine.
For example, in certain cases, it may be desirable to substitute
one or more side groups of the base moiety with a labeling group or
a component of a labeling group, such as one of a donor or acceptor
fluorophore, or other labeling group. Examples of labeled
nucleobases and processes for labeling such groups are described
in, e.g., U.S. Pat. Nos. 5,328,824 and 5,476,928, each of which is
incorporated herein by reference in its entirety for all
purposes.
In the analogs, the S group is optionally a sugar moiety that
provides a suitable backbone for a synthesizing nucleic acid
strand. For example, the sugar moiety is optionally selected from a
D-ribosyl, 2' or 3' D-deoxyribosyl, 2',3'-D-dideoxyribosyl, 2',
3'-D-didehydrodideoxyribosyl, 2' or 3' alkoxyribosyl, 2' or 3'
aminoribosyl, 2' or 3' mercaptoribosyl, 2' or 3' alkothioribosyl,
acyclic, carbocyclic or other modified sugar moieties. A variety of
carbocyclic or acyclic moieties can be incorporated as the "S"
group in place of a sugar moiety, including, e.g., those described
in U.S. Patent Application Publication No. 2003/0124576, which is
incorporated herein by reference in its entirety for all
purposes.
For most cases, the phosphorus containing chain in the analogs,
e.g., a triphosphate in conventional NTPs, is preferably coupled to
the 5' hydroxyl group, as in natural nucleoside triphosphates.
However, in some cases, the phosphorus containing chain is linked
to the S group by the 3' hydroxyl group.
L generally refers to a detectable labeling group that is coupled
to the terminal phosphorus atom via the R.sub.4 (or R.sub.10 or
R.sub.12 etc.) group. The labeling groups employed in the analogs
of the invention may comprise any of a variety of detectable
labels. Detectable labels generally denote a chemical moiety that
provides a basis for detection of the analog compound separate and
apart from the same compound lacking such a labeling group.
Examples of labels include, e.g., optical labels, e.g., labels that
impart a detectable optical property to the analog, electrochemical
labels, e.g., labels that impart a detectable electrical or
electrochemical property to the analog, and physical labels, e.g.,
labels that impart a different physical or spatial property to the
analog, e.g., a mass tag or molecular volume tag. In some cases
individual labels or combinations may be used that impart more than
one of the aforementioned properties to the analogs of the
invention.
Optionally, the labeling groups incorporated into the analogs
comprise optically detectable moieties, such as luminescent,
chemiluminescent, fluorescent, fluorogenic, chromophoric and/or
chromogenic moieties, with fluorescent and/or fluorogenic labels
being preferred. A variety of different label moieties are readily
employed in nucleotide analogs. Such groups include, e.g.,
fluorescein labels, rhodamine labels, cyanine labels (i.e., Cy3,
Cy5, and the like, generally available from the Amersham
Biosciences division of GE Healthcare), the Alexa family of
fluorescent dyes and other fluorescent and fluorogenic dyes
available from Molecular Probes/Invitrogen, Inc. and described in
`The Handbook--A Guide to Fluorescent Probes and Labeling
Technologies, Eleventh Edition` (2010) (available from Invitrogen,
Inc./Molecular Probes). A variety of other fluorescent and
fluorogenic labels for use with nucleoside polyphosphates, and
which would be applicable to the nucleotide analogs incorporated by
the polymerases of the present invention, are described in, e.g.,
U.S. Patent Application Publication No. 2003/0124576, previously
incorporated herein by reference in its entirety for all
purposes.
Additional details regarding labels, analogs, and methods of making
such analogs can be found in U.S. patent application publication
2007-0072196, WO 2007/041342 Labeled Nucleotide Analogs and Uses
Therefor, WO 2009/114182 Labeled Reactants and Their Uses, U.S.
patent application publication 2009-0208957 Alternate Labelling
Strategies for Single Molecule Sequencing, U.S. patent application
Ser. No. 13/218,412 Functionalized Cyanine Dyes, U.S. patent
application Ser. No. 13/218,395 Functionalized Cyanine Dyes, U.S.
patent application Ser. No. 13/218,428 Cyanine Dyes, and U.S.
patent application Ser. No. 13/218,382 Scaffold-Based Polymerase
Enzyme Substrates, each of which is incorporated herein by
reference in its entirety for all purposes.
Thus, in one illustrative example, the analog can be a phosphate
analog (e.g., an analog that has more than the typical number of
phosphates found in nucleoside triphosphates) that includes, e.g.,
an Alexa dye label. For example, an Alexa488 dye can be labeled on
a delta phosphate of a tetraphosphate analog (denoted, e.g.,
A488dC4P or A488dA4P, shown in FIG. 2, for the Alexa488 labeled
tetraphosphate analogs of C and A, respectively), or an Alexa568 or
Alexa633 dye can be used (e.g., A568dC4P and A633dC4P,
respectively, for labeled tetraphosphate analogs of C or A568dT6P
for a labeled hexaphosphate analog of T), or an Alexa546 dye can be
used (e.g., A546dG4P), or an Alexa594 dye can be used (e.g.,
A594dT4P). As additional examples, an Alexa555 dye (e.g., A555dC6P
or A555dA6P), an Alexa 647 dye (e.g., A647dG6P), an Alexa 568 dye
(e.g., A568dT6P), and/or an Alexa660 dye (e.g., A660dA6P or
A660dC6P) can be used in, e.g., single molecule sequencing.
Similarly, to facilitate color separation, a pair of fluorophores
exhibiting FRET (fluorescence resonance energy transfer) can be
labeled on a delta phosphate of a tetraphosphate analog (denoted,
e.g., FAM-amb-A532dG4P or FAM-amb-A594dT4P).
Applications for Enhanced Nucleic Acid Amplification and
Sequencing
Polymerases of the invention, e.g., modified recombinant
polymerases, are optionally used in combination with nucleotides
and/or nucleotide analogs and nucleic acid templates (e.g., DNA,
RNA, or hybrids, analogs, derivatives, or mimetics thereof) to copy
the template nucleic acid. That is, a mixture of the polymerase,
nucleotides/analogs, and optionally other appropriate reagents, the
template and a replication initiating moiety (e.g., primer) is
reacted such that the polymerase synthesizes nucleic acid (e.g.,
extends the primer) in a template-dependent manner. The replication
initiating moiety can be a standard oligonucleotide primer, or,
alternatively, a component of the template, e.g., the template can
be a self-priming single stranded DNA, a nicked double stranded
DNA, or the like. Similarly, a terminal protein can serve as an
initiating moiety. At least one nucleotide analog can be
incorporated into the DNA. The template DNA can be a linear or
circular DNA, and in certain applications, is desirably a circular
template (e.g., for rolling circle replication or for sequencing of
circular templates). Optionally, the composition can be present in
an automated DNA replication and/or sequencing system.
Incorporation of labeled nucleotide analogs by the polymerases of
the invention is particularly useful in a variety of different
nucleic acid analyses, including real-time monitoring of DNA
polymerization. The label can itself be incorporated, or more
preferably, can be released during incorporation of the analog. For
example, analog incorporation can be monitored in real-time by
monitoring label release during incorporation of the analog by the
polymerase. The portion of the analog that is incorporated can be
the same as a natural nucleotide, or can include features of the
analog that differ from a natural nucleotide.
In general, label incorporation or release can be used to indicate
the presence and composition of a growing nucleic acid strand,
e.g., providing evidence of template replication/amplification
and/or sequence of the template. Signaling from the incorporation
can be the result of detecting labeling groups that are liberated
from the incorporated analog, e.g., in a solid phase assay, or can
arise upon the incorporation reaction. For example, in the case of
FRET labels where a bound label is quenched and a free label is
not, release of a label group from the incorporated analog can give
rise to a fluorescent signal. Alternatively, the enzyme may be
labeled with one member of a FRET pair proximal to the active site,
and incorporation of an analog bearing the other member will allow
energy transfer upon incorporation. The use of enzyme bound FRET
components in nucleic acid sequencing applications is described,
e.g., in U.S. Patent Application Publication No. 2003/0044781,
incorporated herein by reference.
In one example reaction of interest, a polymerase reaction can be
isolated within an extremely small observation volume that
effectively results in observation of individual polymerase
molecules. As a result, the incorporation event provides
observation of an incorporating nucleotide analog that is readily
distinguishable from non-incorporated nucleotide analogs. In a
preferred aspect, such small observation volumes are provided by
immobilizing the polymerase enzyme within an optical confinement,
such as a Zero Mode Waveguide (ZMW). For a description of ZMWs and
their application in single molecule analyses, and particularly
nucleic acid sequencing, see, e.g., U.S. Patent Application
Publication No. 2003/0044781 and U.S. Pat. No. 6,917,726, each of
which is incorporated herein by reference in its entirety for all
purposes. See also Levene et al. (2003) "Zero-mode waveguides for
single-molecule analysis at high concentrations" Science
299:682-686, Eid et al. (2009) "Real-time DNA sequencing from
single polymerase molecules" Science 323:133-138, and U.S. Pat.
Nos. 7,056,676, 7,056,661, 7,052,847, and 7,033,764, the full
disclosures of which are incorporated herein by reference in their
entirety for all purposes.
In general, a polymerase enzyme is complexed with the template
strand in the presence of one or more nucleotides and/or one or
more nucleotide analogs. For example, in certain embodiments,
labeled analogs are present representing analogous compounds to
each of the four natural nucleotides, A, T, G and C, e.g., in
separate polymerase reactions, as in classical Sanger sequencing,
or multiplexed together, e.g., in a single reaction, as in
multiplexed sequencing approaches. When a particular base in the
template strand is encountered by the polymerase during the
polymerization reaction, it complexes with an available analog that
is complementary to such nucleotide, and incorporates that analog
into the nascent and growing nucleic acid strand. In one aspect,
incorporation can result in a label being released, e.g., in
polyphosphate analogs, cleaving between the .alpha. and .beta.
phosphorus atoms in the analog, and consequently releasing the
labeling group (or a portion thereof). The incorporation event is
detected, either by virtue of a longer presence of the analog and,
thus, the label, in the complex, or by virtue of release of the
label group into the surrounding medium. Where different labeling
groups are used for each of the types of analogs, e.g., A, T, G or
C, identification of a label of an incorporated analog allows
identification of that analog and consequently, determination of
the complementary nucleotide in the template strand being processed
at that time. Sequential reaction and monitoring permits real-time
monitoring of the polymerization reaction and determination of the
sequence of the template nucleic acid. As noted above, in
particularly preferred aspects, the polymerase enzyme/template
complex is provided immobilized within an optical confinement that
permits observation of an individual complex, e.g., a zero mode
waveguide. For additional information on single molecule sequencing
monitoring incorporation of phosphate-labeled analogs in real time,
see, e.g., Eid et al. (2009) "Real-time DNA sequencing from single
polymerase molecules" Science 323:133-138.
In a first exemplary technique, as schematically illustrated in
FIG. 3A, a nucleic acid synthesis complex, including a polymerase
enzyme 202, a template sequence 204 and a complementary primer
sequence 206, is provided immobilized within an observation region
200 that permits illumination (as shown by hv) and observation of a
small volume that includes the complex without excessive
illumination of the surrounding volume (as illustrated by dashed
line 208). By illuminating and observing only the volume
immediately surrounding the complex, one can readily identify
fluorescently labeled nucleotides that become incorporated during
that synthesis, as such nucleotides are retained within that
observation volume by the polymerase for longer periods than those
nucleotides that are simply randomly diffusing into and out of that
volume.
In particular, as shown in FIG. 3B, when a nucleotide, e.g., A, is
incorporated into DNA by the polymerase, it is retained within the
observation volume for a prolonged period of time, and upon
continued illumination yields a prolonged fluorescent signal (shown
by peak 210). By comparison, randomly diffusing and not
incorporated nucleotides remain within the observation volume for
much shorter periods of time, and thus produce only transient
signals (such as peak 212), many of which go undetected due to
their extremely short duration.
In particularly preferred exemplary systems, the confined
illumination volume is provided through the use of arrays of
optically confined apertures termed zero mode waveguides (ZMWs),
e.g., as shown by confined reaction region 200 (see, e.g., U.S.
Pat. No. 6,917,726, which is incorporated herein by reference in
its entirety for all purposes). For sequencing applications, the
DNA polymerase is typically provided immobilized upon the bottom of
the ZMW, although another component of the complex (e.g., a primer
or template) is optionally immobilized on the bottom of the ZMW to
localize the complex. See, e.g., Korlach et al. (2008) PNAS U.S.A.
105(4):1176-1181 and U.S. patent application publication
2008-0032301, each of which is incorporated herein by reference in
its entirety for all purposes.
In operation, the fluorescently labeled nucleotides (shown as A, C,
G and T) bear one or more fluorescent dye groups on a terminal
phosphate moiety that is cleaved from the nucleotide upon
incorporation. As a result, synthesized nucleic acids do not bear
the build-up of fluorescent labels, as the labeled polyphosphate
groups diffuse away from the complex following incorporation of the
associated nucleotide, nor do such labels interfere with the
incorporation event. See, e.g., Korlach et al. (2008) Nucleosides,
Nucleotides and Nucleic Acids 27:1072-1083.
A fluorescence time trace for a ZMW, showing pulses (peaks)
representing incorporation of different nucleotide analogs, is
presented in FIG. 4. A pulse width and interpulse distance are
illustrated on the trace. The inset schematically illustrates the
catalytic cycle for polymerase-mediated nucleic acid primer
extension according to the exemplary reaction scheme described in
U.S. patent application publication 2012-0034602; the box indicates
the portion of the catalytic cycle that corresponds to the pulse
when sequencing is performed with phosphate-labeled nucleotide
analogs. The remainder of the cycle corresponds to the interpulse
distance.
In a second exemplary technique, the immobilized complex and the
nucleotides to be incorporated are each provided with interactive
labeling components. Upon incorporation, the nucleotide borne
labeling component is brought into sufficient proximity to the
complex borne (or complex proximal) labeling component, such that
these components produce a characteristic signal event. For
example, the polymerase may be provided with a fluorophore that
provides fluorescent resonant energy transfer (FRET) to appropriate
acceptor fluorophores. These acceptor fluorophores are provided
upon the nucleotide to be incorporated, where each type of
nucleotide bears a different acceptor fluorophore, e.g., that
provides a different fluorescent signal. Upon incorporation, the
donor and acceptor are brought close enough together to generate
energy transfer signal. By providing different acceptor labels on
the different types of nucleotides, one obtains a characteristic
FRET-based fluorescent signal for the incorporation of each type of
nucleotide, as the incorporation is occurring.
In a related aspect, a nucleotide analog may include two
interacting fluorophores that operate as a donor/quencher pair,
where one member is present on the nucleobase or other retained
portion of the nucleotide, while the other member is present on a
phosphate group or other portion of the nucleotide that is released
upon incorporation, e.g., a terminal phosphate group. Prior to
incorporation, the donor and quencher are sufficiently proximal on
the same analog as to provide characteristic signal quenching. Upon
incorporation and cleavage of the terminal phosphate groups, e.g.,
bearing a donor fluorophore, the quenching is removed and the
resulting characteristic fluorescent signal of the donor is
observable.
In exploiting the foregoing processes, where the incorporation
reaction occurs too rapidly, it may result in the incorporation
event not being detected, i.e., the event speed exceeds the
detection speed of the monitoring system. The missed detection of
incorporated nucleotides can lead to an increased rate of errors in
sequence determination, as omissions in the real sequence. In order
to mitigate the potential for missed pulses due to short reaction
or product release times, in one aspect, the current invention can
result in increased reaction and/or product release times during
incorporation cycles. Similarly, very short interpulse distances
can occasionally cause pulse merging. An advantage of employing
polymerases with reduced reaction rates, e.g., polymerases
exhibiting decreased rates and/or two slow-step kinetics as
described in U.S. patent application publications 2009-0286245 and
2010-0112645, is an increased frequency of longer, detectable,
binding events. This advantage may also be seen as an increased
ratio of longer, detectable pulses to shorter, non-detectable
pulses, where the pulses represent binding events.
In addition to their use in sequencing, the polymerases of the
invention are also useful in a variety of other genotyping
analyses, e.g., SNP genotyping using single base extension methods,
real time monitoring of amplification, e.g., RT-PCR methods, and
the like. The polymerases of the invention are also useful in
amplifying nucleic acids, e.g., DNAs or RNAs, including, for
example, in applications such as whole genome amplification. For
example, polymerases of the invention that show increased
thermostability or resistance to organic solvents (e.g., DMSO), or
that otherwise exhibit an improved ability to read through damaged,
modified, or other "difficult" stretches of nucleic acid template,
can be suitably employed in whole genome amplification. For review
of whole genome amplification, see, e.g., Silander and Saarela
(2008) "Whole Genome Amplification with Phi29 DNA Polymerase to
Enable Genetic or Genomic Analysis of Samples of Low DNA Yield"
Methods in Molecular Biology 439:1-18 and Pinard et al. (2006)
"Assessment of whole genome amplification-induced bias through
high-throughput, massively parallel whole genome sequencing" BMC
Genomics 7:216. Further details regarding sequencing and nucleic
acid amplification can be found, e.g., in Sambrook, Ausubel, and
Innis, all infra.
Recombinant Polymerases with Increased Phototolerance
The compositions of the invention comprise a modified recombinant
DNA polymerase which exhibits one or more altered properties
desirable in single molecule sequencing applications or other
applications involving nucleic acid synthesis. An exemplary
property of certain polymerases of the invention is increased
phototolerance relative to a wild-type or parental polymerase.
Other exemplary properties include altered kinetic behavior (e.g.,
demonstration of slow catalytic steps), exonuclease deficiency,
increased closed complex stability, altered (e.g., reduced)
branching fraction, altered cofactor selectivity, increased yield,
increased thermostability, increased accuracy, increased speed, and
increased readlength.
As will be understood, polymerases of the invention can display one
of the aforementioned properties alone or can display two or more
of the properties in combination. Moreover, it will be understood
that while a polymerase or group of polymerases may be described
with respect to a particular property, the polymerase(s) may
possess additional modified properties not mentioned in every
instance for ease of discussion. It will also be understood that
particular properties are observed under certain conditions. For
example, a photoprotective mutation can, e.g., confer increased
readlength (as compared to a parental polymerase lacking the
mutation) when observed with an excitation light source at a
constant power or it can confer increased accuracy at a higher
power. A single mutation (e.g., a single amino acid substitution,
deletion, insertion, or the like) may give rise to the one or more
altered properties, or the one or more properties may result from
two or more mutations which act in concert to confer the desired
activity. The recombinant polymerases, mutations, and altered
properties exhibited by the recombinant polymerases are set forth
in greater detail below.
Detection of optical labels in an enzymatic reaction generally
entails directing excitation radiation at the reaction mixture to
excite a labeling group present in the mixture, which is then
separately detectable. However, prolonged exposure of chemical and
biochemical reactants to radiation (e.g., light) energy during the
excitation and detection of optical labels can damage components of
the reaction mixture, e.g., enzymes, proteins, substrates, or the
like. For example, it has been observed that, in template-directed
synthesis of nucleic acids from fluorescently labeled nucleotides
or nucleotide analogs, sustained exposure of the DNA polymerase to
excitation radiation used in the detection of the relevant label
(e.g., fluorophore) reduces the enzyme's processivity and
polymerase activity. Although illuminated reactions typically
proceed under conditions where the reactants (e.g., enzyme
molecules, etc.) are present in excess such that any adverse
effects of photodamage on any single enzyme molecule in the
reaction mix do not, in general, affect operation of the assay, an
increasing number of analyses that entail the use of optical labels
are performed with reactants at very low concentrations. For
example, polymerases can be used to synthesize DNAs from
fluorescently labeled nucleotide analogs in microfluidic or
nanofluidic reaction vessels or channels or in optically confined
reaction volumes, e.g., in a zero-mode waveguide (ZMW) or ZMW array
as described above. Analysis of small, single-analyte reaction
volumes is becoming increasingly important in high-throughput
applications, e.g., in DNA sequencing. However, in such
reactant-limited analyses, any degradation of a critical reagent
such as an enzyme molecule due to photodamage can dramatically
interfere with the analysis.
Polymerases that exhibit decreased sensitivity to photodamage
(increased phototolerance) are thus desirable for use in a variety
of single- or low-number enzyme analyses, including, but not
limited to, DNA sequencing (e.g., single molecule sequencing),
nucleic acid amplification, and others. Exemplary approaches to
producing polymerases with increased resistance to photodamage by,
e.g., replacing residues susceptible to oxidative damage have been
described in U.S. patent application publication 2010-0093555.
Additional approaches are described below.
Without limitation to any particular mechanism, observation of
polymerase performance in single molecule sequencing reactions
using labeled nucleotide analogs has revealed that, in many
instances, photodamage involves collision of the dye moiety of an
analog with the polymerase followed by crosslink formation between
the dye and the polymerase. A novel approach to increasing
polymerase phototolerance thus involves reducing the frequency of
such collisions. In one approach, again without limitation to any
particular mechanism, since the nucleotide analog is negatively
charged, the frequency of collisions between the polymerase and the
label is reduced by introducing negative charges to and/or removing
positive charges from the surface of the polymerase that is within
reach of the dye moiety. An electrostatic surface representation of
.PHI.29 polymerase with a bound analog is shown in FIG. 5 (dark
gray is positively charged surface, and medium gray is negatively
charged). It will be evident that residues playing an essential
role in nucleotide binding and/or catalysis are not preferred sites
for substitution. Exemplary locations where positive surface charge
can be reduced without loss of performance in sequencing reactions
are shown in dark gray in FIG. 6.
Positions of particular interest include, e.g., K131, K132, K135,
H149, G197, 1201, K205, K206, K472, K536, and K539, where positions
are identified relative to wild-type .PHI.29 polymerase (SEQ ID
NO:1). To produce a polymerase with increased phototolerance, a
residue at one (or more) of these positions can be substituted with
another residue, preferably a non-positively charged residue (e.g.,
a negatively charged residue such as Asp or Glu, or an uncharged
polar residue, e.g., Asn, Gln, or Ser). Suitable substitutions at
these positions include, for example, K131E, K131Q, K131S, K131D,
K131A, K131H, K131L, K131Y, K131I, K131N, K131C, K131F, K131G,
K131P, K131R, K131T, K131V, K131W, K135Q, K135S, K135N, H149D,
G197D, G197E, I201E, K205E, K205D, K205A, K206E, K472A, K536Q, and
K539Q.
Decreasing the overall positive surface charge on the polymerase in
the vicinity of the analog binding pocket can, however, affect
binding rate of the analog, resulting in undesirably lengthened
interpulse distances or the like. Increasing positive charge in
areas of the polymerase's surface that are less accessible to the
dye moiety can compensate for this effect by narrowing interpulse
distances and increasing polymerase speed. (It will be evident that
such mutations can be employed to increase speed regardless of the
presence or absence of mutations that decrease speed while
increasing phototolerance.)
Positions of particular interest include, e.g., V141, L142, I504,
E508, D510, L513, and D523, where positions are identified relative
to wild-type .PHI.29 polymerase (SEQ ID NO:1). To increase the
overall positive surface charge, a residue at one or more of these
positions can be substituted with another residue, e.g., with an
uncharged residue where the residue was originally negatively
charged, or more preferably, with a positively charged residue
(e.g., Lys, His, or Arg). Suitable substitutions at these positions
include, for example, V141K, L142K, E508K, D510S, and D510K.
As will be appreciated, recombinant polymerases that exhibit
increased phototolerance and/or speed can also include additional
mutations (e.g., amino acid substitutions, deletions, insertions,
exogenous features at the N- and/or C-terminus, and/or the like)
which confer one or more additional desirable properties, e.g.,
reduced or eliminated exonuclease activity, convenient surface
immobilization, increased closed complex stability, reduced or
increased branching, selectivity for particular metal cofactors,
increased yield, increased thermostability, increased accuracy,
increased speed, and/or increased readlength.
Design and Characterization of Recombinant Polymerases
In addition to methods of using the polymerases and other
compositions herein, the present invention also includes methods of
making the polymerases. (Polymerases made by the methods are also a
feature of the invention, and it will be evident that, although
various design strategies are detailed herein, no limitation of the
resulting polymerases to any particular mechanism is thereby
intended.) As described, methods of making a recombinant DNA
polymerase can include structurally modeling a parental polymerase,
e.g., using any available crystal structure and molecular modeling
software or system. Based on the modeling, one or more amino acid
residue positions in the polymerase are identified as targets for
mutation. For example, one or more feature affecting
phototolerance, closed complex stability, nucleotide access to or
removal from the active site (and, thereby, branching), binding of
a DNA or nucleotide analog, product binding, etc. is identified.
These residues can be, e.g., in the active site or a binding pocket
or in a domain such as the exonuclease, TPR2 or thumb domain (or
interface between domains) or proximal to such domains. The DNA
polymerase is mutated to include different residues at such
positions (e.g., another one of the nineteen other commonly
occurring natural amino acids or a non-natural amino acid, e.g., a
nonpolar and/or aliphatic residue, a polar uncharged residue, an
aromatic residue, a positively charged residue, or a negatively
charged residue), and then screened for an activity of interest
(e.g., phototolerance, processivity, k.sub.off, K.sub.d, branching
fraction, decreased rate constant, balanced rate constants,
accuracy, speed, thermostability, yield, cofactor selectivity,
etc.). It will be evident that catalytic and/or highly conserved
residues are typically (but not necessarily) less preferred targets
for mutation.
Further, as noted above, a polymerase of the invention (e.g., a
.PHI.29-type DNA polymerase that includes E375, K512, L253, and/or
A484 mutations) can be further modified to enhance the properties
of the polymerase. For example, a polymerase comprising a
combination of the above mutations can be mutated at one or more
additional sites to enhance a property already possessed by the
polymerase or to confer a new property not provided by the existing
mutations. Details correlating polymerase structure with desirable
functionalities that can be added to polymerases of the invention
are provided herein. Also provide below are various approaches for
modifying/mutating polymerases of the invention, determining
kinetic parameters or other properties of the modified polymerases,
screening modified polymerases, and adding exogenous features to
the N- and/or C-terminal regions of the polymerases.
Structure-Based Design of Recombinant Polymerases
Structural data for a polymerase can be used to conveniently
identify amino acid residues as candidates for mutagenesis to
create recombinant polymerases, for example, having modified active
site regions and/or modified domain interfaces to increase
phototolerance, reduce reaction rates, reduce branching, improve
complex stability, reduce exonuclease activity, alter cofactor
selectivity, increase stability, improve yield, or confer other
desirable properties. For example, analysis of the
three-dimensional structure of a polymerase such as .PHI.29 can
identify residues that are in the active polymerization site of the
enzyme, residues that form part of the nucleotide analog binding
pocket, and/or amino acids at an interface between domains.
The three-dimensional structures of a large number of DNA
polymerases have been determined by x-ray crystallography and
nuclear magnetic resonance (NMR) spectroscopy, including the
structures of polymerases with bound templates, nucleotides, and/or
nucleotide analogs. Many such structures are freely available for
download from the Protein Data Bank, at (www(dot)rcsb(dot)org/pdb.
Structures, along with domain and homology information, are also
freely available for search and download from the National Center
for Biotechnology Information's Molecular Modeling DataBase, at
www(dot)ncbi(dot)nlm(dot)nih(dot)gov/Structure/MMDB/mmdb(dot)shtml.
The structures of .PHI.29 polymerase, .PHI.29 polymerase complexed
with terminal protein, and .PHI.29 polymerase complexed with
primer-template DNA in the presence and absence of a nucleoside
triphosphate are available; see Kamtekar et al. (2004) "Insights
into strand displacement and processivity from the crystal
structure of the protein-primed DNA polymerase of bacteriophage
.PHI.29" Mol. Cell 16(4): 609-618), Kamtekar et al. (2006) "The
phi29 DNA polymerase:protein-primer structure suggests a model for
the initiation to elongation transition" EMBO J. 25(6):1335-43, and
Berman et al. (2007) "Structures of phi29 DNA polymerase complexed
with substrate: The mechanism of translocation in B-family
polymerases" EMBO J. 26:3494-3505, respectively. The structures of
additional polymerases or complexes can be modeled, for example,
based on homology of the polymerases with polymerases whose
structures have already been determined. Alternatively, the
structure of a given polymerase (e.g., a wild-type or modified
polymerase), optionally complexed with a DNA (e.g., template and/or
primer) and/or nucleotide analog, or the like, can be
determined.
Techniques for crystal structure determination are well known. See,
for example, McPherson (1999) Crystallization of Biological
Macromolecules Cold Spring Harbor Laboratory; Bergfors (1999)
Protein Crystallization International University Line; Mullin
(1993) Crystallization Butterwoth-Heinemann; Stout and Jensen
(1989) X-ray structure determination: a practical guide, 2nd
Edition Wiley Publishers, New York; Ladd and Palmer (1993)
Structure determination by X-ray crystallography, 3rd Edition
Plenum Press, New York; Blundell and Johnson (1976) Protein
Crystallography Academic Press, New York; Glusker and Trueblood
(1985) Crystal structure analysis: A primer. 2nd Ed. Oxford
University Press, New York; International Tables for
Crystallography. Vol. F. Crystallography of Biological
Macromolecules; McPherson (2002) Introduction to Macromolecular
Crystallography Wiley-Liss; McRee and David (1999) Practical
Protein Crystallography, Second Edition Academic Press; Drenth
(1999) Principles of Protein X-Ray Crystallography (Springer
Advanced Texts in Chemistry) Springer-Verlag; Fanchon and
Hendrickson (1991) Chapter 15 of Crystallographic Computing. Volume
5 IUCr/Oxford University Press; Murthy (1996) Chapter 5 of
Crystallographic Methods and Protocols Humana Press; Dauter et al.
(2000) "Novel approach to phasing proteins: derivatization by short
cryo-soaking with halides" Acta Cryst.D56:232-237; Dauter (2002)
"New approaches to high-throughput phasing" Curr. Opin. Structural
Biol. 12:674-678; Chen et al. (1991) "Crystal structure of a bovine
neurophysin-II dipeptide complex at 2.8 .ANG. determined from the
single-wavelength anomalous scattering signal of an incorporated
iodine atom" Proc. Natl Acad. Sci. USA, 88:4240-4244; and Gavira et
al. (2002) "Ab initio crystallographic structure determination of
insulin from protein to electron density without crystal handling"
Acta Cryst.D58:1147-1154.
In addition, a variety of programs to facilitate data collection,
phase determination, model building and refinement, and the like
are publicly available. Examples include, but are not limited to,
the HKL2000 package (Otwinowski and Minor (1997) "Processing of
X-ray Diffraction Data Collected in Oscillation Mode" Methods in
Enzymology 276:307-326), the CCP4 package (Collaborative
Computational Project (1994) "The CCP4 suite: programs for protein
crystallography" Acta Crystallogr D 50:760-763), SOLVE and RESOLVE
(Terwilliger and Berendzen (1999) Acta Crystallogr D 55 (Pt
4):849-861), SHELXS and SHELXD (Schneider and Sheldrick (2002)
"Substructure solution with SHELXD" Acta Crystallogr D Biol
Crystallogr 58:1772-1779), Refmac5 (Murshudov et al. (1997)
"Refinement of Macromolecular Structures by the Maximum-Likelihood
Method" Acta Crystallogr D 53:240-255), PRODRG (van Aalten et al.
(1996) "PRODRG, a program for generating molecular topologies and
unique molecular descriptors from coordinates of small molecules" J
Comput Aided Mol Des 10:255-262), and Coot (Elmsley et al. (2010)
"Features and Development of Coot" Acta Cryst D 66:486-501.
Techniques for structure determination by NMR spectroscopy are
similarly well described in the literature. See, e.g., Cavanagh et
al. (1995) Protein NMR Spectroscopy: Principles and Practice,
Academic Press; Levitt (2001) Spin Dynamics: Basics of Nuclear
Magnetic Resonance, John Wiley & Sons; Evans (1995)
Biomolecular NMR Spectroscopy, Oxford University Press; Wuthrich
(1986) NMR of Proteins and Nucleic Acids (Baker Lecture Series),
Kurt Wiley-Interscience; Neuhaus and Williamson (2000) The Nuclear
Overhauser Effect in Structural and Conformational Analysis, 2nd
Edition, Wiley-VCH; Macomber (1998) A Complete Introduction to
Modern NMR Spectroscopy, Wiley-Interscience; Downing (2004) Protein
NMR Techniques (Methods in Molecular Biology), 2nd edition, Humana
Press; Clore and Gronenborn (1994) NMR of Proteins (Topics in
Molecular and Structural Biology), CRC Press; Reid (1997) Protein
NMR Techniques, Humana Press; Krishna and Berliner (2003) Protein
NMR for the Millenium (Biological Magnetic Resonance), Kluwer
Academic Publishers; Kiihne and De Groot (2001) Perspectives on
Solid State NMR in Biology (Focus on Structural Biology, 1), Kluwer
Academic Publishers; Jones et al. (1993) Spectroscopic Methods and
Analyses: NMR, Mass Spectrometry, and Related Techniques (Methods
in Molecular Biology, Vol. 17), Humana Press; Goto and Kay (2000)
Curr. Opin. Struct. Biol. 10:585; Gardner (1998) Annu. Rev.
Biophys. Biomol. Struct. 27:357; Wuthrich (2003) Angew. Chem. Int.
Ed. 42:3340; Bax (1994) Curr. Opin. Struct. Biol. 4:738; Pervushin
et al. (1997) Proc. Natl. Acad. Sci. U.S.A. 94:12366; Fiaux et al.
(2002) Nature 418:207; Fernandez and Wider (2003) Curr. Opin.
Struct. Biol. 13:570; Ellman et al. (1992) J. Am. Chem. Soc.
114:7959; Wider (2000) BioTechniques 29:1278-1294; Pellecchia et
al. (2002) Nature Rev. Drug Discov. (2002) 1:211-219; Arora and
Tamm (2001) Curr. Opin. Struct. Biol. 11:540-547; Flaux et al.
(2002) Nature 418:207-211; Pellecchia et al. (2001) J. Am. Chem.
Soc. 123:4633-4634; and Pervushin et al. (1997) Proc. Natl. Acad.
Sci. USA 94:12366-12371.
The structure of a polymerase or of a polymerase bound to a DNA or
with a given nucleotide analog incorporated into the active site
can, as noted, be directly determined, e.g., by x-ray
crystallography or NMR spectroscopy, or the structure can be
modeled based on the structure of the polymerase and/or a structure
of a polymerase with a natural nucleotide bound. The active site or
other relevant domain of the polymerase can be identified, for
example, by homology with other polymerases, examination of
polymerase-template or polymerase-nucleotide co-complexes,
biochemical analysis of mutant polymerases, and/or the like. The
position of a nucleotide analog (as opposed to an available
nucleotide structure) in the active site can be modeled, for
example, by projecting the location of non-natural features of the
analog (e.g., additional phosphate or phosphonate groups in the
phosphorus containing chain linked to the nucleotide, e.g., tetra,
penta or hexa phosphate groups, detectable labeling groups, e.g.,
fluorescent dyes, or the like) based on the previously determined
location of another nucleotide or nucleotide analog in the active
site.
Such modeling of the nucleotide analog or template (or both) in the
active site can involve simple visual inspection of a model of the
polymerase, for example, using molecular graphics software such as
the PyMOL viewer (open source, freely available on the World Wide
Web at www(dot)pymol(dot)org), Insight II, or Discovery Studio 2.1
(commercially available from Accelrys at
(www(dot)accelrys(dot)com/products/discovery-studio).
Alternatively, modeling of the active site complex of the
polymerase or a putative mutant polymerase, for example, can
involve computer-assisted docking, molecular dynamics, free energy
minimization, and/or like calculations. Such modeling techniques
have been well described in the literature; see, e.g., Babine and
Abdel-Meguid (eds.) (2004) Protein Crystallography in Drug Design,
Wiley-VCH, Weinheim; Lyne (2002) "Structure-based virtual
screening: An overview" Drug Discov. Today 7:1047-1055; Molecular
Modeling for Beginners, at
(www(dot)usm(dot)maine(dot)edu/.about.rhodes/SPVTut/index(dot)html;
and Methods for Protein Simulations and Drug Design at
(www(dot)dddc(dot)ac(dot)cn/embo04; and references therein.
Software to facilitate such modeling is widely available, for
example, the CHARMm simulation package, available academically from
Harvard University or commercially from Accelrys (at
www(dot)accelrys(dot)com), the Discover simulation package
(included in Insight II, supra), and Dynama (available at
(www(dot)cs(dot)gsu(dot)edu/.about.cscrwh/progs/progs(dot)html).
See also an extensive list of modeling software at
(www(dot)netsci(dot)org/Resources/Software/Modeling/MMMD/top(dot)html.
Visual inspection and/or computational analysis of a polymerase
model, including optional comparison of models of the polymerase in
different states, can identify relevant features of the polymerase,
including, for example, residues that can be mutated to increase
phototolerance or polymerase speed, as detailed above.
In another example, residues from domains that are in close
proximity to one another are mutated to alter inter-domain
interactions. In .PHI.29, Q183 in the exonuclease domain can
contact the back of the fingers domain (e.g., Q183 is close to
I378, particularly when the fingers are open). Mutating this
residue can thus alter the equilibrium between the open and closed
conformations of the polymerase. A Q183F substitution, for example,
significantly increases mean readlength, although it also reduces
accuracy somewhat. This substitution can therefore be of interest
in polymerases for applications where readlength is of greater
priority than accuracy, e.g., for scaffolding genome assembly.
Other substitutions at this position include, e.g., Q183W and Q183T
(which also increase readlength), as well as Q183H.
As described in U.S. patent application publication 2012-0034602,
substitutions at position L253 of .PHI.29 can affect cofactor
selectivity. Introducing an A437G substitution into the polymerase
can increase polymerase speed and can also increase the range of
useful substitutions at position L253. For example, a combination
of L253H and A437G substitutions can reduce pulse width and
pausing, increase readlength, and enhance Mg.sup.++ tolerance. As
shown in FIG. 8, examination of a crystal structure of a
recombinant .PHI.29 polymerase including D12A, D66A, Y224K, E239G,
L253H, E375Y, A437G, A484E, D510K, and K512Y substitutions reveals
that the histidine at position 253 forms a hydrogen bond with the
backbone carbonyl of residue 437. Formation of the hydrogen bond is
enabled by the A437G substitution.
Substitution of V250 can also increase the range of functional
substitutions at position L253. For example, replacement of valine
at position 250 with a smaller residue, e.g., alanine, can
accommodate a larger side chain at position L253. Exemplary
combinations include, e.g., V250A with L253H or L253F. A V250A
substitution can also increase readlength.
Amino acid sequence data, e.g., for members of a family of
polymerases, can be used in conjunction with structural data to
identify particular residues as candidates for mutagenesis. As one
example, residues that differ between family members and that are
close to the active site can be mutated. For example, as shown in
FIG. 1, wild-type .PHI.29 has an alanine at position 256 while
wild-type M2Y has a serine at the corresponding position (position
253 of M2Y, SEQ ID NO:2). Introducing an S253A substitution into
M2Y, where positions are numbered with respect to SEQ ID NO:2, can
increase readlength and decrease pulse width, improving performance
in single molecule sequencing assays. An A256S substitution can be
introduced into .PHI.29, where positions are numbered with respect
to SEQ ID NO:1, e.g., to increase pulse width. As another example,
wild-type .PHI.29 has a tyrosine at position 224 while wild-type
M2Y has a lysine at the corresponding position (position 221 of
M2Y, SEQ ID NO:2). A Y224K substitution can be introduced into
.PHI.29, where positions are numbered with respect to SEQ ID NO:1,
or a K221Y substitution can be introduced into M2Y, where positions
are numbered with respect to SEQ ID NO:2.
Combining Mutations
As noted repeatedly, the various mutations described herein can be
combined in recombinant polymerases of the invention. Combination
of mutations can be random, or more desirably, guided by the
properties of the particular mutations and the characteristics
desired for the resulting polymerase. Additional mutations can also
be introduced into a polymerase to compensate for deleterious
effects of otherwise desirable mutations.
A large number of exemplary mutations and the properties they
confer are described herein, and it will be evident that these
mutations can be favorably combined in many different combinations.
Exemplary combinations are also provided herein, e.g., in Tables 3
and 4 and FIG. 7, and an example of strategies by which additional
favorable combinations are readily derived follows. For the sake of
simplicity, a few exemplary combinations using only a few exemplary
mutations are discussed, but it will be evident that any of the
mutations described herein can be employed in such strategies to
produce polymerases with desirable properties.
For example, where a recombinant polymerase is desired to
incorporate phosphate-labeled phosphate analogs in a
Mg.sup.++-containing single molecule sequencing reaction, one or
more substitutions that enhance analog binding (e.g., E375Y, K512Y,
and/or A484E) and one or more substitutions that alter metal
cofactor usage (e.g., L253A, L253H, or L253S) can be incorporated.
One or more substitutions that increase phototolerance (e.g.,
K131E, K131Q, and/or K135Q) can be included. Exemplary combinations
thus include K131E, L253A and A484E; K131E, L253A, E375Y, and
K512Y; K131E, L253A, E375Y, A484E, and K512Y; K135Q, L253A and
A484E; K135Q, L253A, E375Y, and K512Y; and K135Q, L253A, E375Y,
A484E, and K512Y. Polymerase speed can be enhanced by inclusion of
substitutions such as A437G, E508K, V141K, L142K, D510K, and/or
V250I, providing combinations such as A437G, L253A, and A484E;
A437G, E375Y, and K512Y; K131E, L253A, A484E, and D510K; K135Q,
L253A, A484E, and D510K; K131E, Y148I, L253A, and A484E; K135Q,
Y148I, L253A, and A484E; K131E, Y148I, L253A, E375Y, A484E, and
K512Y; and K135Q, Y148I, L253A, E375Y, A484E, and K512Y. Stability
and/or yield can be increased by inclusion of substitutions such as
E239G, V250I, and/or Y224K, producing combinations such as K131E,
E239G, L253A, A484E, and D510K; K135Q, E239G, L253A, A484E, and
D510K; K131E, E239G, L253A, E375Y, A484E, D510K, and K512Y; K135Q,
E239G, L253A, E375Y, A484E, D510K, and K512Y; K131E, Y224K, E239G,
L253A, E375Y, A484E, D510K, and K512Y; and K135Q, Y224K, E239G,
L253A, E375Y, A484E, D510K, and K512Y. Accuracy can be enhanced by
inclusion of substitutions such as E515Q, D235E, and/or Y148I,
providing combinations such as K131E, Y148I, Y224K, E239G, V250I,
L253A, E375Y, A484E, D510K, and K512Y; K131E, Y148I, Y224K, E239G,
V250I, L253H, E375Y, A437G, A484E, and K512Y; K135Q, Y148I, Y224K,
E239G, V250I, L253H, E375Y, A437G, A484E, and K512Y; K131E, Y148I,
Y224K, E239G, V250I, L253A, E375Y, A437G, A484E, D510K, K512Y, and
E515Q; K135Q, Y148I, Y224K, E239G, V250I, L253A, E375Y, A437G,
A484E, D510K, K512Y, and E515Q; K135Q, Y148I, Y224K, E239G, V250I,
L253A, E375Y, A484E, D510K, and K512Y; K131E, Y148I, Y224K, E239G,
V250I, L253A, E375Y, A484E, D510K, K512Y, and E515Q; and K135Q,
Y148I, Y224K, E239G, V250I, L253A, E375Y, A484E, D510K, K512Y, and
E515Q.
Additional exemplary combinations of substitutions that can be
present in a polymerase of the invention include, but are not
limited to: E239G, L253A, E375Y, A437G, A484E, D510K, K512Y, and
E515Q; E239G, V250I, L253A, E375Y, A437G, A484E, D510K, K512Y, and
E515Q; E239G, L253A, E375Y, A437N, A484E, D510K, K512Y, and E515Q;
E239G, V250I, L253A, E375Y, A437N, A484E, D510K, K512Y, and E515Q;
E239G, V250A, L253H, E375Y, A437G, A484E, D510K, K512Y, and E515Q;
E239G, V250A, L253H, E375Y, A437N, A484E, D510K, K512Y, and E515Q;
Y224K, E239G, L253A, E375Y, A437G, A484E, D510K, K512Y, and E515Q;
Y224K, E239G, V250I, L253A, E375Y, A437G, A484E, D510K, K512Y, and
E515Q; Y224K, E239G, L253A, E375Y, A437N, A484E, D510K, K512Y, and
E515Q; Y224K, E239G, V250I, L253A, E375Y, A437N, A484E, D510K,
K512Y, and E515Q; Y224K, E239G, V250A, L253H, E375Y, A437G, A484E,
D510K, K512Y, and E515Q; Y224K, E239G, V250A, L253H, E375Y, A437N,
A484E, D510K, K512Y, and E515Q; K131E, E239G, L253A, E375Y, A437G,
A484E, D510K, K512Y, and E515Q; K131E, E239G, V250I, L253A, E375Y,
A437G, A484E, D510K, K512Y, and E515Q; K131E, E239G, L253A, E375Y,
A437N, A484E, D510K, K512Y, and E515Q; K131E, E239G, V250I, L253A,
E375Y, A437N, A484E, D510K, K512Y, and E515Q; K131E, E239G, V250A,
L253H, E375Y, A437G, A484E, D510K, K512Y, and E515Q; K131E, E239G,
V250A, L253H, E375Y, A437N, A484E, D510K, K512Y, and E515Q; K131E,
Y224K, E239G, L253A, E375Y, A437G, A484E, D510K, K512Y, and E515Q;
K131E, Y224K, E239G, V250I, L253A, E375Y, A437G, A484E, D510K,
K512Y, and E515Q; K131E, Y224K, E239G, L253A, E375Y, A437N, A484E,
D510K, K512Y, and E515Q; K131E, Y224K, E239G, V250I, L253A, E375Y,
A437N, A484E, D510K, K512Y, and E515Q; K131E, Y224K, E239G, V250A,
L253H, E375Y, A437G, A484E, D510K, K512Y, and E515Q; and K131E,
Y224K, E239G, V250A, L253H, E375Y, A437N, A484E, D510K, K512Y, and
E515Q.
Many other such recombinant polymerases, including these mutations
and/or those described elsewhere herein, will be readily apparent
and are features of the invention.
Mutating Polymerases
Various types of mutagenesis are optionally used in the present
invention, e.g., to modify polymerases to produce variants, e.g.,
in accordance with polymerase models and model predictions as
discussed above, or using random or semi-random mutational
approaches. In general, any available mutagenesis procedure can be
used for making polymerase mutants. Such mutagenesis procedures
optionally include selection of mutant nucleic acids and
polypeptides for one or more activity of interest (e.g., increased
phototolerance, reduced reaction rates, decreased exonuclease
activity, increased complex stability, decreased branching
fraction, altered metal cofactor selectivity, improved
processivity, increased thermostability, increased yield, increased
accuracy, and/or improved k.sub.off, K.sub.m, V.sub.max, k.sub.cat
etc., e.g., for a given nucleotide analog). Procedures that can be
used include, but are not limited to: site-directed point
mutagenesis, random point mutagenesis, in vitro or in vivo
homologous recombination (DNA shuffling and combinatorial overlap
PCR), mutagenesis using uracil containing templates,
oligonucleotide-directed mutagenesis, phosphorothioate-modified DNA
mutagenesis, mutagenesis using gapped duplex DNA, point mismatch
repair, mutagenesis using repair-deficient host strains,
restriction-selection and restriction-purification, deletion
mutagenesis, mutagenesis by total gene synthesis, degenerate PCR,
double-strand break repair, and many others known to persons of
skill. The starting polymerase for mutation can be any of those
noted herein, including available polymerase mutants such as those
identified e.g., in WO 2007/076057 POLYMERASES FOR NUCLEOTIDE
ANALOGUE INCORPORATION by Hanzel et al.; WO 2008/051530 POLYMERASE
ENZYMES AND REAGENTS FOR ENHANCED NUCLEIC ACID SEQUENCING; U.S.
patent application publication 2010-0075332 ENGINEERING POLYMERASES
AND REACTION CONDITIONS FOR MODIFIED INCORPORATION PROPERTIES by
Pranav Patel et al.; U.S. patent application publication
2010-0093555 ENZYMES RESISTANT TO PHOTODAMAGE by Keith Bjornson et
al.; U.S. patent application publication 2010-0112645 GENERATION OF
MODIFIED POLYMERASES FOR IMPROVED ACCURACY IN SINGLE MOLECULE
SEQUENCING by Sonya Clark et al.; U.S. patent application
publication 2011-0189659 GENERATION OF MODIFIED POLYMERASES FOR
IMPROVED ACCURACY IN SINGLE MOLECULE SEQUENCING by Sonya Clark et
al.; U.S. patent application publication 2012-0034602 RECOMBINANT
POLYMERASES FOR IMPROVED SINGLE MOLECULE SEQUENCING; Hanzel et al.
WO 2007/075987 ACTIVE SURFACE COUPLED POLYMERASES; and Hanzel et
al. 2007/075873 PROTEIN ENGINEERING STRATEGIES TO OPTIMIZE ACTIVITY
OF SURFACE ATTACHED PROTEINS.
Optionally, mutagenesis can be guided by known information from a
naturally occurring polymerase molecule, or of a known altered or
mutated polymerase (e.g., using an existing mutant polymerase as
noted in the preceding references), e.g., sequence, sequence
comparisons, physical properties, crystal structure and/or the like
as discussed above. However, in another class of embodiments,
modification can be essentially random (e.g., as in classical or
"family" DNA shuffling, see, e.g., Crameri et al. (1998) "DNA
shuffling of a family of genes from diverse species accelerates
directed evolution" Nature 391:288-291).
Additional information on mutation formats is found in: Sambrook et
al., Molecular Cloning--A Laboratory Manual (3rd Ed.), Vol. 1-3,
Cold Spring Harbor Laboratory, Cold Spring Harbor, N. Y., 2000
("Sambrook"); Current Protocols in Molecular Biology, F. M. Ausubel
et al., eds., Current Protocols, a joint venture between Greene
Publishing Associates, Inc. and John Wiley & Sons, Inc.,
(supplemented through 2012) ("Ausubel")) and PCR Protocols A Guide
to Methods and Applications (Innis et al. eds) Academic Press Inc.
San Diego, Calif. (1990) ("Innis"). The following publications and
references cited within provide additional detail on mutation
formats: Arnold, Protein engineering for unusual environments,
Current Opinion in Biotechnology 4:450-455 (1993); Bass et al.,
Mutant Trp repressors with new DNA-binding specificities, Science
242:240-245 (1988); Bordo and Argos (1991) Suggestions for "Safe"
Residue Substitutions in Site-directed Mutagenesis 217:721-729;
Botstein & Shortle, Strategies and applications of in vitro
mutagenesis, Science 229:1193-1201(1985); Carter et al., Improved
oligonucleotide site-directed mutagenesis using M13 vectors, Nucl.
Acids Res. 13: 4431-4443 (1985); Carter, Site-directed mutagenesis,
Biochem. J. 237:1-7 (1986); Carter, Improved
oligonucleotide-directed mutagenesis using M13 vectors, Methods in
Enzymol. 154: 382-403 (1987); Dale et al., Oligonucleotide-directed
random mutagenesis using the phosphorothioate method, Methods Mol.
Biol. 57:369-374 (1996); Eghtedarzadeh & Henikoff, Use of
oligonucleotides to generate large deletions, Nucl. Acids Res. 14:
5115 (1986); Fritz et al., Oligonucleotide-directed construction of
mutations: a gapped duplex DNA procedure without enzymatic
reactions in vitro, Nucl. Acids Res. 16: 6987-6999 (1988);
Grundstrom et al., Oligonucleotide-directed mutagenesis by
microscale `shot-gun` gene synthesis, Nucl. Acids Res. 13:
3305-3316 (1985); Hayes (2002) Combining Computational and
Experimental Screening for rapid Optimization of Protein Properties
PNAS 99(25) 15926-15931; Kunkel, The efficiency of oligonucleotide
directed mutagenesis, in Nucleic Acids & Molecular Biology
(Eckstein, F. and Lilley, D. M. J. eds., Springer Verlag, Berlin))
(1987); Kunkel, Rapid and efficient site-specific mutagenesis
without phenotypic selection, Proc. Natl. Acad. Sci. USA 82:488-492
(1985); Kunkel et al., Rapid and efficient site-specific
mutagenesis without phenotypic selection, Methods in Enzymol. 154,
367-382 (1987); Kramer et al., The gapped duplex DNA approach to
oligonucleotide-directed mutation construction, Nucl. Acids Res.
12: 9441-9456 (1984); Kramer & Fritz Oligonucleotide-directed
construction of mutations via gapped duplex DNA, Methods in
Enzymol. 154:350-367 (1987); Kramer et al., Point Mismatch Repair,
Cell 38:879-887 (1984); Kramer et al., Improved enzymatic in vitro
reactions in the gapped duplex DNA approach to
oligonucleotide-directed construction of mutations, Nucl. Acids
Res. 16: 7207 (1988); Ling et al., Approaches to DNA mutagenesis:
an overview, Anal Biochem. 254(2): 157-178 (1997); Lorimer and
Pastan Nucleic Acids Res. 23, 3067-8 (1995); Mandecki,
Oligonucleotide-directed double-strand break repair in plasmids of
Escherichia coli: a method for site-specific mutagenesis, Proc.
Natl. Acad. Sci. USA, 83:7177-7181 (1986); Nakamaye & Eckstein,
Inhibition of restriction endonuclease Nci I cleavage by
phosphorothioate groups and its application to
oligonucleotide-directed mutagenesis, Nucl. Acids Res. 14:
9679-9698 (1986); Nambiar et al., Total synthesis and cloning of a
gene coding for the ribonuclease S protein, Science 223: 1299-1301
(1984); Sakamar and Khorana, Total synthesis and expression of a
gene for the a-subunit of bovine rod outer segment guanine
nucleotide-binding protein (transducin), Nucl. Acids Res. 14:
6361-6372 (1988); Sayers et al., Y-T Exonucleases in
phosphorothioate-based oligonucleotide-directed mutagenesis, Nucl.
Acids Res. 16:791-802 (1988); Sayers et al., Strand specific
cleavage of phosphorothioate-containing DNA by reaction with
restriction endonucleases in the presence of ethidium bromide,
(1988) Nucl. Acids Res. 16: 803-814; Sieber, et al., Nature
Biotechnology, 19:456-460 (2001); Smith, In vitro mutagenesis, Ann.
Rev. Genet. 19:423-462(1985); Methods in Enzymol. 100: 468-500
(1983); Methods in Enzymol. 154: 329-350 (1987); Stemmer, Nature
370, 389-91 (1994); Taylor et al., The use of
phosphorothioate-modified DNA in restriction enzyme reactions to
prepare nicked DNA, Nucl. Acids Res. 13: 8749-8764 (1985); Taylor
et al., The rapid generation of oligonucleotide-directed mutations
at high frequency using phosphorothioate-modified DNA, Nucl. Acids
Res. 13: 8765-8787 (1985); Wells et al., Importance of
hydrogen-bond formation in stabilizing the transition state of
subtilisin, Phil. Trans. R. Soc. Lond. A 317: 415-423 (1986); Wells
et al., Cassette mutagenesis: an efficient method for generation of
multiple mutations at defined sites, Gene 34:315-323 (1985); Zoller
& Smith, Oligonucleotide-directed mutagenesis using M13-derived
vectors: an efficient and general procedure for the production of
point mutations in any DNA fragment, Nucleic Acids Res.
10:6487-6500 (1982); Zoller & Smith, Oligonucleotide-directed
mutagenesis of DNA fragments cloned into M13 vectors, Methods in
Enzymol. 100:468-500 (1983); Zoller & Smith,
Oligonucleotide-directed mutagenesis: a simple method using two
oligonucleotide primers and a single-stranded DNA template, Methods
in Enzymol. 154:329-350 (1987); Clackson et al. (1991) "Making
antibody fragments using phage display libraries" Nature
352:624-628; Gibbs et al. (2001) "Degenerate oligonucleotide gene
shuffling (DOGS): a method for enhancing the frequency of
recombination with family shuffling" Gene 271:13-20; and Hiraga and
Arnold (2003) "General method for sequence-independent
site-directed chimeragenesis: J. Mol. Biol. 330:287-296. Additional
details on many of the above methods can be found in Methods in
Enzymology Volume 154, which also describes useful controls for
trouble-shooting problems with various mutagenesis methods.
Determining Kinetic Parameters
The polymerases of the invention can be screened or otherwise
tested to determine whether the polymerase displays a modified
activity for or with a nucleotide analog or template as compared to
a parental DNA polymerase (e.g., a corresponding wild-type or
available mutant polymerase from which the recombinant polymerase
of the invention was derived). For example, branching fraction, a
reaction rate constant, k.sub.off, k.sub.cat, K.sub.m, V.sub.max,
k.sub.cat/K.sub.m, V.sub.max/K.sub.m, k.sub.pol, and/or K.sub.d of
the recombinant DNA polymerase for the nucleotide (or analog) or
template nucleic acid can be determined. The specificity constant
k.sub.cat/K.sub.m is also a useful measure, e.g., for assessing
branch rate. k.sub.cat/K.sub.m is a measure of substrate binding
that leads to product formation (and, thus, includes terms defining
binding K.sub.d and inversely predicts branching fraction
formation).
As is well-known in the art, for enzymes obeying simple
Michaelis-Menten kinetics, kinetic parameters are readily derived
from rates of catalysis measured at different substrate
concentrations. The Michaelis-Menten equation,
V=V.sub.max[S]([S]+K.sub.m).sup.-1, relates the concentration of
free substrate ([S], approximated by the total substrate
concentration), the maximal rate (V.sub.max, attained when the
enzyme is saturated with substrate), and the Michaelis constant
(K.sub.m, equal to the substrate concentration at which the
reaction rate is half of its maximal value), to the reaction rate
(V).
For many enzymes, K.sub.m is equal to the dissociation constant of
the enzyme-substrate complex and is thus a measure of the strength
of the enzyme-substrate complex. For such an enzyme, in a
comparison of K.sub.ms, a lower K.sub.m represents a complex with
stronger binding, while a higher Km represents a complex with
weaker binding. The ratio k.sub.cat/K.sub.m, sometimes called the
specificity constant, can be thought of as the second order rate
constant times the probability of that substrate being converted to
product once bound. The larger the specificity constant, the more
efficient the enzyme is in binding the substrate and converting it
to product. The specificity constant is inversely proportional to
the branching rate, as branching rate is the rate at which the
enzyme binds substrate (e.g., nucleotide) but does not convert it
to product (e.g., a DNA polymer).
k.sub.cat (also called the turnover number of the enzyme) can be
determined if the total enzyme concentration ([E.sub.T], i.e., the
concentration of active sites) is known, since
V.sub.max=k.sub.cat[E.sub.T]. For situations in which the total
enzyme concentration is difficult to measure, the ratio
V.sub.max/K.sub.m is often used instead as a measure of efficiency.
K.sub.m and V.sub.max can be determined, for example, from a
Lineweaver-Burk plot of 1/V against 1/[S], where the y intercept
represents 1/V.sub.max, the x intercept -1/K.sub.m, and the slope
K.sub.m/V.sub.max, or from an Eadie-Hofstee plot of V against
V/[S], where the y intercept represents V.sub.max, the x intercept
V.sub.max/K.sub.m, and the slope -K.sub.m. Software packages such
as KinetAsyst.TM. or Enzfit (Biosoft, Cambridge, UK) can facilitate
the determination of kinetic parameters from catalytic rate
data.
For enzymes such as polymerases that have multiple substrates,
varying the concentration of only one substrate while holding the
others in suitable excess (e.g., effectively constant)
concentration typically yields normal Michaelis-Menten
kinetics.
Details regarding k.sub.off determination are described, e.g., in
U.S. patent application publication 2012-0034602. In general, the
dissociation rate can be measured in any manner that detects the
polymerase/DNA complex over time. This includes stopped-flow
spectroscopy, or even simply taking aliquots over time and testing
for polymerase activity on the template of interest. Free
polymerase is captured with a polymerase trap after dissociation,
e.g., by incubation in the presence of heparin or an excess of
competitor DNA (e.g., non-specific salmon sperm DNA, or the
like).
In one embodiment, using pre-steady-state kinetics, the nucleotide
concentration dependence of the rate constant k.sub.obs (the
observed first-order rate constant for dNTP incorporation) provides
an estimate of the K.sub.m for a ground state binding and the
maximum rate of polymerization (k.sub.pol). The k.sub.obs is
measured using a burst assay. The results of the assay are fitted
with the Burst equation; Product=A[1-exp(-k.sub.obs*t)]+k.sub.ss*t
where A represents amplitude an estimate of the concentration of
the enzyme active sites, k.sub.ss is the observed steady-state rate
constant and t is the reaction incubation time. The K.sub.m for
dNTP binding to the polymerase-DNA complex and the k.sub.pol are
calculated by fitting the dNTP concentration dependent change in
the k.sub.obs using the equation
k.sub.obs=(k.sub.pol*[S])*(K.sub.m+[S]).sup.-1 where [S] is the
substrate concentration. Results are optionally obtained from a
rapid-quench experiment (also called a quench-flow measurement),
for example, based on the methods described in Johnson (1986)
"Rapid kinetic analysis of mechanochemical
adenosinetriphosphatases" Methods Enzymol. 134:677-705, Patel et
al. (1991) "Pre-steady-state kinetic analysis of processive DNA
replication including complete characterization of an
exonuclease-deficient mutant" Biochemistry 30(2):511-25, and Tsai
and Johnson (2006) "A new paradigm for DNA polymerase specificity"
Biochemistry 45(32):9675-87.
Parameters such as rate of binding of a nucleotide analog or
template by the recombinant polymerase, rate of product release by
the recombinant polymerase, or branching rate of the recombinant
polymerase can also be determined, and optionally compared to that
of a parental polymerase (e.g., a corresponding wild-type
polymerase).
For a more thorough discussion of enzyme kinetics, see, e.g., Berg,
Tymoczko, and Stryer (2002) Biochemistry, Fifth Edition, W. H.
Freeman; Creighton (1984) Proteins: Structures and Molecular
Principles, W. H. Freeman; and Fersht (1985) Enzyme Structure and
Mechanism. Second Edition, W. H. Freeman.
In one aspect, the improved activity of the enzymes of the
invention is compared with a given parental polymerase. For
example, in the case of enzymes derived from a .PHI.29 parental
enzyme, where the improvement being sought is an increase in
stability of the closed complex, an improved enzyme of the
invention would have a lower k.sub.off than the parental enzyme,
e.g., wild type .PHI.29. Such comparisons are made under equivalent
reaction conditions, e.g., equal concentrations of the parental and
modified polymerase, equal substrate concentrations, equivalent
solution conditions (pH, salt concentration, presence of divalent
cations, etc.), temperature, and the like. In one aspect, the
improved activity of the enzymes of the invention is measured with
reference to a model analog or analog set and compared with a given
parental enzyme. Optionally, the improved activity of the enzymes
of the invention is measured under specified reaction conditions.
While the foregoing may be used as a characterization tool, it in
no way is intended as a specifically limiting reaction of the
invention.
Optionally, the polymerase exhibits a K.sub.m for a
phosphate-labeled nucleotide analog that is less than a K.sub.m
observed for a wild-type polymerase for the analog to facilitate
applications in which the polymerase incorporates the analog, e.g.,
during SMS. For example, the modified recombinant polymerase can
exhibit a K.sub.m for the phosphate-labeled nucleotide analog that
is less than 75%, less than 50%, or less than 25% than that of
wild-type or parental polymerase such as a wild type .PHI.29. In
one specific class of examples, the polymerases of the invention
have a K.sub.m of about 10 .mu.M or less for a non-natural
nucleotide analog such as a phosphate labeled analog.
Screening Polymerases
Screening or other protocols can be used to determine whether a
polymerase displays a modified activity, e.g., for a nucleotide
analog, as compared to a parental DNA polymerase. For example,
branching fraction, rate constant, k.sub.off, k.sub.cat, K.sub.m,
V.sub.max, or k.sub.cat/K.sub.m of the recombinant DNA polymerase
for the template or nucleotide or analog can be determined as
discussed above. As another example, activity can be assayed
indirectly. Assays for properties such as protein yield,
thermostability, and the like are described, e.g., in U.S. patent
application publication 2012-0034602. Performance of a recombinant
polymerase in a sequencing reaction, e.g., a single molecule
sequencing reaction, can be examined to assay properties such as
speed, pulse width, interpulse distance, accuracy, readlength, etc.
as described herein. Phototolerance can be assessed by monitoring
polymerase performance (e.g., in a single molecule sequencing
reaction) during or after exposure of the polymerase to light,
e.g., excitation light of a specified wavelength at a given
intensity for a given time, e.g., as compared to a wild-type or
other parental polymerase.
In one desirable aspect, a library of recombinant DNA polymerases
can be made and screened for these properties. For example, a
plurality of members of the library can be made to include one or
more mutation that increases phototolerance, alters (e.g.,
decreases) reaction rate constants, improves closed complex
stability, decreases branching fraction, alters cofactor
selectivity, or increases yield, thermostability, accuracy, speed,
or readlength and/or randomly generated mutations (e.g., where
different members include different mutations or different
combinations of mutations), and the library can then be screened
for the properties of interest (e.g., increased phototolerance,
decreased rate constant, decreased branching fraction, increased
closed complex stability, etc.). In general, the library can be
screened to identify at least one member comprising a modified
activity of interest.
Libraries of polymerases can be either physical or logical in
nature. Moreover, any of a wide variety of library formats can be
used. For example, polymerases can be fixed to solid surfaces in
arrays of proteins. Similarly, liquid phase arrays of polymerases
(e.g., in microwell plates) can be constructed for convenient
high-throughput fluid manipulations of solutions comprising
polymerases. Liquid, emulsion, or gel-phase libraries of cells that
express recombinant polymerases can also be constructed, e.g., in
microwell plates, or on agar plates. Phage display libraries of
polymerases or polymerase domains (e.g., including the active site
region or interdomain stability regions) can be produced. Likewise,
yeast display libraries can be used. Instructions in making and
using libraries can be found, e.g., in Sambrook, Ausubel and
Berger, referenced herein.
For the generation of libraries involving fluid transfer to or from
microtiter plates, a fluid handling station is optionally used.
Several "off the shelf" fluid handling stations for performing such
transfers are commercially available, including e.g., the Zymate
systems from Caliper Life Sciences (Hopkinton, Mass.) and other
stations which utilize automatic pipettors, e.g., in conjunction
with the robotics for plate movement (e.g., the ORCA.RTM. robot,
which is used in a variety of laboratory systems available, e.g.,
from Beckman Coulter, Inc. (Fullerton, Calif.).
In an alternate embodiment, fluid handling is performed in
microchips, e.g., involving transfer of materials from microwell
plates or other wells through microchannels on the chips to
destination sites (microchannel regions, wells, chambers or the
like). Commercially available microfluidic systems include those
from Hewlett-Packard/Agilent Technologies (e.g., the HP2100
bioanalyzer) and the Caliper High Throughput Screening System. The
Caliper High Throughput Screening System provides one example
interface between standard microwell library formats and Labchip
technologies. RainDance Technologies' nanodroplet platform provides
another method for handling large numbers of spatially separated
reactions. Furthermore, the patent and technical literature
includes many examples of microfluidic systems which can interface
directly with microwell plates for fluid handling.
Tags and Other Optional Polymerase Features
The recombinant DNA polymerase optionally includes additional
features exogenous or heterologous to the polymerase. For example,
the recombinant polymerase optionally includes one or more tags,
e.g., purification, substrate binding, or other tags, such as a
polyhistidine tag, a His10 tag, a His6 tag, an alanine tag, an
Ala10 tag, an Ala16 tag, a biotin tag, a biotin ligase recognition
sequence or other biotin attachment site (e.g., a BiTag or a Btag
or variant thereof, e.g., BtagV1-11), a GST tag, an S Tag, a
SNAP-tag, an HA tag, a DSB (Sso7D) tag, a lysine tag, a NanoTag, a
Cmyc tag, a tag or linker comprising the amino acids glycine and
serine, a tag or linker comprising the amino acids glycine, serine,
alanine and histidine, a tag or linker comprising the amino acids
glycine, arginine, lysine, glutamine and proline, a plurality of
polyhistidine tags, a plurality of His10 tags, a plurality of His6
tags, a plurality of alanine tags, a plurality of Ala10 tags, a
plurality of Ala16 tags, a plurality of biotin tags, a plurality of
GST tags, a plurality of BiTags, a plurality of S Tags, a plurality
of SNAP-tags, a plurality of HA tags, a plurality of DSB (Sso7D)
tags, a plurality of lysine tags, a plurality of NanoTags, a
plurality of Cmyc tags, a plurality of tags or linkers comprising
the amino acids glycine and serine, a plurality of tags or linkers
comprising the amino acids glycine, serine, alanine and histidine,
a plurality of tags or linkers comprising the amino acids glycine,
arginine, lysine, glutamine and proline, biotin, avidin, an
antibody or antibody domain, antibody fragment, antigen, receptor,
receptor domain, receptor fragment, maltose binding protein,
ligand, one or more protease site (e.g., Factor Xa, enterokinase,
or thrombin site), a dye, an acceptor, a quencher, a DNA binding
domain (e.g., a helix-hairpin-helix domain from topoisomerase V),
or combination thereof. See, e.g., U.S. patent application
publication 2012-0034602 for sequences of a number of suitable tags
and linkers, including BtagV1-11. The one or more exogenous or
heterologous features can find use not only for purification
purposes, immobilization of the polymerase to a substrate, and the
like, but can also be useful for altering one or more properties of
the polymerase.
The one or more exogenous or heterologous features can be included
internal to the polymerase, at the N-terminal region of the
polymerase, at the C-terminal region of the polymerase, or at a
combination thereof (e.g., at both the N-terminal and C-terminal
regions of the polymerase). Where the polymerase includes an
exogenous or heterologous feature at both the N-terminal and
C-terminal regions, the exogenous or heterologous features can be
the same (e.g., a polyhistidine tag, e.g., a His10 tag, at both the
N- and C-terminal regions) or different (e.g., a biotin ligase
recognition sequence at the N-terminal region and a polyhistidine
tag, e.g., His10 tag, at the C-terminal region). Optionally, a
terminal region (e.g., the N- or C-terminal region) of a polymerase
of the invention can comprise two or more exogenous or heterologous
features which can be the same or different (e.g., a biotin ligase
recognition sequence and a polyhistidine tag at the N-terminal
region, a biotin ligase recognition sequence, a polyhistidine tag,
and a Factor Xa recognition site at the N-terminal region, and the
like). As a few examples, the polymerase can include a
polyhistidine tag at the C-terminal region, a biotin ligase
recognition sequence at the N-terminal region and a polyhistidine
tag at the C-terminal region, a biotin ligase recognition sequence
and a polyhistidine tag at the N-terminal region, a biotin ligase
recognition sequence and a polyhistidine tag at the N-terminal
region and a polyhistidine tag at the C-terminal region, or a
polyhistidine tag and a biotin ligase recognition sequence at the
C-terminal region.
For convenience, an exogenous or heterologous feature will often be
expressed as a fusion domain of the overall polymerase protein,
e.g., as a conventional in-frame fusion of a polypeptide sequence
with the active polymerase enzyme (e.g., a polyhistidine tag fused
in frame to an active polymerase enzyme sequence). However,
features such as tags can be added chemically to the polymerase,
e.g., by using an available amino acid residue of the enzyme or by
incorporating an amino acid into the protein that provides a
suitable attachment site for the coupling domain. Suitable residues
of the enzyme can include, e.g., histidine, cysteine, or serine
residues (providing for N, S, or O linked coupling reactions).
Optionally, one or more cysteines present in the parental
polymerase (e.g., up to all of the cysteines present on the
polymerase's surface) can be replaced with a different amino acid;
either a single reactive surface cysteine can be left unsubstituted
or a single reactive surface cysteine can be introduced in place of
another residue, for convenient addition of a feature, e.g., for
surface immobilization through thiol labeling (e.g., addition of
maleimide biotin, or maleimide and an alkyne for click labeling).
Unnatural amino acids that comprise unique reactive sites can also
be added to the enzyme, e.g., by expressing the enzyme in a system
that comprises an orthogonal tRNA and an orthogonal synthetase that
loads the unnatural amino acid in response to a selector codon.
The exogenous or heterologous features can find use, e.g., in the
context of binding a polymerase in an active form to a surface,
e.g., to orient and/or protect the polymerase active site when the
polymerase is bound to a surface. In general, surface binding
elements and purification tags that can be added to the polymerase
(e.g., recombinantly or chemically) include, e.g., biotin
attachment sites (e.g., biotin ligase recognition sequences such as
Btags or BiTag), polyhistidine tags, His6 tags, His10 tags, biotin,
avidin, GST sequences, modified GST sequences, e.g., that are less
likely to form dimers, S tags, SNAP-tags, antibodies or antibody
domains, antibody fragments, antigens, receptors, receptor domains,
receptor fragments, ligands, and combinations thereof.
One aspect of the invention includes DNA polymerases that can be
coupled to a surface without substantial loss of activity (e.g., in
an active form). DNA polymerases can be coupled to the surface
through a single surface coupling domain or through multiple
surface coupling domains which act in concert to increase binding
affinity of the polymerase for the surface and to orient the
polymerase relative to the surface. For example, the active site
can be oriented distal to the surface, thereby making it accessible
to a polymerase substrate (template, nucleotides, etc.). This
orientation also tends to reduce surface denaturation effects in
the region of the active site. In a related aspect, activity of the
enzyme can be protected by making the coupling domains large,
thereby serving to further insulate the active site from surface
binding effects. Further details regarding the immobilization of a
polymerase to a surface (e.g., the surface of a zero mode
waveguide) in an active form are found in WO 2007/075987 ACTIVE
SURFACE COUPLED POLYMERASES by Hanzel et al., and WO 2007/075873
PROTEIN ENGINEERING STRATEGIES TO OPTIMIZE ACTIVITY OF SURFACE
ATTACHED PROTEINS by Hanzel et al. Further details on attaching
tags is available in the art. See, e.g., U.S. Pat. Nos. 5,723,584
and 5,874,239 and U.S. patent application publication 2011/0306096
for additional information on attaching biotinylation peptides to
recombinant proteins.
The polymerase immobilized on a surface in an active form can be
coupled to the surface through one or a plurality of artificial or
recombinant surface coupling domains as discussed above, and
typically displays a k.sub.cat/K.sub.m (or V.sub.max/K.sub.m) that
is at least about 1%, at least about 10%, at least about 25%, at
least about 50%, or at least about 75% as high as a corresponding
active polymerase in solution.
Exonuclease-Deficient Recombinant Polymerases
Many native DNA polymerases have a proof-reading exonuclease
function which can yield substantial data analysis problems in
processes that utilize real time observation of incorporation
events as a method of identifying sequence information, e.g.,
single molecule sequencing applications. Even where exonuclease
activity does not introduce such problems in single molecule
sequencing, reduction of exonuclease activity can be desirable
since it can increase accuracy (in some cases at the expense of
readlength).
Accordingly, recombinant polymerases of the invention optionally
include one or more mutations (e.g., substitutions, insertions,
and/or deletions) relative to the parental polymerase that reduce
or eliminate endogenous exonuclease activity. For example, relative
to the wild-type .PHI.29 DNA polymerase of SEQ ID NO:1, one or more
of positions N62, D12, E14, T15, H61, D66, D169, K143, Y148, and
H149 is optionally mutated to reduce exonuclease activity.
Exemplary mutations that can reduce exonuclease activity include,
e.g., N62D, N62H, D12A, T15I, E14I, E14A, D66A, K143D, D145A and
D169A substitutions, as well as addition of an exogenous feature at
the C-terminus (e.g., a polyhistidine tag). Additional exemplary
substitutions in the exonuclease domain include N62S, D12N, D12R,
D12M, E14Q, H61K, H61D, H61A, D66R, D66N, D66Q, D66K, D66M, D169N,
K143R, Y148I, Y148K, Y148A, Y148C, Y148D, Y148E, Y148F, Y148G,
Y148H, Y148L, Y148M, Y148N, Y148P, Y148Q, Y148R, Y148S, Y148T,
Y148V, Y148W, and H149M. The polymerases of the invention
optionally comprise one or more of these mutations. For example, in
one aspect, the polymerase is a .PHI.29-type polymerase that
includes one or more mutations in the N-terminal exonuclease domain
(residues 5-189 as numbered with respect to wild-type .PHI.29).
Making and Isolating Recombinant Polymerases
Generally, nucleic acids encoding a polymerase of the invention can
be made by cloning, recombination, in vitro synthesis, in vitro
amplification and/or other available methods. A variety of
recombinant methods can be used for expressing an expression vector
that encodes a polymerase of the invention. Methods for making
recombinant nucleic acids, expression and isolation of expressed
products are well known and described in the art. A number of
exemplary mutations and combinations of mutations, as well as
strategies for design of desirable mutations, are described herein.
Methods for making and selecting mutations in the active site of
polymerases, including for modifying steric features in or near the
active site to permit improved access by nucleotide analogs are
found hereinabove and, e.g., in WO 2007/076057 POLYMERASES FOR
NUCLEOTIDE ANALOG INCORPORATION by Hanzel et al. and WO 2008/051530
POLYMERASE ENZYMES AND REAGENTS FOR ENHANCED NUCLEIC ACID
SEQUENCING by Rank et al.
Additional useful references for mutation, recombinant and in vitro
nucleic acid manipulation methods (including cloning, expression,
PCR, and the like) include Berger and Kimmel, Guide to Molecular
Cloning Techniques, Methods in Enzymology volume 152 Academic
Press, Inc., San Diego, Calif. (Berger); Kaufman et al. (2003)
Handbook of Molecular and Cellular Methods in Biology and Medicine
Second Edition Ceske (ed) CRC Press (Kaufman); and The Nucleic Acid
Protocols Handbook Ralph Rapley (ed) (2000) Cold Spring Harbor,
Humana Press Inc (Rapley); Chen et al. (ed) PCR Cloning Protocols,
Second Edition (Methods in Molecular Biology, volume 192) Humana
Press; and in Viljoen et al. (2005) Molecular Diagnostic PCR
Handbook Springer, ISBN 1402034032.
In addition, a plethora of kits are commercially available for the
purification of plasmids or other relevant nucleic acids from
cells, (see, e.g., EasyPrep.TM., FlexiPrep.TM., both from Pharmacia
Biotech; StrataClean.TM., from Stratagene; and, QIAprep.TM. from
Qiagen). Any isolated and/or purified nucleic acid can be further
manipulated to produce other nucleic acids, used to transfect
cells, incorporated into related vectors to infect organisms for
expression, and/or the like. Typical cloning vectors contain
transcription and translation terminators, transcription and
translation initiation sequences, and promoters useful for
regulation of the expression of the particular target nucleic acid.
The vectors optionally comprise generic expression cassettes
containing at least one independent terminator sequence, sequences
permitting replication of the cassette in eukaryotes, or
prokaryotes, or both, (e.g., shuttle vectors) and selection markers
for both prokaryotic and eukaryotic systems. Vectors are suitable
for replication and integration in prokaryotes, eukaryotes, or
both.
Other useful references, e.g. for cell isolation and culture (e.g.,
for subsequent nucleic acid isolation) include Freshney (1994)
Culture of Animal Cells, a Manual of Basic Technique, third
edition, Wiley-Liss, New York and the references cited therein;
Payne et al. (1992) Plant Cell and Tissue Culture in Liquid Systems
John Wiley & Sons, Inc. New York, N.Y.; Gamborg and Phillips
(eds) (1995) Plant Cell. Tissue and Organ Culture; Fundamental
Methods Springer Lab Manual, Springer-Verlag (Berlin Heidelberg New
York) and Atlas and Parks (eds) The Handbook of Microbiological
Media (1993) CRC Press, Boca Raton, Fla.
Nucleic acids encoding the recombinant polymerases of the invention
are also a feature of the invention. A particular amino acid can be
encoded by multiple codons, and certain translation systems (e.g.,
prokaryotic or eukaryotic cells) often exhibit codon bias, e.g.,
different organisms often prefer one of the several synonymous
codons that encode the same amino acid. As such, nucleic acids of
the invention are optionally "codon optimized," meaning that the
nucleic acids are synthesized to include codons that are preferred
by the particular translation system being employed to express the
polymerase. For example, when it is desirable to express the
polymerase in a bacterial cell (or even a particular strain of
bacteria), the nucleic acid can be synthesized to include codons
most frequently found in the genome of that bacterial cell, for
efficient expression of the polymerase. A similar strategy can be
employed when it is desirable to express the polymerase in a
eukaryotic cell, e.g., the nucleic acid can include codons
preferred by that eukaryotic cell.
A variety of protein isolation and detection methods are known and
can be used to isolate polymerases, e.g., from recombinant cultures
of cells expressing the recombinant polymerases of the invention. A
variety of protein isolation and detection methods are well known
in the art, including, e.g., those set forth in R. Scopes, Protein
Purification, Springer-Verlag, N.Y. (1982); Deutscher, Methods in
Enzymology Vol. 182: Guide to Protein Purification, Academic Press,
Inc. N.Y. (1990); Sandana (1997) Bioseparation of Proteins,
Academic Press, Inc.; Bollag et al. (1996) Protein Methods,
2.sup.nd Edition Wiley-Liss, NY; Walker (1996) The Protein
Protocols Handbook Humana Press, NJ, Harris and Angal (1990)
Protein Purification Applications: A Practical Approach IRL Press
at Oxford, Oxford, England; Harris and Angal Protein Purification
Methods: A Practical Approach IRL Press at Oxford, Oxford, England;
Scopes (1993) Protein Purification: Principles and Practice
3.sup.rd Edition Springer Verlag, NY; Janson and Ryden (1998)
Protein Purification: Principles, High Resolution Methods and
Applications, Second Edition Wiley-VCH, NY; and Walker (1998)
Protein Protocols on CD-ROM Humana Press, NJ; and the references
cited therein. Additional details regarding protein purification
and detection methods can be found in Satinder Ahuja ed., Handbook
of Bioseparations, Academic Press (2000).
Kits
The present invention also features kits that incorporate the
polymerases of the invention, optionally with additional useful
reagents such as one or more nucleotides and/or nucleotide analogs,
e.g., for sequencing, nucleic acid amplification, or the like. Such
kits can include the polymerase of the invention packaged in a
fashion to enable use of the polymerase (e.g., the polymerase
immobilized in a ZMW array), optionally with a set of different
nucleotide analogs of the invention, e.g., those that are analogous
to A, T, G, and C, e.g., where one or more of the analogs comprise
a detectable moiety, to permit identification in the presence of
the analogs. Depending upon the desired application, the kits of
the invention optionally include additional reagents, such as
natural nucleotides, a control template, and other reagents, such
as buffer solutions and/or salt solutions, including, e.g.,
divalent metal ions such as Ca.sup.++, Mg.sup.++, Mn.sup.++ and/or
Fe.sup.++, and standard solutions, e.g., dye standards for detector
calibration. Such kits also typically include instructions for use
of the compounds and other reagents in accordance with the desired
application methods, e.g., nucleic acid sequencing, amplification
and the like.
Nucleic Acid and Polypeptide Sequences and Variants
As described herein, the invention also features polynucleotide
sequences encoding, e.g., a polymerase as described herein.
Examples of polymerase sequences that include features found
herein, e.g., as in Tables 3-6, are provided. However, one of skill
in the art will immediately appreciate that the invention is not
limited to the specifically exemplified sequences. For example, one
of skill will appreciate that the invention also provides, e.g.,
many related sequences with the functions described herein, e.g.,
polynucleotides and polypeptides encoding conservative variants of
a polymerase of Tables 3-6 or FIG. 7 or any other specifically
listed polymerase herein. Combinations of any of the mutations
noted herein or combinations of any of the mutations herein in
combination with those noted in other available references relating
to improved polymerases, such as Hanzel et al. WO 2007/076057
POLYMERASES FOR NUCLEOTIDE ANALOGUE INCORPORATION; Rank et al. WO
2008/051530 POLYMERASE ENZYMES AND REAGENTS FOR ENHANCED NUCLEIC
ACID SEQUENCING; Hanzel et al. WO 2007/075987 ACTIVE SURFACE
COUPLED POLYMERASES; Hanzel et al. WO 2007/075873 PROTEIN
ENGINEERING STRATEGIES TO OPTIMIZE ACTIVITY OF SURFACE ATTACHED
PROTEINS; U.S. patent application publication 2010-0075332
ENGINEERING POLYMERASES AND REACTION CONDITIONS FOR MODIFIED
INCORPORATION PROPERTIES by Pranav Patel et al.; U.S. patent
application publication 2010-0093555 ENZYMES RESISTANT TO
PHOTODAMAGE by Keith Bjornson et al.; U.S. patent application
publication 2010-0112645 GENERATION OF MODIFIED POLYMERASES FOR
IMPROVED ACCURACY IN SINGLE MOLECULE SEQUENCING by Sonya Clark et
al.; U.S. patent application publication 2011-0189659 GENERATION OF
MODIFIED POLYMERASES FOR IMPROVED ACCURACY IN SINGLE MOLECULE
SEQUENCING by Sonya Clark et al.; and U.S. patent application
publication 2012-0034602 RECOMBINANT POLYMERASES FOR IMPROVED
SINGLE MOLECULE SEQUENCING are also features of the invention.
Accordingly, the invention provides a variety of polypeptides
(polymerases) and polynucleotides (nucleic acids that encode
polymerases). Exemplary polynucleotides of the invention include,
e.g., any polynucleotide that encodes a polymerase of Tables 3-6 or
FIG. 7 or otherwise described herein. Because of the degeneracy of
the genetic code, many polynucleotides equivalently encode a given
polymerase sequence. Similarly, an artificial or recombinant
nucleic acid that hybridizes to a polynucleotide indicated above
under highly stringent conditions over substantially the entire
length of the nucleic acid (and is other than a naturally occurring
polynucleotide) is a polynucleotide of the invention. In one
embodiment, a composition includes a polypeptide of the invention
and an excipient (e.g., buffer, water, pharmaceutically acceptable
excipient, etc.). The invention also provides an antibody or
antisera specifically immunoreactive with a polypeptide of the
invention (e.g., that specifically recognizes a feature of the
polymerase that confers decreased branching or increased complex
stability.
In certain embodiments, a vector (e.g., a plasmid, a cosmid, a
phage, a virus, etc.) comprises a polynucleotide of the invention.
In one embodiment, the vector is an expression vector. In another
embodiment, the expression vector includes a promoter operably
linked to one or more of the polynucleotides of the invention. In
another embodiment, a cell comprises a vector that includes a
polynucleotide of the invention.
One of skill will also appreciate that many variants of the
disclosed sequences are included in the invention. For example,
conservative variations of the disclosed sequences that yield a
functionally similar sequence are included in the invention.
Variants of the nucleic acid polynucleotide sequences, wherein the
variants hybridize to at least one disclosed sequence, are
considered to be included in the invention. Unique subsequences of
the sequences disclosed herein, as determined by, e.g., standard
sequence comparison techniques, are also included in the
invention.
Conservative Variations
Owing to the degeneracy of the genetic code, "silent substitutions"
(i.e., substitutions in a nucleic acid sequence which do not result
in an alteration in an encoded polypeptide) are an implied feature
of every nucleic acid sequence that encodes an amino acid sequence.
Similarly, "conservative amino acid substitutions," where one or a
limited number of amino acids in an amino acid sequence (other than
residues noted, e.g., in Tables 3-6 and FIG. 7 or elsewhere herein,
as being relevant to a feature or property of interest) are
substituted with different amino acids with highly similar
properties, are also readily identified as being highly similar to
a disclosed construct. Such conservative variations of each
disclosed sequence are a feature of the present invention.
"Conservative variations" of a particular nucleic acid sequence
refers to those nucleic acids which encode identical or essentially
identical amino acid sequences, or, where the nucleic acid does not
encode an amino acid sequence, to essentially identical sequences.
One of skill will recognize that individual substitutions,
deletions or additions which alter, add or delete a single amino
acid or a small percentage of amino acids (typically less than 5%,
more typically less than 4%, 2% or 1%) in an encoded sequence are
"conservatively modified variations" where the alterations result
in the deletion of an amino acid, addition of an amino acid, or
substitution of an amino acid with a chemically similar amino acid,
while retaining the relevant mutational feature (for example, the
conservative substitution can be of a residue distal to the active
site region, or distal to an interdomain stability region). Thus,
"conservative variations" of a listed polypeptide sequence of the
present invention include substitutions of a small percentage,
typically less than 5%, more typically less than 2% or 1%, of the
amino acids of the polypeptide sequence, with an amino acid of the
same conservative substitution group. Finally, the addition of
sequences which do not alter the encoded activity of a nucleic acid
molecule, such as the addition of a non-functional or tagging
sequence (introns in the nucleic acid, poly His or similar
sequences in the encoded polypeptide, etc.), is a conservative
variation of the basic nucleic acid or polypeptide.
Conservative substitution tables providing functionally similar
amino acids are well known in the art, where one amino acid residue
is substituted for another amino acid residue having similar
chemical properties (e.g., aromatic side chains or positively
charged side chains), and therefore does not substantially change
the functional properties of the polypeptide molecule. The
following sets forth example groups that contain natural amino
acids of like chemical properties, where substitutions within a
group is a "conservative substitution".
TABLE-US-00001 TABLE 1 Conservative amino acid substitutions
Nonpolar Positively Negatively and/or Polar, Aromatic Charged
Charged Aliphatic Side Uncharged Side Side Side Chains Side Chains
Chains Chains Chains Glycine Serine Phenylalanine Lysine Aspartate
Alanine Threonine Tyrosine Arginine Glutamate Valine Cysteine
Tryptophan Histidine Leucine Methionine Isoleucine Asparagine
Proline Glutamine
Nucleic Acid Hybridization
Comparative hybridization can be used to identify nucleic acids of
the invention, including conservative variations of nucleic acids
of the invention. In addition, target nucleic acids which hybridize
to a nucleic acid of the invention under high, ultra-high and
ultra-ultra high stringency conditions, where the nucleic acids
encode mutants corresponding to those noted in Tables 3-6 and FIG.
7 or other listed polymerases, are a feature of the invention.
Examples of such nucleic acids include those with one or a few
silent or conservative nucleic acid substitutions as compared to a
given nucleic acid sequence encoding a polymerase of Tables 3-6 and
FIG. 7 (or other exemplified polymerase), where any conservative
substitutions are for residues other than those noted in Tables 3-6
and FIG. 7 or elsewhere as being relevant to a feature of interest
(increased phototolerance, improved analog binding, etc.).
A test nucleic acid 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.times.-10.times. as
high as that observed for hybridization to any of the unmatched
target nucleic acids.
Nucleic acids "hybridize" when they associate, typically in
solution. Nucleic acids hybridize due to a variety of well
characterized physico-chemical forces, such as hydrogen bonding,
solvent exclusion, base stacking and the like. An extensive guide
to the hybridization of nucleic acids is found in Tijssen (1993)
Laboratory Techniques in Biochemistry and Molecular
Biology--Hybridization with Nucleic Acid Probes part I chapter 2,
"Overview of principles of hybridization and the strategy of
nucleic acid probe assays," (Elsevier, New York), as well as in
Current Protocols in Molecular Biology, Ausubel et al., eds.,
Current Protocols, a joint venture between Greene Publishing
Associates, Inc. and John Wiley & Sons, Inc., (supplemented
through 2012); Hames and Higgins (1995) Gene Probes 1 IRL Press at
Oxford University Press, Oxford, England, (Hames and Higgins 1) and
Hames and Higgins (1995) Gene Probes 2 IRL Press at Oxford
University Press, Oxford, England (Hames and Higgins 2) provide
details on the synthesis, labeling, detection and quantification of
DNA and RNA, including oligonucleotides.
An example of stringent hybridization conditions for hybridization
of complementary nucleic acids which have more than 100
complementary residues on a filter in a Southern or northern blot
is 50% formalin with 1 mg of heparin at 42.degree. C., with the
hybridization being carried out overnight. An example of stringent
wash conditions is a 0.2.times.SSC wash at 65.degree. C. for 15
minutes (see, Sambrook, supra for a description of SSC buffer).
Often the high stringency wash is preceded by a low stringency wash
to remove background probe signal. An example low stringency wash
is 2.times.SSC at 40.degree. C. for 15 minutes. In general, a
signal to noise ratio of 5.times. (or higher) than that observed
for an unrelated probe in the particular hybridization assay
indicates detection of a specific hybridization.
"Stringent hybridization wash conditions" in the context of nucleic
acid hybridization experiments such as Southern and northern
hybridizations are sequence dependent, and are different under
different environmental parameters. An extensive guide to the
hybridization of nucleic acids is found in Tijssen (1993), supra.
and in Hames and Higgins, 1 and 2. Stringent hybridization and wash
conditions can easily be determined empirically for any test
nucleic acid. For example, in determining stringent hybridization
and wash conditions, the hybridization and wash conditions are
gradually increased (e.g., by increasing temperature, decreasing
salt concentration, increasing detergent concentration and/or
increasing the concentration of organic solvents such as formalin
in the hybridization or wash), until a selected set of criteria are
met. For example, in highly stringent hybridization and wash
conditions, the hybridization and wash conditions are gradually
increased until a probe binds to a perfectly matched complementary
target with a signal to noise ratio that is at least 5.times. as
high as that observed for hybridization of the probe to an
unmatched target.
"Very stringent" conditions are selected to be equal to the thermal
melting point (T.sub.m) for a particular probe. 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.
"Ultra high-stringency" hybridization and wash conditions are those
in which the stringency of hybridization and wash conditions are
increased until the signal to noise ratio for binding of the probe
to the perfectly matched complementary target nucleic acid is at
least 10.times. as high as that observed for hybridization to any
of the unmatched target nucleic acids. A target nucleic acid which
hybridizes to a probe under such conditions, with a signal to noise
ratio of at least 1/2 that of the perfectly matched complementary
target nucleic acid is said to bind to the probe under ultra-high
stringency conditions.
Similarly, even higher levels of stringency can be determined by
gradually increasing the hybridization and/or wash conditions of
the relevant hybridization assay. For example, those in which the
stringency of hybridization and wash conditions are increased until
the signal to noise ratio for binding of the probe to the perfectly
matched complementary target nucleic acid is at least 10.times.,
20.times., 50.times., 100.times., or 500.times. or more as high as
that observed for hybridization to any of the unmatched target
nucleic acids. A target nucleic acid which hybridizes to a probe
under such conditions, with a signal to noise ratio of at least 1/2
that of the perfectly matched complementary target nucleic acid is
said to bind to the probe under ultra-ultra-high stringency
conditions.
Nucleic acids that do not hybridize to each other under stringent
conditions are still substantially identical if the polypeptides
which they encode are substantially identical. This occurs, e.g.,
when a copy of a nucleic acid is created using the maximum codon
degeneracy permitted by the genetic code.
Unique Subsequences
In some aspects, the invention provides a nucleic acid that
comprises a unique subsequence in a nucleic acid that encodes a
polymerase of Tables 3-6 and FIG. 7 or others described herein. The
unique subsequence may be unique as compared to a nucleic acid
corresponding to, e.g., a wild type .PHI.29-type polymerase.
Alignment can be performed using, e.g., BLAST set to default
parameters. Any unique subsequence is useful, e.g., as a probe to
identify the nucleic acids of the invention.
Similarly, the invention includes a polypeptide which comprises a
unique subsequence in a polymerase of Tables 3-6 and FIG. 7 or
otherwise detailed herein. Here, the unique subsequence is unique
as compared to, e.g., a wild type .PHI.29-type polymerase or
previously characterized mutation thereof.
The invention also provides for target nucleic acids which
hybridize under stringent conditions to a unique coding
oligonucleotide which encodes a unique subsequence in a polypeptide
selected from the modified polymerase sequences of the invention,
wherein the unique subsequence is unique as compared to a
polypeptide corresponding to a wild type .PHI.29-type polymerase.
Unique sequences are determined as noted above.
Sequence Comparison. Identity, and Homology
The terms "identical" or "percent identity," 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 one of the sequence comparison algorithms described below (or
other algorithms available to persons of skill) or by visual
inspection.
The phrase "substantially identical," in the context of two nucleic
acids or polypeptides (e.g., DNAs encoding a polymerase, or the
amino acid sequence of a polymerase) refers to two or more
sequences or subsequences that have at least about 60%, about 80%,
about 90%, about 95%, about 98%, about 99% or more nucleotide or
amino acid residue identity, when compared and aligned for maximum
correspondence, as measured using a sequence comparison algorithm
or by visual inspection. Such "substantially identical" sequences
are typically considered to be "homologous," without reference to
actual ancestry. Preferably, the "substantial identity" exists over
a region of the sequences that is at least about 50 residues in
length, more preferably over a region of at least about 100
residues, and most preferably, the sequences are substantially
identical over at least about 150 residues, or over the full length
of the two sequences to be compared.
Proteins and/or protein sequences are "homologous" when they are
derived, naturally or artificially, from a common ancestral protein
or protein sequence. Similarly, nucleic acids and/or nucleic acid
sequences are homologous when they are derived, naturally or
artificially, from a common ancestral nucleic acid or nucleic acid
sequence. Homology is generally inferred from sequence similarity
between two or more nucleic acids or proteins (or sequences
thereof). The precise percentage of similarity between sequences
that is useful in establishing homology varies with the nucleic
acid and protein at issue, but as little as 25% sequence similarity
over 50, 100, 150 or more residues is routinely used to establish
homology. Higher levels of sequence similarity, e.g., 30%, 40%,
50%, 60%, 70%, 75%, 80%, 90%, 95%, 97%, 98%, or 99% or more
identity, can also be used to establish homology. Methods for
determining sequence similarity percentages (e.g., BLASTP and
BLASTN using default parameters) are described herein and are
generally available.
For sequence comparison and homology determination, typically one
sequence acts as a reference sequence to which test sequences are
compared. When using a sequence comparison algorithm, test and
reference sequences are input into a computer, subsequence
coordinates are designated, if necessary, and sequence algorithm
program parameters are designated. The sequence comparison
algorithm then calculates the percent sequence identity for the
test sequence(s) relative to the reference sequence, based on the
designated program parameters.
Optimal alignment of sequences for comparison can be conducted,
e.g., by the local homology algorithm of Smith & Waterman, Adv.
Appl. Math. 2:482 (1981), by the homology alignment algorithm of
Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search
for similarity method of Pearson & Lipman, Proc. Nat'l. Acad.
Sci. USA 85:2444 (1988), by computerized implementations of these
algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin
Genetics Software Package, Genetics Computer Group, 575 Science
Dr., Madison, Wis.), or by visual inspection (see generally Current
Protocols in Molecular Biology, Ausubel et al., eds., Current
Protocols, a joint venture between Greene Publishing Associates,
Inc. and John Wiley & Sons, Inc., supplemented through
2012).
One example of an algorithm that is suitable for determining
percent sequence identity and sequence similarity is the BLAST
algorithm, which is described in Altschul et al., J. Mol. Biol.
215:403-410 (1990). Software for performing BLAST analyses is
publicly available through the National Center for Biotechnology
Information. This algorithm involves first identifying high scoring
sequence pairs (HSPs) by identifying short words of length W in the
query sequence, which either match or satisfy some positive-valued
threshold score T when aligned with a word of the same length in a
database sequence. T is referred to as the neighborhood word score
threshold (Altschul et al., supra). These initial neighborhood word
hits act as seeds for initiating searches to find longer HSPs
containing them. The word hits are then extended in both directions
along each sequence for as far as the cumulative alignment score
can be increased. Cumulative scores are calculated using, for
nucleotide sequences, the parameters M (reward score for a pair of
matching residues; always >0) and N (penalty score for
mismatching residues; always <0). For amino acid sequences, a
scoring matrix is used to calculate the cumulative score. Extension
of the word hits in each direction are halted when: the cumulative
alignment score falls off by the quantity X from its maximum
achieved value; the cumulative score goes to zero or below, due to
the accumulation of one or more negative-scoring residue
alignments; or the end of either sequence is reached. The BLAST
algorithm parameters W, T, and X determine the sensitivity and
speed of the alignment. The BLASTN program (for nucleotide
sequences) uses as defaults a wordlength (W) of 11, an expectation
(E) of 10, a cutoff of 100, M=5, N=-4, and a comparison of both
strands. For amino acid sequences, the BLASTP program uses as
defaults a wordlength (W) of 3, an expectation (E) of 10, and the
BLOSUM62 scoring matrix (see Henikoff & Henikoff (1989) Proc.
Natl. Acad. Sci. USA 89:10915).
In addition to calculating percent sequence identity, the BLAST
algorithm also performs a statistical analysis of the similarity
between two sequences (see, e.g., Karlin & Altschul (1993)
Proc. Nat'l. Acad. Sci. USA 90:5873-5787). One measure of
similarity provided by the BLAST algorithm is the smallest sum
probability (P(N)), which provides an indication of the probability
by which a match between two nucleotide or amino acid sequences
would occur by chance. For example, a nucleic acid is considered
similar to a reference sequence if the smallest sum probability in
a comparison of the test nucleic acid to the reference nucleic acid
is less than about 0.1, more preferably less than about 0.01, and
most preferably less than about 0.001.
For reference, the amino acid sequence of a wild-type .PHI.29
polymerase is presented in Table 2, along with the sequences of
several other wild-type .PHI.29-type polymerases.
TABLE-US-00002 TABLE 2 Amino acid sequence of exemplary wild-type
.PHI.29-type polymerases. .PHI.29
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIEDHSEYKIGNS SEQ ID
LDEFMAWVLKVQADLYFHNLKFDGAFIINWLERNGFKWSADGL NO: 1
PNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFP
VKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQI
IAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLS
LGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQM
YSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPT
IQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYN
YVEISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLN
SLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMG
VFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKD
IVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEG
SPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPV QVPGGVVLVDDTFTIK M2Y
MSRKMFSCDFETTTKLDDCRVWAYGYMEIGNLDNYKIGNSLDE SEQ ID
FMQWVMEIQADLYFHNLKFDGAFIVNWLEQHGFKWSNEGLPNT NO: 2
YNTIISKMGQWYMIDICFGYKGKRKLHTVIYDSLKKLPFPVKK
IAKDFQLPLLKGDIDYHTERPVGHEITPEEYEYIKNDIEIIAR
ALDIQFKQGLDRMTAGSDSLKGFKDILSTKKFNKVFPKLSLPM
DKEIRKAYRGGFTWLNDKYKEKEIGEGMVFDVNSLYPSQMYSR
PLPYGAPIVFQGKYEKDEQYPLYIQRIRFEFELKEGYIPTIQI
KKNPFFKGNEYLKNSGVEPVELYLTNVDLELIQEHYELYNVEY
IDGFKFREKTGLFKDFIDKWTYVKTHEEGAKKQLAKLMLNSLY
GKFASNPDVTGKVPYLKDDGSLGFRVGDEEYKDPVYTPMGVFI
TAWARFTTITAAQACYDRIIYCDTDSIHLTGTEVPEIIKDIVD
PKKLGYWAHESTFKRAKYLRQKTYIQDIYVKEVDGKLKECSPD
EATTTKFSVKCAGMTDTIKKKVTFDNFAVGFSSMGKPKPVQVN GGVVLVDSVFTIK B103
MPRKMFSCDFETTTKLDDCRVWAYGYMEIGNLDNYKIGNSLDE SEQ ID
FMQWVMEIQADLYFHNLKFDGAFIVNWLEHHGFKWSNEGLPNT NO: 3
YNTIISKMGQWYMIDICFGYKGKRKLHTVIYDSLKKLPFPVKK
IAKDFQLPLLKGDIDYHAERPVGHEITPEEYEYIKNDIEIIAR
ALDIQFKQGLDRMTAGSDSLKGFKDILSTKKFNKVFPKLSLPM
DKEIRRAYRGGFTWLNDKYKEKEIGEGMVFDVNSLYPSQMYSR
PLPYGAPIVFQGKYEKDEQYPLYIQRIRFEFELKEGYIPTIQI
KKNPFFKGNEYLKNSGAEPVELYLTNVDLELIQEHYEMYNVEY
IDGFKFREKTGLFKEFIDKWTYVKTHEKGAKKQLAKLMFDSLY
GKFASNPDVTGKVPYLKEDGSLGFRVGDEEYKDPVYTPMGVFI
TAWARFTTITAAQACYDRIIYCDTDSIHLTGTEVPEIIKDIVD
PKKLGYWAHESTFKRAKYLRQKTYIQDIYAKEVDGKLIECSPD
EATTTKFSVKCAGMTDTIKKKVTFDNFRVGFSSTGKPKPVQVN GGVVLVDSVFTIK GA-1
MARSVYVCDFETTTDPEDCRLWAWGWMDIYNTDKWSYGEDIDS SEQ ID
FMEWALNSNSDIYFHNLKFDGSFILPWWLRNGYVHTEEDRTNT NO: 4
PKEFTTTISGMGQWYAVDVCINTRGKNKNHVVFYDSLKKLPFK
VEQIAKGFGLPVLKGDIDYKKYRPVGYVMDDNEIEYLKHDLLI
VALALRSMFDNDFTSMTVGSDALNTYKEMLGVKQWEKYFPVLS
LKVNSEIRKAYKGGFTWVNPKYQGETVYGGMVFDVNSMYPAMM
KNKLLPYGEPVMFKGEYKKNVEYPLYIQQVRCFFELKKDKIPC
IQIKGNARFGQNEYLSTSGDEYVDLYVTNVDWELIKKHYDIFE
EEFIGGFMFKGFIGFFDEYIDRFMEIKNSPDSSAEQSLQAKLM
LNSLYGKFATNPDITGKVPYLDENGVLKFRKGELKERDPVYTP
MGCFITAYARENILSNAQKLYPRFIYADTDSIHVEGLGEVDAI
KDVIDPKKLGYWDHEATFQRARYVRQKTYFIETTWKENDKGKL
VVCEPQDATKVKPKIACAGMSDAIKERIRFNEFKIGYSTHGSL KPKNVLGGVVLMDYPFAIK
AV-1 MVRQSTIASPARGGVRRSHKKVPSFCADFETTTDEDDCRVWSW SEQ ID
GIIQVGKLQNYVDGISLDGFMSHISERASHIYFHNLAFDGTFI NO: 5
LDWLLKHGYRWTKENPGVKEFTSLISRMGKYYSITVVFETGFR
VEFRDSFKKLPMSVSAIAKAFNLHDQKLEIDYEKPRPIGYIPT
EQEKRYQRNDVAIVAQALEVQFAEKMTKLTAGSDSLATYKKMT
GKLFIRRFPILSPEIDTEIRKAYRGGFTYADPRYAKKLNGKGS
VYDVNSLYPSVMRTALLPYGEPIYSEGAPRTNRPLYIASITFT
AKLKPNHIPCIQIKKNLSFNPTQYLEEVKEPTTVVATNIDIEL
WKKHYDFKIYSWNGTFEFRGSHGFFDTYVDHFMEIKKNSTGGL
RQIAKLHLNSLYGKFATNPDITGKHPTLKDNRVSLVMNEPETR
DPVYTPMGVFITAYARKKTISAAQDNYETFAYADTDSLHLIGP
TTPPDSLWVDPVELGAWKHESSFTKSVYIRAKQYAEEIGGKLD
VHIAGMPRNVAATLTLEDMLHGGTWNGKLIPVRVPGGTVLKDT TFTLKID CP-1
MTCYYAGDFETTTNEEETEVWLSCFAKVIDYDKLDTFKVNTSL SEQ ID
EDFLKSLYLDLDKTYTETGEDEFIIFFHNLKFDGSFLLSFFLN NO: 6
NDIECTYFINDMGVWYSITLEFPDFTLTFRDSLKILNFSIATM
AGLFKMPIAKGTTPLLKHKPEVIKPEWIDYIHVDVAILARGIF
AMYYEENFTKYTSASEALTEFKRIFRKSKRKFRDFFPILDEKV
DDFCRKHIVGAGRLPTLKHRGRTLNQLIDIYDINSMYPATMLQ
NALPIGIPKRYKGKPKEIKEDHYYIYHIKADFDLKRGYLPTIQ
IKKKLDALRIGVRTSDYVTTSKNEVIDLYLTNFDLDLFLKHYD
ATIMYVETLEFQTESDLFDDYITTYRYKKENAQSPAEKQKAKI
MLNSLYGKFGAKIISVKKLAYLDDKGILRFKNDDEEEVQPVYA
PVALFVTSIARHFIISNAQENYDNFLYADTDSLHLFHSDSLVL
DIDPSEFGKWAHEGRAVKAKYLRSKLYIEELIQEDGTTHLDVK
GAGMTPEIKEKITFENFVIGATFEGKRASKQIKGGTLIYETTF KIRETDYLV
Exemplary Mutation Combinations
A list of exemplary polymerase mutation combinations, and optional
corresponding exogenous or heterologous features at the N- and/or
C-terminal region of the polymerase, is provided in Tables 3 and 4.
Positions of amino acid substitutions are identified relative to a
wild-type .PHI.29 DNA polymerase (SEQ ID NO:1) for the recombinant
polymerases in Table 3 and relative to a wild-type M2Y DNA
polymerase (SEQ ID NO:2) for the recombinant polymerases in Table
4. Polymerases of the invention (including those provided in Tables
3 and 4) can include any exogenous or heterologous feature (or
combination of such features), e.g., at the N- and/or C-terminal
region. For example, it will be understood that polymerase mutants
in Tables 3 and 4 that do not include, e.g., a C-terminal
polyhistidine tag can be modified to include a polyhistidine tag at
the C-terminal region, alone or in combination with any of the
exogenous or heterologous features described herein. Similarly,
some or all of the exogenous features listed in Tables 3 and 4 can
be omitted, or substituted or combined with any of the other
exogenous features described herein, and still result in a
polymerase of the invention. As will be appreciated, the numbering
of amino acid residues is with respect to a particular reference
polymerase, such as the wild-type sequence of the .PHI.29
polymerase (SEQ ID NO:1); actual position of a mutation within a
molecule of the invention may vary based upon the nature of the
various modifications that the enzyme includes relative to the wild
type .PHI.29 enzyme, e.g., deletions and/or additions to the
molecule, either at the termini or within the molecule itself.
TABLE-US-00003 TABLE 3 Exemplary mutations introduced into a
.PHI.29 DNA polymerase. Positions are identified relative to SEQ ID
NO: 1. N-terminal region C-terminal region feature(s) Mutations
feature(s) K131E Y148I Y224K E239G V250I L253A E375Y His10 A437G
A484E D510K K512Y E515Q GGGSGGGSGGGS BtagV7 K135Q Y148I Y224K E239G
V250I L253A E375Y His10 A437G A484E D510K K512Y E515Q GGGSGGGSGGGS
BtagV7 K131E Y148I Y224K D235E E239G V250A L253H His10 E375Y A437G
A484E D510K K512Y E515Q GGGSGGGSGGGS BtagV7 Y148I Y224K E239G L253S
E375Y A437G A484E His10 D510K K512Y E515Q GGGSGGGSGGGS BtagV7 Y148I
Q183F D235E E239G L253H E375Y A437G His10 A484E D510K K512Y E515Q
GGGSGGGSGGGS BtagV7 BtagV7 His10 Y148I Y224K E239G V250I L253H
E375Y A437G His10 A484E D510K K512Y Y148I Y224K E239G V250I L253A
E375Y A437G His10 A484E D510K K512Y E515Q GGGSGGGSGGGS BtagV7 K131E
Y148I Y224K D235E E239G L253H E375Y His10 A437G A484E D510K K512Y
E515Q GGGSGGGSGGGS BtagV7 Y148I Y224K D235E E239G L253H E375Y A437G
His10co BtagV7 A484E D510K K512Y E515Q Y148I Y224K E239G V250I
L253A E375Y A437G His10 A484E D510K K512Y GGGSGGGSGGGS BtagV7
BtagV7 His10 Y148I Y224K E239G V250I L253A E375Y A437G His10 A484E
D510K K512Y BtagV7 His10 K131E Y148I Y224K E239G V250I L253A E375Y
His10 A484E D510K K512Y BtagV7 His10 K135Q Y148I Y224K E239G V250I
L253A E375Y His10 A484E D510K K512Y BtagV7 His10 Y148I Y224K E239G
L253H E375Y A437G A484E His10 D510K K512Y K131E K135Q V141K L142K
Y148I Y224K E239G His10 V250I L253A E375Y A437G A484E E508K D510K
GGGSGGGSGGGS K512Y E515Q K536Q BtagV7 K131E Y148I Y224K E239G V250I
L253A E375Y His10 A437G A484E E508K D510K K512Y E515Q GGGSGGGSGGGS
BtagV7 BtagV7 His10 K131Q Y148I Y224K E239G V250I L253A E375Y His10
A484E D510K K512Y
TABLE-US-00004 TABLE 4 Exemplary mutations introduced into an M2Y
DNA polymerase. Positions are identified relative to SEQ ID NO: 2.
N-terminal C-terminal region region feature(s) Mutations feature(s)
BtagV7 L250A S253A E372Y A481E K509Y His10 His10 Y145I E236G V247I
L250A S253A E372Y His10 A434G A481E D507K K509Y E512Q GGGSGGGSGGGS
BtagV7 BtagV7 K132Q Y145I E236G V247I L250A E372Y His10 His10 A434G
A481E D507K K509Y E512Q
The amino acid sequences of recombinant .PHI.29 and M2Y polymerases
harboring the exemplary mutation combinations of Tables 3 and 4 are
provided in Tables 5 and 6. Table 5 includes the polymerase portion
of the molecule as well as the one or more exogenous features at
the N- and/or C-terminal region of the polymerase, while Table 6
includes the amino acid sequence of the polymerase portion
only.
TABLE-US-00005 TABLE 5 Amino acid sequences of exemplary
recombinant .PHI.29 and M2Y polymerases including N- and C-terminal
exogenous features. Amino acid positions are identified relative to
SEQ ID NO: 1 for recombinant .PHI.29 polymerases (denoted by
"Phi29") or relative to SEQ ID NO: 2 for recombinant M2Y
polymerases (denoted by "M2"). SEQ ID NO Amino Acid Sequence 7
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K131E_Y148I_Y224K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI E239G_V250I_L253A_E375Y_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A437G_A484E_D510K_K512Y_
LGYKGKRKIHTVIYDSLKKLPFPVEKIAKDFKLTVLKG E515Q.His10.GGGSGGGSGGGS.
DIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK BtagV7
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGRY
TTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKGY
LVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV
GFSRKMKPKPVQVPGGVVLVDDTFTIKGHHHHHHH HHHGGGSGGGSGGGSGLNDFFEAQKIEWHE
8 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K135Q_Y148I_Y224K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI E239G_V250I_L253A_E375Y_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A437G_A484E_D510K_K512Y_
LGYKGKRKIHTVIYDSLKKLPFPVKKIAQDFKLTVLK E515Q.His10.GGGSGGGSGGGS.
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK BtagV7
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKGY
LVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV
GFSRKMKPKPVQVPGGVVLVDDTFTIKGHHHHHHH HHHGGGSGGGSGGGSGLNDFFEAQKIEWHE
9 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K131E_Y148I_Y224K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI D235E_E239G_V250A_L253H_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC E375Y_A437G_A484E_D510K_
LGYKGKRKIHTVIYDSLKKLPFPVEKIAKDFKLTVLK K512Y_E515Q.His10.
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK GGGSGGGSGGGS.BtagV7
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNERFKGKEIGEGMVFDANSHY
PAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCE
FELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLS
NVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFID
KWTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTG
KVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWG
RYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVD
PKKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKG
YLVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFK
VGFSRKMKPKPVQVPGGVVLVDDTFTIKGHHHHHH HHHHGGGSGGGSGGGSGLNDFFEAQKIEWHE
10 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.Y148I_Y224K_E239G_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI L253S_E375Y_A437G_A484E_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC D510K_K512Y_E515Q.His10.
LGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLK GGGSGGGSGGGS.BtagV7
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDVNSSY
PAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCE
FELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLS
NVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFID
KWTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTG
KVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWG
RYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVD
PKKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKG
YLVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFK
VGFSRKMKPKPVQVPGGVVLVDDTFTIKGHHHHHH HHHHGGGSGGGSGGGSGLNDFFEAQKIEWHE
11 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.Y148I_Q183F_D235E_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI E239G_L253H_E375Y_A437G_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A484E_D510K_K512Y_E515Q.
LGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLK His10.GGGSGGGSGGGS.
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK BtagV7
FGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRYAYRGGFTWLNERFKGKEIGEGMVFDVNSHY
PAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCE
FELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLS
NVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFID
KWTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTG
KVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWG
RYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVD
PKKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKG
YLVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFK
VGFSRKMKPKPVQVPGGVVLVDDTFTIKGHHHHHH HHHHGGGSGGGSGGGSGLNDFFEAQKIEWHE
12 MSVDGLNDFFEAQKIEWHEAMGHHHHHHHHHHSS BtagV7.His10.Phi29.Y148I_
GHIEGRHMKHMPRKMYSCDFETTTKVEDCRVWAY Y224K_E239G_V250I_L253H_
GYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHN E375Y_A437G_A484E_D510K_
LKFDGAFIINWLERNGFKWSADGLPNTYNTIISRMGQ K512Y.His10
WYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKD
FKLTVLKGDIDIHKERPVGYKITPEEYAYIKNDIQIIAE
ALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFP
TLSLGLDKEVRKAYRGGFTWLNDRFKGKEIGEGMV
FDINSHYPAQMYSRLLPYGEPIVFEGKYVWDEDYPL
HIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGE
IADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTG
LFKDFIDKWTYIKTTSYGAIKQLAKLMLNSLYGKFAS
NPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMG
VFITAWGRYTTITAAQACYDRIIYCDTDSIHLTGTEIP
DVIKDIVDPKKLGYWEHESTFKRAKYLRQKTYIQDIY
MKEVKGYLVEGSPDDYTDIKFSVKCAGMTDKIKKE
VTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIKG HHHHHHHHHH 13
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.Y148I_Y224K_E239G_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI V250I_L253A_E375Y_A437G_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A484E_D510K_K512Y_E515Q.
LGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLK His10.GGGSGGGSGGGS.
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK BtagV7
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKGY
LVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV
GFSRKMKPKPVQVPGGVVLVDDTFTIKGHHHHHHH HHHGGGSGGGSGGGSGLNDFFEAQKIEWHE
14 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K131E_Y148I_Y224K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI D235E_E239G_L253H_E375Y_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A437G_A484E_D510K_K512Y_
LGYKGKRKIHTVIYDSLKKLPFPVEKIAKDFKLTVLK E515Q.His10.
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK GGGSGGGSGGGS.BtagV7
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNERFKGKEIGEGMVFDVNSHY
PAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCE
FELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLS
NVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFID
KWTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTG
KVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWG
RYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVD
PKKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKG
YLVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFK
VGFSRKMKPKPVQVPGGVVLVDDTFTIKGHHHHHH HHHHGGGSGGGSGGGSGLNDFFEAQKIEWHE
15 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.Y148I_Y224K_D235E_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI E239G_L253H_E375Y_A437G_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A484E_D510K_K512Y_E515Q.
LGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLK His10.BtagV7
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNERFKGKEIGEGMVFDVNSHY
PAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCE
FELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLS
NVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFID
KWTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTG
KVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWG
RYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVD
PKKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKG
YLVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFK
VGFSRKMKPKPVQVPGGVVLVDDTFTIKGHHHHHH HHHHGGGSGGGSGGGSGLNDFFEAQKIEWHE
16 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.Y148I_Y224K_E239G_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI V250I_L253A_E375Y_A437G_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A484E_D510K_K512Y.His10.
LGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLK GGGSGGGSGGGS.BtagV7
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKGY
LVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV
GFSRKMKPKPVQVPGGVVLVDDTFTIKGHHHHHHH HHHGGGSGGGSGGGSGLNDFFEAQKIEWHE
17 MSVDGLNDFFEAQKIEWHEAMGHHHHHHHHHHSS BtagV7.His10.CTerm_
GHIEGRHMKHMPRKMYSCDFETTTKVEDCRVWAY His10.Phi29.Y148I_Y224K_
GYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHN E239G_V250I_L253A_E375Y_
LKFDGAFIINWLERNGFKWSADGLPNTYNTIISRMGQ A437G_A484E_D510K_K512Y
WYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKD
FKLTVLKGDIDIHKERPVGYKITPEEYAYIKNDIQIIAE
ALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFP
TLSLGLDKEVRKAYRGGFTWLNDRFKGKEIGEGMV
FDINSAYPAQMYSRLLPYGEPIVFEGKYVWDEDYPL
HIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGE
IADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTG
LFKDFIDKWTYIKTTSYGAIKQLAKLMLNSLYGKFAS
NPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMG
VFITAWGRYTTITAAQACYDRIIYCDTDSIHLTGTEIP
DVIKDIVDPKKLGYWEHESTFKRAKYLRQKTYIQDIY
MKEVKGYLVEGSPDDYTDIKFSVKCAGMTDKIKKE
VTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIKG HHHHHHHHHH 18
MSVDGLNDFFEAQKIEWHEAMGHHHHHHHHHHSS BtagV7.His10.CTerm_
GHIEGRHMKHMPRKMYSCDFETTTKVEDCRVWAY His10.Phi29.K131E_Y148I_
GYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHN Y224K_E239G_V250I_L253A_
LKFDGAFIINWLERNGFKWSADGLPNTYNTIISRMGQ E375Y_A484E_D510K_K512Y
WYMIDICLGYKGKRKIHTVIYDSLKKLPFPVEKIAKD
FKLTVLKGDIDIHKERPVGYKITPEEYAYIKNDIQIIAE
ALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFP
TLSLGLDKEVRKAYRGGFTWLNDRFKGKEIGEGMV
FDINSAYPAQMYSRLLPYGEPIVFEGKYVWDEDYPL
HIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGE
IADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTG
LFKDFIDKWTYIKTTSYGAIKQLAKLMLNSLYGKFAS
NPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMG
VFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIP
DVIKDIVDPKKLGYWEHESTFKRAKYLRQKTYIQDIY
MKEVKGYLVEGSPDDYTDIKFSVKCAGMTDKIKKE
VTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIKG HHHHHHHHHH 19
MSVDGLNDFFEAQKIEWHEAMGHHHHHHHHHHSS BtagV7.His10.CTerm_
GHIEGRHMKHMPRKMYSCDFETTTKVEDCRVWAY His10.Phi29.K135Q_Y148I_
GYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHN Y224K_E239G_V250I_L253A_
LKFDGAFIINWLERNGFKWSADGLPNTYNTIISRMGQ E375Y_A484E_D510K_K512Y
WYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAQD
FKLTVLKGDIDIHKERPVGYKITPEEYAYIKNDIQIIAE
ALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFP
TLSLGLDKEVRKAYRGGFTWLNDRFKGKEIGEGMV
FDINSAYPAQMYSRLLPYGEPIVFEGKYVWDEDYPL
HIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGE
IADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTG
LFKDFIDKWTYIKTTSYGAIKQLAKLMLNSLYGKFAS
NPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMG
VFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIP
DVIKDIVDPKKLGYWEHESTFKRAKYLRQKTYIQDIY
MKEVKGYLVEGSPDDYTDIKFSVKCAGMTDKIKKE
VTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIKG HHHHHHHHHH 20
MSVDGLNDFFEAQKIEWHEAMGHHHHHHHHHHSS BtagV7.His10.CTerm_
GHIEGRHMSRKMFSCDFETTTKLDDCRVWAYGYME His10.M2.L250A_S253A_
IGNLDNYKIGNSLDEFMQWVMEIQADLYFHNLKFDG
E372Y_A481E_K509Y AFIVNWLEQHGFKWSNEGLPNTYNTIISKMGQWYMI
DICFGYKGKRKLHTVIYDSLKKLPFPVKKIAKDFQLP
LLKGDIDYHTERPVGHEITPEEYEYIKNDIEIIARALDI
QFKQGLDRMTAGSDSLKGFKDILSTKKFNKVFPKLS
LPMDKEIRKAYRGGFTWLNDKYKEKEIGEGMVFDV
NSAYPAQMYSRPLPYGAPIVFQGKYEKDEQYPLYIQ
RIRFEFELKEGYIPTIQIKKNPFFKGNEYLKNSGVEPV
ELYLTNVDLELIQEHYELYNVEYIDGFKFREKTGLFK
DFIDKWTYVKTHEYGAKKQLAKLMLNSLYGKFASN
PDVTGKVPYLKDDGSLGFRVGDEEYKDPVYTPMGV
FITAWARFTTITAAQACYDRIIYCDTDSIHLTGTEVPEI
IKDIVDPKKLGYWEHESTFKRAKYLRQKTYIQDIYVK
EVDGYLKECSPDEATTTKFSVKCAGMTDTIKKKVTF
DNFAVGFSSMGKPKPVQVNGGVVLVDSVFTIKGHH HHHHHHHH 21
MSVDGLNDFFEAQKIEWHEAMGHHHHHHHHHHSS BtagV7.His10.CTerm_
GHIEGRHMKHMPRKMYSCDFETTTKVEDCRVWAY His10.Phi29.Y148I_Y224K_
GYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHN E239G_L253H_E375Y_A437G_
LKFDGAFIINWLERNGFKWSADGLPNTYNTIISRMGQ A484E_D510K_K512Y
WYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKD
FKLTVLKGDIDIHKERPVGYKITPEEYAYIKNDIQIIAE
ALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFP
TLSLGLDKEVRKAYRGGFTWLNDRFKGKEIGEGMV
FDVNSHYPAQMYSRLLPYGEPIVFEGKYVWDEDYPL
HIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGE
IADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTG
LFKDFIDKWTYIKTTSYGAIKQLAKLMLNSLYGKFAS
NPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMG
VFITAWGRYTTITAAQACYDRIIYCDTDSIHLTGTEIP
DVIKDIVDPKKLGYWEHESTFKRAKYLRQKTYIQDIY
MKEVKGYLVEGSPDDYTDIKFSVKCAGMTDKIKKE
VTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIKG HHHHHHHHHH 22
MSRKMFSCDFETTTKLDDCRVWAYGYMEIGNLDNY M2.Y145I_E236G_V247I_
KIGNSLDEFMQWVMEIQADLYFHNLKFDGAFIVNWL L250A_S253A_E372Y_A434G_
EQHGFKWSNEGLPNTYNTIISKMGQWYMIDICFGYK A481E_D507K_K509Y_E512Q.
GKRKLHTVIYDSLKKLPFPVKKIAKDFQLPLLKGDIDI His10.GGGSGGGSGGGS.
HTERPVGHEITPEEYEYIKNDIEIIARALDIQFKQGLDR BtagV7
MTAGSDSLKGFKDILSTKKFNKVFPKLSLPMDKEIRK
AYRGGFTWLNDKYKGKEIGEGMVFDINSAYPAQMY
SRPLPYGAPIVFQGKYEKDEQYPLYIQRIRFEFELKEG
YIPTIQIKKNPFFKGNEYLKNSGVEPVELYLTNVDLEL
IQEHYELYNVEYIDGFKFREKTGLFKDFIDKWTYVKT
HEYGAKKQLAKLMLNSLYGKFASNPDVTGKVPYLK
DDGSLGFRVGDEEYKDPVYTPMGVFITAWGRFTTIT
AAQACYDRIIYCDTDSIHLTGTEVPEIIKDIVDPKKLG
YWEHESTFKRAKYLRQKTYIQDIYVKEVKGYLKQCS
PDEATTTKFSVKCAGMTDTIKKKVTFDNFAVGFSSM
GKPKPVQVNGGVVLVDSVFTIKGHHHHHHHHHHGG GSGGGSGGGSGLNDFFEAQKIEWHE 23
MSVDGLNDFFEAQKIEWHEAMGHHHHHHHHHHSS BtagV7.His10.M2.K132Q_
GHIEGRHMSRKMFSCDFETTTKLDDCRVWAYGYME Y145I_E236G_V247I_L250A_
IGNLDNYKIGNSLDEFMQWVMEIQADLYFHNLKFDG E372Y_A434G_A481E_D507K_
AFIVNWLEQHGFKWSNEGLPNTYNTIISKMGQWYMI K509Y_E512Q.His10
DICFGYKGKRKLHTVIYDSLKKLPFPVKKIAQDFQLP
LLKGDIDIHTERPVGHEITPEEYEYIKNDIEIIARALDIQ
FKQGLDRMTAGSDSLKGFKDILSTKKFNKVFPKLSLP
MDKEIRKAYRGGFTWLNDKYKGKEIGEGMVFDINS
AYPSQMYSRPLPYGAPIVFQGKYEKDEQYPLYIQRIR
FEFELKEGYIPTIQIKKNPFFKGNEYLKNSGVEPVELY
LTNVDLELIQEHYELYNVEYIDGFKFREKTGLFKDFI
DKWTYVKTHEYGAKKQLAKLMLNSLYGKFASNPD
VTGKVPYLKDDGSLGFRVGDEEYKDPVYTPMGVFIT
AWGRFTTITAAQACYDRIIYCDTDSIHLTGTEVPEIIK
DIVDPKKLGYWEHESTFKRAKYLRQKTYIQDIYVKE
VKGYLKQCSPDEATTTKFSVKCAGMTDTIKKKVTFD
NFAVGFSSMGKPKPVQVNGGVVLVDSVFTIKGHHH HHHHHHH 24
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K131E_K135Q_V141K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI L142K_Y148I_Y224K_E239G_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC V250I_L253A_E375Y_A437G_
LGYKGKRKIHTVIYDSLKKLPFPVEKIAQDFKLTKKK A484E_E508K_D510K_K512Y_
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK E515Q_K536Q.His10.
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD GGGSGGGSGGGS.BtagV7
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKKVKGY
LVQGSPDDYTDIKFSVKCAGMTDQIKKEVTFENFKV
GFSRKMKPKPVQVPGGVVLVDDTFTIKGHHHHHHH HHHGGGSGGGSGGGSGLNDFFEAQKIEWHE
25 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K131E_Y148I_Y224K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI E239G_V250I_L253A_E375Y_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A437G_A484E_E508K_D510K_
LGYKGKRKIHTVIYDSLKKLPFPVEKIAKDFKLTVLK K512Y_E515Q.His10.
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK GGGSGGGSGGGS.BtagV7
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKKVKGY
LVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV
GFSRKMKPKPVQVPGGVVLVDDTFTIKGHHHHHHH HHHGGGSGGGSGGGSGLNDFFEAQKIEWHE
26 MSVDGLNDFFEAQKIEWHEAMGHHHHHHHHHHSS BtagV7.His10.Phi29.K131Q_
GHIEGRHMKHMPRKMYSCDFETTTKVEDCRVWAY Y148I_Y224K_E239G_V250I_
GYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHN L253A_E375Y_A484E_D510K_
LKFDGAFIINWLERNGFKWSADGLPNTYNTIISRMGQ K512Y.His10
WYMIDICLGYKGKRKIHTVIYDSLKKLPFPVQKIAKD
FKLTVLKGDIDIHKERPVGYKITPEEYAYIKNDIQIIAE
ALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFP
TLSLGLDKEVRKAYRGGFTWLNDRFKGKEIGEGMV
FDINSAYPAQMYSRLLPYGEPIVFEGKYVWDEDYPL
HIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGE
IADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTG
LFKDFIDKWTYIKTTSYGAIKQLAKLMLNSLYGKFAS
NPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMG
VFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIP
DVIKDIVDPKKLGYWEHESTFKRAKYLRQKTYIQDIY
MKEVKGYLVEGSPDDYTDIKFSVKCAGMTDKIKKE
VTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIKG HHHHHHHHHH
TABLE-US-00006 TABLE 6 Amino acid sequences of exemplary
recombinant .PHI.29 and M2Y polymerases. Amino acid positions are
identified relative to SEQ ID NO: 1 for recombinant .PHI.29
polymerases (denoted by "Phi29") or relative to SEQ ID NO: 2 for
recombinant M2Y polymerases (denoted by "M2"). SEQ ID NO Amino Acid
Sequence 27 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED
Phi29.K131E_Y148I_Y224K_ HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI
E239G_V250I_L253A_ INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC
E375Y_A437G_A484E_ LGYKGKRKIHTVIYDSLKKLPFPVEKIAKDFKLTVLK
D510K_K512Y_E515Q GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKGY
LVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV GFSRKMKPKPVQVPGGVVLVDDTFTIK 28
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K135Q_Y148I_Y224K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI E239G_V250I_L253A_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC E375Y_A437G_A484E_
LGYKGKRKIHTVIYDSLKKLPFPVKKIAQDFKLTVLK D510K_K512Y_E515Q
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKGY
LVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV GFSRKMKPKPVQVPGGVVLVDDTFTIK 29
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K131E_Y148I_Y224K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI D235E_E239G_V250A_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC L253H_E375Y_A437G_
LGYKGKRKIHTVIYDSLKKLPFPVEKIAKDFKLTVLK A484E_D510K_K512Y_
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK E515Q
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNERFKGKEIGEGMVFDANSHY
PAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCE
FELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLS
NVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFID
KWTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTG
KVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWG
RYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVD
PKKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKG
YLVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFK VGFSRKMKPKPVQVPGGVVLVDDTFTIK
30 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.Y148I_Y224K_E239G_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI L253S_E375Y_A437G_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A484E_D510K_K512Y_
LGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLK E515Q
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDVNSSY
PAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCE
FELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLS
NVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFID
KWTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTG
KVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWG
RYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVD
PKKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKG
YLVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFK VGFSRKMKPKPVQVPGGVVLVDDTFTIK
31 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.Y148I_Q183F_D235E_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI E239G_L253H_E375Y_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A437G_A484E_D510K_
LGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLK K512Y_E515Q
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
FGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRYAYRGGFTWLNERFKGKEIGEGMVFDVNSHY
PAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCE
FELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLS
NVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFID
KWTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTG
KVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWG
RYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVD
PKKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKG
YLVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFK VGFSRKMKPKPVQVPGGVVLVDDTFTIK
32 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.Y148I_Y224K_E239G_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI V250I_L253H_E375Y_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A437G_A484E_D510K_
LGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLK K512Y
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSHYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKGY
LVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV GFSRKMKPKPVQVPGGVVLVDDTFTIK 33
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.Y148I_Y224K_E239G_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI V250I_L253A_E375Y_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A437G_A484E_D510K_
LGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLK K512Y_E515Q
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKGY
LVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV GFSRKMKPKPVQVPGGVVLVDDTFTIK 34
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K131E_Y148I_Y224K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI D235E_E239G_L253H_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC E375Y_A437G_A484E_
LGYKGKRKIHTVIYDSLKKLPFPVEKIAKDFKLTVLK D510K_K512Y_E515Q
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNERFKGKEIGEGMVFDVNSHY
PAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCE
FELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLS
NVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFID
KWTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTG
KVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWG
RYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVD
PKKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKG
YLVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFK VGFSRKMKPKPVQVPGGVVLVDDTFTIK
35 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.Y148I_Y224K_D235E_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI E239G_L253H_E375Y_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A437G_A484E_D510K_
LGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLK K512Y_E515Q
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNERFKGKEIGEGMVFDVNSHY
PAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCE
FELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLS
NVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFID
KWTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTG
KVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWG
RYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVD
PKKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKG
YLVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFK VGFSRKMKPKPVQVPGGVVLVDDTFTIK
36 MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.Y148I_Y224K_E239G_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI V250I_L253A_E375Y_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A437G_A484E_D510K_
LGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLK K512Y
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKGY
LVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV GFSRKMKPKPVQVPGGVVLVDDTFTIK 37
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.Y148I_Y224K_E239G_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI V250I_L253A_E375Y_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC A437G_A484E_D510K_
LGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLK K512Y
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKGY
LVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV GFSRKMKPKPVQVPGGVVLVDDTFTIK 38
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K131E_Y148I_Y224K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI E239G_V250I_L253A_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC E375Y_A484E_D510K_
LGYKGKRKIHTVIYDSLKKLPFPVEKIAKDFKLTVLK K512Y
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWAR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKGY
LVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV GFSRKMKPKPVQVPGGVVLVDDTFTIK 39
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K135Q_Y148I_Y224K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI E239G_V250I_L253A_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC E375Y_A484E_D510K_
LGYKGKRKIHTVIYDSLKKLPFPVKKIAQDFKLTVLK K512Y
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWAR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKGY
LVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV GFSRKMKPKPVQVPGGVVLVDDTFTIK 40
MSRKMFSCDFETTTKLDDCRVWAYGYMEIGNLDNY M2.L250A_S253A_E372Y_
KIGNSLDEFMQWVMEIQADLYFHNLKFDGAFIVNWL A481E_K509Y
EQHGFKWSNEGLPNTYNTIISKMGQWYMIDICFGYK
GKRKLHTVIYDSLKKLPFPVKKIAKDFQLPLLKGDID
YHTERPVGHEITPEEYEYIKNDIEIIARALDIQFKQGLD
RMTAGSDSLKGFKDILSTKKFNKVFPKLSLPMDKEIR
KAYRGGFTWLNDKYKEKEIGEGMVFDVNSAYPAQ
MYSRPLPYGAPIVFQGKYEKDEQYPLYIQRIRFEFEL
KEGYIPTIQIKKNPFFKGNEYLKNSGVEPVELYLTNV
DLELIQEHYELYNVEYIDGFKFREKTGLFKDFIDKWT
YVKTHEYGAKKQLAKLMLNSLYGKFASNPDVTGKV
PYLKDDGSLGFRVGDEEYKDPVYTPMGVFITAWARF
TTITAAQACYDRIIYCDTDSIHLTGTEVPEIIKDIVDPK
KLGYWEHESTFKRAKYLRQKTYIQDIYVKEVDGYLK
ECSPDEATTTKFSVKCAGMTDTIKKKVTFDNFAVGF SSMGKPKPVQVNGGVVLVDSVFTIK 41
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.Y148I_Y224K_E239G_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI L253H_E375Y_A437G_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC
A484E_D510K_K512Y LGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLK
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDVNSHY
PAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCE
FELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLS
NVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFID
KWTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTG
KVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWG
RYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVD
PKKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKG
YLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFK VGFSRKMKPKPVQVPGGVVLVDDTFTIK
42 MSRKMFSCDFETTTKLDDCRVWAYGYMEIGNLDNY M2.Y145I_E236G_V247I_
KIGNSLDEFMQWVMEIQADLYFHNLKFDGAFIVNWL L250A_S253A_E372Y_
EQHGFKWSNEGLPNTYNTIISKMGQWYMIDICFGYK A434G_A481E_D507K_
GKRKLHTVIYDSLKKLPFPVKKIAKDFQLPLLKGDIDI K509Y_E512Q
HTERPVGHEITPEEYEYIKNDIEIIARALDIQFKQGLDR
MTAGSDSLKGFKDILSTKKFNKVFPKLSLPMDKEIRK
AYRGGFTWLNDKYKGKEIGEGMVFDINSAYPAQMY
SRPLPYGAPIVFQGKYEKDEQYPLYIQRIRFEFELKEG
YIPTIQIKKNPFFKGNEYLKNSGVEPVELYLTNVDLEL
IQEHYELYNVEYIDGFKFREKTGLFKDFIDKWTYVKT
HEYGAKKQLAKLMLNSLYGKFASNPDVTGKVPYLK
DDGSLGFRVGDEEYKDPVYTPMGVFITAWGRFTTIT
AAQACYDRIIYCDTDSIHLTGTEVPEIIKDIVDPKKLG
YWEHESTFKRAKYLRQKTYIQDIYVKEVKGYLKQCS
PDEATTTKFSVKCAGMTDTIKKKVTFDNFAVGFSSM GKPKPVQVNGGVVLVDSVFTIK 43
MSRKMFSCDFETTTKLDDCRVWAYGYMEIGNLDNY M2.K132Q_Y145I_E236G_
KIGNSLDEFMQWVMEIQADLYFHNLKFDGAFIVNWL V247I_L250A_E372Y_
EQHGFKWSNEGLPNTYNTIISKMGQWYMIDICFGYK A434G_A481E_D507K_
GKRKLHTVIYDSLKKLPFPVKKIAQDFQLPLLKGDIDI K509Y_E512Q
HTERPVGHEITPEEYEYIKNDIEIIARALDIQFKQGLDR
MTAGSDSLKGFKDILSTKKFNKVFPKLSLPMDKEIRK
AYRGGFTWLNDKYKGKEIGEGMVFDINSAYPSQMY
SRPLPYGAPIVFQGKYEKDEQYPLYIQRIRFEFELKEG
YIPTIQIKKNPFFKGNEYLKNSGVEPVELYLTNVDLEL
IQEHYELYNVEYIDGFKFREKTGLFKDFIDKWTYVKT
HEYGAKKQLAKLMLNSLYGKFASNPDVTGKVPYLK
DDGSLGFRVGDEEYKDPVYTPMGVFITAWGRFTTIT
AAQACYDRIIYCDTDSIHLTGTEVPEIIKDIVDPKKLG
YWEHESTFKRAKYLRQKTYIQDIYVKEVKGYLKQCS
PDEATTTKFSVKCAGMTDTIKKKVTFDNFAVGFSSM GKPKPVQVNGGVVLVDSVFTIK 44
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K131E_K135Q_V141K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI L142K_Y148I_Y224K_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC E239G_V250I_L253A_
LGYKGKRKIHTVIYDSLKKLPFPVEKIAQDFKLTKKK E375Y_A437G_A484E_
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK E508K_D510K_K512Y_
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD E515Q_K536Q
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKKVKGY
LVQGSPDDYTDIKFSVKCAGMTDQIKKEVTFENFKV GFSRKMKPKPVQVPGGVVLVDDTFTIK 45
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K131E_Y148I_Y224K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI E239G_V250I_L253A_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC E375Y_A437G_A484E_
LGYKGKRKIHTVIYDSLKKLPFPVEKIAKDFKLTVLK E508K_D510K_K512Y_
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK E515Q
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWGR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKKVKGY
LVQGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV GFSRKMKPKPVQVPGGVVLVDDTFTIK 46
MKHMPRKMYSCDFETTTKVEDCRVWAYGYMNIED Phi29.K131Q_Y148I_Y224K_
HSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFI E239G_V250I_L253A_
INWLERNGFKWSADGLPNTYNTIISRMGQWYMIDIC E375Y_A484E_D510K_
LGYKGKRKIHTVIYDSLKKLPFPVQKIAKDFKLTVLK K512Y
GDIDIHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFK
QGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLD
KEVRKAYRGGFTWLNDRFKGKEIGEGMVFDINSAYP
AQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEF
ELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSN
VDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDK
WTYIKTTSYGAIKQLAKLMLNSLYGKFASNPDVTGK
VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWAR
YTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDP
KKLGYWEHESTFKRAKYLRQKTYIQDIYMKEVKGY
LVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKV
GFSRKMKPKPVQVPGGVVLVDDTFTIK
Additional exemplary polymerase mutations and/or combinations
thereof are provided in FIG. 7. In FIG. 7, positions of the
mutations are identified relative to a wild-type .PHI.29 DNA
polymerase (SEQ ID NO:1) where the name of the polymerase includes
"Phi29," and where the name of the polymerase includes "M2"
positions are identified relative to a wild-type M2Y polymerase
(SEQ ID NO:2). Where the feature "topo V fusion" is listed, it
indicates that the polymerase includes a fusion as described in de
Vega et al. (2010) "Improvement of .PHI.29 DNA polymerase
amplification performance by fusion of DNA binding motifs" Proc
Natl Acad Sci USA 107:16506-16511. Where the feature "Maltose
Binding Fusion Protein" is listed, it indicates that the polymerase
includes a fusion with maltose binding protein as known in the art.
The notation "pET16.BtagV7co.His10co," where the tags are listing
in the N-terminal position, indicates that the polymerase includes
N-terminal biotin and His10 tags. The feature "Cterm_His10co" is
the same as listing the His10 in the C terminal position; both
terms indicate that the polymerase includes a C-terminal His10 tag.
"pET16" or "pET11" refers to a vector used to produce a recombinant
.PHI.29 polymerase comprising the indicated mutations, and "co"
indicates that the polynucleotide sequence encoding certain
features (e.g., a His10 tag or BtagV7) has been codon optimized;
neither notation is relevant to the structure of the
polymerase.
The mutations or combinations of mutations shown in FIG. 7 are not
limited to use in a .PHI.29 or M2Y polymerase. Essentially any of
these mutations, any combination of these mutations, and/or any
combination of these mutations with the other mutations disclosed
or referenced herein can be introduced into a polymerase (e.g., a
.PHI.29-type polymerase) to produce a modified recombinant
polymerase in accordance with the invention. Similarly, polymerases
of the invention including the mutations or mutation combinations
provided in FIG. 7 can include any exogenous or heterologous
feature (or combination of such features), e.g., at the N- and/or
C-terminal region. Similarly, some or all of the exogenous features
listed in FIG. 7 can be omitted, or substituted or combined with
any of the other exogenous features described herein, and still
result in a polymerase of the invention. As will be appreciated,
the numbering of amino acid residues is with respect to a
particular reference polymerase, such as the wild-type sequence of
the .PHI.29 polymerase (SEQ ID NO:1) or M2Y polymerase (SEQ ID
NO:2); actual position of a mutation within a molecule of the
invention may vary based upon the nature of the various
modifications that the enzyme includes relative to the wild type
.PHI.29 enzyme, e.g., deletions and/or additions to the molecule,
either at the termini or within the molecule itself.
EXAMPLES
It is understood that the examples and embodiments described herein
are for illustrative purposes only and that various modifications
or changes in light thereof will be suggested to persons skilled in
the art and are to be included within the spirit and purview of
this application and scope of the appended claims. Accordingly, the
following examples are offered to illustrate, but not to limit, the
claimed invention.
Example 1
Characterization of Exemplary Recombinant Polymerases in Single
Molecule Sequencing Reactions
Recombinant polymerases based on .PHI.29 or M2Y polymerase and
including various combinations of mutations were expressed and
purified as described below. The polymerases were characterized by
use in single molecule sequencing. Single molecule sequencing data
was obtained with recombinant .PHI.29 and M2Y polymerases including
the mutation combinations listed in FIG. 7. Exemplary data are
presented in Table 7. Data for each polymerase is presented along
with data for a control polymerase, acquired from the same chip for
comparison. nReads represents the number of ZMWs from which single
molecule sequencing data was obtained. Accuracy and readlength are
determined using data for those reads meeting selected performance
criteria.
TABLE-US-00007 TABLE 7 Single molecule sequencing with the
exemplary recombinant .PHI.29 and M2Y polymerases listed in Tables
3-5. Accu- Con- Con- Control Control Read racy trol trol Read-
Accu- Pol..sup.a nReads length.sup.b (%) Pol..sup.c nReads length
racy 7 2696 1893 85.5 13 3089 1677 84.9 8 1958 1907 83.5 13 1927
1628 83.1 9 2324 2655 81.9 14 2623 2358 81.7 10 1782 1805 82 22
1434 1587 82.1 11 2278 3111 81.7 15 2481 2284 83.1 12 1347 1815
80.4 C1 2701 1207 83.8 13 2570 1744 85 17 2479 1823 83.4 14 1802
2089 83.5 15 4921 1915 83.1 15 2585 1617 83.6 C1 1886 1029 83.8 16
1264 2076 84.5 17 1400 1981 83.7 17 2123 1507 84.9 C1 1715 1145
85.1 18 2134 1289 84.3 C1 2282 1145 84.3 19 3001 1450 84.9 C1 2072
1261 84.8 20 868 976 82.8 C2 2231 908 83.8 21 2540 1470 81.2 C1 972
878 83.3 22 2119 2063 82.7 13 1802 2180 83.5 23 1772 996 82.8 C3
817 870 82.5 24 2330 2020 83 7 1376 2063 83.1 25 2644 1847 83 7
1427 1747 83.7 26 2098 1333 83.4 C1 2080 1197 83.4 .sup.aSEQ ID NO
of exemplary polymerase (see Table 5). .sup.bReadlength in
nucleotides. .sup.cSEQ ID NO of control polymerase (see Table 5).
Additional control polymerases are C1: .PHI.29 BtagV7 His10 Y148I
Y224K E239G V250I L253A E375Y A484E D510K K512Y His10, C2: .PHI.29
BtagV7 His10 L253A E375Y A484E K512Y His10, and C3: M2Y BtagV7
His10 Y145I E236G V247I L250A E372Y A434G A481E D507K K509Y E512Q
His10, where positions are identified relative to SEQ ID NO:1 for
Cl and C2 and relative to SEQ ID NO:2 for C3.
Materials and Methods
Molecular Cloning
The phi29 and M2Y polymerase genes were cloned into either pET16 or
pET11 (Novagen). Primers for specified mutations are designed and
introduced into the gene using the Phusion Hot Start DNA Polymerase
Kit (New England Biolabs). A PCR reaction is performed to
incorporate mutations and product is purified using ZR-96 DNA Clean
and Concentration Kits (Zymo Research). PCR products are digested
with NdeI/BamHI and ligated into the vector. Plasmids are
transformed into TOP10 E. coli competent cells, plated on selective
media and incubated at 37.degree. C. overnight. Colonies are
selected and plasmid is purified using Qiagen miniprep kits.
Plasmids are then sequenced (Sequetech).
Protein Purification
Plasmid containing the recombinant polymerase gene is transformed
into BL21 Star21 CDE3+Biotin Ligase cells (Invitrogen) using heat
shock. Transformed cells are grown in selective media overnight at
37.degree. C. 200 .mu.L of the overnight culture are diluted into 4
mL of Overnight Express Instant TB Medium (EMD Chemicals) and grown
at 37.degree. C. until controls reach O.D. value of 4-6. Cultures
are then incubated at 18.degree. C. for 16 hours. Following this
incubation, cells are harvested, resuspended in buffer, and frozen
at -80.degree. C. Cells are thawed. The resulting lysate is
centrifuged and supernatant is collected. Polymerase is purified
over nickel followed by heparin columns. The resulting proteins are
run on gels and quantified by SYPRO.RTM. staining.
Single Molecule Sequencing
Enzymes are characterized by single molecule sequencing basically
as described in Eid et al. (2009) Science 323:133-138 (including
supplemental information), using reagents similar to those
commercially available in SMRT.TM. sequencing kits (Pacific
Biosciences of California, Inc.). Each enzyme is initially screened
with a single 5-7 minute movie, followed by secondary screening
with 30 minute replicates where applicable. Data presented in Table
7 are from 30 minute movies. Enzymes are evaluated, e.g., based on
readlength and accuracy compared to control enzymes.
While the foregoing invention has been described in some detail for
purposes of clarity and understanding, it will be clear to one
skilled in the art from a reading of this disclosure that various
changes in form and detail can be made without departing from the
true scope of the invention. For example, all the techniques and
apparatus described above can be used in various combinations. All
publications, patents, patent applications, and/or other documents
cited in this application are incorporated by reference in their
entirety for all purposes to the same extent as if each individual
publication, patent, patent application, and/or other document were
individually indicated to be incorporated by reference for all
purposes.
SEQUENCE LISTINGS
1
461575PRTBacteriophage 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
5752572PRTBacteriophage M2Y 2Met 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 5703572PRTBacteriophage B103
3Met 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 5704578PRTBacteriophage GA-1 4Met Ala Arg Ser Val Tyr Val
Cys Asp Phe Glu Thr Thr Thr Asp Pro1 5 10 15Glu Asp Cys Arg Leu Trp
Ala Trp Gly Trp Met Asp Ile Tyr Asn Thr 20 25 30Asp Lys Trp Ser Tyr
Gly Glu Asp Ile Asp Ser Phe Met Glu Trp Ala 35 40 45Leu Asn Ser Asn
Ser Asp Ile Tyr Phe His Asn Leu Lys Phe Asp Gly 50 55 60Ser Phe Ile
Leu Pro Trp Trp Leu Arg Asn Gly Tyr Val His Thr Glu65 70 75 80Glu
Asp Arg Thr Asn Thr Pro Lys Glu Phe Thr Thr Thr Ile Ser Gly 85 90
95Met Gly Gln Trp Tyr Ala Val Asp Val Cys Ile Asn Thr Arg Gly Lys
100 105 110Asn Lys Asn His Val Val Phe Tyr Asp Ser Leu Lys Lys Leu
Pro Phe 115 120 125Lys Val Glu Gln Ile Ala Lys Gly Phe Gly Leu Pro
Val Leu Lys Gly 130 135 140Asp Ile Asp Tyr Lys Lys Tyr Arg Pro Val
Gly Tyr Val Met Asp Asp145 150 155 160Asn Glu Ile Glu Tyr Leu Lys
His Asp Leu Leu Ile Val Ala Leu Ala 165 170 175Leu Arg Ser Met Phe
Asp Asn Asp Phe Thr Ser Met Thr Val Gly Ser 180 185 190Asp Ala Leu
Asn Thr Tyr Lys Glu Met Leu Gly Val Lys Gln Trp Glu 195 200 205Lys
Tyr Phe Pro Val Leu Ser Leu Lys Val Asn Ser Glu Ile Arg Lys 210 215
220Ala Tyr Lys Gly Gly Phe Thr Trp Val Asn Pro Lys Tyr Gln Gly
Glu225 230 235 240Thr Val Tyr Gly Gly Met Val Phe Asp Val Asn Ser
Met Tyr Pro Ala 245 250 255Met Met Lys Asn Lys Leu Leu Pro Tyr Gly
Glu Pro Val Met Phe Lys 260 265 270Gly Glu Tyr Lys Lys Asn Val Glu
Tyr Pro Leu Tyr Ile Gln Gln Val 275 280 285Arg Cys Phe Phe Glu Leu
Lys Lys Asp Lys Ile Pro Cys Ile Gln Ile 290 295 300Lys Gly Asn Ala
Arg Phe Gly Gln Asn Glu Tyr Leu Ser Thr Ser Gly305 310 315 320Asp
Glu Tyr Val Asp Leu Tyr Val Thr Asn Val Asp Trp Glu Leu Ile 325 330
335Lys Lys His Tyr Asp Ile Phe Glu Glu Glu Phe Ile Gly Gly Phe Met
340 345 350Phe Lys Gly Phe Ile Gly Phe Phe Asp Glu Tyr Ile Asp Arg
Phe Met 355 360 365Glu Ile Lys Asn Ser Pro Asp Ser Ser Ala Glu Gln
Ser Leu Gln Ala 370 375 380Lys Leu Met Leu Asn Ser Leu Tyr Gly Lys
Phe Ala Thr Asn Pro Asp385 390 395 400Ile Thr Gly Lys Val Pro Tyr
Leu Asp Glu Asn Gly Val Leu Lys Phe 405 410 415Arg Lys Gly Glu Leu
Lys Glu Arg Asp Pro Val Tyr Thr Pro Met Gly 420 425 430Cys Phe Ile
Thr Ala Tyr Ala Arg Glu Asn Ile Leu Ser Asn Ala Gln 435 440 445Lys
Leu Tyr Pro Arg Phe Ile Tyr Ala Asp Thr Asp Ser Ile His Val 450 455
460Glu Gly Leu Gly Glu Val Asp Ala Ile Lys Asp Val Ile Asp Pro
Lys465 470 475 480Lys Leu Gly Tyr Trp Asp His Glu Ala Thr Phe Gln
Arg Ala Arg Tyr 485 490 495Val Arg Gln Lys Thr Tyr Phe Ile Glu Thr
Thr Trp Lys Glu Asn Asp 500 505 510Lys Gly Lys Leu Val Val Cys Glu
Pro Gln Asp Ala Thr Lys Val Lys 515 520 525Pro Lys Ile Ala Cys Ala
Gly Met Ser Asp Ala Ile Lys Glu Arg Ile 530 535 540Arg Phe Asn Glu
Phe Lys Ile Gly Tyr Ser Thr His Gly Ser Leu Lys545 550 555 560Pro
Lys Asn Val Leu Gly Gly Val Val Leu Met Asp Tyr Pro Phe Ala 565 570
575Ile Lys5566PRTBacteriophage AV-1 5Met Val Arg Gln Ser Thr Ile
Ala Ser Pro Ala Arg Gly Gly Val Arg1 5 10 15Arg Ser His Lys Lys Val
Pro Ser Phe Cys Ala Asp Phe Glu Thr Thr 20 25 30Thr Asp Glu Asp Asp
Cys Arg Val Trp Ser Trp Gly Ile Ile Gln Val 35 40 45Gly Lys Leu Gln
Asn Tyr Val Asp Gly Ile Ser Leu Asp Gly Phe Met 50 55 60Ser His Ile
Ser Glu Arg Ala Ser His Ile Tyr Phe His Asn Leu Ala65 70 75 80Phe
Asp Gly Thr Phe Ile Leu Asp Trp Leu Leu Lys His Gly Tyr Arg 85 90
95Trp Thr Lys Glu Asn Pro Gly Val Lys Glu Phe Thr Ser Leu Ile Ser
100 105 110Arg Met Gly Lys Tyr Tyr Ser Ile Thr Val Val Phe Glu Thr
Gly Phe 115 120 125Arg Val Glu Phe Arg Asp Ser Phe Lys Lys Leu Pro
Met Ser Val Ser 130 135 140Ala Ile Ala Lys Ala Phe Asn Leu His Asp
Gln Lys Leu Glu Ile Asp145 150 155 160Tyr Glu Lys Pro Arg Pro
Ile Gly Tyr Ile Pro Thr Glu Gln Glu Lys 165 170 175Arg Tyr Gln Arg
Asn Asp Val Ala Ile Val Ala Gln Ala Leu Glu Val 180 185 190Gln Phe
Ala Glu Lys Met Thr Lys Leu Thr Ala Gly Ser Asp Ser Leu 195 200
205Ala Thr Tyr Lys Lys Met Thr Gly Lys Leu Phe Ile Arg Arg Phe Pro
210 215 220Ile Leu Ser Pro Glu Ile Asp Thr Glu Ile Arg Lys Ala Tyr
Arg Gly225 230 235 240Gly Phe Thr Tyr Ala Asp Pro Arg Tyr Ala Lys
Lys Leu Asn Gly Lys 245 250 255Gly Ser Val Tyr Asp Val Asn Ser Leu
Tyr Pro Ser Val Met Arg Thr 260 265 270Ala Leu Leu Pro Tyr Gly Glu
Pro Ile Tyr Ser Glu Gly Ala Pro Arg 275 280 285Thr Asn Arg Pro Leu
Tyr Ile Ala Ser Ile Thr Phe Thr Ala Lys Leu 290 295 300Lys Pro Asn
His Ile Pro Cys Ile Gln Ile Lys Lys Asn Leu Ser Phe305 310 315
320Asn Pro Thr Gln Tyr Leu Glu Glu Val Lys Glu Pro Thr Thr Val Val
325 330 335Ala Thr Asn Ile Asp Ile Glu Leu Trp Lys Lys His Tyr Asp
Phe Lys 340 345 350Ile Tyr Ser Trp Asn Gly Thr Phe Glu Phe Arg Gly
Ser His Gly Phe 355 360 365Phe Asp Thr Tyr Val Asp His Phe Met Glu
Ile Lys Lys Asn Ser Thr 370 375 380Gly Gly Leu Arg Gln Ile Ala Lys
Leu His Leu Asn Ser Leu Tyr Gly385 390 395 400Lys Phe Ala Thr Asn
Pro Asp Ile Thr Gly Lys His Pro Thr Leu Lys 405 410 415Asp Asn Arg
Val Ser Leu Val Met Asn Glu Pro Glu Thr Arg Asp Pro 420 425 430Val
Tyr Thr Pro Met Gly Val Phe Ile Thr Ala Tyr Ala Arg Lys Lys 435 440
445Thr Ile Ser Ala Ala Gln Asp Asn Tyr Glu Thr Phe Ala Tyr Ala Asp
450 455 460Thr Asp Ser Leu His Leu Ile Gly Pro Thr Thr Pro Pro Asp
Ser Leu465 470 475 480Trp Val Asp Pro Val Glu Leu Gly Ala Trp Lys
His Glu Ser Ser Phe 485 490 495Thr Lys Ser Val Tyr Ile Arg Ala Lys
Gln Tyr Ala Glu Glu Ile Gly 500 505 510Gly Lys Leu Asp Val His Ile
Ala Gly Met Pro Arg Asn Val Ala Ala 515 520 525Thr Leu Thr Leu Glu
Asp Met Leu His Gly Gly Thr Trp Asn Gly Lys 530 535 540Leu Ile Pro
Val Arg Val Pro Gly Gly Thr Val Leu Lys Asp Thr Thr545 550 555
560Phe Thr Leu Lys Ile Asp 5656568PRTBacteriophage CP-1 6Met Thr
Cys Tyr Tyr Ala Gly Asp Phe Glu Thr Thr Thr Asn Glu Glu1 5 10 15Glu
Thr Glu Val Trp Leu Ser Cys Phe Ala Lys Val Ile Asp Tyr Asp 20 25
30Lys Leu Asp Thr Phe Lys Val Asn Thr Ser Leu Glu Asp Phe Leu Lys
35 40 45Ser Leu Tyr Leu Asp Leu Asp Lys Thr Tyr Thr Glu Thr Gly Glu
Asp 50 55 60Glu Phe Ile Ile Phe Phe His Asn Leu Lys Phe Asp Gly Ser
Phe Leu65 70 75 80Leu Ser Phe Phe Leu Asn Asn Asp Ile Glu Cys Thr
Tyr Phe Ile Asn 85 90 95Asp Met Gly Val Trp Tyr Ser Ile Thr Leu Glu
Phe Pro Asp Phe Thr 100 105 110Leu Thr Phe Arg Asp Ser Leu Lys Ile
Leu Asn Phe Ser Ile Ala Thr 115 120 125Met Ala Gly Leu Phe Lys Met
Pro Ile Ala Lys Gly Thr Thr Pro Leu 130 135 140Leu Lys His Lys Pro
Glu Val Ile Lys Pro Glu Trp Ile Asp Tyr Ile145 150 155 160His Val
Asp Val Ala Ile Leu Ala Arg Gly Ile Phe Ala Met Tyr Tyr 165 170
175Glu Glu Asn Phe Thr Lys Tyr Thr Ser Ala Ser Glu Ala Leu Thr Glu
180 185 190Phe Lys Arg Ile Phe Arg Lys Ser Lys Arg Lys Phe Arg Asp
Phe Phe 195 200 205Pro Ile Leu Asp Glu Lys Val Asp Asp Phe Cys Arg
Lys His Ile Val 210 215 220Gly Ala Gly Arg Leu Pro Thr Leu Lys His
Arg Gly Arg Thr Leu Asn225 230 235 240Gln Leu Ile Asp Ile Tyr Asp
Ile Asn Ser Met Tyr Pro Ala Thr Met 245 250 255Leu Gln Asn Ala Leu
Pro Ile Gly Ile Pro Lys Arg Tyr Lys Gly Lys 260 265 270Pro Lys Glu
Ile Lys Glu Asp His Tyr Tyr Ile Tyr His Ile Lys Ala 275 280 285Asp
Phe Asp Leu Lys Arg Gly Tyr Leu Pro Thr Ile Gln Ile Lys Lys 290 295
300Lys Leu Asp Ala Leu Arg Ile Gly Val Arg Thr Ser Asp Tyr Val
Thr305 310 315 320Thr Ser Lys Asn Glu Val Ile Asp Leu Tyr Leu Thr
Asn Phe Asp Leu 325 330 335Asp Leu Phe Leu Lys His Tyr Asp Ala Thr
Ile Met Tyr Val Glu Thr 340 345 350Leu Glu Phe Gln Thr Glu Ser Asp
Leu Phe Asp Asp Tyr Ile Thr Thr 355 360 365Tyr Arg Tyr Lys Lys Glu
Asn Ala Gln Ser Pro Ala Glu Lys Gln Lys 370 375 380Ala Lys Ile Met
Leu Asn Ser Leu Tyr Gly Lys Phe Gly Ala Lys Ile385 390 395 400Ile
Ser Val Lys Lys Leu Ala Tyr Leu Asp Asp Lys Gly Ile Leu Arg 405 410
415Phe Lys Asn Asp Asp Glu Glu Glu Val Gln Pro Val Tyr Ala Pro Val
420 425 430Ala Leu Phe Val Thr Ser Ile Ala Arg His Phe Ile Ile Ser
Asn Ala 435 440 445Gln Glu Asn Tyr Asp Asn Phe Leu Tyr Ala Asp Thr
Asp Ser Leu His 450 455 460Leu Phe His Ser Asp Ser Leu Val Leu Asp
Ile Asp Pro Ser Glu Phe465 470 475 480Gly Lys Trp Ala His Glu Gly
Arg Ala Val Lys Ala Lys Tyr Leu Arg 485 490 495Ser Lys Leu Tyr Ile
Glu Glu Leu Ile Gln Glu Asp Gly Thr Thr His 500 505 510Leu Asp Val
Lys Gly Ala Gly Met Thr Pro Glu Ile Lys Glu Lys Ile 515 520 525Thr
Phe Glu Asn Phe Val Ile Gly Ala Thr Phe Glu Gly Lys Arg Ala 530 535
540Ser Lys Gln Ile Lys Gly Gly Thr Leu Ile Tyr Glu Thr Thr Phe
Lys545 550 555 560Ile Arg Glu Thr Asp Tyr Leu Val
5657613PRTArtificialmutant recombinant phi29-type DNA polymerase
7Met 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 Glu Lys Ile
Ala Lys Asp Phe Lys Leu Thr Val Leu Lys Gly 130 135 140Asp Ile Asp
Ile 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 Lys 210 215 220Ala Tyr Arg Gly Gly Phe Thr Trp
Leu Asn Asp Arg Phe Lys Gly Lys225 230 235 240Glu Ile Gly Glu Gly
Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Gly 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 Glu 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 Lys Gly Tyr 500 505 510Leu
Val Gln 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 Gly 565 570 575His His His His His His His His His
His Gly Gly Gly Ser Gly Gly 580 585 590Gly Ser Gly Gly Gly Ser Gly
Leu Asn Asp Phe Phe Glu Ala Gln Lys 595 600 605Ile Glu Trp His Glu
6108613PRTArtificialmutant recombinant phi29-type DNA polymerase
8Met 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 Gln Asp Phe Lys Leu Thr Val Leu Lys Gly 130 135 140Asp Ile Asp
Ile 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 Lys 210 215 220Ala Tyr Arg Gly Gly Phe Thr Trp
Leu Asn Asp Arg Phe Lys Gly Lys225 230 235 240Glu Ile Gly Glu Gly
Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Gly 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 Glu 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 Lys Gly Tyr 500 505 510Leu
Val Gln 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 Gly 565 570 575His His His His His His His His His
His Gly Gly Gly Ser Gly Gly 580 585 590Gly Ser Gly Gly Gly Ser Gly
Leu Asn Asp Phe Phe Glu Ala Gln Lys 595 600 605Ile Glu Trp His Glu
6109613PRTArtificialmutant recombinant phi29-type DNA polymerase
9Met 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 Glu Lys Ile
Ala Lys Asp Phe Lys Leu Thr Val Leu Lys Gly 130 135 140Asp Ile Asp
Ile 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 Lys 210 215 220Ala Tyr Arg Gly Gly Phe Thr Trp
Leu Asn Glu Arg Phe Lys Gly Lys225 230 235 240Glu Ile Gly Glu Gly
Met Val Phe Asp Ala Asn Ser His 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 Tyr 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 Gly 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 Glu 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 Lys
Gly Tyr 500 505 510Leu Val Gln 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 Gly 565 570 575His His His
His His His His His His His Gly Gly Gly Ser Gly Gly 580 585 590Gly
Ser Gly Gly Gly Ser Gly Leu Asn Asp Phe Phe Glu Ala Gln Lys 595 600
605Ile Glu Trp His Glu 61010613PRTArtificialmutant recombinant
phi29-type DNA polymerase 10Met 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 Ile 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 Lys 210 215 220Ala Tyr Arg
Gly Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys Gly Lys225 230 235
240Glu Ile Gly Glu Gly Met Val Phe Asp Val Asn Ser Ser 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 Tyr 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 Gly 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 Glu 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 Lys
Gly Tyr 500 505 510Leu Val Gln 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 Gly 565 570 575His His His
His His His His His His His Gly Gly Gly Ser Gly Gly 580 585 590Gly
Ser Gly Gly Gly Ser Gly Leu Asn Asp Phe Phe Glu Ala Gln Lys 595 600
605Ile Glu Trp His Glu 61011613PRTArtificialmutant recombinant
phi29-type DNA polymerase 11Met 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 Ile 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 Phe 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 Glu Arg Phe Lys Gly Lys225 230 235
240Glu Ile Gly Glu Gly Met Val Phe Asp Val Asn Ser His 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 Tyr 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 Gly 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 Glu 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 Lys
Gly Tyr 500 505 510Leu Val Gln 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 Gly 565 570 575His His His
His His His His His His His Gly Gly Gly Ser Gly Gly 580 585 590Gly
Ser Gly Gly Gly Ser Gly Leu Asn Asp Phe Phe Glu Ala Gln Lys 595 600
605Ile Glu Trp His Glu 61012627PRTArtificialmutant recombinant
phi29-type DNA polymerase 12Met Ser Val Asp Gly Leu Asn Asp Phe Phe
Glu Ala Gln Lys Ile Glu1 5 10 15Trp His Glu Ala Met Gly His His His
His His His His His His His 20 25 30Ser Ser Gly His Ile Glu Gly Arg
His Met Lys His Met Pro Arg Lys 35 40 45Met Tyr Ser Cys Asp Phe Glu
Thr Thr Thr Lys Val Glu Asp Cys Arg 50 55 60Val Trp Ala Tyr Gly Tyr
Met Asn Ile Glu Asp His Ser Glu Tyr Lys65 70 75 80Ile Gly Asn Ser
Leu Asp Glu Phe Met Ala Trp Val Leu Lys Val Gln 85 90 95Ala Asp Leu
Tyr Phe His Asn Leu Lys Phe Asp Gly Ala Phe Ile Ile 100 105 110Asn
Trp Leu Glu Arg Asn Gly Phe Lys Trp Ser Ala Asp Gly Leu Pro 115 120
125Asn Thr Tyr Asn Thr Ile Ile Ser Arg Met Gly Gln Trp Tyr Met Ile
130 135 140Asp Ile Cys Leu Gly Tyr Lys Gly Lys Arg Lys Ile His Thr
Val Ile145 150 155 160Tyr Asp Ser Leu Lys Lys Leu Pro Phe Pro Val
Lys Lys Ile Ala Lys 165 170 175Asp Phe Lys Leu Thr Val Leu Lys Gly
Asp Ile Asp Ile His Lys Glu 180 185 190Arg Pro Val Gly Tyr Lys Ile
Thr Pro Glu Glu Tyr Ala Tyr Ile Lys 195 200 205Asn Asp Ile Gln Ile
Ile Ala Glu Ala Leu Leu Ile Gln Phe Lys Gln 210 215 220Gly Leu Asp
Arg Met Thr Ala Gly Ser Asp Ser Leu Lys Gly Phe Lys225 230 235
240Asp Ile Ile Thr Thr Lys Lys Phe Lys Lys Val Phe Pro Thr Leu Ser
245 250 255Leu Gly Leu Asp Lys Glu Val Arg Lys Ala Tyr Arg Gly Gly
Phe Thr 260 265 270Trp Leu Asn Asp Arg Phe Lys Gly Lys Glu Ile Gly
Glu Gly Met Val 275 280 285Phe Asp Ile Asn Ser His Tyr Pro Ala Gln
Met Tyr Ser Arg Leu Leu 290 295 300Pro Tyr Gly Glu Pro Ile Val Phe
Glu Gly Lys Tyr Val Trp Asp Glu305 310 315 320Asp Tyr Pro Leu His
Ile Gln His Ile Arg Cys Glu Phe Glu Leu Lys 325 330 335Glu Gly Tyr
Ile Pro Thr Ile Gln Ile Lys Arg Ser Arg Phe Tyr Lys 340 345 350Gly
Asn Glu Tyr Leu Lys Ser Ser Gly Gly Glu Ile Ala Asp Leu Trp 355 360
365Leu Ser Asn Val Asp Leu Glu Leu Met Lys Glu His Tyr Asp Leu Tyr
370 375 380Asn Val Glu Tyr Ile Ser Gly Leu Lys Phe Lys Ala Thr Thr
Gly Leu385 390 395 400Phe Lys Asp Phe Ile Asp Lys Trp Thr Tyr Ile
Lys Thr Thr Ser Tyr 405 410 415Gly Ala Ile Lys Gln Leu Ala Lys Leu
Met Leu Asn Ser Leu Tyr Gly 420 425 430Lys Phe Ala Ser Asn Pro Asp
Val Thr Gly Lys Val Pro Tyr Leu Lys 435 440 445Glu Asn Gly Ala Leu
Gly Phe Arg Leu Gly Glu Glu Glu Thr Lys Asp 450 455 460Pro Val Tyr
Thr Pro Met Gly Val Phe Ile Thr Ala Trp Gly Arg Tyr465 470 475
480Thr Thr Ile Thr Ala Ala Gln Ala Cys Tyr Asp Arg Ile Ile Tyr Cys
485 490 495Asp Thr Asp Ser Ile His Leu Thr Gly Thr Glu Ile Pro Asp
Val Ile 500 505 510Lys Asp Ile Val Asp Pro Lys Lys Leu Gly Tyr Trp
Glu His Glu Ser 515 520 525Thr Phe Lys Arg Ala Lys Tyr Leu Arg Gln
Lys Thr Tyr Ile Gln Asp 530 535 540Ile Tyr Met Lys Glu Val Lys Gly
Tyr Leu Val Glu Gly Ser Pro Asp545 550 555 560Asp Tyr Thr Asp Ile
Lys Phe Ser Val Lys Cys Ala Gly Met Thr Asp 565 570 575Lys Ile Lys
Lys Glu Val Thr Phe Glu Asn Phe Lys Val Gly Phe Ser 580 585 590Arg
Lys Met Lys Pro Lys Pro Val Gln Val Pro Gly Gly Val Val Leu 595 600
605Val Asp Asp Thr Phe Thr Ile Lys Gly His His His His His His His
610 615 620His His His62513613PRTArtificialmutant recombinant
phi29-type DNA polymerase 13Met 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 Ile 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 Lys 210 215 220Ala Tyr Arg
Gly Gly
Phe Thr Trp Leu Asn Asp Arg Phe Lys Gly Lys225 230 235 240Glu Ile
Gly Glu Gly Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Gly 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 Glu 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 Lys Gly Tyr
500 505 510Leu Val Gln 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 Gly 565 570 575His His His His His
His His His His His Gly Gly Gly Ser Gly Gly 580 585 590Gly Ser Gly
Gly Gly Ser Gly Leu Asn Asp Phe Phe Glu Ala Gln Lys 595 600 605Ile
Glu Trp His Glu 61014613PRTArtificialmutant recombinant phi29-type
DNA polymerase 14Met 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 Glu Lys Ile Ala Lys Asp Phe Lys Leu Thr Val Leu Lys Gly 130 135
140Asp Ile Asp Ile 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 Lys 210 215 220Ala Tyr Arg Gly
Gly Phe Thr Trp Leu Asn Glu Arg Phe Lys Gly Lys225 230 235 240Glu
Ile Gly Glu Gly Met Val Phe Asp Val Asn Ser His 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 Tyr 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 Gly 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 Glu 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 Lys Gly Tyr
500 505 510Leu Val Gln 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 Gly 565 570 575His His His His His
His His His His His Gly Gly Gly Ser Gly Gly 580 585 590Gly Ser Gly
Gly Gly Ser Gly Leu Asn Asp Phe Phe Glu Ala Gln Lys 595 600 605Ile
Glu Trp His Glu 61015613PRTArtificialmutant recombinant phi29-type
DNA polymerase 15Met 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 Ile 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 Lys 210 215 220Ala Tyr Arg Gly
Gly Phe Thr Trp Leu Asn Glu Arg Phe Lys Gly Lys225 230 235 240Glu
Ile Gly Glu Gly Met Val Phe Asp Val Asn Ser His 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 Tyr 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 Gly 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 Glu 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 Lys Gly Tyr
500 505 510Leu Val Gln 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 Gly 565 570 575His His His His His
His His His His His Gly Gly Gly Ser Gly Gly 580 585 590Gly Ser Gly
Gly Gly Ser Gly Leu Asn Asp Phe Phe Glu Ala Gln Lys 595 600 605Ile
Glu Trp His Glu 61016613PRTArtificialmutant recombinant phi29-type
DNA polymerase 16Met 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 Ile 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 Lys 210 215 220Ala Tyr Arg Gly
Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys Gly Lys225 230 235 240Glu
Ile Gly Glu Gly Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Gly 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 Glu 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 Lys Gly Tyr
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 Gly 565 570 575His His His His His
His His His His His Gly Gly Gly Ser Gly Gly 580 585 590Gly Ser Gly
Gly Gly Ser Gly Leu Asn Asp Phe Phe Glu Ala Gln Lys 595 600 605Ile
Glu Trp His Glu 61017627PRTArtificialmutant recombinant phi29-type
DNA polymerase 17Met Ser Val Asp Gly Leu Asn Asp Phe Phe Glu Ala
Gln Lys Ile Glu1 5 10 15Trp His Glu Ala Met Gly His His His His His
His His His His His 20 25 30Ser Ser Gly His Ile Glu Gly Arg His Met
Lys His Met Pro Arg Lys 35 40 45Met Tyr Ser Cys Asp Phe Glu Thr Thr
Thr Lys Val Glu Asp Cys Arg 50 55 60Val Trp Ala Tyr Gly Tyr Met Asn
Ile Glu Asp His Ser Glu Tyr Lys65 70 75 80Ile Gly Asn Ser Leu Asp
Glu Phe Met Ala Trp Val Leu Lys Val Gln 85 90 95Ala Asp Leu Tyr Phe
His Asn Leu Lys Phe Asp Gly Ala Phe Ile Ile 100 105 110Asn Trp Leu
Glu Arg Asn Gly Phe Lys Trp Ser Ala Asp Gly Leu Pro 115 120 125Asn
Thr Tyr Asn Thr Ile Ile Ser Arg Met Gly Gln Trp Tyr Met Ile 130 135
140Asp Ile Cys Leu Gly Tyr Lys Gly Lys Arg Lys Ile His Thr Val
Ile145 150 155 160Tyr Asp Ser Leu Lys Lys Leu Pro Phe Pro Val Lys
Lys Ile Ala Lys 165 170 175Asp Phe Lys Leu Thr Val Leu Lys Gly Asp
Ile Asp Ile His Lys Glu 180 185 190Arg Pro Val Gly Tyr Lys Ile Thr
Pro Glu Glu Tyr Ala Tyr Ile Lys 195 200 205Asn Asp Ile Gln Ile Ile
Ala Glu Ala Leu Leu Ile Gln Phe
Lys Gln 210 215 220Gly Leu Asp Arg Met Thr Ala Gly Ser Asp Ser Leu
Lys Gly Phe Lys225 230 235 240Asp Ile Ile Thr Thr Lys Lys Phe Lys
Lys Val Phe Pro Thr Leu Ser 245 250 255Leu Gly Leu Asp Lys Glu Val
Arg Lys Ala Tyr Arg Gly Gly Phe Thr 260 265 270Trp Leu Asn Asp Arg
Phe Lys Gly Lys Glu Ile Gly Glu Gly Met Val 275 280 285Phe Asp Ile
Asn Ser Ala Tyr Pro Ala Gln Met Tyr Ser Arg Leu Leu 290 295 300Pro
Tyr Gly Glu Pro Ile Val Phe Glu Gly Lys Tyr Val Trp Asp Glu305 310
315 320Asp Tyr Pro Leu His Ile Gln His Ile Arg Cys Glu Phe Glu Leu
Lys 325 330 335Glu Gly Tyr Ile Pro Thr Ile Gln Ile Lys Arg Ser Arg
Phe Tyr Lys 340 345 350Gly Asn Glu Tyr Leu Lys Ser Ser Gly Gly Glu
Ile Ala Asp Leu Trp 355 360 365Leu Ser Asn Val Asp Leu Glu Leu Met
Lys Glu His Tyr Asp Leu Tyr 370 375 380Asn Val Glu Tyr Ile Ser Gly
Leu Lys Phe Lys Ala Thr Thr Gly Leu385 390 395 400Phe Lys Asp Phe
Ile Asp Lys Trp Thr Tyr Ile Lys Thr Thr Ser Tyr 405 410 415Gly Ala
Ile Lys Gln Leu Ala Lys Leu Met Leu Asn Ser Leu Tyr Gly 420 425
430Lys Phe Ala Ser Asn Pro Asp Val Thr Gly Lys Val Pro Tyr Leu Lys
435 440 445Glu Asn Gly Ala Leu Gly Phe Arg Leu Gly Glu Glu Glu Thr
Lys Asp 450 455 460Pro Val Tyr Thr Pro Met Gly Val Phe Ile Thr Ala
Trp Gly Arg Tyr465 470 475 480Thr Thr Ile Thr Ala Ala Gln Ala Cys
Tyr Asp Arg Ile Ile Tyr Cys 485 490 495Asp Thr Asp Ser Ile His Leu
Thr Gly Thr Glu Ile Pro Asp Val Ile 500 505 510Lys Asp Ile Val Asp
Pro Lys Lys Leu Gly Tyr Trp Glu His Glu Ser 515 520 525Thr Phe Lys
Arg Ala Lys Tyr Leu Arg Gln Lys Thr Tyr Ile Gln Asp 530 535 540Ile
Tyr Met Lys Glu Val Lys Gly Tyr Leu Val Glu Gly Ser Pro Asp545 550
555 560Asp Tyr Thr Asp Ile Lys Phe Ser Val Lys Cys Ala Gly Met Thr
Asp 565 570 575Lys Ile Lys Lys Glu Val Thr Phe Glu Asn Phe Lys Val
Gly Phe Ser 580 585 590Arg Lys Met Lys Pro Lys Pro Val Gln Val Pro
Gly Gly Val Val Leu 595 600 605Val Asp Asp Thr Phe Thr Ile Lys Gly
His His His His His His His 610 615 620His His
His62518627PRTArtificialmutant recombinant phi29-type DNA
polymerase 18Met Ser Val Asp Gly Leu Asn Asp Phe Phe Glu Ala Gln
Lys Ile Glu1 5 10 15Trp His Glu Ala Met Gly His His His His His His
His His His His 20 25 30Ser Ser Gly His Ile Glu Gly Arg His Met Lys
His Met Pro Arg Lys 35 40 45Met Tyr Ser Cys Asp Phe Glu Thr Thr Thr
Lys Val Glu Asp Cys Arg 50 55 60Val Trp Ala Tyr Gly Tyr Met Asn Ile
Glu Asp His Ser Glu Tyr Lys65 70 75 80Ile Gly Asn Ser Leu Asp Glu
Phe Met Ala Trp Val Leu Lys Val Gln 85 90 95Ala Asp Leu Tyr Phe His
Asn Leu Lys Phe Asp Gly Ala Phe Ile Ile 100 105 110Asn Trp Leu Glu
Arg Asn Gly Phe Lys Trp Ser Ala Asp Gly Leu Pro 115 120 125Asn Thr
Tyr Asn Thr Ile Ile Ser Arg Met Gly Gln Trp Tyr Met Ile 130 135
140Asp Ile Cys Leu Gly Tyr Lys Gly Lys Arg Lys Ile His Thr Val
Ile145 150 155 160Tyr Asp Ser Leu Lys Lys Leu Pro Phe Pro Val Glu
Lys Ile Ala Lys 165 170 175Asp Phe Lys Leu Thr Val Leu Lys Gly Asp
Ile Asp Ile His Lys Glu 180 185 190Arg Pro Val Gly Tyr Lys Ile Thr
Pro Glu Glu Tyr Ala Tyr Ile Lys 195 200 205Asn Asp Ile Gln Ile Ile
Ala Glu Ala Leu Leu Ile Gln Phe Lys Gln 210 215 220Gly Leu Asp Arg
Met Thr Ala Gly Ser Asp Ser Leu Lys Gly Phe Lys225 230 235 240Asp
Ile Ile Thr Thr Lys Lys Phe Lys Lys Val Phe Pro Thr Leu Ser 245 250
255Leu Gly Leu Asp Lys Glu Val Arg Lys Ala Tyr Arg Gly Gly Phe Thr
260 265 270Trp Leu Asn Asp Arg Phe Lys Gly Lys Glu Ile Gly Glu Gly
Met Val 275 280 285Phe Asp Ile Asn Ser Ala Tyr Pro Ala Gln Met Tyr
Ser Arg Leu Leu 290 295 300Pro Tyr Gly Glu Pro Ile Val Phe Glu Gly
Lys Tyr Val Trp Asp Glu305 310 315 320Asp Tyr Pro Leu His Ile Gln
His Ile Arg Cys Glu Phe Glu Leu Lys 325 330 335Glu Gly Tyr Ile Pro
Thr Ile Gln Ile Lys Arg Ser Arg Phe Tyr Lys 340 345 350Gly Asn Glu
Tyr Leu Lys Ser Ser Gly Gly Glu Ile Ala Asp Leu Trp 355 360 365Leu
Ser Asn Val Asp Leu Glu Leu Met Lys Glu His Tyr Asp Leu Tyr 370 375
380Asn Val Glu Tyr Ile Ser Gly Leu Lys Phe Lys Ala Thr Thr Gly
Leu385 390 395 400Phe Lys Asp Phe Ile Asp Lys Trp Thr Tyr Ile Lys
Thr Thr Ser Tyr 405 410 415Gly Ala Ile Lys Gln Leu Ala Lys Leu Met
Leu Asn Ser Leu Tyr Gly 420 425 430Lys Phe Ala Ser Asn Pro Asp Val
Thr Gly Lys Val Pro Tyr Leu Lys 435 440 445Glu Asn Gly Ala Leu Gly
Phe Arg Leu Gly Glu Glu Glu Thr Lys Asp 450 455 460Pro Val Tyr Thr
Pro Met Gly Val Phe Ile Thr Ala Trp Ala Arg Tyr465 470 475 480Thr
Thr Ile Thr Ala Ala Gln Ala Cys Tyr Asp Arg Ile Ile Tyr Cys 485 490
495Asp Thr Asp Ser Ile His Leu Thr Gly Thr Glu Ile Pro Asp Val Ile
500 505 510Lys Asp Ile Val Asp Pro Lys Lys Leu Gly Tyr Trp Glu His
Glu Ser 515 520 525Thr Phe Lys Arg Ala Lys Tyr Leu Arg Gln Lys Thr
Tyr Ile Gln Asp 530 535 540Ile Tyr Met Lys Glu Val Lys Gly Tyr Leu
Val Glu Gly Ser Pro Asp545 550 555 560Asp Tyr Thr Asp Ile Lys Phe
Ser Val Lys Cys Ala Gly Met Thr Asp 565 570 575Lys Ile Lys Lys Glu
Val Thr Phe Glu Asn Phe Lys Val Gly Phe Ser 580 585 590Arg Lys Met
Lys Pro Lys Pro Val Gln Val Pro Gly Gly Val Val Leu 595 600 605Val
Asp Asp Thr Phe Thr Ile Lys Gly His His His His His His His 610 615
620His His His62519627PRTArtificialmutant recombinant phi29-type
DNA polymerase 19Met Ser Val Asp Gly Leu Asn Asp Phe Phe Glu Ala
Gln Lys Ile Glu1 5 10 15Trp His Glu Ala Met Gly His His His His His
His His His His His 20 25 30Ser Ser Gly His Ile Glu Gly Arg His Met
Lys His Met Pro Arg Lys 35 40 45Met Tyr Ser Cys Asp Phe Glu Thr Thr
Thr Lys Val Glu Asp Cys Arg 50 55 60Val Trp Ala Tyr Gly Tyr Met Asn
Ile Glu Asp His Ser Glu Tyr Lys65 70 75 80Ile Gly Asn Ser Leu Asp
Glu Phe Met Ala Trp Val Leu Lys Val Gln 85 90 95Ala Asp Leu Tyr Phe
His Asn Leu Lys Phe Asp Gly Ala Phe Ile Ile 100 105 110Asn Trp Leu
Glu Arg Asn Gly Phe Lys Trp Ser Ala Asp Gly Leu Pro 115 120 125Asn
Thr Tyr Asn Thr Ile Ile Ser Arg Met Gly Gln Trp Tyr Met Ile 130 135
140Asp Ile Cys Leu Gly Tyr Lys Gly Lys Arg Lys Ile His Thr Val
Ile145 150 155 160Tyr Asp Ser Leu Lys Lys Leu Pro Phe Pro Val Lys
Lys Ile Ala Gln 165 170 175Asp Phe Lys Leu Thr Val Leu Lys Gly Asp
Ile Asp Ile His Lys Glu 180 185 190Arg Pro Val Gly Tyr Lys Ile Thr
Pro Glu Glu Tyr Ala Tyr Ile Lys 195 200 205Asn Asp Ile Gln Ile Ile
Ala Glu Ala Leu Leu Ile Gln Phe Lys Gln 210 215 220Gly Leu Asp Arg
Met Thr Ala Gly Ser Asp Ser Leu Lys Gly Phe Lys225 230 235 240Asp
Ile Ile Thr Thr Lys Lys Phe Lys Lys Val Phe Pro Thr Leu Ser 245 250
255Leu Gly Leu Asp Lys Glu Val Arg Lys Ala Tyr Arg Gly Gly Phe Thr
260 265 270Trp Leu Asn Asp Arg Phe Lys Gly Lys Glu Ile Gly Glu Gly
Met Val 275 280 285Phe Asp Ile Asn Ser Ala Tyr Pro Ala Gln Met Tyr
Ser Arg Leu Leu 290 295 300Pro Tyr Gly Glu Pro Ile Val Phe Glu Gly
Lys Tyr Val Trp Asp Glu305 310 315 320Asp Tyr Pro Leu His Ile Gln
His Ile Arg Cys Glu Phe Glu Leu Lys 325 330 335Glu Gly Tyr Ile Pro
Thr Ile Gln Ile Lys Arg Ser Arg Phe Tyr Lys 340 345 350Gly Asn Glu
Tyr Leu Lys Ser Ser Gly Gly Glu Ile Ala Asp Leu Trp 355 360 365Leu
Ser Asn Val Asp Leu Glu Leu Met Lys Glu His Tyr Asp Leu Tyr 370 375
380Asn Val Glu Tyr Ile Ser Gly Leu Lys Phe Lys Ala Thr Thr Gly
Leu385 390 395 400Phe Lys Asp Phe Ile Asp Lys Trp Thr Tyr Ile Lys
Thr Thr Ser Tyr 405 410 415Gly Ala Ile Lys Gln Leu Ala Lys Leu Met
Leu Asn Ser Leu Tyr Gly 420 425 430Lys Phe Ala Ser Asn Pro Asp Val
Thr Gly Lys Val Pro Tyr Leu Lys 435 440 445Glu Asn Gly Ala Leu Gly
Phe Arg Leu Gly Glu Glu Glu Thr Lys Asp 450 455 460Pro Val Tyr Thr
Pro Met Gly Val Phe Ile Thr Ala Trp Ala Arg Tyr465 470 475 480Thr
Thr Ile Thr Ala Ala Gln Ala Cys Tyr Asp Arg Ile Ile Tyr Cys 485 490
495Asp Thr Asp Ser Ile His Leu Thr Gly Thr Glu Ile Pro Asp Val Ile
500 505 510Lys Asp Ile Val Asp Pro Lys Lys Leu Gly Tyr Trp Glu His
Glu Ser 515 520 525Thr Phe Lys Arg Ala Lys Tyr Leu Arg Gln Lys Thr
Tyr Ile Gln Asp 530 535 540Ile Tyr Met Lys Glu Val Lys Gly Tyr Leu
Val Glu Gly Ser Pro Asp545 550 555 560Asp Tyr Thr Asp Ile Lys Phe
Ser Val Lys Cys Ala Gly Met Thr Asp 565 570 575Lys Ile Lys Lys Glu
Val Thr Phe Glu Asn Phe Lys Val Gly Phe Ser 580 585 590Arg Lys Met
Lys Pro Lys Pro Val Gln Val Pro Gly Gly Val Val Leu 595 600 605Val
Asp Asp Thr Phe Thr Ile Lys Gly His His His His His His His 610 615
620His His His62520624PRTArtificialmutant recombinant phi29-type
DNA polymerase 20Met Ser Val Asp Gly Leu Asn Asp Phe Phe Glu Ala
Gln Lys Ile Glu1 5 10 15Trp His Glu Ala Met Gly His His His His His
His His His His His 20 25 30Ser Ser Gly His Ile Glu Gly Arg His Met
Ser Arg Lys Met Phe Ser 35 40 45Cys Asp Phe Glu Thr Thr Thr Lys Leu
Asp Asp Cys Arg Val Trp Ala 50 55 60Tyr Gly Tyr Met Glu Ile Gly Asn
Leu Asp Asn Tyr Lys Ile Gly Asn65 70 75 80Ser Leu Asp Glu Phe Met
Gln Trp Val Met Glu Ile Gln Ala Asp Leu 85 90 95Tyr Phe His Asn Leu
Lys Phe Asp Gly Ala Phe Ile Val Asn Trp Leu 100 105 110Glu Gln His
Gly Phe Lys Trp Ser Asn Glu Gly Leu Pro Asn Thr Tyr 115 120 125Asn
Thr Ile Ile Ser Lys Met Gly Gln Trp Tyr Met Ile Asp Ile Cys 130 135
140Phe Gly Tyr Lys Gly Lys Arg Lys Leu His Thr Val Ile Tyr Asp
Ser145 150 155 160Leu Lys Lys Leu Pro Phe Pro Val Lys Lys Ile Ala
Lys Asp Phe Gln 165 170 175Leu Pro Leu Leu Lys Gly Asp Ile Asp Tyr
His Thr Glu Arg Pro Val 180 185 190Gly His Glu Ile Thr Pro Glu Glu
Tyr Glu Tyr Ile Lys Asn Asp Ile 195 200 205Glu Ile Ile Ala Arg Ala
Leu Asp Ile Gln Phe Lys Gln Gly Leu Asp 210 215 220Arg Met Thr Ala
Gly Ser Asp Ser Leu Lys Gly Phe Lys Asp Ile Leu225 230 235 240Ser
Thr Lys Lys Phe Asn Lys Val Phe Pro Lys Leu Ser Leu Pro Met 245 250
255Asp Lys Glu Ile Arg Lys Ala Tyr Arg Gly Gly Phe Thr Trp Leu Asn
260 265 270Asp Lys Tyr Lys Glu Lys Glu Ile Gly Glu Gly Met Val Phe
Asp Val 275 280 285Asn Ser Ala Tyr Pro Ala Gln Met Tyr Ser Arg Pro
Leu Pro Tyr Gly 290 295 300Ala Pro Ile Val Phe Gln Gly Lys Tyr Glu
Lys Asp Glu Gln Tyr Pro305 310 315 320Leu Tyr Ile Gln Arg Ile Arg
Phe Glu Phe Glu Leu Lys Glu Gly Tyr 325 330 335Ile Pro Thr Ile Gln
Ile Lys Lys Asn Pro Phe Phe Lys Gly Asn Glu 340 345 350Tyr Leu Lys
Asn Ser Gly Val Glu Pro Val Glu Leu Tyr Leu Thr Asn 355 360 365Val
Asp Leu Glu Leu Ile Gln Glu His Tyr Glu Leu Tyr Asn Val Glu 370 375
380Tyr Ile Asp Gly Phe Lys Phe Arg Glu Lys Thr Gly Leu Phe Lys
Asp385 390 395 400Phe Ile Asp Lys Trp Thr Tyr Val Lys Thr His Glu
Tyr Gly Ala Lys 405 410 415Lys Gln Leu Ala Lys Leu Met Leu Asn Ser
Leu Tyr Gly Lys Phe Ala 420 425 430Ser Asn Pro Asp Val Thr Gly Lys
Val Pro Tyr Leu Lys Asp Asp Gly 435 440 445Ser Leu Gly Phe Arg Val
Gly Asp Glu Glu Tyr Lys Asp Pro Val Tyr 450 455 460Thr Pro Met Gly
Val Phe Ile Thr Ala Trp Ala Arg Phe Thr Thr Ile465 470 475 480Thr
Ala Ala Gln Ala Cys Tyr Asp Arg Ile Ile Tyr Cys Asp Thr Asp 485 490
495Ser Ile His Leu Thr Gly Thr Glu Val Pro Glu Ile Ile Lys Asp Ile
500 505 510Val Asp Pro Lys Lys Leu Gly Tyr Trp Glu His Glu Ser Thr
Phe Lys 515 520 525Arg Ala Lys Tyr Leu Arg Gln Lys Thr Tyr Ile Gln
Asp Ile Tyr Val 530 535 540Lys Glu Val Asp Gly Tyr Leu Lys Glu Cys
Ser Pro Asp Glu Ala Thr545 550 555 560Thr Thr Lys Phe Ser Val Lys
Cys Ala Gly Met Thr Asp Thr Ile Lys 565 570 575Lys Lys Val Thr Phe
Asp Asn Phe Ala Val Gly Phe Ser Ser Met Gly 580 585 590Lys Pro Lys
Pro Val Gln Val Asn Gly Gly Val Val Leu Val Asp Ser 595 600 605Val
Phe Thr Ile Lys Gly His His His His His His His His His His 610 615
62021627PRTArtificialmutant recombinant phi29-type DNA polymerase
21Met Ser Val Asp Gly Leu Asn Asp Phe Phe Glu Ala Gln Lys Ile Glu1
5 10 15Trp His Glu Ala Met Gly His His His His His His His His His
His 20 25 30Ser Ser Gly His Ile Glu Gly Arg His Met Lys His Met Pro
Arg Lys 35 40 45Met Tyr Ser Cys Asp Phe Glu Thr Thr Thr Lys Val Glu
Asp Cys Arg 50 55 60Val Trp Ala Tyr Gly Tyr Met Asn Ile Glu Asp His
Ser Glu Tyr Lys65 70 75 80Ile Gly Asn Ser Leu Asp Glu Phe Met Ala
Trp Val Leu Lys Val Gln 85 90 95Ala Asp Leu Tyr Phe His Asn Leu Lys
Phe Asp Gly Ala Phe Ile Ile 100 105 110Asn Trp Leu Glu Arg Asn Gly
Phe Lys Trp Ser Ala Asp Gly Leu Pro 115 120 125Asn Thr Tyr Asn Thr
Ile Ile Ser Arg Met Gly Gln Trp Tyr Met Ile 130 135 140Asp Ile Cys
Leu Gly Tyr Lys Gly Lys Arg Lys Ile His Thr Val Ile145 150
155 160Tyr Asp Ser Leu Lys Lys Leu Pro Phe Pro Val Lys Lys Ile Ala
Lys 165 170 175Asp Phe Lys Leu Thr Val Leu Lys Gly Asp Ile Asp Ile
His Lys Glu 180 185 190Arg Pro Val Gly Tyr Lys Ile Thr Pro Glu Glu
Tyr Ala Tyr Ile Lys 195 200 205Asn Asp Ile Gln Ile Ile Ala Glu Ala
Leu Leu Ile Gln Phe Lys Gln 210 215 220Gly Leu Asp Arg Met Thr Ala
Gly Ser Asp Ser Leu Lys Gly Phe Lys225 230 235 240Asp Ile Ile Thr
Thr Lys Lys Phe Lys Lys Val Phe Pro Thr Leu Ser 245 250 255Leu Gly
Leu Asp Lys Glu Val Arg Lys Ala Tyr Arg Gly Gly Phe Thr 260 265
270Trp Leu Asn Asp Arg Phe Lys Gly Lys Glu Ile Gly Glu Gly Met Val
275 280 285Phe Asp Val Asn Ser His Tyr Pro Ala Gln Met Tyr Ser Arg
Leu Leu 290 295 300Pro Tyr Gly Glu Pro Ile Val Phe Glu Gly Lys Tyr
Val Trp Asp Glu305 310 315 320Asp Tyr Pro Leu His Ile Gln His Ile
Arg Cys Glu Phe Glu Leu Lys 325 330 335Glu Gly Tyr Ile Pro Thr Ile
Gln Ile Lys Arg Ser Arg Phe Tyr Lys 340 345 350Gly Asn Glu Tyr Leu
Lys Ser Ser Gly Gly Glu Ile Ala Asp Leu Trp 355 360 365Leu Ser Asn
Val Asp Leu Glu Leu Met Lys Glu His Tyr Asp Leu Tyr 370 375 380Asn
Val Glu Tyr Ile Ser Gly Leu Lys Phe Lys Ala Thr Thr Gly Leu385 390
395 400Phe Lys Asp Phe Ile Asp Lys Trp Thr Tyr Ile Lys Thr Thr Ser
Tyr 405 410 415Gly Ala Ile Lys Gln Leu Ala Lys Leu Met Leu Asn Ser
Leu Tyr Gly 420 425 430Lys Phe Ala Ser Asn Pro Asp Val Thr Gly Lys
Val Pro Tyr Leu Lys 435 440 445Glu Asn Gly Ala Leu Gly Phe Arg Leu
Gly Glu Glu Glu Thr Lys Asp 450 455 460Pro Val Tyr Thr Pro Met Gly
Val Phe Ile Thr Ala Trp Gly Arg Tyr465 470 475 480Thr Thr Ile Thr
Ala Ala Gln Ala Cys Tyr Asp Arg Ile Ile Tyr Cys 485 490 495Asp Thr
Asp Ser Ile His Leu Thr Gly Thr Glu Ile Pro Asp Val Ile 500 505
510Lys Asp Ile Val Asp Pro Lys Lys Leu Gly Tyr Trp Glu His Glu Ser
515 520 525Thr Phe Lys Arg Ala Lys Tyr Leu Arg Gln Lys Thr Tyr Ile
Gln Asp 530 535 540Ile Tyr Met Lys Glu Val Lys Gly Tyr Leu Val Glu
Gly Ser Pro Asp545 550 555 560Asp Tyr Thr Asp Ile Lys Phe Ser Val
Lys Cys Ala Gly Met Thr Asp 565 570 575Lys Ile Lys Lys Glu Val Thr
Phe Glu Asn Phe Lys Val Gly Phe Ser 580 585 590Arg Lys Met Lys Pro
Lys Pro Val Gln Val Pro Gly Gly Val Val Leu 595 600 605Val Asp Asp
Thr Phe Thr Ile Lys Gly His His His His His His His 610 615 620His
His His62522610PRTArtificialmutant recombinant phi29-type DNA
polymerase 22Met 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
140Ile 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 Gly Lys Glu Ile Gly225 230 235 240Glu
Gly Met Val Phe Asp Ile Asn Ser Ala Tyr Pro Ala 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 Tyr 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 Gly 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 480Glu
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 Lys Gly Tyr Leu Lys Gln
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 Gly His His His 565 570 575His His His His His
His His Gly Gly Gly Ser Gly Gly Gly Ser Gly 580 585 590Gly Gly Ser
Gly Leu Asn Asp Phe Phe Glu Ala Gln Lys Ile Glu Trp 595 600 605His
Glu 61023624PRTArtificialmutant recombinant phi29-type DNA
polymerase 23Met Ser Val Asp Gly Leu Asn Asp Phe Phe Glu Ala Gln
Lys Ile Glu1 5 10 15Trp His Glu Ala Met Gly His His His His His His
His His His His 20 25 30Ser Ser Gly His Ile Glu Gly Arg His Met Ser
Arg Lys Met Phe Ser 35 40 45Cys Asp Phe Glu Thr Thr Thr Lys Leu Asp
Asp Cys Arg Val Trp Ala 50 55 60Tyr Gly Tyr Met Glu Ile Gly Asn Leu
Asp Asn Tyr Lys Ile Gly Asn65 70 75 80Ser Leu Asp Glu Phe Met Gln
Trp Val Met Glu Ile Gln Ala Asp Leu 85 90 95Tyr Phe His Asn Leu Lys
Phe Asp Gly Ala Phe Ile Val Asn Trp Leu 100 105 110Glu Gln His Gly
Phe Lys Trp Ser Asn Glu Gly Leu Pro Asn Thr Tyr 115 120 125Asn Thr
Ile Ile Ser Lys Met Gly Gln Trp Tyr Met Ile Asp Ile Cys 130 135
140Phe Gly Tyr Lys Gly Lys Arg Lys Leu His Thr Val Ile Tyr Asp
Ser145 150 155 160Leu Lys Lys Leu Pro Phe Pro Val Lys Lys Ile Ala
Gln Asp Phe Gln 165 170 175Leu Pro Leu Leu Lys Gly Asp Ile Asp Ile
His Thr Glu Arg Pro Val 180 185 190Gly His Glu Ile Thr Pro Glu Glu
Tyr Glu Tyr Ile Lys Asn Asp Ile 195 200 205Glu Ile Ile Ala Arg Ala
Leu Asp Ile Gln Phe Lys Gln Gly Leu Asp 210 215 220Arg Met Thr Ala
Gly Ser Asp Ser Leu Lys Gly Phe Lys Asp Ile Leu225 230 235 240Ser
Thr Lys Lys Phe Asn Lys Val Phe Pro Lys Leu Ser Leu Pro Met 245 250
255Asp Lys Glu Ile Arg Lys Ala Tyr Arg Gly Gly Phe Thr Trp Leu Asn
260 265 270Asp Lys Tyr Lys Gly Lys Glu Ile Gly Glu Gly Met Val Phe
Asp Ile 275 280 285Asn Ser Ala Tyr Pro Ser Gln Met Tyr Ser Arg Pro
Leu Pro Tyr Gly 290 295 300Ala Pro Ile Val Phe Gln Gly Lys Tyr Glu
Lys Asp Glu Gln Tyr Pro305 310 315 320Leu Tyr Ile Gln Arg Ile Arg
Phe Glu Phe Glu Leu Lys Glu Gly Tyr 325 330 335Ile Pro Thr Ile Gln
Ile Lys Lys Asn Pro Phe Phe Lys Gly Asn Glu 340 345 350Tyr Leu Lys
Asn Ser Gly Val Glu Pro Val Glu Leu Tyr Leu Thr Asn 355 360 365Val
Asp Leu Glu Leu Ile Gln Glu His Tyr Glu Leu Tyr Asn Val Glu 370 375
380Tyr Ile Asp Gly Phe Lys Phe Arg Glu Lys Thr Gly Leu Phe Lys
Asp385 390 395 400Phe Ile Asp Lys Trp Thr Tyr Val Lys Thr His Glu
Tyr Gly Ala Lys 405 410 415Lys Gln Leu Ala Lys Leu Met Leu Asn Ser
Leu Tyr Gly Lys Phe Ala 420 425 430Ser Asn Pro Asp Val Thr Gly Lys
Val Pro Tyr Leu Lys Asp Asp Gly 435 440 445Ser Leu Gly Phe Arg Val
Gly Asp Glu Glu Tyr Lys Asp Pro Val Tyr 450 455 460Thr Pro Met Gly
Val Phe Ile Thr Ala Trp Gly Arg Phe Thr Thr Ile465 470 475 480Thr
Ala Ala Gln Ala Cys Tyr Asp Arg Ile Ile Tyr Cys Asp Thr Asp 485 490
495Ser Ile His Leu Thr Gly Thr Glu Val Pro Glu Ile Ile Lys Asp Ile
500 505 510Val Asp Pro Lys Lys Leu Gly Tyr Trp Glu His Glu Ser Thr
Phe Lys 515 520 525Arg Ala Lys Tyr Leu Arg Gln Lys Thr Tyr Ile Gln
Asp Ile Tyr Val 530 535 540Lys Glu Val Lys Gly Tyr Leu Lys Gln Cys
Ser Pro Asp Glu Ala Thr545 550 555 560Thr Thr Lys Phe Ser Val Lys
Cys Ala Gly Met Thr Asp Thr Ile Lys 565 570 575Lys Lys Val Thr Phe
Asp Asn Phe Ala Val Gly Phe Ser Ser Met Gly 580 585 590Lys Pro Lys
Pro Val Gln Val Asn Gly Gly Val Val Leu Val Asp Ser 595 600 605Val
Phe Thr Ile Lys Gly His His His His His His His His His His 610 615
62024613PRTArtificialmutant recombinant phi29-type DNA polymerase
24Met 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 Glu Lys Ile
Ala Gln Asp Phe Lys Leu Thr Lys Lys Lys Gly 130 135 140Asp Ile Asp
Ile 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 Lys 210 215 220Ala Tyr Arg Gly Gly Phe Thr Trp
Leu Asn Asp Arg Phe Lys Gly Lys225 230 235 240Glu Ile Gly Glu Gly
Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Gly 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 Glu 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 Lys Val Lys Gly Tyr 500 505 510Leu
Val Gln Gly Ser Pro Asp Asp Tyr Thr Asp Ile Lys Phe Ser Val 515 520
525Lys Cys Ala Gly Met Thr Asp Gln 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 Gly 565 570 575His His His His His His His His His
His Gly Gly Gly Ser Gly Gly 580 585 590Gly Ser Gly Gly Gly Ser Gly
Leu Asn Asp Phe Phe Glu Ala Gln Lys 595 600 605Ile Glu Trp His Glu
61025613PRTArtificialmutant recombinant phi29-type DNA polymerase
25Met 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 Glu Lys Ile Ala Lys Asp Phe Lys Leu Thr Val Leu Lys Gly
130 135 140Asp Ile Asp Ile 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 Lys 210 215 220Ala Tyr Arg
Gly Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys Gly Lys225 230 235
240Glu Ile Gly Glu Gly Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Gly 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 Glu 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 Lys Val Lys
Gly Tyr 500 505 510Leu Val Gln 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 Gly 565 570 575His His His
His His His His His His His Gly Gly Gly Ser Gly Gly 580 585 590Gly
Ser Gly Gly Gly Ser Gly Leu Asn Asp Phe Phe Glu Ala Gln Lys 595 600
605Ile Glu Trp His Glu 61026627PRTArtificialmutant recombinant
phi29-type DNA polymerase 26Met Ser Val Asp Gly Leu Asn Asp Phe Phe
Glu Ala Gln Lys Ile Glu1 5 10 15Trp His Glu Ala Met Gly His His His
His His His His His His His 20 25 30Ser Ser Gly His Ile Glu Gly Arg
His Met Lys His Met Pro Arg Lys 35 40 45Met Tyr Ser Cys Asp Phe Glu
Thr Thr Thr Lys Val Glu Asp Cys Arg 50 55 60Val Trp Ala Tyr Gly Tyr
Met Asn Ile Glu Asp His Ser Glu Tyr Lys65 70 75 80Ile Gly Asn Ser
Leu Asp Glu Phe Met Ala Trp Val Leu Lys Val Gln 85 90 95Ala Asp Leu
Tyr Phe His Asn Leu Lys Phe Asp Gly Ala Phe Ile Ile 100 105 110Asn
Trp Leu Glu Arg Asn Gly Phe Lys Trp Ser Ala Asp Gly Leu Pro 115 120
125Asn Thr Tyr Asn Thr Ile Ile Ser Arg Met Gly Gln Trp Tyr Met Ile
130 135 140Asp Ile Cys Leu Gly Tyr Lys Gly Lys Arg Lys Ile His Thr
Val Ile145 150 155 160Tyr Asp Ser Leu Lys Lys Leu Pro Phe Pro Val
Gln Lys Ile Ala Lys 165 170 175Asp Phe Lys Leu Thr Val Leu Lys Gly
Asp Ile Asp Ile His Lys Glu 180 185 190Arg Pro Val Gly Tyr Lys Ile
Thr Pro Glu Glu Tyr Ala Tyr Ile Lys 195 200 205Asn Asp Ile Gln Ile
Ile Ala Glu Ala Leu Leu Ile Gln Phe Lys Gln 210 215 220Gly Leu Asp
Arg Met Thr Ala Gly Ser Asp Ser Leu Lys Gly Phe Lys225 230 235
240Asp Ile Ile Thr Thr Lys Lys Phe Lys Lys Val Phe Pro Thr Leu Ser
245 250 255Leu Gly Leu Asp Lys Glu Val Arg Lys Ala Tyr Arg Gly Gly
Phe Thr 260 265 270Trp Leu Asn Asp Arg Phe Lys Gly Lys Glu Ile Gly
Glu Gly Met Val 275 280 285Phe Asp Ile Asn Ser Ala Tyr Pro Ala Gln
Met Tyr Ser Arg Leu Leu 290 295 300Pro Tyr Gly Glu Pro Ile Val Phe
Glu Gly Lys Tyr Val Trp Asp Glu305 310 315 320Asp Tyr Pro Leu His
Ile Gln His Ile Arg Cys Glu Phe Glu Leu Lys 325 330 335Glu Gly Tyr
Ile Pro Thr Ile Gln Ile Lys Arg Ser Arg Phe Tyr Lys 340 345 350Gly
Asn Glu Tyr Leu Lys Ser Ser Gly Gly Glu Ile Ala Asp Leu Trp 355 360
365Leu Ser Asn Val Asp Leu Glu Leu Met Lys Glu His Tyr Asp Leu Tyr
370 375 380Asn Val Glu Tyr Ile Ser Gly Leu Lys Phe Lys Ala Thr Thr
Gly Leu385 390 395 400Phe Lys Asp Phe Ile Asp Lys Trp Thr Tyr Ile
Lys Thr Thr Ser Tyr 405 410 415Gly Ala Ile Lys Gln Leu Ala Lys Leu
Met Leu Asn Ser Leu Tyr Gly 420 425 430Lys Phe Ala Ser Asn Pro Asp
Val Thr Gly Lys Val Pro Tyr Leu Lys 435 440 445Glu Asn Gly Ala Leu
Gly Phe Arg Leu Gly Glu Glu Glu Thr Lys Asp 450 455 460Pro Val Tyr
Thr Pro Met Gly Val Phe Ile Thr Ala Trp Ala Arg Tyr465 470 475
480Thr Thr Ile Thr Ala Ala Gln Ala Cys Tyr Asp Arg Ile Ile Tyr Cys
485 490 495Asp Thr Asp Ser Ile His Leu Thr Gly Thr Glu Ile Pro Asp
Val Ile 500 505 510Lys Asp Ile Val Asp Pro Lys Lys Leu Gly Tyr Trp
Glu His Glu Ser 515 520 525Thr Phe Lys Arg Ala Lys Tyr Leu Arg Gln
Lys Thr Tyr Ile Gln Asp 530 535 540Ile Tyr Met Lys Glu Val Lys Gly
Tyr Leu Val Glu Gly Ser Pro Asp545 550 555 560Asp Tyr Thr Asp Ile
Lys Phe Ser Val Lys Cys Ala Gly Met Thr Asp 565 570 575Lys Ile Lys
Lys Glu Val Thr Phe Glu Asn Phe Lys Val Gly Phe Ser 580 585 590Arg
Lys Met Lys Pro Lys Pro Val Gln Val Pro Gly Gly Val Val Leu 595 600
605Val Asp Asp Thr Phe Thr Ile Lys Gly His His His His His His His
610 615 620His His His62527575PRTArtificialmutant recombinant
phi29-type DNA polymerase 27Met 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 Glu Lys Ile Ala Lys Asp Phe Lys Leu Thr Val Leu Lys Gly
130 135 140Asp Ile Asp Ile 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 Lys 210 215 220Ala Tyr Arg
Gly Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys Gly Lys225 230 235
240Glu Ile Gly Glu Gly Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Gly 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 Glu 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 Lys
Gly Tyr 500 505 510Leu Val Gln 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
57528575PRTArtificialmutant recombinant phi29-type DNA polymerase
28Met 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 Gln Asp Phe Lys Leu Thr Val Leu Lys Gly 130 135 140Asp Ile Asp
Ile 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 Lys 210 215 220Ala Tyr Arg Gly Gly Phe Thr Trp
Leu Asn Asp Arg Phe Lys Gly Lys225 230 235 240Glu Ile Gly Glu Gly
Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Gly 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 Glu 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 Lys Gly Tyr 500 505 510Leu
Val Gln 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 57529575PRTArtificialmutant recombinant
phi29-type DNA polymerase 29Met 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 Glu Lys Ile Ala Lys Asp Phe Lys Leu Thr Val Leu Lys Gly
130 135 140Asp Ile Asp Ile 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 Lys 210 215 220Ala Tyr Arg Gly Gly Phe Thr Trp Leu Asn
Glu Arg Phe Lys Gly Lys225 230 235 240Glu Ile Gly Glu Gly Met Val
Phe Asp Ala Asn Ser His 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
Tyr 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 Gly 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 Glu 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 Lys Gly Tyr 500 505 510Leu Val Gln
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 57530575PRTArtificialmutant recombinant
phi29-type DNA polymerase 30Met 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 Ile 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 Lys 210 215 220Ala Tyr Arg
Gly Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys Gly Lys225 230 235
240Glu Ile Gly Glu Gly Met Val Phe Asp Val Asn Ser Ser 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 Tyr 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 Gly 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 Glu 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 Lys
Gly Tyr 500 505 510Leu Val Gln 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
57531575PRTArtificialmutant recombinant phi29-type DNA polymerase
31Met 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
Ile 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 Phe 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 Glu Arg Phe Lys Gly Lys225 230 235 240Glu Ile Gly Glu Gly
Met Val Phe Asp Val Asn Ser His 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 Tyr 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 Gly 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 Glu 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 Lys Gly Tyr 500 505 510Leu
Val Gln 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 57532575PRTArtificialmutant recombinant
phi29-type DNA polymerase 32Met 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 Ile 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 Lys 210 215 220Ala Tyr Arg
Gly Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys Gly Lys225 230 235
240Glu Ile Gly Glu Gly Met Val Phe Asp Ile Asn Ser His 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 Tyr 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 Gly 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 Glu 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 Lys
Gly Tyr 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
57533575PRTArtificialmutant recombinant phi29-type DNA polymerase
33Met 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
Ile 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 Lys 210 215 220Ala Tyr Arg Gly Gly Phe Thr Trp
Leu Asn Asp Arg Phe Lys Gly Lys225 230 235 240Glu Ile Gly Glu Gly
Met Val Phe Asp Ile Asn Ser Ala 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
Tyr 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 Gly 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 Glu 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 Lys Gly Tyr 500 505 510Leu Val Gln
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 57534575PRTArtificialmutant recombinant
phi29-type DNA polymerase 34Met 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 Glu Lys Ile Ala Lys Asp Phe Lys Leu Thr Val Leu Lys Gly
130 135 140Asp Ile Asp Ile 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 Lys 210 215 220Ala Tyr Arg
Gly Gly Phe Thr Trp Leu Asn Glu Arg Phe Lys Gly Lys225 230 235
240Glu Ile Gly Glu Gly Met Val Phe Asp Val Asn Ser His 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 Tyr 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 Gly 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 Glu 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 Lys
Gly Tyr 500 505 510Leu Val Gln 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
57535575PRTArtificialmutant recombinant phi29-type DNA polymerase
35Met 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
Ile 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 Lys 210 215 220Ala Tyr Arg Gly Gly Phe Thr Trp
Leu Asn Glu Arg Phe Lys Gly Lys225 230 235 240Glu Ile Gly Glu Gly
Met Val Phe Asp Val Asn Ser His 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 Tyr 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 Gly 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 Glu 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 Lys Gly Tyr 500 505 510Leu
Val Gln 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 57536575PRTArtificialmutant recombinant
phi29-type DNA polymerase 36Met 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 Ile 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 Lys 210 215 220Ala Tyr Arg
Gly Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys Gly Lys225 230 235
240Glu Ile Gly Glu Gly Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Gly 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 Glu 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 Lys
Gly Tyr 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
57537575PRTArtificialmutant recombinant phi29-type DNA polymerase
37Met 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
Ile 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 Lys 210 215 220Ala Tyr Arg Gly Gly Phe Thr Trp
Leu Asn Asp Arg Phe Lys Gly Lys225 230 235 240Glu Ile Gly Glu Gly
Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Gly 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 Glu 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 Lys Gly Tyr 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 57538575PRTArtificialmutant recombinant phi29-type DNA
polymerase 38Met 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
Glu Lys Ile Ala Lys Asp Phe Lys Leu Thr Val Leu Lys Gly 130 135
140Asp Ile Asp Ile 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 Lys 210 215 220Ala Tyr Arg Gly
Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys Gly Lys225 230 235 240Glu
Ile Gly Glu Gly Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Glu 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 Lys Gly Tyr
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 57539575PRTArtificialmutant
recombinant phi29-type DNA polymerase 39Met 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 Gln Asp Phe Lys Leu Thr
Val Leu Lys Gly 130 135 140Asp Ile Asp Ile 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 Lys 210 215
220Ala Tyr Arg Gly Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys Gly
Lys225 230 235 240Glu Ile Gly Glu Gly Met Val Phe Asp Ile Asn Ser
Ala 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 Tyr 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 Glu 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 Lys Gly Tyr 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
57540572PRTArtificialmutant recombinant phi29-type DNA polymerase
40Met 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 Ala Tyr Pro Ala 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 Tyr 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 480Glu 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 Tyr 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 57041575PRTArtificialmutant recombinant phi29-type DNA
polymerase 41Met 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 Ile 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 Lys 210 215 220Ala Tyr Arg Gly
Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys Gly Lys225 230 235 240Glu
Ile Gly Glu Gly Met Val Phe Asp Val Asn Ser His 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 Tyr 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 Gly 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 Glu 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 Lys Gly Tyr
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
57542572PRTArtificialmutant recombinant phi29-type DNA polymerase
42Met 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 140Ile 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 Gly Lys Glu Ile Gly225 230 235 240Glu Gly Met Val Phe
Asp Ile Asn Ser Ala Tyr Pro Ala 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 Tyr 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 Gly 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 480Glu 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 Lys Gly Tyr Leu Lys Gln 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 57043572PRTArtificialmutant recombinant phi29-type DNA
polymerase 43Met 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 Gln Asp Phe Gln Leu Pro Leu Leu Lys Gly Asp Ile Asp 130 135
140Ile 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 Gly Lys Glu Ile Gly225 230 235 240Glu
Gly Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Gly 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 480Glu
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 Lys Gly Tyr Leu Lys Gln
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 57044575PRTArtificialmutant recombinant
phi29-type DNA polymerase 44Met 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 Glu Lys Ile Ala Gln Asp Phe Lys Leu Thr Lys Lys Lys Gly
130 135 140Asp Ile Asp Ile 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 Lys 210 215 220Ala Tyr Arg
Gly Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys Gly Lys225 230 235
240Glu Ile Gly Glu Gly Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Gly 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 Glu 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 Lys Val Lys
Gly Tyr 500 505 510Leu Val Gln Gly Ser Pro Asp Asp Tyr Thr Asp Ile
Lys Phe Ser Val 515 520 525Lys Cys Ala Gly Met Thr Asp Gln 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
57545575PRTArtificialmutant recombinant phi29-type DNA polymerase
45Met 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 Glu Lys Ile
Ala Lys Asp Phe Lys Leu Thr Val Leu Lys Gly 130 135 140Asp Ile Asp
Ile 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 Lys 210 215 220Ala Tyr Arg Gly Gly Phe Thr Trp
Leu Asn Asp Arg Phe Lys Gly Lys225 230 235 240Glu Ile Gly Glu Gly
Met Val Phe Asp Ile Asn Ser Ala 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 Tyr 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 Gly 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 Glu 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 Lys Val Lys Gly Tyr 500 505 510Leu
Val Gln 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 57546575PRTArtificialmutant recombinant
phi29-type DNA polymerase 46Met 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 Gln Lys Ile Ala Lys Asp Phe Lys
Leu Thr Val Leu Lys Gly 130 135 140Asp Ile Asp Ile 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 Lys
210 215 220Ala Tyr Arg Gly Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys
Gly Lys225 230 235 240Glu Ile Gly Glu Gly Met Val Phe Asp Ile Asn
Ser Ala 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 Tyr 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 Glu 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 Lys Gly Tyr 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
570 575
* * * * *
References