U.S. patent application number 13/982024 was filed with the patent office on 2014-03-20 for methods for reducing nucleic acid damage.
This patent application is currently assigned to ILLUMINA, INC.. The applicant listed for this patent is ILLUMINA, INC.. Invention is credited to Epameinondas Fritzilas, Niall Anthony Gormley, Kevin Hall, Avgousta Ioannou, Kay Klausing, John Moore, Roberto Rigatti, Min-Jui Richard Shen, Vincent Peter Smith.
Application Number | 20140080721 13/982024 |
Document ID | / |
Family ID | 46577814 |
Filed Date | 2014-03-20 |
United States Patent
Application |
20140080721 |
Kind Code |
A1 |
Klausing; Kay ; et
al. |
March 20, 2014 |
METHODS FOR REDUCING NUCLEIC ACID DAMAGE
Abstract
Provided herein is a method of inhibiting degradation of nucleic
acids during a nucleic acid processing step selected from
fragmentation and detection comprising contacting the nucleic acids
with a solution comprising gallic acid, analogues, derivatives
thereof or mixtures thereof, during the processing step, wherein
the contacting inhibits degradation of the nucleic acids. Also
provided herein is a method of inhibiting light-induced degradation
of nucleic acids. Additionally, provided herein is a method of
reducing or inhibiting nucleic acid damage during preparation of a
nucleic acid sample comprising fragmenting the nucleic acid
sequences in the sample in a solution comprising one of more
compounds, the compounds inhibiting degradation of the nucleic acid
sequences in the sample.
Inventors: |
Klausing; Kay; (San Diego,
CA) ; Shen; Min-Jui Richard; (San Diego, CA) ;
Moore; John; (San Diego, CA) ; Smith; Vincent
Peter; (Essex, GB) ; Hall; Kevin; (Essex,
GB) ; Gormley; Niall Anthony; (Essex, GB) ;
Ioannou; Avgousta; (Essex, GB) ; Fritzilas;
Epameinondas; (Essex, GB) ; Rigatti; Roberto;
(Essex, GB) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
ILLUMINA, INC. |
San Diego |
CA |
US |
|
|
Assignee: |
ILLUMINA, INC.
San Diego
CA
|
Family ID: |
46577814 |
Appl. No.: |
13/982024 |
Filed: |
January 12, 2012 |
PCT Filed: |
January 12, 2012 |
PCT NO: |
PCT/US12/21040 |
371 Date: |
November 25, 2013 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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13018255 |
Jan 31, 2011 |
|
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13982024 |
|
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61438522 |
Feb 1, 2011 |
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Current U.S.
Class: |
506/4 ; 435/6.12;
506/2 |
Current CPC
Class: |
C12Q 1/6832 20130101;
C12Q 1/6832 20130101; C12Q 1/6869 20130101; C12N 15/1003 20130101;
C40B 20/04 20130101; C12Q 2527/127 20130101; C12Q 2527/125
20130101; C12Q 1/6874 20130101; C12Q 2523/319 20130101 |
Class at
Publication: |
506/4 ; 435/6.12;
506/2 |
International
Class: |
C12N 15/10 20060101
C12N015/10 |
Claims
1. A method of inhibiting degradation of nucleic acids during a
nucleic acid processing step selected from fragmentation and
detection comprising contacting the nucleic acids with a solution
comprising gallic acid, analogues, derivatives, or mixtures thereof
during the processing step, wherein the contacting inhibits
degradation of the nucleic acids.
2. The method of claim 1, wherein the nucleic acids are in an array
of nucleic acids attached to a support.
3. The method of claim 1, wherein the gallic acid, analogues,
derivatives, or mixtures thereof is present in a concentration
ranging from between about 10 mM to about 200 mM.
4-6. (canceled)
7. The method of claim 1, wherein the processing step is a
detection processing step.
8. The method of claim 7, wherein the detection processing step
comprises irradiating the nucleic acids.
9. The method of claim 8, wherein the irradiating is conducted in a
range from about 360 nm to about 800 nm.
10. The method of claim 8, wherein the irradiating is conducted
with a light source having power in a range between about 5 to
about 500 milliwatts.
11. The method of claim 8, wherein the irradiating is conducted for
a time period of about 0.1 seconds to about 10 minutes.
12. The method of claim 1, wherein the degradation is light-induced
degradation.
13. The method of claim 12, wherein the light-induced degradation
comprises removal of a nucleic acid member from the array of
nucleic acids.
14. The method of claim 7, further comprising adding a
fluorescently tagged nucleotide to the array and repeating the
detection processing step.
15. The method of claim 14, wherein the adding the fluorescently
tagged nucleotide comprises using a polymerase to add a single
fluorescently tagged nucleotide.
16. The method of claim 14, further comprising repeating the
detection processing and addition steps for at least 50, 75 or 100
cycles.
17. The method of claim 7, wherein the solution reduces the
detection error rate by greater than 20, 40, or 50% compared to a
control.
18. The method of claim 1, wherein the processing step is
fragmentation.
19. The method of claim 18, wherein the nucleic acids are being
prepared for sequencing.
20. The method of claim 19, wherein the fidelity of the sequence
information in the nucleic acids is improved as compared to nucleic
acids fragmented in the absence of the solution.
21. The method of claim 18, further comprising treating the nucleic
acids with an enzyme that cleaves nucleic acid sequences comprising
damaged nucleic acids to remove any damaged nucleic acids.
22. The method of claim 21, wherein the enzyme is
formamidopyrimidine DNA glycosylase (FPG).
23. The method of claim 18, further comprising treating the sample
with an antibody that selectively binds one or more types of
damaged nucleic acids to remove any damaged nucleic acids.
24. The method of claim 23, wherein the antibody binds 8-oxo-G.
25-27. (canceled)
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of, U.S. Provisional
Application No. 61/438,522, filed Feb. 1, 2011. This application is
also a continuation-in-part of and claims priority to U.S.
application Ser. No. 13/018,255, filed Jan. 31, 2011. These
applications are incorporated herein by reference in their
entireties.
BACKGROUND
[0002] Methods for processing nucleic acid samples for and during
sequencing and other techniques can expose the nucleic acids to a
variety of harmful conditions that degrade or damage the nucleic
acids resulting in nucleic acid samples that are unable to be
further processed or, e.g., in the case of sequencing, can result
in high error rates.
[0003] For example, methods for preparing nucleic acid samples for
sequencing and other techniques often involves fragmentation of
larger nucleic acid sequences into smaller nucleic acid sequences
that can lead to damaged nucleic acids resulting in
misidentification of the nucleic acids during, e.g., sequencing
techniques.
[0004] By way of another example, methods used to detect and
characterize nucleic acid structures may employ tagging schemes
that rely on electromagnetic radiation (EM) emission of an excited
state light-absorbing chromophore that can result in nucleic acid
damage. Examples of such photoluminescent processes include
phosphorescence and fluorescence emission. Fluorescence detection,
for example, has been used in DNA sequencing to great effect due,
in part, to the high degree of sensitivity allowing single molecule
detection.
[0005] Performing iterative fluorescent detection steps in an array
context, such as sequencing by synthesis, can cause fluorescence
signal intensity loss (see, for example, Fedurco et al.
WO2006/064199). This problem was addressed, in part, by the
addition of ascorbate to a detection solution to increase the
number of useful detection cycles from about eight to ten cycles,
in the absence of ascorbate, to about 25 cycles in the presence of
ascorbate. The possible mechanisms that underlie this signal loss
are numerous, and can include cleavage of individual nucleic acid
members from the support.
[0006] There are a number of pathways by which nucleic acid damage
can occur during irradiation in fluorescence detection.
Fluorescence emission normally occurs with the emission of light of
a longer wavelength (lower energy), than the original irradiating
source. However, under conditions in which intense EM radiation is
being absorbed by the fluorophore, such as in laser-induced
fluorescence (LIF), it is possible for a molecule to absorb two
photons, which can lead to the emission of higher energy radiation
of smaller wavelengths than the original excitation source. This
multiple photon absorption can cause the fluorophore to emit EM
radiation in the UV-visible region which can contribute to nucleic
acid base dimerization and/or the generation of reactive oxygen
species.
[0007] For example, it has been indicated that exposure of whole
cells to ultraviolet (UV) radiation can cause DNA damage via the
direct photochemical [2+2] photocycloaddition reaction of thymine
or cytosine to provide cyclobutane pyrimidine dimers, such as TT,
TC, and CC. Such direct photocycloaddition reactions can occur in
the UV B and UV C regions which extend from about 100 nm to about
315 nm.
[0008] In the UV A region through a portion of the visible region,
spanning from about 315 nm to about 500 nm, a complex mixture of
indirect mechanisms can also cause DNA damage through
photosensitization of other cellular components. Such indirect
mechanisms can result in pyrimidine dimer formation and oxidative
DNA modification via reactive species such as singlet oxygen,
superoxide anion, and iron-promoted hydroxyl radical formation.
Finally, it also has also been indicated that reactive singlet
oxygen can be generated by fluorescence quenching of an excited
state fluorophore by triplet oxygen. Any combination of direct or
indirect pyrimidine dimerization and nucleic acid damage due to
various reactive oxygen species observed in whole cells can be the
underlying cause of fluorescence signal intensity loss observed in
the array context.
[0009] There is a need to reduce or inhibit nucleic acid damage
during processing of the nucleic acids for and during sequencing
and other techniques. For example, there is a need to reduce
nucleic acid damage during fragmentation. In addition, there is a
need to further reduce fluorescent signal intensity loss for
applications in sequencing by synthesis to facilitate sequencing of
long nucleotide sequences, including sequences of 50, 75, 100, 200,
and 500 nucleotides or more. Moreover, solutions to fluorescent
signal intensity loss in the context of sequencing are readily
applicable to other nucleic acid detection platforms that employ
multiple irradiation steps.
SUMMARY
[0010] Provided herein is a method of inhibiting degradation of
nucleic acids during a nucleic acid processing step selected from
fragmentation and detection comprising contacting the nucleic acids
with a solution comprising gallic acid, analogues, derivatives
thereof or mixtures thereof, during the processing step, wherein
the contacting inhibits degradation of the nucleic acids.
[0011] Also provided herein is a method of inhibiting light-induced
degradation of nucleic acids. The method includes irradiating a
portion of said nucleic acids in the presence of a solution
comprising one or more compounds, e.g., polyphenolic compounds.
Also provided is a method of detecting a nucleic acid having a
fluorescent tag. The method includes irradiating at least a portion
of said nucleic acid with light, wherein said light comprises a
suitable wavelength to induce a fluorescence emission, detecting
the fluorescence emission. Optionally, the compound is gallic acid,
analogues or derivatives thereof, e.g., a lower alkyl ester
thereof, or mixtures thereof.
[0012] Provided herein is a method of reducing or inhibiting
nucleic acid damage during preparation of a nucleic acid sample
comprising fragmenting the nucleic acid sequences in the sample in
a solution comprising one of more compounds, the compounds
inhibiting degradation of the nucleic acid sequences in the sample.
Also provided is a method of removing damaged nucleic acids from a
sample comprising nucleic acid sequences, the method comprising
providing a sample of nucleic acid sequences, and (i) treating the
sample with an enzyme that that cleaves damaged nucleic acid
sequences or (ii) treating the sample with an antibody that
selectively binds one or more types of damaged nucleic acids,
wherein treating the sample removes the damaged nucleic acids from
the sample.
[0013] The details of one or more embodiments are set forth in the
accompanying drawings and the description below. Other features,
objects, and advantages will be apparent from the description and
drawings, and from the claims.
BRIEF DESCRIPTION OF THE DRAWINGS
[0014] FIG. 1 shows a graphic representation of the relative
effectiveness of representative polyphenolic compounds, and related
structures, in providing protection from light-induced degradation.
Increased effectiveness is shown from top (least) to bottom
(most).
[0015] FIG. 2 shows a graphic representation of the relative
effectiveness of representative polyphenolic compounds, and related
structures, in providing protection from light-induced degradation.
Increased effectiveness is shown from top (least) to bottom
(most).
[0016] FIG. 3 shows a graph plotting error versus cluster passing
filter (PF) number.
[0017] FIG. 4 shows coverage plots in a control sequence, in the
presence of gallic acid, in the presence of urea, and in the
presence of gallic acid and urea, over 75 cycles.
[0018] FIG. 5 shows coverage plots in a control sequence, in the
presence of gallic acid, in the presence of urea, and in the
presence of gallic acid and urea, over 100 cycles.
[0019] FIG. 6 is a graph showing that DNA fragmentation by Covaris
shearing has a max Q value that decreases with increased duration
of shearing.
[0020] FIG. 7 is a graph showing the mutation profile of DNA after
fragmentation by Covaris shearing in the presence of gallic acid
(L1), in the presence of ascorbate (L2), no treatment (L7), and
HindIII control digestion treatment (L8). L4 and L6 show the
mutation profile of DNA after fragmentation by Covaris shearing
followed by treatment with FPG (L4) or PreCR treatment (L6).
[0021] FIG. 8 is a graph showing the mutation profile of DNA after
fragmentation by Covaris shearing in the presence of gallic acid
(L1), in the presence of ascorbate (L2), no treatment (L7), and
HindIII control digestion treatment (L8). L4 and L6 show the
mutation profile of DNA after fragmentation by Covaris shearing
followed by treatment with FPG (L4) or PreCR treatment (L6).
DETAILED DESCRIPTION
[0022] The present application provides, in part, a method of
inhibiting degradation of nucleic acids during a nucleic acid
processing step selected from fragmentation and detection
comprising contacting the nucleic acids with a solution comprising
gallic acid an analogue or derivative thereof or mixtures thereof,
during the processing step, wherein the contacting inhibits
degradation of the nucleic acids. Optionally, the nucleic acids are
in an array of nucleic acids attached to a support. Optionally, the
solution further comprises one or more compounds that further
inhibits degradation of the nucleic acids selected from the group
consisting of urea, ascorbic acid or analogues or derivatives
thereof.
[0023] Optionally, the processing step is a detection processing
step. Thus, the present application also provides a method of
inhibiting light-induced degradation of nucleic acids during a
detection step that includes irradiating a portion of the nucleic
acids in the presence of a solution having one or more compounds,
e.g., a polyphenolic compound. The presence of the one or more
compounds in the solution inhibits the amount of light-induced
degradation of the nucleic acids.
[0024] The present application is also directed, in part, to a
method of detecting a nucleic acid having a fluorescent tag that
includes a) irradiating the nucleic acid with light having a
suitable wavelength to induce a fluorescence emission; b) detecting
the fluorescence emission; and repeating these steps iteratively.
The irradiating step is carried out in the presence of a solution
that includes a polyphenolic compound and serves to reduce
light-induced degradation of the nucleic acid.
[0025] Optionally, the processing step is fragmentation. Nucleic
acid samples can be fragmented prior to a variety of techniques
including without limitation, high throughput or rapid sequencing
techniques such as, sequencing by synthesis and sequencing by
ligation, nucleic acid microarray detection techniques such as gene
chips and DNA microarrays, and quantitative polymerase chain
reaction (Q-PCR) techniques such as real time polymerase chain
reaction (PCR) and multiplex PCR. However, fragmentation of nucleic
acid samples, for example, by shearing (e.g., hydroshearing,
nebulization, sonication or acoustic shearing), results in nucleic
acid damage. Thus, provided herein is a method of reducing or
inhibiting nucleic acid damage during preparation of a nucleic acid
sample comprising fragmenting the nucleic acid sequences in the
sample in a solution comprising one of more compounds, the
compounds inhibiting degradation of the nucleic acid sequences in
the sample. Also provided is a method of inhibiting nucleic acid
degradation during preparation of a nucleic acid sample comprising
fragmenting the nucleic acid sequences in the sample in the
presence of one or more compounds, the compounds inhibiting nucleic
acid degradation of the nucleic acid sequences in the sample.
[0026] As stated above, optionally, the nucleic acid sample is
being prepared for sequencing. The fidelity of the sequence
information in the sample is improved as compared to a nucleic acid
sample prepared in the absence of the compounds. Thus, also
provided herein is a method of improving the fidelity of nucleic
acid sequence information during sequencing. The method includes
providing a library of nucleic acid sequences to be sequenced,
fragmenting the library of nucleic acid sequences in the presence
of one or more compounds, the compounds inhibiting nucleic acid
degradation, and sequencing the library of nucleic acid sequences,
the fidelity of the nucleic acid sequence information being
improved as compared to a control. As used throughout, a control or
control value includes the fidelity of sequence information
obtained in a control sample (e.g., a sample prepared in the
absence of the compounds described herein) or can comprise a known
standard.
[0027] Optionally, the provided methods further comprise treating
the sample with an enzyme that cleaves nucleic acid sequences
comprising damaged nucleic acids to remove any damaged nucleic
acids from the sample. Optionally, the provided methods further
comprise treating the sample with an antibody that selectively
binds one or more types of damaged nucleic acids to remove any
damaged nucleic acids from the sample. Thus, in particular
embodiments provided is a method of removing damaged nucleic acids
from a sample comprising nucleic acid sequences. The method
includes providing a sample of nucleic acid sequences and (i)
treating the sample with an enzyme that that cleaves damaged
nucleic acid sequences or (ii) treating the sample with an antibody
that selectively binds one or more types of damaged nucleic acids,
wherein treating the sample removes the damaged nucleic acids from
the sample. Optionally, prior to treating the sample, the sample is
fragmented in the presence of one or more compounds. Optionally,
one compound is used or more than one compound is used. Optionally,
the enzyme is formamidopyrimidine DNA glycosylase (FPG).
Optionally, the antibody binds 8-oxo-G Enzymes that cleave damaged
nucleic acids are known. Further, antibodies that specifically bind
one or more types of damaged nucleic acids are known and are
described in, for example, van Loon and Hubscher, PNAS
106(43):18201-6 (2009), which is incorporated by reference herein
in its entirety.
[0028] Exemplary compounds, exemplified in FIGS. 1 and 2 and Tables
1 and 2, used in the provided solutions protect to nucleic acids
from light-induced degradation that can occur during detection
steps performed in various assays, including for example, base
calling in sequencing by synthesis. The compounds disclosed herein
have been identified as successfully ameliorating the effects of
degradation, including light-induced degradation, among numerous
other classes of compounds that can shut down plausible mechanistic
degradation pathways. Such compounds classes include, without
limitation, hydroxyl radical quenchers, reactive oxygen species
(singlet oxygen, superoxide anion) quenchers, oxygen scavengers,
triplet state quenchers, and hole quenchers.
[0029] In some embodiments, the presence of urea, with or without
ascorbate, in the solution was found to further reduce the amount
of degradation of the nucleic acids when used with a polyphenolic
compound. Table 2 and FIGS. 4 and 5, show this synergy in the
presence of urea and ascorbate. While urea has a significant impact
on reducing degradation when used in conjunction with a
polyphenolic compound, using urea alone has only a minor impact
with respect to any such protective benefits.
[0030] Methods of the invention that employ a solution having a
polyphenolic compound protect the integrity of nucleic acids when
they are exposed to repeated and/or intense irradiation, as might
be employed in a variety of contexts, including without limitation,
high throughput or rapid sequencing techniques such as, sequencing
by synthesis and sequencing by ligation, nucleic acid microarray
detection techniques such as gene chips and DNA microarrays, and
quantitative polymerase chain reaction (Q-PCR) techniques such as
real time polymerase chain reaction (PCR) and multiplex PCR. As
described above, the presence of urea can enhance the protective
role of the polyphenolic compound in any of these contexts. In the
Examples disclosed herein, the use of the solution in sequencing by
synthesis in an array format, in particular, lowered fluorescent
signal decay and provided lower error rates over 50 to 120 cycles
of repeated detection steps.
[0031] The solutions, which can be provided in kit form, can also
be used in fluorescence detection techniques that have been
employed in mechanistic biochemistry. For example, fluorescence
polarization has been indicated as a powerful technique in studying
molecular interactions, including without limitation,
receptor-ligand interactions, such as hormone-receptor
interactions, protein-peptide interactions, and DNA-protein
interactions. For example, Singleton et al. Tetrahedron 63(17):
(2007) incorporated a fluorescent guanine analog into
oligonucleotides in studying RecA protein interactions with DNA.
The detection solution employed in the methods disclosed herein can
be used in real-time kinetic measurements where fluorophores are
employed. The protective effects against light-induced degradation
afforded by the detection solution need not be limited to the
protection of nucleic acids. Thus, for example, the detection
solution can also be used to protect the integrity of proteins,
peptides, carbohydrates, and small molecules, any of which can be
susceptible to reactive oxygen species, or the like, generated
under conditions for measuring fluorescence emission.
[0032] As used herein, the term "nucleic acid" is intended to mean
at least two nucleotides covalently linked together. Nucleic acid
encompasses the term oligonucleotide, polynucleotide, and their
grammatical equivalents. A nucleic acid of the present invention
will generally contain phosphodiester bonds, although in some cases
nucleic acid analogs can have alternate backbones, comprising, for
example, phosphoramide (Beaucage et al., Tetrahedron 49(10): 1925
(1993) and references therein; Letsinger, J. Org. Chem. 35:3800
(1970); Sprinzl et al., Eur. J. Biochem. 81:579 (1977); Letsinger
et al., Nucl. Acids Res. 14:3487 (1986); Sawai et al, Chem. Lett.
805 (1984), Letsinger et al., J. Am. Chem. Soc. 110:4470 (1988);
and Pauwels et al., Chemica Scripta 26:141 91986)),
phosphorothioate (Mag et al., Nucleic Acids Res. 19:1437 (1991);
and U.S. Pat. No. 5,644,048), phosphorodithioate (Briu et al., J.
Am. Chem. Soc. 111:2321 (1989), O-methylphosphoroamidite linkages
(see Eckstein, Oligonucleotides and Analogues: A Practical
Approach, Oxford University Press), and peptide nucleic acid
backbones and linkages (see Egholm, J. Am. Chem. Soc. 114:1895
(1992); Meier et al., Chem. Int. Ed. Other analog nucleic acids
include those with positive backbones (Denpcy et al., Proc. Natl.
Acad. Sci. USA 92:6097 (1995); non-ionic backbones (U.S. Pat. Nos.
5,386,023, 5,637,684, 5,602,240, 5,216,141 and 4,469,863;
Kiedrowshi et al., Angew. Chem. Intl. Ed. English 30:423 (1991);
Letsinger et al., J. Am. Chem. Soc. 110:4470 (1988); Letsinger et
al., Nucleoside & Nucleotide 13:1597 (1994); Chapters 2 and 3,
ASC Symposium Series 580, "Carbohydrate Modifications in Antisense
Research," Ed. Y. S. Sanghui and P. Dan Cook; Mesmaeker et al.,
Bioorganic & Medicinal Chem. Lett. 4:395 (1994); Jeffs et al.,
J. Biomolecular NMR 34:17 (1994); Tetrahedron Lett. 37:743 (1996))
and non-ribose backbones, including those described in U.S. Pat.
Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium
Series 580, "Carbohydrate Modifications in Antisense Research", Ed.
Y. S. Sanghui and P. Dan Cook. Nucleic acids containing one or more
carbocyclic sugars are also included within the definition of
nucleic acids (see Jenkins et al., Chem. Soc. Rev. (1995) pp.
169-176). Several nucleic acid analogs are described in Rawls, C
& E News Jun. 2, 1997 page 35. All of these references are
hereby expressly incorporated by reference. These modifications of
the ribose-phosphate backbone may be done to facilitate the
addition of labels, or to increase the stability and half-life of
such molecules in physiological environments.
[0033] A nucleic acid will generally contain a specific sequence of
four nucleotide bases: adenine (A); cytosine (C); guanine (G); and
thymine (T). Uracil (U) can also be present, for example, as a
natural replacement for thymine when the nucleic acid is RNA.
Uracil can also be used in DNA. A nucleic acid used in the
invention can also include native or non-native bases. In this
regard, a native deoxyribonucleic acid can have one or more bases
selected from the group consisting of adenine, thymine, cytosine or
guanine and a ribonucleic acid can have one or more bases selected
from the group consisting of uracil, adenine, cytosine or guanine.
It will be understood that a deoxyribonucleic acid used in the
methods or compositions set forth herein can include uracil bases
and a ribonucleic acid can include a thymine base. Exemplary
non-native bases that can be included in a nucleic acid, whether
having a native backbone or analog structure, include, without
limitation, inosine, xathanine, hypoxathanine, isocytosine,
isoguanine, 2-aminopurine, 5-methylcytosine, 5-hydroxymethyl
cytosine, 2-aminoadenine, 6-methyl adenine, 6-methyl guanine,
2-propyl guanine, 2-propyl adenine, 2-thioLiracil, 2-thiothymine,
2-thiocytosine, 15-halouracil, 15-halocytosine, 5-propynyl uracil,
5-propynyl cytosine, 6-azo uracil, 6-azo cytosine, 6-azo thymine,
5-uracil, 4-thiouracil, 8-halo adenine or guanine, 8-amino adenine
or guanine, 8-thiol adenine or guanine, 8-thioalkyl adenine or
guanine, 8-hydroxyl adenine or guanine, 5-halo substituted uracil
or cytosine, 7-methylguanine, 7-methyladenine, 8-azaguanine,
8-azaadenine, 7-deazaguanine, 7-deazaadenine, 3-deazaguanine,
3-deazaadenine or the like. A particular embodiment can utilize
isocytosine and isoguanine in a nucleic acid in order to reduce
non-specific hybridization, as generally described in U.S. Pat. No.
5,681,702.
[0034] A non-native base used in a nucleic acid can have universal
base pairing activity, wherein it is capable of base pairing with
any other naturally occurring base. Exemplary bases having
universal base pairing activity include 3-nitropyrrole and
5-nitroindole. Other bases that can be used include those that have
base pairing activity with a subset of the naturally occurring
bases such as inosine, which basepairs with cytosine, adenine or
uracil.
[0035] As used herein the term "array of nucleic acids" means a
solid support having a plurality of spatially distinguishable
nucleic acids disposed thereon or therein. The nucleic acids can be
disposed in an ordered or random pattern of features. An individual
feature can be, for example, a spatially isolated nucleic acid
molecule, or an ensemble of nucleic acid molecules such as a
cluster. An array can be a composite array comprising a plurality
of individual arrays configured to allow processing of multiple
samples. The individual arrays, referred to herein as "sub-arrays,"
include groups of nucleic acid features. Sub-arrays appear in
distinct regions with in a larger array. The sub-arrays themselves
can be ordered or non-ordered. Such sub-arrays can be optionally
spatially addressable. Sub-arrays can include clusters of identical
nucleic acids. An example of a composite array composed of
individual sub-arrays is a microtiter plate having wells in which
the plate as a whole is an array of nucleic acids (or composite
array) while each individual well represents a sub-array within the
larger composite array.
[0036] As used herein the term "nucleic acid member" means a single
nucleic acid bound to a support that is part of an array and/or
part of a sub-array within a composite array.
[0037] As used herein the term "support" refers to a substrate for
immobilizing an array of nucleic acids. A "support" is a material
having a rigid or semi-rigid surface to which a nucleic acid array
can be attached or upon which nucleic acids can be synthesized
and/or modified. Supports can include any resin, microbead, glass,
controlled pore glass (CPG), polymer support, membrane, paper,
plastic, plastic tube or tablet, plastic bead, glass bead, slide,
ceramic, silicon chip, multi-well plate, nylon membrane, fiber
optic, and PVDF membrane.
[0038] A support can include any flat wafer-like substrates and
flat substrates having wells, such as a microtiter plate, including
96-well plates. Exemplary flat substrates include chips, slides,
etched substrates, microtiter plates, and flow cell reactors,
including multi-lane flow cell reactors having multiple
microfluidic channels, such as the eight channel flow cell used in
the cBot sequencing workstation (Illumina, Inc., San Diego,
Calif.).
[0039] A support can also include beads, including magnetic beads,
hollow beads, and solid beads. Beads can be used in conjunction
with flat supports, such flat supports optionally also containing
wells. Beads, or alternatively microspheres, refer generally to a
small body made of a rigid or semi-rigid material. The body can
have a shape characterized, for example, as a sphere, oval,
microsphere, or other recognized particle shape whether having
regular or irregular dimensions. The sizes of beads, in particular,
include, without limitation, about 1 nm, about 2 nm, about 3 nm,
about 5 nm, about 10 nm, about 20 nm, about 30 nm, about 40 nm,
about 60 nm, about 100 nm, about 150 nm or about 200 nm in
diameter. Other particles can be used in ways similar to those
described herein for beads and microspheres.
[0040] The composition of a support can vary, depending for
example, on the format, chemistry and/or method of attachment
and/or on the method of nucleic acid synthesis. Support materials
that can be used in accordance with the present disclosure include,
but are not limited to, polypropylene, polyethylene, polybutylene,
polyurethanes, nylon, metals, and other suitable materials.
Exemplary compositions include supports, and chemical
functionalities imparted thereto, used in polypeptide,
polynucleotide and/or organic moiety synthesis. Such compositions
include, for example, plastics, ceramics, glass, polystyrene,
melamine, methylstyrene, acrylic polymers, paramagnetic materials,
thoria sol, carbon graphite, titanium dioxide, latex or
cross-linked dextrans such as Sepharose.TM., cellulose, nylon,
cross-linked micelles and Teflon.TM., as well as any other
materials which can be found described in, for example,
"Microsphere Detection Guide" from Bangs Laboratories, Fishers 1N,
which is incorporated herein by reference. A support particle can
be made of cross-linked starch, dextrans, cellulose, proteins,
organic polymers including styrene polymers including polystyrene
and methylstyrene as well as other styrene co-polymers, plastics,
glass, ceramics, acrylic polymers, magnetically responsive
materials, colloids, thoriasol, carbon graphite, titanium dioxide,
nylon, latex, or TEFLON.RTM.. "Microsphere Detection Guide" from
Bangs Laboratories, Fishers, Inc., hereby incorporated by reference
in its entirety, is a helpful guide. Further exemplary supports
within the scope of the present disclosure include, for example,
those described in US Application Publication No. 2002/0102578 and
U.S. Pat. No. 6,429,027, both of which are incorporated herein by
reference in their entirety.
[0041] As used herein, nucleic acid damage or degradation refers to
the modification of a nucleic acid base, whether native or
non-native, from its originally intended form. By way of example,
nucleic acid damage or degradation refers to a situation wherein
guanine is converted to 8-oxo-guanine, for example, by reactive
oxygen species generated during nucleic acid sample manipulation.
Other types of nucleic acid damage include, but are not limited to,
abasic sites and thymine and cytosine homo- and
heterodimerization.
[0042] An abasic site is defined as a nucleoside position in a
polynucleotide chain from which the base component has been
removed. Abasic sites can occur naturally in DNA under
physiological conditions by hydrolysis of nucleoside residues, but
may also be formed under artificial conditions. Once formed, abasic
sites may be cleaved (e.g. by treatment with an endonuclease or
other single-stranded cleaving enzyme, exposure to heat or alkali),
providing a means for site-specific cleavage of a polynucleotide
strand.
[0043] As used herein the term "light-induced degradation" means
the light-induced damage to one or more nucleic acids in an array
of nucleic acids by exposure to illumination. Such degradation
includes the complete or partial removal of individual nucleic
acids from the support to which the array is attached. For example,
light-induced degradation can include cleavage of the
phosphodiester backbone at any of the nucleotides within an
individual nucleic acid. Such degradation can also include removal
of or reaction of a nucleic acid base or fluorescent tag causing a
loss in hybridization or fluorescence function. Light-induced
degradation can also include photo-induced crosslinking of
nucleotides. The result of light-induced degradation can manifest
as a decrease in fluorescence detection sensitivity in one or more
regions or sub-arrays of an array nucleic acids when cycling
through repeated detection steps, as might be observed, for
example, when performing sequencing by synthesis, sequencing by
ligation and microarray scanning When used in conjunction with the
term "inhibiting," this refers to a complete or partial block in
the extent of damage, for example, as can be quantified by the
observed strength of fluorescent emission. Light damage can be
measured, for example, as a function of fluorescence signal
intensity versus number of repeated irradiation (detection) steps
performed on the array of nucleic acids. This process is sometimes
referred to as T intensity decay. Another assessment of light
damage can be measured as a function of error rate versus number of
repeated irradiation (detection) steps performed on the array of
nucleic acids.
[0044] As used herein the term "detection error rate" refers to a
measure of the frequency of error in the identification of one or
more fluorescently tagged nucleic acids in an array and/or
sub-array of nucleic acids. For example, when measuring
fluorescence in a scheme employing multi-color fluorescent tags, an
error can arise by misidentification of a tagged sub-array when,
for example, the signal-to-noise is eroded due to light-induced
degradation of a plurality of nucleic acid members in the
sub-array. Thus, the detection error rate is increased with the
continual loss of individual nucleic acid members of an array or
sub-array over numerous repeated cycles of irradiation.
[0045] As used herein the term "irradiating" refers to exposing an
array of nucleic acids to illumination. The exposure can be for the
purpose of fluorescence detection, for example. Irradiation can be
performed with a laser or similar light source. Irradiation can be
performed over a select section of the UV-visible spectrum and can
employ one or more wavelength band filters. Irradiating can be
performed over a period of time to collect sufficient fluorescent
emission data. The term "intense" when used in reference to
illumination refers to the amount of power that is employed during
irradiation of a portion of an array of nucleic acids. Intense
laser irradiation include an amount between about 5 milliWatts to
about 500 milliWatts and a powerdensity in an amount from between
about 1 to about 200 W/mm.sup.2.
[0046] As used herein the term "solution" refers to a solution
containing compounds or compounds described herein that reduce
fragmentation-induced nucleic acid degradation or damage. The
solution is used during preparation of a nucleic acid sample for
further manipulation in, for example, nucleic acid sequencing
techniques. Compounds or compounds for use according to the
provided methods can be supplied as a liquid or in the form of a
solid to be dissolved in a suitable solvent prior to use.
[0047] A solution as used herein can also be referred to as a
detection solution when the processing step is a detection
processing step. As used herein the term "detection solution" means
a solution containing compounds of the present invention that
reduce light-induced degradation upon exposure of an array of
nucleic acids to illumination. The detection solution is the
solution that is used during a detection step employing
irradiation.
[0048] As used herein the term "buffer," when used alone refers to
any other buffer solution not used as a detection solution. Buffer
solutions include those used in polymerase reactions,
hybridizations, washing, or any other operation performed prior to
the use of the detection solution employed in the invention.
[0049] As used herein the term "polyphenolic compound" refers to an
aromatic compound having multiple hydroxyl groups (i.e. phenolic
groups) on a benzene or other aromatic ring. The benzene, or other
aromatic ring, can be optionally substituted with other
substituents and/or fused rings. Exemplary polyphenolic compounds
include, without limitation, gallic acid and lower alkyl esters
thereof, monomethyl ethers thereof, and combinations of lower alkyl
esters and monomethyl ethers thereof, pyrogallol, and
hydroquinones, such as t-butyl hydroquinone (TBHQ),
2,4,5-trihydroxybutyrophenone (THBP).
[0050] As used herein the term "lower alkyl ester" refers to a
C1-C6 alkyl chain ester of a carboxylic acid. In some embodiments,
a "lower alkyl ester" refers to a C1-C4 alkyl chain ester of a
carboxylic acid. Representative esters include methyl, ethyl,
propyl, butyl, pentyl, and hexyl esters. Any of the forgoing esters
can be optionally branched. Such branched esters include iso-propyl
esters, sec-butyl esters, iso-butyl esters and tert-butyl esters,
for example.
[0051] In some embodiments, the present invention provides a method
of inhibiting light-induced degradation of nucleic acids during a
detection step that includes irradiating the nucleic acids in the
presence of a solution having a polyphenolic compound. The solution
inhibits the amount of light-induced degradation of the nucleic
acids.
[0052] In some embodiments, the present invention provides a method
of detecting a nucleic acid having a fluorescent tag that includes
a) irradiating the nucleic acid with light having a suitable
wavelength to induce a fluorescence emission; b) detecting said
fluorescence emission; and c) repeating steps a) and b). The
irradiating step is carried out in the presence of a detection
solution that includes a polyphenolic compound. The detection
solution inhibits light-induced degradation of the nucleic acid. In
some embodiments, the detection solution includes gallic acid, a
lower alkyl ester thereof, or mixtures thereof. In still other
embodiments, the detection solution includes a mixture of 1) gallic
acid, a lower alkyl ester thereof, or mixtures thereof and 2) one
or more compound(s) selected from urea, ascorbic acid or salt
thereof, and isoascorbic acid or salt thereof.
[0053] Methods of the present application include a solution for
use during an irradiation step. The solution includes a
polyphenolic compound which can be any aromatic system having two
or more phenolic hydroxyl groups, any one of which can also be a
lower alkyl ether. Polyphenolic compounds can belong to any number
of structural classes such as lignans, tannins, gallocatechins, and
flavanoids, such as flavonols, flavones, catechins, flavanones,
anthocyanidins, and isoflavonoids. Polyphenolic compounds of the
present invention can exist in a glycosylated form with one or more
sugar residues attached to the polyphenolic compound. Such
glycosylated forms can confer useful solubility properties in
water, for example. Exemplary polyphenolic compounds include,
without limitation, apigenin, astragalin, aurantinidin, azaleatin,
butin, caffeic acid, catechin, cyanidin, epicatechin,
epigallocatechin, gallocatechin, gallic acid and lower alkyl esters
thereof, pyrogallol, delphinidin, ellagic acid, eriodictyol,
homoeriodictyol, europinidin, fisetin, ferulic acid, galangin,
genistein gossypetin, hesperitin, hesperidin, hydroquinones, such
as p-hydroquinone, t-butyl hydroquinone (TBHQ),
2,4,5-trihydroxybutyrophenone (THBP), hydroxytyrosol, isorhamnetin,
isosakuranetin, kaempferol, kaempferide, luteolin, luteolinidin,
malvidin, myricetin, morin, naringenin, naringin, natsudaidain,
pachypodol, pelargonidin, peonidin, petunidin, phloroglucinol,
pinocembrin, poncirin, pterocarpans, pyrocatechol, quercetin,
resorcinol, rhamnazin, rhamnetin, rosinidin, rutin, sinapyl
alcohol, sakuranetin, sakuranin, sterubin, and tannic acid. In some
embodiments, the polyphenolic compound can include gallic acid, a
lower alkyl ester thereof, such as methyl gallate, ethyl gallate,
propyl gallate, monomethyl ethers thereof, and combinations of
lower alkyl esters and monomethyl ethers thereof, or mixtures
thereof.
[0054] Optionally, in the solutions of the provided methods, at
least one of the one or more compounds is ascorbic acid or a salt,
analogue, or derivative thereof. The use of ascorbate in a
detection solution for sequencing has been described in Fedurco et
al., WO2006/064199, which is incorporated by reference herein in
its entirety. Unless otherwise stated the terms ascorbate and
ascorbic acid as used herein refer to both the L-isomer and the
D-isomer, and mixtures, including racemic mixtures, thereof. Both
optical isomers are capable of functioning as compounds in the
provided methods. An exemplary salt includes sodium ascorbate, e.g.
sodium L-ascorbate. There are numerous known ascorbate analogues
and derivatives having activity which can be used in the provided
methods. Suitable derivatives and analogues include those in which
the 5- and/or 6-hydroxy group is esterified or otherwise
derivatized. Alternatively, the 5- and/or 6-hydroxy group may be
replaced with an alternative functional group, such as halo or
amino. Other derivatives are those in which the 5- and/or 6-hydroxy
group is absent and (i.e. with a hydrogen atom in place of the
hydroxyl group). Representative examples of such derivatives
include, but are not limited to, 6-O-tosyl-L-ascorbate,
5-deoxy-L-ascorbate, 6-bromo-6-deoxy-L-ascorbate,
6-amino-6-deoxy-L-ascorbate, L-ascorbic acid 6-carboxylate, and
6-O-ascorbyl alkanoates such as 6-ascorbyl palmitate (palmitoyl
ascorbate).
[0055] As mentioned above, optionally, at least one of the one or
more compounds is gallic acid, a derivative or analogue thereof or
combinations thereof. The use of gallic acid in a detection
solution for sequencing has been described in U.S. Ser. No.
13/018,255, which is incorporated by reference herein in its
entirety. Derivatives include, but are not limited to, lower alkyl
esters or monomethyl ethers of gallic acid. As used herein the term
lower alkyl ester refers to a C1-C6 alkyl chain ester of a
carboxylic acid. In some embodiments, a lower alkyl ester refers to
a C1-C4 alkyl chain ester of a carboxylic acid. Representative
esters include methyl, ethyl, propyl, butyl, pentyl, and hexyl
esters. Any of the forgoing esters can be optionally branched. Such
branched esters include iso-propyl esters, sec-butyl esters,
iso-butyl esters and tert-butyl esters, for example.
[0056] It will also be recognized that other ester derivatives of
gallic acid can be useful in the invention where sufficient water
solubility is conferred to the gallate ester. In some embodiments,
additional solubility can be realized by use of a small amount of a
co-solvent such as dimethyl sulfoxide (DMSO). By employing such
co-solvents in small quantities, the use of any gallate ester can
be effective in reducing light-induced degradation of nucleic
acids. In some embodiments, a water solubilizing ester group can be
employed, such as a PEG ester of gallic acid. In such embodiments,
the gallate ester can benefit from the improved antioxidant
activity of an ester over a carboxylic acid, without sacrificing
the useful water solubility of the carboxylic acid functional
group.
[0057] Optionally, a combination of two or more compound may be
used in the solution. Preferably, at least one of the compounds in
such combinations is gallic acid or an analogue or derivative
thereof.
[0058] The one or more compounds or compounds will be present in
the solution at a concentration range from between about 0.1 mM to
about 5 M, inclusive. For example, the one or more compounds or
compounds will be present in the solution at a concentration range
including 0.1 mM, 0.5 mM, 1 mM, 5 mM, 10 mM, 20 mM, 30 mM, 40 mM,
50 mM, 60 mM, 70 mM, 80 mM, 90 mM, 100 mM, 200 mM, 300 mM, 400 mM,
500 mM, 1M, 2M, 3M, 4M, and 5M, and any concentration in between
about 0.1 mM and about 5 M, inclusive. For example, when employing
gallic acid, its analogues, derivatives, or mixtures thereof, this
component of the solution can be present in a concentration ranging
from between about 0.1 mM to about 200 mM.
[0059] In some embodiments, degradation can include oxidative
damage, such as disclosed in Cooke et al. FASEB J. 17 (10):
1195-1214 (2003), which is incorporated herein by reference in its
entirety. For example, in the case of light-induced degradation, it
can include cleavage of the phosphodiester backbone at any of the
nucleotides of a nucleic acid. Other degradation pathways can
include the formation of 8-oxo-2'-deoxyguanosine, the removal of or
reaction of a nucleic acid base or fluorescent tag causing a loss
in hybridization or fluorescence function, and the photo-induced
cross-linking of nucleotides. Degradation by reactive oxygen
radical species such as hydroxyl radical can damage nucleic acids
by hydrogen atom abstraction processes, such as from the methyl
group of thymine or from the C--H bonds of 2'-deoxyribose. Oxygen
radical species can also oxidize nucleotides by reaction with
unsaturations in nucleic acid bases, for example.
[0060] The solution having a polyphenolic compound can inhibit
light-induced damage of nucleic acids by various mechanisms.
Without being bound by theory, the polyphenolic compound can act as
a more rapid fluorescence quencher of the excited fluorophore than
oxygen, thus reducing or preventing the formation of singlet oxygen
as indicated in Equation 1:
##STR00001##
[0061] As indicated in equation 1, singlet state excited
fluorophore S.sub.1 can react preferentially with a polyphenolic
compound (PP) in lieu of reaction with oxygen, to provide a return
of the fluorophore to the singlet ground state S.sub.0 while
forming an excited state of the polyphenolic compound (PP*). One
skilled in the art will recognize that the return to ground state
S.sub.0 can alternatively proceed via intersystem-crossing to a
triplet excited state of the fluorophore T.sub.1 (not shown). This
non-radiative pathway to the triplet state of the fluorophore can
be promoted by interaction with the polyphenolic compound.
Ultimately, the energy transferred to the polyphenolic compound can
be effectively dissipated.
[0062] Alternatively, any singlet oxygen generated by fluorescence
quenching with oxygen can react with the polyphenolic compound to
preserve the integrity of the nucleic acids. Similarly, any
reactive oxygen species such as superoxide anion or hydroxyl
radical formation formed via multiple photon absorption, as
described above, can also be quenched by the polyphenolic compound
present in the detection solution. Yet another possible mechanism
by which the polyphenolic compound can reduce or prevent
light-induced degradation is by intercepting and dissipating any
high energy UV-visible radiation generated by multiple photon
absorption by the fluorophore. In such a mechanism, the formation
of reactive oxygen species and/or the indirect pyrimidine
dimerization caused by high energy emission is reduced or
prevented. Finally, one skilled in the art will appreciate that
these high energy photochemical processes can operate in any
combination.
[0063] As described above, inhibiting these light-induced
degradation processes refers to a complete or partial blocking of
the extent of damage, for example, as can be quantified by the
observed strength of fluorescent emission with repeated exposure to
intense illumination. Light-induce degradation can be measured, for
example, as a function of fluorescence signal intensity versus
number of repeated irradiation (detection) steps performed on the
array of nucleic acids, such as in the sequencing by synthesis
examples described herein below. This process is sometimes referred
to as intensity decay. Another assessment of light-induced nucleic
acid damage can be measured as a function of error rate versus
number of repeated irradiation (detection) steps performed in an
array of nucleic acids.
[0064] Still another assessment of light-induced damage can be to
assay for nucleic acid degradation products. For example,
measurement of 8-oxo-2'-deoxyguanosine is commonly used to assess
oxidative damage to nucleic acids. Damage can also be assessed by
quantifying the degree of thymine and cytosine homo- and
heterodimerization. When employing detection methods on solid
support, the inhibition of damage can be readily assessed by
comparing arrays irradiated in the presence and absence of the
detection solution and measuring a fluorescence signal intensity
loss with repeated cycles of irradiation.
[0065] In some embodiments, methods of the present invention can be
applied to nucleic acids in solution, while in other embodiments,
methods of the invention can be applied to nucleic acids attached
to a support, such as in an array format. When employing nucleic
acids on a support, the nucleic acids can be present in ordered or
non-ordered arrays. When using the solution having a one or more of
the provided compounds, the amount of nucleic acids cleaved off a
support can be reduced. Thus, in some embodiments, the
light-induced degradation includes removal of a nucleic acid member
from an array of nucleic acids.
[0066] Optionally, the processing step is a detection processing
step and the detection processing step may include irradiating the
nucleic acids. When performing a detection step, irradiating the
nucleic acids includes the use of an appropriate light source to
excite a tag, such as a fluorescence tag. One skilled in the art
will recognize that there are numerous tags available and that the
conditions of the irradiation, such as choice of wavelength for
irradiation and detection, will be guided by the choice of tags
being employed in the nucleic acid detection process. The tags can
be the same for each type of nucleotide, or each nucleotide type
can have a unique tag. The tag is used in the identification of a
particular incorporated of nucleotide within the nucleic acid.
Thus, for example modified adenine, guanine, cytosine and thymine
can all have attached a different fluorophore to allow them to be
discriminated from one another readily. When sequencing on arrays,
a mixture of tagged and untagged nucleotides can be used. Suitable
tags include, but are not limited to, fluorescent tags, mass
labels, magnetic labels and the like. By way of example, tags
include biotin, dinitrophenol and fluorescein. Exemplary tagged
nucleotides for use in the present methods are described in WO
04/018497, and U.S. Pat. Nos. 7,541,444 and 7,057,026, which are
incorporated by reference herein in their entireties.
[0067] Detectable tags such as fluorophores can be linked to
nucleotides via the nucleic acid base using a suitable linker.
Suitable fluorophores include those described in WO 2007/135368,
which is incorporated by reference herein in its entirety. The
linker can be acid labile, photolabile or contain a disulfide
linkage. Exemplary tags and linkages include those disclosed in
WO03/048387. Other linkages, in particular phosphine-cleavable
azide-containing linkers, can be employed in the invention as
described in WO2004/018493.
[0068] Irradiation is carried out with an irradiation source which
can include, for example, a laser or other source to generate
sufficient excitation light intensity to produce detectable
emission. The irradiation source can be used in conjunction with
any combination of wavelength filters. The irradiation step can be
pulsed in some embodiments, or continuous in other embodiments. The
intensity of a light source can be in a range between about 5 milli
Watts to about 500 milli Watts. The light source can be a
high-energy short arc-discharge lamp for example. Exemplary
discharge lamps include mercury burners, ranging in wattage from 50
to 200 Watts, and the xenon burners that range from 75 to 150
Watts, and LEDs. The exact choice of light source intensity can
depend on the extinction coefficient of the fluorophore. Larger
extinction coefficients indicate that the absorption of a photon,
also referred to as quanta, at a given wavelength region is more
likely. The quantum yield denotes the ratio of photons emitted to
photons absorbed, and is usually a value between 0.1 and 1.0. The
quantum yield is a measure of emission efficiency. Quantum yield
values below 1 result from the loss of energy through non-radiative
pathways, such as heat or a photochemical reaction, rather than
fluorescence emission. Extinction coefficient, quantum yield, the
intensity of the light source, and fluorescence lifetime are all
important factors that contribute to the intensity and utility of
fluorescence emission.
[0069] Methods of the invention can include an irradiation step
conducted in a range from about 360 nm to about 800 nm, with a
light source having power in a range between about 5 to about 500 m
watts. As described above, between about 360 to about 800 nm,
light-induced degradation can be ameliorated by the presence of the
detection solution. This facilitates the use of multiple
fluorophores for simultaneous fluorescent emission detection. Thus,
method of the invention can be carried out while incorporating the
four common bases with differential tags. The irradiation step can
be conducted for a time period of about 0.1 seconds to about 10
minutes. 175-500 ms on GA, 2 mm/s scan speed. Such irradiation
times can include pulsed or continuous irradiation.
[0070] When performing multiple steps incorporating differentially
labeled nucleotides, methods of the invention can include replacing
a solution with the provided solution (e.g., detection solution)
prior to the irradiation step. For example, in sequencing by
synthesis the solution used in adding the tagged nucleotide can be
replaced with the detection solution prior to irradiation. In other
embodiments, the detection solution can be used throughout each of
the steps in sequencing by synthesis, including wash steps, in
addition to the detection step.
[0071] Fluorescent light emitted from the fluorophore can be
detected at the appropriate wavelength using a suitable detection
system such as, for example, a Charge-Coupled-Device (CCD) camera,
which can optionally be coupled to a magnifying device, a
fluorescent imager or a confocal microscope. An alternate suitable
detection system employs a complementary metal-oxide-semiconductor
(CMOS) detector. If sequencing is carried out on an array,
detection of an incorporated base can be carried out by using a
confocal scanning microscope to scan the surface of the array with
a laser, to image fluorescent labels attached to the incorporated
nucleotides. Alternatively, a sensitive 2-D detector, such as a
charge-coupled detector (CCD), can be used to visualize the signals
generated. This technique is particularly useful with single
molecule arrays. Other techniques such as scanning near-field
optical microscopy (SNOM) are available and can be used when
imaging dense arrays. For a description of scanning near-field
optical microscopy, see Moyer et al., Laser Focus World 29:10,
1993. An additional technique that can be used is surface-specific
total internal reflection fluorescence microscopy (TIRFM); see, for
example, Vale et al., Nature, (1996) 380: 451-453).
[0072] When employing solutions of the invention to sequencing by
synthesis, for example, the method can include adding an additional
fluorescently tagged nucleotide to the array and repeating the
detection steps each cycle. Methods of the invention employing
repeated nucleotide addition and detection steps can include at
least 25 cycles in some embodiments, at least 75 cycles in other
embodiments, and at least 100 cycles in yet other embodiments.
Methods of the invention include repeating adding and detection
steps for a number of cycles in a range from between about 100
cycles to about 1,000 cycles, in some embodiments, from between
about 100 cycles to about 500 cycles, in other embodiments, and
from between about 100 cycles to about 300 cycles, in yet other
embodiments.
[0073] The ability to accurately sequence 25 or more, 50 or more,
75 or more, or 100 or more consecutive nucleotides in a sequencing
reaction is a significant advantage in applications such as genome
re-alignment.
[0074] In some embodiments, an array of nucleic acids includes a
primer template. Nucleic acid "sequencing-by-synthesis" involves
sequential addition of one or more nucleotides to a growing
polynucleotide chain in the 5' to 3' direction using a polymerase
in order to form an extended polynucleotide chain complementary to
a template nucleic acid to be sequenced. Exemplary sequencing
methods are described, for example, in Bentley et al., Nature
456:53-59 (2008), WO 04/018497; U.S. Pat. No. 7,057,026; WO
91/06678; WO 07/123,744; U.S. Pat. No. 7,329,492; U.S. Pat. No.
7,211,414; U.S. Pat. No. 7,315,019; U.S. Pat. No. 7,405,281, and US
2008/0108082, each of which is incorporated herein by reference.
The identity of the base present in one or more of the added
nucleotide (s) is determined in the detection step. The identity of
the added base can be determined after each nucleotide
incorporation step. The sequence of the template can then be
inferred using conventional Watson-Crick base-pairing rules. For
the avoidance of doubt "sequencing" can also encompass
incorporation and identification of a single nucleotide.
Determination of the identity of a single base can be useful, for
example, in the scoring of single nucleotide polymorphisms.
[0075] The nucleic acid template for a sequencing reaction can
include a double-stranded region having a free 3' hydroxyl group
which serves as a primer or initiation point for the addition of
further nucleotides in the sequencing reaction. The region of the
template to be sequenced will overhang this free 3' hydroxyl group
on the complementary strand. The primer bearing the free 3'
hydroxyl group can be added as a separate component (e.g. a
conventional oligonucleotide sequencing primer) which hybridizes to
a region of the template to be sequenced. Alternatively, the primer
and the template strand to be sequenced can each form part of a
partially self-complementary nucleic acid strand capable of forming
an intramolecular duplex, such as for example a hairpin loop
structure. Nucleotides are added successively to the free 3'
hydroxyl group, resulting in synthesis of a polynucleotide chain in
the 5' to 3' direction. After each nucleotide addition the nature
of the base which has been added can be determined, thus providing
sequence information for the nucleic acid template.
[0076] Incorporation of a nucleotide into a nucleic acid strand (or
polynucleotide) refers to joining of the nucleotide to the free 3'
hydroxyl group of the nucleic acid strand via formation of a
phosphodiester linkage with the 5' phosphate group of the
nucleotide. The nucleic acid template to be sequenced can be DNA or
RNA, or even a hybrid molecule that includes both deoxynucleotides
and ribonucleotides. The nucleic acid can include naturally
occurring and/or non-naturally occurring nucleotides and natural or
non-natural backbone linkages.
[0077] Nucleic acid templates to be sequenced can be attached to a
solid support via any suitable linkage method known in the art.
Linkage can be via covalent attachment, for example. If the
templates are "arrayed" on a solid support then the array can take
any convenient form. Thus, the method of the invention is
applicable to all types of "high density" arrays, including
single-molecule arrays and clustered arrays.
[0078] In some embodiments, the solution reduces a detection error
rate, when sequencing, by greater than 20% relative to a control
lacking the compound. The detection error rate is further reduced
in the presence of one or more compound(s) selected from urea,
ascorbic acid or salt thereof, and isoascorbic acid or salt thereof
in the solution. In further embodiments, the solution reduces a
detection error rate by greater than 40% relative to a control
lacking the polyphenolic compound, which error rate is also
enhanced by the presence of one or more compound(s) selected from
urea, ascorbic acid or salt thereof, and isoascorbic acid or salt
thereof. In still further embodiments, the solution reduces a
detection error rate by greater than 50% relative to a control
lacking the polyphenolic compound.
[0079] Error rates can be determined, for example, as described in
Bentley, et al., "Accurate whole human genome sequencing using
reversible terminator chemistry" Nature 456:53-59 (2008). The error
rate is the sequencing error per cycle as determined by alignment
of the phiX sequence against a phiX standard genome using the ELAND
algorithm that is part of the standard pipeline analysis as
described in the Pipeline User Guide (Illumina, Inc., San Diego,
Calif.) and Bentley et al., Nature 456:53-59 (2008).
[0080] In some embodiments, the present invention provides a method
of inhibiting light-induced degradation of nucleic acids during a
detection step that includes irradiating a portion of the nucleic
acids in the presence of a solution that includes gallic acid,
analogues, derivatives, a lower alkyl ester thereof, or mixtures
thereof. The solution reduces the amount of light-induced
degradation of the nucleic acids. The use of gallic acid and its
derivatives are shown below in Examples I and II. Gallic acid in
its free form is capable of ionizing to carboxylate and its
effectiveness as an inhibitor of light-induced degradation can
therefore be dependent on the pH of the system. By comparison,
lower gallate esters can demonstrate a relatively constant
effectiveness over a range of pHs.
[0081] Without being bound by theory, one skilled in the art will
recognize that a carboxylic acid group is modestly more electron
withdrawing than an ester. Thus, if gallic acid and related
compounds are serving in an antioxidant role, one might expect an
ester to perform slightly better than a carboxylic acid in reducing
light-induced degradation. However, this benefit of gallate esters
can be ameliorated by the need for water solubility of the ester.
In this regard, the ionizable carboxylic acid is useful to confer
water solubility. As such, in some embodiments, detection solutions
of the present invention provide gallic acid, lower alkyl esters of
gallic acid, or mixtures thereof.
[0082] One skilled in the art will also recognize that other ester
derivatives of gallic acid can be useful in the invention where
sufficient water solubility is conferred to the gallate ester. In
some embodiments, additional solubility can be realized by use of a
small amount of a co-solvent such as dimethyl sulfoxide (DMSO). By
employing such co-solvents in small quantities, the use of any
gallate ester can be effective in reducing light-induced
degradation of nucleic acids. In some embodiments, a water
solubilizing ester group can be employed, such as a PEG ester of
gallic acid. In such embodiments, the gallate ester can benefit
from the improved antioxidant activity of an ester over a
carboxylic acid, without sacrificing the useful water solubility of
the carboxylic acid functional group.
[0083] In yet further embodiments, the present invention provides a
method of inhibiting light-induced degradation of nucleic acids
during a detection step that includes the nucleic acids in the
presence of a detection solution that includes 1) gallic acid, a
lower alkyl ester thereof, or mixtures thereof, and 2) one or more
compound(s) selected from urea, ascorbic acid or salt thereof, and
isoascorbic acid or salt thereof. This detection solution reduces
the amount of light-induced degradation of the nucleic acids. As
demonstrated in Examples I and II, urea has shown a synergism in
reducing light-induced degradation of nucleic acids. Unsubstituted
urea, (NH.sub.2).sub.2CO, is not generally classified as an
antioxidant, and thus the role of urea in providing a synergistic
effect in reducing light-induced degradation is not readily
attributable to antioxidant activity. For example, it has been
indicated that urea affords no apparent protection against reactive
oxygen species at physiological concentrations (Glazer, FASEB J.
2:2487-2491 (1988)). Moreover, it has been indicated that urea
affords no apparent protection against reaction with singlet oxygen
(Dahl et al. Photochem. Photobiol. 47(3):357-362 (1988)). Urea
absorbs in the UV-visible region substantially only below 245 nm.
In this region of the UV spectrum pyrimidine dimerization is a
significant pathway with respect to light-induced nucleic acid
damage. However, the role of urea in providing additional
protection against light-induced damage under the conditions of
fluorescence detection, as provided in the Examples, are not yet
fully understood.
[0084] In some embodiments, the present invention is directed to a
kit for use in accordance with the aforementioned methods. Thus,
provided herein is a kit that can include one or more of the
compounds and (i) antibodies, and/or (ii) enzymes described herein
and combinations thereof. The compounds can include gallic acid,
analogues, derivatives, a lower alkyl ester thereof, or mixtures
thereof. In some embodiments, the kit can further include
additional compounds, buffers or other agents and/or a set of
instructions for carrying out preparation of a solution for use in
nucleic acid sample preparation. Additionally or alternatively, the
kit can include one or more nucleotides, an enzyme capable of
catalyzing incorporation of the nucleotides into a nucleic acid
strand complementary to a nucleic acid template to be sequenced,
and a polyphenolic compound suitable for preparing a solution. The
polyphenolic compound can include gallic acid, analogues,
derivatives, a lower alkyl ester thereof, or mixtures thereof. In
some embodiments, the kit further includes a secondary compound
selected from urea, ascorbic acid or salt thereof, and isoascorbic
acid or salt thereof. The kit can further include buffer salts and
a set of instructions for carrying out preparation of a solution
for use in fluorescence experiments.
[0085] Embodiments described herein can be used in a variety of
known methods and/or compositions for detecting nucleic acids,
wherein light-induced degradation of nucleic acids occurs or is
suspected to occur. For example, the methods and compositions
described herein are particularly useful when a detection method
requires repeated or prolonged exposure of nucleic acids to light.
In particular, detection of fluorescently tagged nucleic acids is
often used by irradiating a sample with light that has a suitable
wavelength to induce a fluorescent emission from a nucleic acids
that contains a fluorescent tag. During the irradiation steps of
these methods, as described herein, damage to the nucleic acids can
occur. The repeated or prolonged exposure can result in a decrease
in fluorescence detection sensitivity, which can manifest, for
example, as an increase in detection error rates and reduced
signal-to-noise ratios. Non-limiting examples of methods wherein
the methods and/or compositions for detecting nucleic acids that
have repeated or prolonged exposure to light include high
throughput or rapid sequencing techniques such as, sequencing by
synthesis and sequencing by ligation, nucleic acid microarray
detection techniques such as, gene chips and DNA microarrays, and
quantitative polymerase chain reaction (Q-PCR) techniques such as,
real time polymerase chain reaction (PCR) and multiplex PCR.
[0086] One useful method for high throughput or rapid sequencing is
sequencing by synthesis (SBS). SBS techniques that require repeated
or prolonged irradiation of nucleic acids with light include, but
are not limited to, the Genome Analyzer systems (Illumina Inc., San
Diego, Calif.) and the True Single Molecule Sequencing (tSMS).TM.
systems (Helicos BioSciences Corporation, Cambridge, Mass.).
Briefly, a number of sequencing by synthesis reactions are used to
elucidate the identity of a plurality of bases at target positions
within a target sequence. All of these reactions rely on the use of
a target nucleic acid sequence having at least two domains; a first
domain to which a sequencing primer will hybridize, and an adjacent
second domain, for which sequence information is desired. Upon
formation of an assay complex, extension enzymes are used to add
dNTPs to a sequencing primer that is hybridized to first domain,
and each addition of dNTPs is read to determine the identity of the
added dNTP. This may proceed for many cycles. SBS techniques such
as, the Genome Analyzer systems (Illumina Inc., San Diego, Calif.)
and the True Single Molecule Sequencing (tSMS).TM. systems (Helicos
BioSciences Corporation, Cambridge, Mass.), utilize labeled
nucleotides to determine the sequence of a target nucleic acid
molecule. A target nucleic acid molecule can be hybridized with a
primer and incubated in the presence of a polymerase and a labeled
nucleotide containing a blocking group. The primer is extended such
that the nucleotide is incorporated. The presence of the blocking
group permits only one round of incorporation, that is, the
incorporation of a single nucleotide. The presence of the label
permits identification of the incorporated nucleotide. A plurality
of homogenous single nucleotide bases can be added during each
cycle, such as used in the True Single Molecule Sequencing
(tSMS).TM. systems (Helicos BioSciences Corporation, Cambridge,
Mass.) or, alternatively, all four nucleotide bases can be added
during each cycle simultaneously, such as used in the Genome
Analyzer systems (Illumina Inc., San Diego, Calif.), particularly
when each base is associated with a distinguishable label. After
identifying the incorporated nucleotide by its corresponding label,
both the label and the blocking group can be removed, thereby
allowing a subsequent round of incorporation and identification.
Determining the identity of the added nucleotide base includes
repeated exposure of the newly added labeled bases a light source
that can induce a detectable emission due the addition of a
specific nucleotide base, i.e. dATP, dCTP, dGTP or dTTP. The
methods and compositions disclosed herein are particularly useful
for such SBS techniques.
[0087] Another useful method for high throughput or rapid
sequencing technique is sequencing by ligation. Sequencing by
ligation is a well known method for sequencing that requires
repeated or prolonged irradiation of di-base probes with light.
Exemplary systems that use sequencing by synthesis include the
SOLiD.TM. system by Applied Biosystems (Life Technologies,
Carlsbad, Calif.). Briefly, methods for sequencing by ligation
include hybridizing sequencing primers to adapter sequences
immobilized to templated beads. A set of four fluorescently labeled
di-base probes compete for ligation to the sequencing primer.
Specificity of the di-base probe is achieved by interrogating every
1st and 2nd base in each ligation reaction. Following a series of
ligation cycles, the extension product is removed and the template
is reset with a sequencing primer complementary to the n-1 position
for a second round of ligation cycles. Multiple cycles of ligation,
detection and cleavage are performed with the number of cycles
determining the eventual read length. Sequencing by ligation
methods have been developed by Applied Biosystems in its Agencourt
platform (see Ronaghi et al., Science 281:363 (1998); Dressman et
al., Proc. Natl. Acad. Sci. USA 100:8817-8822 (2003); Mitra et al.,
Proc. Natl. Acad. Sci. USA 100:55926-5931 (2003)).
[0088] In addition, the methods and solutions described herein can
be particularly useful for sequencing from an array of nucleic
acids, where multiple sequences can be read simultaneously from
multiple positions on the array since each nucleotide at each
position can be identified based on its identifiable label.
Exemplary methods are described in US 2009/0088327; US
2010/0028885; and US 2009/0325172, each of which is incorporated
herein by reference.
[0089] Other methods know in the art where repeated or prolonged
irradiation of nucleic acids with light include nucleic acid
microarray detection techniques, such as gene chips and DNA
microarrays. It is well known in the art that reliability and
consistency problems exist when scanning nucleic acid microarrays,
particularly when scanning the same microarray more than once.
However, multiple scans can be required in order to obtain the full
dynamic range of the labeled nucleic acids, for example, when using
a microarray to determine gene expression levels. A single scan
attempts to capture the whole range of expression in the given
samples. This may not give the true picture of the expression of
the whole set of genes when a wide range of expression is present.
For example, a gene in the sample may express as few as 200 copies,
whereas a separate gene in the same sample may express 50,000
copies. In this aspect, the methods and compositions described
herein are particularly useful in maintaining the integrity of the
nucleic acids over multiple scans.
[0090] Examples of nucleic acid microarray detection techniques
known in the art include, but are not limited to, LabCard (ACLARA
Bio Sciences Inc., Santa Clara, Calif.); GeneChip (Affymetrix, Inc,
Santa Clara, Calif.); LabChip (Caliper Technologies Corp,
Hopkinton, Mass.); microarrays produced by SurePrint technology
(Agilent Technologies, Santa Clara, Calif.); a low-density array
with electrochemical sensing (Clinical Micro Sensors Inc.,
Pasadena, Calif.); LabCD System (Tecan Trading AG, Zurich,
Switzerland.); Omni Grid (Gene Machines, Stillwater, Okla.); Q
Array (Genetix Ltd., Boston, Mass.); a high-throughput, automated
mass spectrometry systems with liquid-phase expression technology
(GeneTrace Systems, Inc., Menlo Park, Calif.); a thermal jet
spotting system (Hewlett Packard Company; Palo Alto, Calif.); Hyseq
HyChip (Hyseq, Inc., Sunnyvale, Calif.); BeadArray (Illumina, Inc.,
San Diego, Calif.); GEM (Incyte Microarray Systems, Fremont,
Calif.); a high-throughput microarrying system that can dispense
from 12 to 64 spots onto multiple glass slides (Intelligent
Bio-Instruments, Waltham, Mass.); Molecular Biology Workstation and
NanoChip (Nanogen, Inc., San Diego, Calif.); a micro fluidic glass
chip (Orchid Cellmark, Inc., Dayton, Ohio); BioChip Arrayer with
four PiezoTip piezoelectric drop-on-demand tips (Packard
Instruments, Inc., Meriden, Conn.)); FlexJet (Rosetta Inpharmatic,
Inc., Kirkland, Wash.); MALDI-TOF mass spectrometer (Sequenome, San
Diego, Calif.); ChipMaker 2 and ChipMaker 3 (Arrayit Corporation,
Sunnyvale, Calif.); and GenoSensor (Abbot Molecular, Des Plaines,
Ill.) as identified and described in Heller, Annu. Rev. Biomed.
Eng. 4:129-153 (2002). Examples of gene chips or a microarrays are
also described in U.S. Patent Publ. Nos.: 2007-0111322,
2007-0099198, 2007-0084997, 2007-0059769 and 2007-0059765 and U.S.
Pat. Nos. 7,138,506, 7,070,740, and 6,989,267.
[0091] Quantitative polymerase chain reaction (Q-PCR) techniques
such as, real time polymerase chain reaction (PCR) and multiplex
PCR are well known methods of characterizing and quantifying
nucleic acids. Such techniques require repeated or prolonged
exposure of nucleic acids to light, wherein the methods and
compositions described herein are useful for inhibiting
light-induce degradation. Five of the most popular chemistries for
performing real-time PCR and/or multiplex PCR include TagMan.RTM.
(Life Technologies, Carlsbad, Calif.), Molecular Beacons, FRET
probes, Scorpions.RTM. (Sigma-Aldrich, Inc, St. Louis, Mo.) and
SYBR.RTM. Green (Life Technologies, Carlsbad, Calif.). All of these
chemistries allow detection of PCR products via the generation of a
fluorescent signal. TagMan.RTM. probes, Molecular Beacons, FRET
probes and Scorpions.RTM. depend on Forster Resonance Energy
Transfer (FRET) to generate the fluorescence signal via the
coupling of a fluorogenic dye molecule and a quencher moiety to the
same or different oligonucleotide substrates. SYBR.RTM. Green is a
fluorogenic dye that exhibits little fluorescence when in solution,
but emits a strong fluorescent signal upon binding to
double-stranded DNA.
[0092] TagMan.RTM. probes depend on the 5'-nuclease activity of the
DNA polymerase used for PCR to hydrolyze an oligonucleotide that is
hybridized to the target amplicon. TagMan.RTM. probes are dual
labeled oligonucleotides that have a fluorescent reporter dye
attached to the 5' end and a quencher moiety coupled to the 3' end.
Typically, TagMan.RTM. probes consist of a 18-22 bp oligonucleotide
probe. These probes are designed to hybridize to an internal region
of a PCR product. In the unhybridized state, the proximity of the
fluorescent reporter dye and the quench molecules prevents the
detection of fluorescent signal from the probe. When conducting a
real time PCR experiment, a TagMan.RTM. probe, complementary to the
target sequence is added to the PCR reaction mixture. During PCR,
the probe anneals specifically between the forward and reverse
primer to an internal region of the PCR product. When the
polymerase replicates a template on which a TagMan.RTM. probe is
bound, the 5'-nuclease activity of the polymerase cleaves the
probe. This decouples the fluorescent and quenching dyes and FRET
no longer occurs. Thus, fluorescence increases in each cycle,
proportional to the amount of probe cleavage.
[0093] Like TaqMan.RTM. probes, Molecular Beacons also use FRET to
detect and quantitate the synthesized PCR product via a fluorophore
coupled to the 5' end and a quench attached to the 3' end of an
oligonucleotide substrate. A Molecular Beacon consists of 4 parts,
namely a loop, stem, a 5' fluorophore and a 3' quencher. The loop
is typically a 18-30 base pair region of the molecular beacon which
is complementary to the target sequence. The stem sequence lies on
both ends of the loop and is typically 5-7 bp long. Both the stem
sequences are complementary to each other. The 5' end of the
Molecular Beacon contains a fluorophore and the 3' end of the
molecular beacon contains a quencher dye that when the beacon is in
a closed loop shape, prevents the fluorophore from emitting light.
When a Molecular Beacon hybridizes to a target, the fluorescent dye
and quencher are separated, FRET does not occur, and the
fluorescent dye emits light upon irradiation. However, unlike
TaqMan probes, Molecular Beacons are designed to remain intact
during the amplification reaction, and must rebind to the target in
every cycle for signal measurement. Molecular beacons can report
the presence of specific nucleic acids from a homogeneous solution.
For quantitative PCR, molecular beacons bind to the amplified
target following each cycle of amplification and the resulting
signal is proportional to the amount of template.
[0094] FRET probes are a pair of fluorescent probes designed to
hybridize to adjacent regions on the target DNA as described by
Didenko, Biotechniques 31(5):1106-1121 (2001). Fluorophores are so
chosen that the emission spectrum of one overlaps significantly
with the excitation spectrum of the other. During PCR, the two
different oligonucleotides hybridize to adjacent regions of the
target DNA such that the fluorophores, which are coupled to the
oligonucleotides, are in close proximity in the hybrid structure.
The donor fluorophore is excited by an external light source, then
passes part of its excitation energy to the adjacent acceptor
fluorophore. The excited acceptor fluorophore emits light at a
different wavelength which can then be detected in specific
channels and measured. The light source cannot excite the acceptor
dye.
[0095] With Scorpion.RTM. probes, sequence-specific priming and PCR
product detection is achieved using a single oligonucleotide as
described in Bates et al., Molecular Plant Pathology 2(5):275-280
(2001); Hart et al., J. Clin. Microbiol. 39(9):3204-12 (2001), and
Thelwell et al., Nucleic Acids Research 28(19):3752-61 (2000).
Scorpion.RTM. primers are bi-functional molecules in which a primer
is covalently linked to the probe. The Scorpion.RTM. probe
maintains a stem-loop configuration in the unhybridized state. A
fluorophore is attached to the 5' end and is quenched by a moiety
coupled to the 3' end. The 3' portion of the stem also contains
sequence that is complementary to the extension product of the
primer. This sequence is linked to the 5' end of a specific primer
via a non-amplifiable monomer. In the absence of the target, the
quencher nearly absorbs the fluorescence emitted by the
fluorophore. In the initial PCR cycles, the primer hybridizes to
the target and extension occurs due to the action of polymerase.
After extension of the Scorpion.RTM. primer, the specific probe
sequence is able to bind to its complement within the extended
amplicon thus opening up the hairpin loop and separating the
fluorophore and the quencher, which leads to an increase in
fluorescence emitted. The fluorescence can be detected and measured
in the reaction tube during each successive cycle of
amplification.
[0096] SYBR.RTM. Green provides one of the simplest and most
economical format for detecting and quantitating PCR products in
real-time reactions. SYBR.RTM. Green is an asymmetrical cyanine dye
as described by Zipper et al., Nucleic Acids Res. 32(12):e103
(2004). SYBR.RTM. Green preferentially binds double-stranded DNA,
but will stain single-stranded DNA with lower performance. The
resulting DNA-dye-complex absorbs blue light (.lamda.max=488 nm)
and emits green light (.lamda.max=522 nm). Since the dye
preferentially binds to double-stranded DNA, there is no need to
design a probe for any particular target being analyzed. However,
detection by SYBR Green requires extensive optimization. Since the
dye cannot distinguish between specific and non-specific product
accumulated during PCR, as any PCR product accumulates,
fluorescence increases. The advantages of SYBR.RTM. Green are that
it is inexpensive, easy to use, and sensitive. The disadvantage is
that SYBR.RTM. Green will bind to any double-stranded DNA in the
reaction, including primer-dimers and other non-specific reaction
products, which results in an overestimation of the target
concentration. For single PCR product reactions with well designed
primers, SYBR.RTM. Green can work extremely well, with spurious
non-specific background only showing up in very late cycles.
Similar cyanine dyes are known in the art and include SYBR.RTM.
Green II, SYBR Gold, YO (Oxazole Yellow), TO (Thiazole Orange), and
PG (PicoGreen).
[0097] TagMan.RTM. probes, Molecular Beacons and Scorpions.RTM.
allow multiple DNA species to be measured in the same sample, also
known as multiplex PCR, since fluorescent dyes with different
emission spectra may be attached to the different probes. Multiplex
PCR allows internal controls to be co-amplified and permits allele
discrimination in single-tube, homogeneous assays. These
hybridization probes afford a level of discrimination impossible to
obtain with SYBR Green, since they will only hybridize to true
targets in a PCR and not to primer-dimers or other spurious
products. However, multiplex PCR will also require additional
repeated and prolonged irradiation steps in order quantitate the
multiple fluorescent emissions from a single sample. Accordingly,
the methods and compositions described herein are useful for
inhibiting light-induced nucleic acid degradation.
[0098] Disclosed are materials, compositions, and components that
can be used for, can be used in conjunction with, can be used in
preparation for, or are products of the disclosed methods and
compositions. These and other materials are disclosed herein, and
it is understood that when combinations, subsets, interactions,
groups, etc. of these materials are disclosed that while specific
reference of each various individual and collective combinations
and permutation may not be explicitly disclosed, each is
specifically contemplated and described herein. For example, if a
chimeric animal is disclosed and discussed and a number of
modifications that can be made to the chimeric animal are
discussed, each and every combination and permutation of the
chimeric animal, and the modifications that are possible are
specifically contemplated unless specifically indicated to the
contrary. Likewise, any subset or combination of these is also
specifically contemplated and disclosed. This concept applies to
all aspects of this disclosure including, but not limited to, steps
in methods of using the disclosed compositions or animals. Thus, if
there are a variety of additional steps that can be performed it is
understood that each of these additional steps can be performed
with any specific method steps or combination of method steps of
the disclosed methods, and that each such combination or subset of
combinations is specifically contemplated and should be considered
disclosed.
[0099] Throughout this application, various publications are
referenced. The disclosures of these publications in their
entireties are hereby incorporated by reference into this
application.
[0100] A number of embodiments have been described. Nevertheless,
it will be understood that various modifications may be made.
Accordingly, other embodiments are within the scope of the claims
below.
EXAMPLES
Example I
Error Rate and 20 Cycle Intensity
[0101] This Example shows error rates with repeated detection
cycles in a sequencing by synthesis format using an eight lane
flowcell. The data in this example was generated using the standard
procedure of setting up a sequencing run on HiSeq instruments
(Illumina Inc., San Diego, Calif.) according to the HiSeq UserGuide
and using standard Illumina Sequencing reagents, except for the
detection solution. Methods for the standard protocols are
available from Illumina, Inc. and referenced in Bentley et al.,
Nature 456:53-59 (2008), which is incorporated by reference herein
in its entirety. Briefly, a plurality of fluorescently labeled
modified nucleotides is used to sequence clusters of amplified DNA
present on the surface of a flow cell. To initiate the first
sequencing cycle, one or more differently labeled nucleotides, and
appropriate reagents, e.g., DNA polymerase, etc., are flowed
into/through the flow cell by a fluid flow system. After
incorporation, non-incorporated nucleotides are washed away by
flowing a wash solution through the flow cell. A detection solution
is then flowed through the flow cell while lasers are used to
excite the nucleic acids and induce fluorescence. A deblocking
reagent is then added to the flow cell to remove reversible
terminator groups from the DNA strands that were extended and
detected. The deblocking reagent is then washed away by flowing a
wash solution through the flow cell. The flow cell is then ready
for a further cycle of sequencing starting with introduction of a
labeled nucleotide as set forth above. The fluidic and detection
steps are repeated several times to complete a sequencing run.
[0102] To generate the detection solution used in the experiments,
the test compounds were added from powder to the detection solution
to the indicated final solutions in Table 1 and the pH was checked
and adjusted if needed. The "Image_Cycle_Pump" feature was used to
test 3 compounds per run such that lanes 1 and 2 were scanned in
control detection solution, lanes 3 and 4 in detection solution
containing a first test compound, lanes 5 and 6 in detection
solution containing a second test compound and lanes 7 and 8 in
detection solution containing a third test compound. The intensity
decay and error rates were compared between the lanes that received
control detection solution and those that received detection
solution containing the test compounds.
Example II
Error over Cluster PF
[0103] This Example shows a gallic acid dose response using 20
(lanes 3 and 4) 40 (lanes 5 and 6) and 80 mM (lanes 7 and 8) with
lanes 1 and 2 being the no gallic acid controls.
[0104] This experiment was carried out exactly as described above
in Example I. FIG. 3 shows a graph plotting error versus cluster
passing filter (PF) number. The graph in FIG. 3 shows a significant
dose-dependent improvement in error rates (y axis) for all gallic
acid concentrations. The graphs also shows an improvement in
clusters passing filters with an optimum of 40 mM-at 80 mM the
number of clusters passing filter is reduced compared to 40 mM.
Example III
Coverage Plots
[0105] This Example shows the errors per position in a reference
sequence.
[0106] This experiment was carried out exactly as described in
Example I. FIG. 4 shows coverage plots for a control sequence, in
the presence of gallic acid, in the presence of urea, and in the
presence of gallic acid and urea, over 75 cycles. FIG. 5 shows
coverage plots for a control sequence, in the presence of gallic
acid, in the presence of urea, and in the presence of gallic acid
and urea, over 100 cycles. Coverage plots analyze error (Y axis)
per position in a given genome (x axis, using phiX genome as
standard). The data shows that the phiX genome contains hot-spots
with significantly higher error rate than the rest of the genome.
Gallic acid in the detection solution reduces the error rate
certain hot spot significantly while not affecting other hot spot
as much. Urea by itself has very little effecting reducing the
error rates but show a remarkable synergy with gallic acid that
almost eliminates the error in most hotspots and even lowers the
error of the dominant hot spot (around position 4300) while each of
the compounds alone have no effect.
TABLE-US-00001 TABLE 1 Entry Concentration Error cycle20 number
Compound mM Rate Int 1 1,4-Dihydroxy-2,6-dimethoxybenzene 10 0.81
73.91 2 1,4-Dihydroxy-2-Naphthoic Acid 10 5.22 64.32 3
2,2,6,6-Tetramethyl-4-piperidinol 10 3.11 50.47 4 2,3 Dihydroxy
Benzoic Acid 50 0.63 78.86 5 3,5 Dihydroxy Benzoic Acid 10 0.62
75.66 6 3,4 Dihydroxy Benzoic Acid 10 0.73 78.60 7
2-Phenyl-5-benzimidazole sulfonic acid 30 0.97 79.28 8
3,4,5-Trihydroxybenzamide 10 2.08 76.71 9 3,4-Diaminobenzoic acid
10 2.01 80.47 10 3-Aminobenzoic Acid 10 0.33 75.59 11
3-Amino-4-Hydroxybenzoic Acid 10 1.66 80.72 12 3-Hydroxybenzoic
Acid 10 2.23 70.79 13 3-Hydroxy-4-Nitrobenzoic Acid 10 3.72 73.50
14 3-Hydroxyanthranilic Acid 10 0.85 81.59 15 3-HydroxyCinnamic
Acid 10 1.49 76.84 16 4-Aminosalicylic Acid 10 1.75 80.08 17
4-Amino Benzoic Acid 10 0.57 74.85 18 4-Amino3-Hydroxybenzoic Acid
10 1.61 79.21 19 4-Amino-3-Methoxybenzoic acid 10 2.36 74.98 20
4-Hydroxybenzoic Acid 10 2.01 74.76 21 4-Hydroxy-3-Nitrobenzoic
acid 10 3.09 75.91 22 4-Hydroxycinnamic Acid 10 1.92 68.78 23
5-benzoyl-4-hydroxy-2-methoxy benzene sulfonic acid 10 2.58 75.53
24 1-Aza-3,7-dioxabucyclo{3,3,0]-octane-5-methanol 30 0.38 78.19 25
Benzoic Acid 100 2.24 71.98 26 Bis
[2,2,6,6-Tetramethyl-4-piperidone] sebacate 20 0.92 76.17 27
Caffeic Acid 10 0.41 76.60 28 Catechol 10 1.58 78.54 29 Chlorogenic
Acid 10 0.86 79.65 30 1,4-Diazabicyclo[2,2,2]octane 10 1.02 76.32
31 Diaminotoluene sulfate 10 0.56 76.08 32 Diethyldithiocarbamate
25 1.39 76.28 33 N,N-Diethylhydroxylamine 30 0.43 78.94 34
Diethyldithiocarbamate 10 1.46 79.30 35 N,N-Diethylhydroxylamine 10
1.41 76.66 36 1,4-Dimethylpiperazine 10 1.03 76.17 37
Diethylenetriaminepentaacetic acid 10 1.28 68.53 38
5-Ethoxysalicylic acid 10 0.50 75.31 39 Ethylgallate 10 0.36 85.89
40 Ferulic Acid 10 0.77 72.58 41 Gallic Acid 100 1.39 87.37 42
Gallic acid 200 0.82 78.83 43 Gallic acid 20 0.58 84.30 44 Gallic
Acid 50 0.39 84.98 45 Glutathione 10 0.75 74.70 46 Histidine 10
0.92 76.18 47 5-methoxysalicylic acid 10 0.76 73.57 48 Hesperidin
methyl chalcone 30 0.26 79.84 49 Hydrazine 10 0.63 75.32 50
Hydroquinone 10 0.92 79.48 51 Laurylgallate 10 1.69 65.94 52
.alpha.-Lipoic acid 10 1.01 76.32 53 .beta.-Mercaptoethylamine
hydrochloride 10 1.75 72.29 54 Melatonin 1 0.43 72.42 55 Methyl
3,4,5-trihydroxy-benzoate 20 0.97 82.34 56 Methyl
3,4,5-trihydroxy-benzoate 10 0.47 82.60 57 Methoxyhydroquinone 10
0.90 77.17 58 N-AcetylCysteine 10 2.97 76.56 59
Nordihydroguaiaretic Acid 10 1.25 68.60 60 2Phenylbenzimidazole
sulfonic acid 30 0.30 78.37 61 p-Coumaric Acid 10 1.63 77.05 62
1,4-Phenylenediamine dihydrochloride 10 1.58 79.04 63 Propylgallate
30 1.96 73.40 64 Phthalic acid 10 0.73 73.97 65
.alpha.-(4-Pyridyl-N-oxide)N-tert-butylnitrone 10 1.72 70.99 66
Propylgallate 10 0.38 84.45 67 Pyridoxine 100 1.95 72.53 68
QuinicAcid 100 1.79 68.36 69 Quercetin 1 0.50 77.43 70 Rutin 1 0.42
74.18 71 Salicylate 10 0.64 76.49 72 Selenomethionine 10 3.34 62.84
73 Sodium Selenite 30 1.46 78.66 74 Sodium Sulfite 10 0.63 75.84 75
Spermine 100 0.29 54.69 76 Sulfanilic Acid 10 1.57 76.47 77
Syringic Acid 10 1.12 82.32 78 Tert-Butylhydroquinone 10 1.33 84.93
79 4-Hydroxy-2,2,6,6-tetramethylpiperidine 1-oxyl 10 1.97 71.31 80
Terephthalic acid 10 0.86 74.54 81 Tetrachloro-1,4-benzoquinone 10
4.03 54.01 82 2,4,5-Trihydroxybutrophenone 10 1.02 84.56 83
1,3,5-Tris(2-hydroxyethyl)isocyanurate 10 1.75 76.86 84 Thiourea
100 15.31 51.62 85 2,2,6,6-Tetramethyl-4-piperidone hydrochloride
10 1.89 69.38 86 6-Hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic
acid 10 0.84 74.97 87 L-Tryptophan 10 1.69 76.44
TABLE-US-00002 TABLE 2 Entry Error cycle20 number Compound Rate Int
1 Ethylgallate 10 mM + 10 mM Bis [2,2,6,6-Tetramethyl-4-piperidone]
sebacate 0.57 88.89 2 Ethylgallate 10 mM + 10 mM
Diethyldithiocarbamate 0.50 90.48 3 Ethylgallate 10 mM + 10 mM
N,N-Diethylhydroxylamine 0.49 69.01 4 Ethylgallate 10 mM + 10 mM
2Phenylbenzimidazole sulfonic acid 0.35 70.58 5 Ethylgallate 10 mM
+ 10 mM Pyrogallol 0.31 72.78 6 Ethylgallate 10 mM + 25 mM
NaAscorbate 0.34 85.64 7 Ethylgallate 10 mM + 30 mM Hydroquinone
0.45 90.58 8 Ethylgallate 10 mM + 50 mM Gallic Acid 0.34 87.25 9
gallic acid 100 mM + 250 mM mannitol 0.31 77.08 10 gallic acid 100
mM + 2M Urea 0.17 80.90
Example IV
Nucleic Acid Damage can be Prevented by Inclusion of a Compound
During Nucleic Acid Fragmentation
[0107] The fidelity with which a sequenced library matches the
original genome sequence can vary depending on the frequency of
base mutation occurring at any stage from the extraction of the
nucleic acid to its sequencing on a sequencing platform. This
frequency places an upper limit on the probability of a sequenced
base being correct. For example, if a mutation occurs one in a
thousand times, then the maximum confidence (probability) that any
base is correct is one in a 10.sup.3, i.e., a max of Q30. DNA
fragmented by Covaris shearing has been observed to have a max Q
value that decreases with increasing duration of shearing. See FIG.
6. To determine whether a compound can be used to increase the
fidelity with which a sequence library matches the original genome
sequence, data was generated using pools of plasmid DNA. Twelve
plasmids were pooled, each plasmid having a different 50 basepair
(bp) insert within the template cassette. The pool was sheared in a
Covaris S2 then subjected to clustering by standard means followed
by paired 75 base reads on a GA sequencer (Illmunia, Inc., San
Diego, Calif.). Maximum quality scores were then calculated from
the data. Specifically, 1 .mu.g of pooled plasmid DNA was sheared
using Covaris in the absence of or presence of compounds as
follows: a) 1 .mu.g input DNA was fragmented in the presence of 50
mM gallic acid; or b) 1 .mu.g input DNA was fragmented in the
presence of 50 mM ascorbate. The solutions were made by addition of
60 .mu.l of a 100 mM stock solution of gallic acid or ascorbate to
10 .mu.l DNA (1 .mu.g) and the volume was made up to 120 .mu.l with
TE (Tris, EDTA) buffer. The covaris parameters used were as
follows: duty cycle: 20%, intensity: 5, cycles/burst: 200 and time:
240 seconds. These samples were then put onto the flow cell for
sequencing without further treatment. As shown in Table 1 below and
FIGS. 7 and 8, nucleic acid damage can be prevented by inclusion of
gallic acid or ascorbate during the shearing reaction.
TABLE-US-00003 TABLE 3 Effect of Gallic Acid and Ascorbate During
Nucleic Acid Fragmentation. Sample Max Q Detection Max Q System Max
Q Gallic Acid 43 63 43 Ascorbate 43 65 44 No Treatment 38 67 38
Control HindIII 44 60 43 Digested DNA
Example V
Damaged Nucleic Acids can be Cleared by Enzymatic Treatment
[0108] To determine whether damaged nucleic acids can be cleared by
enzymatic cleavage, 3 ng of accuracy pool DNA were sheared using
Covaris. The Covaris parameters used were as follows: duty cycle:
20%, intensity: 5, cycles/burst: 200 and time: 240 seconds.
Following this, the sample was divided into tubes of 1 ng each. One
tube (1 ng) was treated with FPG enzyme as follows: 10 .mu.l of FPG
enzyme (80 units) were added to 1 .mu.g of DNA in 1.times.NEB
buffer 1, supplemented with bovine serum albumin (BSA) to a final
volume of 200 .mu.l. Alternatively, one tube was treated with
PreCR.TM. Repair Mix (NEB, Ipswich, Mass.). The reactions were
incubated for 30 minutes at 37.degree. C. The reactions were then
cleaned up using the Qiagen PCR purification kit and eluted in 30
.mu.l EB buffer (10 mM Tris-Cl, pH 8.5). As shown in Table 2 below
and FIGS. 2 and 3, treatment of Covaris sheared DNA with FPG (an
enzyme that cleaves DNA at 8-oxo-G lesions) restores the Max Q
value of the sample from 38 to 43 and, thus, removes damaged
nucleic acids from the sample.
TABLE-US-00004 TABLE 4 Effect of FPG Following Nucleic Acid
Fragmentation. Sample Max Q Detection Max Q System Max Q FPG
Treatment 43 65 43 PreCR Treatment 38 64 37 No Treatment 38 67 38
Control HindIII 44 60 43 Digested DNA
* * * * *