U.S. patent application number 15/698992 was filed with the patent office on 2018-01-04 for reagents and methods of pcr.
The applicant listed for this patent is Brandeis University. Invention is credited to Yanwei Jia, John E. Rice, Nicholas Rice, Lawrence J. Wangh.
Application Number | 20180002739 15/698992 |
Document ID | / |
Family ID | 42244601 |
Filed Date | 2018-01-04 |
United States Patent
Application |
20180002739 |
Kind Code |
A1 |
Wangh; Lawrence J. ; et
al. |
January 4, 2018 |
REAGENTS AND METHODS OF PCR
Abstract
Modified double-stranded oligonucleotides that have terminal
regions on each of their strands, that have a hybrid length of 6-50
nucleotides long, that have a melting temperature Tm of at least
32.degree. C., and that include 2-4 modifying groups, each
covalently attached to a different terminal region, preferably to a
terminal nucleotide, said modifying groups being polycyclic
substituents that do not have bulky portions that are non-planar,
said modified oligonucleotide being capable of binding to the 5'
exonuclease domains of DNA polymerases and, when included in a PCR
or other primer-dependent DNA amplification reaction at a
concentration, generally not more than 2000 nM, that is effective
for at least one of the functions of suppressing mispriming,
increasing polymerase selectivity against 3' terminal mismatches.
increasing polymerase selectivity against AT-rich 3' ends, reducing
scatter among replicates, suppressing polymerase 5' exonuclease
activity, and inhibiting polymerase activity; as well as
amplification reaction mixtures containing such modified
double-stranded oligonucleotides, and amplification reactions,
amplification assays and kits that include such modified
double-stranded oligonucleotides.
Inventors: |
Wangh; Lawrence J.;
(Auburndale, MA) ; Rice; John E.; (Quincy, MA)
; Rice; Nicholas; (Quincy, MA) ; Jia; Yanwei;
(Waltham, MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Brandeis University |
Waltham |
MA |
US |
|
|
Family ID: |
42244601 |
Appl. No.: |
15/698992 |
Filed: |
September 8, 2017 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14715299 |
May 18, 2015 |
9758813 |
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15698992 |
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13256038 |
Nov 22, 2011 |
9034605 |
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PCT/US10/27011 |
Mar 11, 2010 |
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14715299 |
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61202565 |
Mar 12, 2009 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q 1/6853 20130101;
C12Q 2531/107 20130101; C12Q 2545/114 20130101; C12Q 2527/107
20130101; C12Q 2531/107 20130101; C12Q 2527/107 20130101; C12Q
2545/114 20130101; C12Q 1/6806 20130101; C12Q 1/6853 20130101; C12Q
1/6806 20130101 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68 |
Claims
1. In a reaction mixture for a primer-dependent DNA amplification
reaction including primer extension by a DNA polymerase for
amplifying at least one DNA target sequence, said reaction mixture
including at least one primer pair, a DNA polymerase and dNTP's,
the improvement comprising including in the reaction mixture prior
to the start of amplification at least one double-stranded
oligonucleotide additive that has a hybrid length of 6-50
nucleotides long, that is at least fifty percent double-stranded at
32.degree. C., that has terminal regions on each of its strands and
includes 1-4 modifying groups, each covalently attached to a
different terminal region, said modifying groups being polycyclic
moieties that do not have bulky portions that are non-planar,
wherein said at least one double-stranded oligonucleotide additive
is included at a concentration relative to the concentration of
said DNA polymeras that is effective for at least one of the
functions of suppressing mispriming, increasing polymerase
selectivity against hybrids having recessed 3' terminal sequences
that are not perfectly complementary, increasing polymerase
selectivity against hybrids having recessed 3' terminal sequences
that are AT-rich, reducing scatter among replicate reactions,
inhibiting polymerase 5' exonuclease activity, and inhibiting
polymerase activity; provided that, if the additive is a primer or
detection probe for any target sequence, it includes at least three
modifying groups.
2. The amplification reaction mixture of claim 1 wherein the at
least one modifying groups is 2-4 modifying groups.
3. The amplification reaction mixture of claim 2 wherein the 2-4
modifying groups is three modifying groups.
4. The amplification reaction mixture of claim 3 wherein the
additive includes a first strand that is a primer or probe for said
at least one target sequence and a reverse complement strand that
is partially complementary to the first strand.
5. The amplification reaction mixture of claim 2 wherein the 2-4
modifying groups is four modifying groups.
6. The amplification reaction mixture of any of claims 1-5 wherein
the modifying groups are covalently linked to terminal nucleotides
of said at least one double-stranded oligonucleotide additive.
7. The amplification reaction mixture of any of claims 1-6 wherein
the modifying groups are Dabcyl.
8. The amplification reaction mixture of claim 2 wherein the at
least one additive is a mixture of two additives.
9. The amplification reaction mixture of claim 8 wherein the
mixture consists of three strands.
10. The amplification reaction mixture of any of claims 1-9,
wherein the at least one double-stranded oligonucleotide additive
consists of natural nucleotides.
11. The amplification reaction mixture of any of claims 1-9 wherein
the at least one double-stranded oligonucleotide additive is
DNA.
12. The amplification reaction mixture according to any of claims
1-3 and 5-11 wherein the at least one additive is not a primer or
probe for said at least one target sequence.
13. The amplification reaction mixture according to any of claims
1-12 wherein the concentration of said at least one double-stranded
oligonucleotide additive is not more than 1000 nM.
14. The amplification reaction mixture according to any of claims
1-13, further including a reverse transcriptase.
15. The amplification reaction mixture of claim 1 wherein the at
least one double-stranded additive includes from one to four
single-stranded overhangs.
16. The amplification reaction mixture of claim 15 wherein the at
least one double-stranded additive comprises at least one strand
that, when not hybridized, forms a stem-loop structure.
17. A method for amplifying at least one DNA target sequence
comprising contacting said at least and DNA target sequence with an
amplification reaction mixture according to claim 1 and subjecting
the reaction mixture to a primer-dependent DNA amplification
reaction having a primer annealing temperature and a primer
extension temperature.
18. The method of claim 17 wherein contacting the at least one DNA
target sequence with the reaction mixture consists of adding the at
least one DNA target sequence in single-stranded form to the
reaction mixture.
19. The method of claim 17 that includes reverse transcribing RNA
to obtain the at least one DNA target sequence.
20. The method of claim 17 wherein the at least one modifier is 2-4
modifiers.
21. The method of claim 20 wherein the double-stranded
oligonucleotide has a melting temperature, Tm, that is in the range
of the primer annealing temperature to not more than 5.degree. C.
below the primer annealing temperature.
22. The method of claim 20 wherein the double-stranded
oligonucleotide has a melting temperature, Tm, that is higher than
the primer annealing temperature.
23. The method of claim 17 wherein the additive has three modifying
groups and includes a first strand that is a primer or probe for
said at least one target sequence and a reverse complement strand
that is partially complementary to the first strand.
24. The method of claim 20 wherein said at least one additive is a
mixture of two additives.
25. The method of claim 22 wherein the mixture includes a first
additive having a double-stranded oligonucleotide that has a Tm
that is in the range of the primer annealing temperature to not
more than 5.degree. C. below the primer annealing temperature and a
second additive having a double-stranded oligonucleotide that has a
Tm that is higher than the primer annealing temperature.
26. The method of claim 25 wherein each additive includes 3-4
modifying groups.
27. The method according to any of claims 17-26, wherein the
primer-dependent amplification reaction is a polymerase chain
reaction (PCR) amplification reaction.
28. The method according to any of claims 17-26, wherein the
primer-dependent amplification is a LATE-PCR amplification
reaction.
29. The method according to any of claims 17-28 wherein the at
least one DNA target sequence is reverse transcribed from an RNA
target sequence.
30. An amplification assay that includes amplification according to
any of claims 17-29 and fluorescence detection of single-stranded
products of the reaction, double-stranded products of the reaction,
or both, either in real time during amplification or end point
following amplification, wherein double-stranded products of the
reaction are detected with a fluorescent DNA dye, single-stranded
products of the reaction are detected with at least one
fluorescently labeled hybridization probe, or both.
31. A kit of reagents amplifying at least one DNA target sequence,
said kit including the reagents for a reaction mixture according to
any of claims 1-16.
32. The kit according claim 31 further including reverse
transcriptase.
33. The kit according to claim 31 or claim 32 further including a
DNA dye.
34. The kit according to any of claims 31-33 further including a
fluorescently labeled detection probe for said at least one target
sequence.
35. A modified double-stranded oligonucleotide that has terminal
regions on each of its strands, that has a hybrid length of 6-50
nucleotides long, that is at least fifty percent double-stranded at
32.degree. C., and that includes 2-4 modifying groups, each
covalently attached to a different terminal region, said modifying
groups being polycyclic moieties that do not have bulky portions
that are non-planar, said modified oligonucleotide being capable of
inhibiting the 5' exonuclease domains of DNA polymerases.
36. The modified oligonucleotide of claim 35 wherein the
double-stranded oligonucleotide is DNA.
37. The modified oligonucleotide of claim 35 or claim 36 wherein
said modifying groups are attached to terminal nucleotides.
38. A mixture of two modified double-stranded oligonucleotides
according to any of claims 35-37.
39. The mixture of claim 38 wherein the two double-stranded
oligonucleotides comprise three strands.
40. The amplification reaction mixture of claim 1, wherein the DNA
polymerase is thermostable.
Description
CROSS-REFERENCE FOR RELATED PATENT APPLICATIONS
[0001] This application is a continuation of U.S. patent
application Ser. No. 13/256,038, filed Mar. 11, 2010, which is a
371 US National Entry of International Patent Application Serial
Number PCT/US2010/027011, filed Mar. 11, 2010, which claims benefit
to U.S. provisional patent application No. 61/202,565, filed Mar.
12, 2009 to Zhang, which is hereby incorporated by reference in its
entirety.
SEQUENCE LISTING
[0002] The instant application contains a Sequence Listing which
has been submitted in ASCII format via EFS-Web and is hereby
incorporated by reference in its entirety.
FIELD
[0003] Nucleic acid amplification reactions and assays including
both real-time and end point homogeneous polymerase chain reaction
(PCR) monoplex and multiplex amplification assays are provided.
BACKGROUND
[0004] Amplification and amplification assays using DNA primers and
a DNA polymerase are well-known for amplifying and for detecting
nucleic acid target sequences. Methods for exponential
amplification include the polymerase chain reaction (PCR), strand
displacement amplification (SDA), nucleic acid sequence based
amplification (NASBA), transcription-mediated amplification (TMA),
and rolling circle amplification (RCA). Certain of these
primer-dependent amplification methods, such as PCR, include
thermal cycling, while others, such as NASBA, are isothermal. Among
numerous DNA polymerases commonly used are Thermus aquaticus DNA
polymerase (Taq polymerase) and reverse transcriptase. The design
of linear DNA oligonucleotide amplification primers is generally
accomplished with the aid of a computer program designed for that
purpose. Among the available programs that can be utilized are
PRIDE (Haas et al., Nucl. Acids Res. 26:3006-3012 1998); OLIGO
(Rychlik et al., Nucl. Acids Res 17(21):8543-51 1989); OSP (Hilber
et al., OSP: a computer program for choosing PCR and DNA sequencing
primers. PCR Methods Appl. 1(2):124-128 1991); Primo (Li et al.,
Genomics 40(3):476-85 1997); and Primer Master (Proutski et al.,
Comput Appl Biosci 12(3):253-5 1996).
[0005] Nucleic acid amplification employing PCR is well known, as
are assays that include PCR amplification. See U.S. Pat. Nos.
4,683,202, 4,683,195 and 4,965,188, and, generally, PCR PROTOCOLS,
a guide to Methods and Applications, Innis et al. eds., Academic
Press (San Diego, Calif. (USA) 1990). Homogeneous PCR assays that
do not require washing to remove unbound detector reagents or
probes and thus can be performed without opening amplification
reaction vessels are also well known. Homogeneous PCR assays
include both end-point assays, in which amplified product is
detected at the end of the amplification reaction, and real-time
assays, in which amplified product is detected during some or all
of the thermal cycles as the reaction proceeds. See U.S. Pat. Nos.
5,994,056, 5,487,972, 5,925,517 and 6,150,097.
[0006] PCR amplification reactions, like other amplification
methods referred to above, are generally designed to be symmetric,
that is, to make double-stranded amplicons by utilizing a forward
primer and a reverse primer that are "matched"; that is, they have
melting temperatures that are as close as possible, and they are
added to the reaction in equimolar concentrations. A technique that
has found limited use for making single-stranded DNA directly in a
PCR reaction is "asymmetric PCR." Gyllensten and Erlich,
"Generation of Single-Stranded DNA by the Polymerase Chain Reaction
and Its Application to Direct Sequencing of the HLA-DQA Locus,"
Proc. Natl. Acad. Sci. (USA) 85: 7652-7656 (1988); and U.S. Pat.
No. 5,066,584. Asymmetric PCR differs from symmetric PCR in that
one of the primers is added in limiting amount, typically 1-20
percent of the concentration of the other primer.
[0007] A more recently developed non-symmetric PCR amplification
method is known as "Linear-After-The-Exponential" PCR or, for
short, "LATE-PCR." See Sanchez et al. (2004) PNAS 101: 1933-1938,
Pierce et al. (2005) PNAS 102: 8609-8614, and published
international patent application WO 03/054233 (3 Jul. 2003), which
is incorporated herein by reference in its entirety. LATE-PCR takes
into account the actual, concentration-adjusted melting
temperatures of PCR primers at the start of amplification, referred
to as Tm.sub.[0]. Tm.sub.[0] can be determined empirically, as is
necessary when non-natural nucleotides are used, or calculated. A
variety of fluorescent probes can be used with LATE-PCR, including,
among others: molecular beacons, which are single-strands capable
of forming a stem-loop structure that can close when not bound to
target thereby bringing near to each other a fluorophore on one end
and a quencher on the other end; linear single-stranded probes
having a fluorophore on one end and a quencher on the other end;
FRET probe pairs, which are two labeled, single-stranded probes
that hybridize adjacently on a target sequence, permitting their
labels to pass energy between them by FRET; fluorophore-labeled
linear probes that FRET with a DNA dye; and linear double-stranded
probes in which the fluorophore is on the strand that binds to
target and the quencher is on a complementary strand that binds to
the probe at an equivalent Tm in the absence of a target.
[0008] An undesirable feature of symmetric PCR amplifications is
that, following the exponential phase of amplification,
fluorescence curves obtained by monitoring replicate amplifications
in real time diverge and plateau at different levels. Scatter
indicates that replicates do not have the same reaction efficiency
and reduces detection accuracy. This is a problem for PCR assays
generally, but is particularly undesirable in the case of end-point
assays. Scatter among replicates is considerably reduced but still
present in LATE-PCR assays and asymmetric PCR assays, both of which
have an exponential phase and a linear phase. The scatter in the
linear phase in part reflects the scatter in the plateau at the end
of the exponential amplification when the limiting primer runs
out.
[0009] Another significant problem with primer-dependent
amplification reactions, including PCR amplifications, is
mispriming, which we consider to be manifested in several distinct
types: Type 1, mispriming that occurs during preparation of
reaction mixtures prior to the start of amplification; Type 2,
mispriming that occurs during amplification if the temperature
(which in PCR amplifications means the temperature in any thermal
cycle) is for any reason reduced below the melting temperature of a
primer; and Type 3, mispriming that occurs in the late stages of
amplification, including a PCR amplification, that is continued
after a high concentration of amplicon has been made. When Type 3
mispriming occurs in LATE-PCR and asymmetric reactions, the 3'end
of a single-stranded amplicon primes on another ss-DNA molecule,
thereby converting ss-DNA into ds-DNA. Mispriming in a reaction can
also result in scatter among replicate reactions. Mispriming
includes primer-dimer formation, which can occur during any stage
of amplification.
[0010] Several approaches have been used to address Type 1
mispriming. One approach is to modify the polymerase chemically so
that it is inactive until heated to a high temperature such as
95.degree. C. See U.S. Pat. Nos. 5,677,152 and 5,773,258. Another
approach is to bind an antibody to the polymerase to inhibit the
polymerase until the reaction is heated to a high temperature such
as 95.degree. C. to irreversibly denature the antibody. See U.S.
Pat. No. 5,338,671. Chemically modified and antibody-bound DNA
polymerases are commonly referred to as "hot start" DNA
polymerases. Yet another "hot start" approach is to include an
aptamer in the reaction mixture. See Doug and Jayasena (1996), J.
Mol. Biol. 264: 268-278 and U.S. Pat. No. 6,020,130. An aptamer is
a single-stranded oligonucleotide approximately 30 nucleotides in
length that binds to a polymerase and inhibits its ability to
extend a recessed 3' end at low temperatures. Aptamers are not
irreversibly denatured at 95.degree. C., a typical highest
temperature for a PCR cycle. Eppendorf-5 Prime, Inc. markets a
proprietary ligand that is said to bind to Taq polymerase in a
temperature-dependent manner and to inhibit its binding to
double-stranded DNA at temperatures below about 50.degree. C.
Despite these many attempts, mispriming remains a problem with PCR
amplifications.
[0011] Another type of mispriming during primer-dependent
amplification reactions, including PCR amplifications, is known as
primer-dimer formation and primer-dimer amplification. According to
this phenomenon one primer hybridizes to the other primer or to
another copy of itself and then undergoes extension of the 3' end
to generate a small double-stranded amplicon, which can then
amplify further or can multimerize and amplify further.
Primer-dimer formation can occur in the absence of target.
[0012] Quantitative analysis of amplification reactions, including
PCR amplifications, has been enabled by real-time detection
methods. In PCR amplifications the PCR cycle at which fluorescent
signal becomes visible above the threshold cycle or C.sub.T of
reactions is indicative of starting target concentrations.
End-point analyses are semi-quantitative at best, due in part to
scatter among replicates as the reaction exits exponential
amplification. Electrophoretic analysis of double-stranded
amplicons is semi-quantitative, and may utilize fluorescently
labeled primers. End-point analysis utilizing fluorescently labeled
probes, either allele-discriminating probes or mismatch-tolerant
probes, are also semi-quantitative at best. By reducing scatter and
producing single-stranded product, LATE-PCR offers significant
improvement in end-point analysis, but scatter among replicates is
often not completely eliminated, leaving quantitative and multiplex
detection less accurate and more problematic than desired.
[0013] Design and construction of multiplex PCR assays often
encounters the problem of mispriming, because the use of multiple
pairs of primers in a single reaction geometrically increases the
number of possible unintended interactions of primers and target
sequences or other DNA strands that may be present. Indeed, in
symmetric multiplex PCR assays it is very difficult to design all
primer pairs to have the same melting temperature, and in a
asymmetric or LATE-PCR multiplex PCR assay to design all of the
limiting primers to have a single melting temperature and all of
the excess primers to have a single melting temperature. It
therefore follows that in a multiplex PCR assay the particular
annealing temperature used for one or more thermal cycles is not
likely to be optimal for all pairs of primers. If the primer
annealing step of a PCR cycle is set to permit hybridization of the
lowest Tm primer, the reaction will have reduced stringency for
primers with Higher Tm's, which increases the chance for mispriming
to occur. Moreover, in LATE-PCR assays the limiting primers used
(whether in a monoplex or a multiplex) typically have melting
temperatures 5.degree. C. or more above the melting temperatures of
the excess primers, again making it impossible to match a single
primer annealing temperature to the melting temperature of both
primers.
[0014] A property of DNA polymerases in primer-dependent
amplifications, including PCR amplifications, is a nominal amount
of selectivity, particularly a nominal ability to discriminate
between a target sequence that is perfectly complementary to a
primer and a sequence that is perfectly complementary except for a
mismatch at the 3' terminal nucleotide of the primer. It has been
attempted to take advantage of this nominal selectivity to detect
single-nucleotide mutations, or SNPs, by designing primers having
their 3' terminal nucleotide complementary to the target nucleotide
that is subject to mutation. The amplification assay method known
as the amplification refractory mutation system (ARMS) attempts to
do that (Newton et al., Nucl. Acids Res. 17, 2503-2516 (1989); Wu
et al., Proc. Natl. Acad. Sci. USA 86:2757-2760 (1989)). ARMS
assays are prone to generation of false-positive signals due to
mispriming and primer-dimer formation. Certain mispriming events
may involve a primer that hybridizes incorrectly such that there is
a 3' mismatched nucleotide. Primer-dimer formation may also involve
a mismatched 3' nucleotide. In the last phase of a LATE-PCR
amplification mispriming of a single-stranded amplicon on another
single strand in the reaction mixture may also involve a mismatched
3' nucleotide. Therefore, enhancing a polymerase's discrimination
against a 3' terminal mismatch can, among other effects, reduce
mispriming. Attempts have been made to improve selectivity during
amplification beyond the foregoing nominal selectivity by making
amplification primers themselves more selective. For example, Tyagi
et al. added to the 5' end of a primer a sequence complementary to
the 3' end of the primer to form a stem-loop structure wherein the
loop and the 3' portion of the stem are complementary to the target
strand (U.S. Pat. No. 6,277,607). This approach is not seen to
reduce the difficulty, described above, of designing primers for
multiples assays. Making primers more selective does not, of
course, improve the selectivity of DNA polymerases.
[0015] To improve selectivity, an alternative to modifying primers
is to affect the DNA polymerase itself. U.S. patent application
U.S. Ser. No. 11/242,506 describes a class of reagent additives
that somewhat improve product specificity and that greatly reduce
or in some cases practically eliminate the effects of mispriming in
PCR amplification reactions. This class of reagents is comprised of
single oligonucleotides molecules that are able to fold into
hairpin structures having a stem and a loop when the temperature is
lowered below the melting temperature of the stem. Although the
double-stranded stem closes, the nucleotides at the 3' and 5' ends
tend to unwind. Therefore, these additive reagents are chemically
modified at both their 3' and 5' ends to keep the ends closed. End
closure in this way effectively increases the melting temperature
of the stem. In the closed configuration these reagent additives
interact with DNA polymerase so as to improve selectivity. In the
closed configuration they also inhibit polymerase activity of DNA
polymerases. While these additives out-perform existing "hot-start"
methodologies in all types of PCR and can be used to prevent the
accumulation of undesired products, including primer-dimers and
misprimed amplicons, both at early stages of the reaction and
during LATE-PCR reactions having many cycles (typically 60 cycles
and more), they do have their limitations which are inherent to
their being comprised of a single oligonucleotide. Specifically,
the length of the stem cannot be greater than about 12 nucleotides,
because, if it is, and is also chemically modified at its ends, its
melting temperature becomes so high that it does not readily open
when the PCR is heated to the extension temperature. Even when
added at low concentration, hairpin molecules with long stems and
high Tm tend to inhibit the reaction. Yet another difficulty
inherent to these additives is that they are not linearly
symmetric, i.e. one end of the closed hairpin is open while the
other end is a loop. As described in U.S. patent application U.S.
Ser. No. 11/242,506, molecules with loops comprised of 3-22
nucleotides tend to inhibit amplification more readily than
molecules in which the loop is formed by use of a 3 carbon or 6
carbon linker. It would be desirable to have reagents which are
structurally symmetrical end-to-end.
[0016] Kainz et al. (2000) Biotechniques 28: 278-282 reported that
DNA fragments, double-stranded DNA oligonucleotides, having lengths
of 16-21 nucleotides can inhibit mispriming that occurs at or just
below the optimal annealing temperature of symmetric PCR reactions
and thereby prevent amplification of non-specific products. The DNA
oligomers are reversibly denatured during the melting step of the
PCR cycling. In all cases the assays that Kainz et al. employed
revealed the presence of, and inhibition of, mispriming that takes
place when the temperature is descending to the optimal annealing
temperature after the first melting event at 95.degree. C. This
does not address Type 1 mispriming, as Kainz et al. acknowledged,
and their data reveal that double-stranded fragments that are only
double-stranded when Type 1 mispriming occurs (that is, with
melting temperatures >5.degree. C. below the annealing
temperature of the reaction) fail to prevent mispriming. From Kainz
et al. one infers that their method will likely be even more
unreliable in multiplex reactions because, as explained above, the
annealing temperature cannot simultaneously be optimized for all
pairs of primers. Kainz et al. also acknowledged that, although
they did not observe it in their particular experiments,
double-stranded DNA oligonucleotides may trigger mispriming, if
they become the target for hybridization of one or more primers in
the reaction.
SUMMARY
[0017] One embodiment is a reaction mixture for a primer-dependent
DNA amplification reaction, preferably a PCR amplification
reaction, including primer extension by a DNA polymerase for
amplifying at least one DNA target sequence, said reaction mixture
including at least one primer pair, a thermally stable DNA
polymerase and dNTP's, the improvement comprising including in the
reaction mixture prior to the start of amplification at least one
double-stranded oligonucleotide additive that has terminal regions
on each of its strands, that has a hybrid length of 6-50
nucleotides long, that is at least 50% double-stranded at
32.degree. C., and that includes 1-4 modifying groups, preferably
two, three or four modifying groups, each covalently attached to a
different terminal region, preferably to a terminal nucleotide,
said modifying groups being polycyclic moieties that do not have
bulky portions that are non-planar, wherein said at least one
double-stranded oligonucleotide additive is included at a
concentration that is effective for at least one of the functions
of suppressing mispriming, increasing polymerase selectivity
against hybrids having recessed 3' terminal sequences that are not
perfectly complementary, increasing polymerase selectivity against
hybrids having recessed 3' terminal sequences that are AT-rich,
reducing scatter among replicate reactions, inhibiting polymerase
5' exonuclease activity, and inhibiting polymerase activity;
provided that, if the additive is a primer or detection probe for
any target sequence, it includes at least three modifying
groups.
[0018] Another embodiment is a reaction mixture as described in the
preceding paragraph that includes a mixture of two such
double-stranded additives.
[0019] Another embodiment is a reaction mixture as described above
wherein the additive includes a first strand that is a primer or
probe for said at least one target sequence and a reverse
complement strand that is partially complementary to the first
strand, and wherein the additive includes three of the described
modifying groups.
[0020] Another embodiment is primer-dependent amplification of DNA
(including cDNA) targets, preferably PCR amplification, using
reaction mixtures described above and, where necessary reverse
transcribing RNA to obtain the DNA target sequence to be
amplified.
[0021] Another embodiment is homogeneous detection assays, both
real-time and end-point assays, that include such primer-dependent
amplifications plus fluorescence detection of amplification
products.
[0022] Another embodiment is reagent kits containing primers for at
least one DNA target sequence, dNTPs, a thermally stable DNA
polymerase, and at least one modified double-stranded
oligonucleotide additive as describe above.
[0023] Another embodiment is such reagent kits that also include at
least on fluorescence detection reagent for detecting amplification
reaction products homogeneously.
[0024] Another embodiment is modified double-stranded
oligonucleotides that have terminal regions on each of their
strands, that have a hybrid length of 6-50 nucleotides long, that
is at least 50% double-stranded at 40.degree. C., preferably, but
at least at 32.degree. C., and that include 2-4 modifying groups,
each covalently attached to a different terminal region, preferably
to a terminal nucleotide, said modifying groups being polycyclic
moieties that do not have bulky portions that are non-planar, said
modified oligonucleotide being capable of binding to the 5'
exonuclease domains of DNA polymerases.
[0025] Another embodiment is a primer-dependent DNA amplification
reaction mixture including primer extension by a DNA polymerase for
amplifying at least one DNA target sequence, said reaction mixture
including at least one primer pair, a DNA polymerase and dNTP's,
the improvement comprising including in the reaction mixture prior
to the start of amplification at least one double-stranded
oligonucleotide additive that has a hybrid length of 6-50
nucleotides long, that is at least fifty percent double-stranded at
32.degree. C., that has terminal regions on each of its strands and
includes 1-4 modifying groups, each covalently attached to a
different terminal region, said modifying groups being polycyclic
moieties that do not have bulky portions that are non-planar,
wherein said at least one double-stranded oligonucleotide additive
is included at a concentration relative to the concentration of
said DNA polymerase that is effective for at least one of the
functions of suppressing mispriming, increasing polymerase
selectivity against hybrids having recessed 3' terminal sequences
that are not perfectly complementary, increasing polymerase
selectivity against hybrids having recessed 3' terminal sequences
that are AT-rich, reducing scatter among replicate reactions,
inhibiting polymerase 5' exonuclease activity, and inhibiting
polymerase activity; provided that, if the additive is a primer or
detection probe for any target sequence, it includes at least three
modifying groups.
[0026] Another embodiment is an amplification assay that includes
amplification and fluorescence detection of single-stranded
products of the reaction, double-stranded products of the reaction,
or both, either in real time during amplification or end point
following amplification, wherein double-stranded products of the
reaction are detected with a fluorescent DNA dye, single-stranded
products of the reaction are detected with at least one
fluorescently labeled hybridization probe, or both.
[0027] Another embodiment is a modified double-stranded
oligonucleotide that has terminal regions on each of its strands,
that has a hybrid length of 6-50 nucleotides long, that is at least
fifty percent double-stranded at 32.degree. C., and that includes
2-4 modifying groups, each covalently attached to a different
terminal region, said modifying groups being polycyclic moieties
that do not have bulky portions that are non-planar, said modified
oligonucleotide being capable of inhibiting the 5' exonuclease
domains of DNA polymerases. The modified double-stranded
oligonucleotide may have from one to four single-stranded
overhangs, and, when not hybridized in the double-stranded
oligonucleotide structure, it may comprise either one or two single
strands that form a stem-loop (hairpin) structure, in which case
the stem is 6 or fewer base-pairs long.
BRIEF DESCRIPTION OF THE DRAWINGS
[0028] FIG. 1 presents melt curves for replicates of a LATE-PCR
amplification described in Example 1 utilizing additive 16merA at a
concentration of 300 nM.
[0029] FIG. 2 presents melt curves for replicates of a LATE-PCR
amplification described in Example 1 utilizing additive 16merB at a
concentration of 300 nM.
[0030] FIG. 3 presents melt curves for replicates of a LATE-PCR
amplification described in Example 1 utilizing additive EP049 at a
concentration of 600 nM.
[0031] FIG. 4 presents melt curves for replicates of a LATE-PCR
amplification described in Example 1 utilizing additive EP027 at a
concentration of 100 nM.
[0032] FIG. 5 is a graph of SYBR Green fluorescence as a function
of amplification cycle number for replicates of a LATE-PCR
amplification described in Example 1 utilizing additive EP027 at
concentrations of 100, 300, 600 and 1000 nM.
[0033] FIG. 6 presents melt curves for replicates of a LATE-PCR
amplification described in Example 2 utilizing additive 22merA at a
concentration of 100 nM and additive EP003 at a concentration of
100 nM.
[0034] FIG. 7A is a graph of SYBR Green fluorescence as a function
of amplification cycle number for replicates of a LATE-PCR
amplification described in Example 4 utilizing three-strand
additive mixture EP043 at a total concentration of 600 nM and
strand concentrations of 25/600/575 nM.
[0035] FIG. 7B is a graph of SYBR Green fluorescence as a function
of amplification cycle number for replicates of a LATE-PCR
amplification described in Example 4 utilizing three-strand
additive mixture EP043 at a total concentration of 600 nM and
strand concentrations of 50/600/550 nM.
[0036] FIG. 7C is a graph of SYBR Green fluorescence as a function
of amplification cycle number for replicates of a LATE-PCR
amplification described in Example 4 utilizing three-strand
additive mixture EP043 at a total concentration of 600 nM and
strand concentrations of 75/600/525 nM.
[0037] FIG. 7D is a graph of SYBR Green fluorescence as a function
of amplification cycle number for replicates of a LATE-PCR
amplification described in Example 4 utilizing three-strand
additive mixture EP043 at a total concentration of 600 nM and
strand concentrations of 100/600/500 nM.
[0038] FIG. 8A is a graph of SYBR Green fluorescence as a function
of amplification cycle number for replicates of a LATE-PCR
amplification described in Example 4 utilizing three-strand
additive mixture EP045 at a total concentration of 600 nM and
strand concentrations of 25/600/575 nM.
[0039] FIG. 8B is a graph of SYBR Green fluorescence as a function
of amplification cycle number for replicates of a LATE-PCR
amplification described in Example 4 utilizing three-strand
additive mixture EP045 at a total concentration of 600 nM and
strand concentrations of 50/600/550 nM.
[0040] FIG. 8C is a graph of SYBR Green fluorescence as a function
of amplification cycle number for replicates of a LATE-PCR
amplification described in Example 4 utilizing three-strand
additive mixture EP045 at a total concentration of 600 nM and
strand concentrations of 75/600/525 nM.
[0041] FIG. 8D is a graph of SYBR Green fluorescence as a function
of amplification cycle number for replicates of a LATE-PCR
amplification described in Example 4 utilizing three-strand
additive mixture EP046 at a total concentration of 600 nM and
strand concentrations of 100/600/500 nM.
[0042] FIG. 9A is a graph of fluorescences from two probes as a
function of amplification cycle number for replicates of a LATE-PCR
duplex amplification described in Example 5 utilizing no additive
and an annealing temperature of 65.degree. C.
[0043] FIG. 9B is a graph of fluorescences from two probes as a
function of amplification cycle number for replicates of a LATE-PCR
duplex amplification described in Example 5 utilizing additive
EP020 at a concentration of 400 nM and an annealing temperature of
65.degree. C.
[0044] FIG. 9C is a graph of fluorescences from two probes as a
function of amplification cycle number for replicates of a LATE-PCR
duplex amplification described in Example 5 utilizing additive
EP020 at a concentration of 400 nM and an annealing temperature of
60.7.degree. C.
[0045] FIG. 9D is a graph of fluorescences from two probes as a
function of amplification cycle number for replicates of a LATE-PCR
duplex amplification described in Example 5 utilizing additive
EP013 at a concentration of 300 nM and an annealing temperature of
66. .degree. C.
[0046] FIG. 9E is a graph of fluorescences from two probes as a
function of amplification cycle number for replicates of a LATE-PCR
duplex amplification described in Example 5 utilizing additive
EP013 at a concentration of 300 nM and an annealing temperature of
64.2.degree. C.
[0047] FIG. 9F is a graph of fluorescences from two probes as a
function of amplification cycle number for replicates of a LATE-PCR
duplex amplification described in Example 5 utilizing additive
EP013 at a concentration of 300 nM and an annealing temperature of
60.7.degree. C.
[0048] FIG. 10 is a graph of probe fluorescence as a function of
the number of temperature oscillation cycles for a
primer-independent probe-cleavage assay described in Example 6
utilizing any of several additives or no additive.
[0049] FIG. 11A presents melt curves for probe-amplicon hybrids
resulting from replicates of a LATE-PCR amplification described in
Example 7 with no additive, and for probe alone.
[0050] FIG. 11B presents melt curves for probe-amplicon hybrids
resulting from replicates of a LATE-PCR amplification described in
Example 7 with additive EP013 at 600 nM concentration, and for
probe alone.
[0051] FIG. 12 is an electrophoretic gel showing products of a
12-plex LATE-PCR amplification described in Example 8 starting with
1000 copies of mitochondrial genomic DNA (target sequences) with no
additive, with additive EP011 at a concentration of 300 nM, and
with additive EP011 at a concentration of 600 nM.
[0052] FIG. 13 is a graph of SYBR Green fluorescence as a function
of amplification cycle number for replicates of a LATE-PCR
amplification described in Example 9 utilizing Taq DNA polymerase
with no additive, Taq DNA polymerase and antibody with no additive,
Taq DNA polymerase with additive EP046 at a concentration of 600
nM, and Taq DNA polymerase and antibody with additive EP046 at a
concentration of 600 nM.
[0053] FIG. 14A is a graph of fluorescence from a probe as a
function of amplification cycle number for replicates of a LATE-PCR
amplification with a low-temperature detection step described in
Example 10 utilizing additive EP010 at a concentration of 600 nM,
starting with 1000, 100 and 10 copies of target.
[0054] FIG. 14B presents melt curves for probe-amplicon hybrids
after 40 cycles of a LATE-PCR ColdStop amplification described in
Example 10 utilizing additive EP010 at a concentration of 600 nM.
starting with 1000, 100 and 10 copies of target.
[0055] FIG. 14C presents melt curves for probe-amplicon hybrids
after 70 cycles of a LATE-PCR ColdStop amplification described in
Example 10 utilizing additive EP010 at a concentration of 600 nM.
starting with 1000, 100 and 10 copies of target.
[0056] FIG. 15A is a graph of SYBR Green fluorescence as a function
of amplification cycle number for replicates of a LATE-PCR
amplification described in Example 13 utilizing additive mixture
EP043 at a total concentration of 600 nM and strand concentrations
of 50/600/550 nM, with untailed primer and tailed primer.
[0057] FIG. 15B shows the melt curves of the six amplification
products with additive EP043, where the downward pointing arrow
indicates the melting temperature, 86.degree. C., of the correct
double-stranded DNA product. Circle 153 identifies the one
replicate with untailed primer that showed the correct peak with no
product evolution (flat plateau) in FIG. 15A, and circle 154
identifies the two replicates with tailed primer also showed no
product evolution (flat plateau) in FIG. 15A.
[0058] FIG. 16A presents melt curves for replicates of a LATE-PCR
amplification described in Example 14 utilizing a 5'-Dabcylated
primer but no reverse complement sequence.
[0059] FIG. 16B presents melt curves for replicates of a LATE-PCR
amplification described in Example 14 utilizing a 5'-Dabcylated
primer plus a reverse complement sequence at a concentration of 100
nM.
[0060] FIG. 16C presents melt curves for replicates of a LATE-PCR
amplification described in Example 14 utilizing a 5'-Dabcylated
primer plus a reverse complement sequence at a concentration of 200
nM.
[0061] FIG. 16D presents melt curves for replicates of a LATE-PCR
amplification described in Example 14 utilizing a 5'-Dabcylated
primer plus a reverse complement sequence at a concentration of 300
nM.
[0062] FIG. 17A is a graph of probe fluorescence as a function of
cycle number for replicates of a LATE-PCR amplification with
reverse transcription for an RNA target, described in Example 15,
utilizing additive EP020 at a concentration of 2000 nM.
[0063] FIG. 17B is a graph of probe fluorescence as a function of
cycle number for replicates of a LATE-PCR amplification with
reverse transcription for an RNA target, described in Example 15,
utilizing additive EP010 at a concentration of 200 nM.
[0064] FIG. 17C is a graph of probe fluorescence as a function of
cycle number for replicates of a LATE-PCR amplification with
reverse transcription for an RNA target, described in Example 15,
utilizing additive EP003 at a concentration of 400 nM.
[0065] FIG. 17D is a graph of probe fluorescence as a function of
cycle number for replicates of a LATE-PCR amplification with
reverse transcription for an RNA target, described in Example 15,
utilizing an mixture of additive EP010 at a concentration of 400 nM
and additive EP020 at a concentration of 1000 nM.
[0066] FIG. 17E is a graph of probe fluorescence as a function of
cycle number for replicates of a LATE-PCR amplification with
reverse transcription for an RNA target, described in Example 15,
utilizing a mixture of additive EP003 at a concentration of 400 nM
and additive EP020 at a concentration of 1000 nM.
[0067] FIG. 17F is a graph of probe fluorescence as a function of
cycle number for replicates of a LATE-PCR amplification with
reverse transcription for an RNA target, described in Example 15,
utilizing no additive.
[0068] FIG. 18A is a schematic depiction of a modified
double-stranded additive according to this invention formed from
two linear (random coil) oligonucleotides and having
single-stranded overhangs.
[0069] FIG. 18B is a schematic depiction of a modified
double-stranded additive as in FIG. 18A, but formed from one linear
oligonucleotide and one hairpin-forming oligonucleotide.
[0070] FIG. 18C is a schematic depiction of a modified
double-stranded additive as in FIG. 18A, but formed from two
hairpin-forming oligonucleotides.
[0071] FIG. 19A presents melt curves for products of LATE-PCR
amplifications with Taq polymerase plus antibody, with and without
additive SL04, as described in Example 16.
[0072] FIG. 19B presents melt curves for products of LATE-PCR
amplifications with Taq polymerase plus antibody, with and without
additive SL07, as described in Example 16.
[0073] FIG. 19C presents melt curves for products of LATE-PCR
amplifications with Taq polymerase plus antibody, with and without
additive SL08, as described in Example 16.
[0074] FIG. 19D presents melt curves for products of LATE-PCR
amplifications with Taq polymerase plus antibody, with and without
additive SL09, as described in Example 16.
[0075] FIG. 20 is a graph of probe fluorescence as a function of
the number of temperature oscillation cycles for a
primer-independent probe-cleavage assay described in Example 18
utilizing additive SL06 at different concentrations.
[0076] FIG. 21A is a schematic representation showing the action of
a blocker oligonucleotide to create a 3' terminal mismatch between
a limiting primer and a target to which the primer is perfectly
complementary.
[0077] FIG. 21B is a schematic representation showing the action of
a blocker oligonucleotide to create a 3' terminal mismatch between
a limiting primer and a target to which the primer is perfectly
complementary.
[0078] FIG. 22A is a graph of threshold cycle (C.sub.T) versus
starting concentration of target (Copy Number) for a dilution
series of amplifications without blocker as described in Example
19.
[0079] FIG. 22B is a graph of threshold cycle (C.sub.T) versus
starting concentration of target (Copy Number) for a dilution
series of amplifications with blocker as described in Example
19.
[0080] FIG. 23A is a graph of SYBR Green fluorescence versus
amplification Cycle Number showing the effect of antibody in
amplifications described in Example 20.
[0081] FIG. 23B is a graph of SYBR Green fluorescence versus
amplification Cycle Number showing the effect of additive EP010 in
amplifications described in Example 20.
[0082] FIG. 23C is melt curves of products described in Example 20
made with DNA polymerase only and product made with antibody added
after the first incubation step of the assay.
[0083] FIG. 23D is melt curves of product described in Example 20
made with antibody added prior to the first incubation step of the
assay.
[0084] FIG. 23E is melt curves of products described in Example 20
made with additive EP010 added before and after the first
incubation step of the assay.
DETAILED DESCRIPTION
[0085] References are made to melting temperatures (Tm) of
double-stranded additives, primers and probes. By definition, Tm
means the temperature at which a double-stranded oligonucleotide is
50% double-stranded and 50% single-stranded. For additives, Tm
means a calculated Tm of a double-stranded oligonucleotide not
accounting for any effect of substituent modifiers. Tms of
double-stranded additives presented in this specification were
calculated according to Markhan and Zuker (2005) DINAMELT web
server for nucleic acid melting prediction, Nucleic Acids Res.
33:W577-W581, and Markham and Zuker (2008) UNAFOLD: software for
nucleic acid folding and hybridization. In Keith, J. M., ed.,
BIOINFORMATICS, vol. II, Structure, Functions and Applications, No.
453 in Methods in Molecular Biology, Ch. 1, pages 3-31 (Humana
Press, Totowa, N.J. ISBN 978-1-60327-428-9. In utilizing the
referenced web server, the following inputs were made:
concentration of each strand, in .mu.M, as reported in the
Examples; 70 mM for salt concentration; and 3 mM for magnesium
concentration. Tms of probes and primers in LATE-PCR amplification
reactions the start of amplification are referred to as Tm.sub.[0].
Tm.sub.[0] can be determined empirically, as is necessary when
structured probes are used, or calculated according to the "nearest
neighbor" method (Santa Lucia, J. (1998) PNAS (USA) 95: 1460-1465;
and Allawi, H. T. and Santa Lucia, J. (1997) Biochem. 36:
10581-10594) which is herein incorporated by reference in its
entirety using a salt concentration adjustment. In our work, we use
0.07 M monovalent salt concentration, although other concentrations
can be used.
[0086] References are made to modifying groups being located on
terminal regions oligonucleotide strands. By "terminal regions" it
is meant attached to a terminal 5' or 3' nucleotide or to an
internal nucleotide not more than five, not more than three, or not
more than two nucleotides from a 5' or 3' end. In some embodiments,
terminal modifiers are attached to a 5' or 3' terminal
nucleotide.
[0087] References are made to selectivity. By "selectivity" it is
meant generally the preference of a DNA polymerase to extend
recessed 3' ends when certain conditions are met. Generally
speaking, recessed 3'ends bound to a target sequence are
thermodynamically unstable, that is they alternately bind to and
partially unwind from the strand to which they are hybridized.
These ends can be said to be stable when binding to the target is
favored by formation of more hydrogen bonds and unstable when they
form fewer hydrogen bonds. According to this view, recessed 3'ends
that are perfectly complementary to their targets are more stable
than recessed 3' ends that are not perfectly complementary to their
targets. Similarly, recessed 3' ends that are GC rich are generally
more stable than recessed 3'ends that are AT rich, since GC
dinucleotide pairs form three hydrogen bonds while AT dinucleotide
pairs form two hydrogen bonds.
[0088] In accord with this understanding, one type of selectivity
is the preference of a DNA polymerase to extend a recessed 3' end
of a hybrid when the 3' terminal region, particularly including the
terminal 3' nucleotide, of the recessed 3' end is perfectly
complementary, that is, is hybridized with no mismatch. Stated
another way, this type of selectivity is selectivity against a 3'
terminal priming sequence that is not perfectly matched to its
target. Selectivity against 3' terminal-region mismatches applies
to primer-target hybrids, where it signifies the preference of a
polymerase for a primer-target hybrid that is perfectly
complementary at the 3' end of the primer over a primer-target
hybrid having a mismatch at, for example, the 3' terminal
nucleotide. Selectivity against 3' terminal-region mismatches also
applies more generally to hybrids having recessed, extendable 3'
ends formed by any two DNA strands in an amplification reaction
mixture, such as may occur when one amplicon strand hybridizes to
(that is, primes on) another amplicon strand.
[0089] A second type of selectivity is the preference of a DNA
polymerase for a primer (or priming strand) having a 3' terminal
region that is GC-rich rather than AT-rich, or stated another way,
selectivity against a primer or other priming strand whose terminal
region is AT-rich.
[0090] For selectivity of either type, the measure of selectivity
is the difference (.DELTA.C.sub.T) between the threshold cycle
(C.sub.T) of the signal from amplification of the non-preferred
hybrid, for example the hybrid formed by a primer and a mismatched
target and the C.sub.T of the signal from amplification of the
preferred hybrid, for example the hybrid formed by a primer and a
matched target. Improvement in selectivity due to the use of an
additive is the net C.sub.T difference obtained by subtracting the
.DELTA.C.sub.T without any additive from the .DELTA.C.sub.T that
results with the additive.
[0091] Additives that reduce mispriming, inhibit DNA polymerase
activity, increase DNA polymerase selectivity of either type,
inhibit DNA polymerase exonuclease activity, or reduce scatter
among replicate reactions, or any combination of the foregoing in
primer-dependent DNA amplification reactions and nucleic acid
detection assays employing such reactions, including PCR
amplification reactions and PCR amplification assays can be
included.
[0092] Chemical reagents that are soluble in DNA amplification
buffer and include from one to four or from two to four, covalently
bound moieties, which are referred to as modifying groups or, for
short, modifiers, suppress mispriming and enhance polymerase
selectivity for hybrids between primers and fully complementary
target sequences. The covalently bound modifying groups are
polycyclic (including but not limited to aromatic) moieties which,
if bulky, are planar and can be configured to bind to a DNA
polymerase having an exonuclease domain (active or inactivated) so
as to suppress mispriming and enhance polymerase selectivity for
hybrids between primers and fully complementary target
sequences.
[0093] In some embodiments, the quencher Dabcyl can be used as a
modifying group for these reagents.
[0094] These polycyclic moieties can be solubilized by attaching
them to double-stranded oligonucleotides. Certain double-stranded
oligonucleotides with from 1-4 polycyclic moieties, as described
above, can be useful as additives for reducing mispriming,
inhibiting DNA polymerase activity, increasing DNA polymerase
selectivity, inhibiting DNA polymerase exonuclease activity,
reducing scatter among replicates, or any combination of the
foregoing in primer-dependent DNA amplification reactions and
nucleic acid detection assays employing such reactions, including
PCR amplification reactions and PCR amplification assays. The
modified double-stranded oligonucleotides may comprise natural
nucleotides, that is, they may be DNA, RNA, or mixtures of DNA and
RNA. The modified double-stranded oligonucleotides may also
comprise non-natural nucleotides, for example, LNA's and 2'
O-methyl ribonucleotides. The amplification reactions may be
symmetric or non-symmetric, including asymmetric PCR amplification
reactions and, preferably, LATE-PCR reactions.
[0095] The additives can be modified linear double-stranded DNA
oligonucleotides in which the complementary nucleic acid strands
are from 6-50, preferably 12-30, and more preferably 16-26,
nucleotides in length. The modified double-stranded
oligonucleotides may be blunt ended or may contain short overhangs
of 1-8 nucleotides, preferably 1-5 nucleotides, on one or both
ends. FIGS. 18A-18C depict several different embodiments with
non-complementary terminal regions in the strands at one or both
ends of an additive's double-stranded region. For purposes of
illustration, all the constructions are shown with three modifying
groups, M, having a particular placement, but it will be
appreciated that embodiments such as these are not limited to the
placement shown or to the inclusion of three modifier groups. FIG.
18A shows two partially complementary, random coil oligonucleotides
181, 182 that hybridize to form double-stranded additive 183, which
includes double-stranded region 184 and single-stranded overhangs
185, 186. The melting temperature, Tm, of hybrid 184 can be
adjusted by changing its length and GC content. FIG. 18B similarly
shows two partially complementary oligonucleotides 187, 188 that
hybridize to form double-stranded additive 189, which includes
double-stranded region 190 and single-stranded overhangs 191, 192.
Overhangs 191, 192 may comprise sequences that do not hybridize to
one another even at low temperatures. Alternatively, the overhangs
may comprise sequences that hybridize to one another only at low
temperatures (Tm below the Tm of double-stranded region 184, as
determined by degree of complementarity and GC content). The
embodiment depicted in FIG. 18B differs from the embodiment shown
in FIG. 18A in that one oligonucleotide, namely, oligonucleotide
187, when not hybridized to oligonucleotide 188, assumes a hairpin
structure that includes a double-stranded stem 193 up to six
nucleotides in length. FIG. 18C similarly shows two partially
complementary oligonucleotides 194, 195 that hybridize to form
double-stranded additive 196, which includes double-stranded region
197 and single-stranded overhangs 198-201. In the embodiment shown
in FIG. 18C both oligonucleotides 194 and 195, when not hybridized
to one another, assume hairpin structures that include stems 202
and 203, respectively. Examples 16 and 17 utilize the structures
shown in FIG. 18C. For additives in which either or both strands
form a hairpin, or stem-loop, structure, the Tm of each stem is
higher than the Tm of the double-stranded region, to ensure
formation of the hairpin during use, but not so high as to prevent
formation of the double-stranded conformation of the additive in a
reasonable period of time when the temperature of the reaction is
decreased during use. In some embodiments, in which neither
oligonucleotide strand serves as an amplification primer or as a
probe, both 3' ends are blocked to prevent extension by a DNA
polymerase. Blocking may be achieved by covalently linking a
modifying group to the 3' terminal nucleotide of a strand or
otherwise blocking extension, as, for example, by including a 3'
terminal phosphate group. Additives can include double-stranded
oligonucleotides that are at least 50% double-stranded at
32.degree. C., which is as high a temperature as is likely to be
encountered during assembly of an amplification reaction
mixture.
[0096] From 1-4 modifying groups, preferably 2, 3 or 4 groups, are
included in the linear double-stranded oligonucleotides. The
modifiers are covalently attached to additive strands in their
terminal regions, that is, at a terminal nucleotide or at a
nucleotide that is not more than five, preferably not more than
two, nucleotides from a terminal nucleotide. Some embodiments
utilize modifiers attached to terminal nucleotides of the
double-stranded oligonucleotides. The modifiers can be covalently
linked to oligonucleotide strands. Covalent linking of modifying
groups is well known in the art for incorporating fluorophores and
quenchers, for example.
[0097] The modifying groups can be moieties that are polycyclic,
including but not limited to polyaromatic, and, if bulky, have an
overall planar aspect. Examples include digoxigenin, a plant
steroid; coumarin, a bicyclic aromatic; QSY-21, a small
polyaromatic compounds used as quenchers, that are not planar.
Fulvic and humic acids are believed to be included. In some
embodiments, the modifying group is the well-known quencher Dabcyl,
which is polyaromatic, bulky and planar. Thus, modifying groups can
be polycyclic moieties that do not have bulky portions that are
non-planar, and preferably are polyaromatic.
[0098] Additives can include a linear double-stranded DNA
oligonucleotide with various possible configurations of one, two,
three and four modifying groups. With one terminal modifying group,
there are four possible configurations: the modifier may be
attached to the 3' or 5' terminal nucleotide of either strand. With
two terminal modifying groups, there are six possible
configurations; with three terminal modifying groups there are four
possible configurations; and with four modifying groups there is
only one possible configuration. Attachment of modifiers to
internal nucleotides of terminal regions creates additional
possible configurations. In all cases in which a strand is not a
primer and a modifying group is not attached to a strand's 3'
terminal nucleotide, that nucleotide is otherwise blocked, as by a
phosphate group (identified in sequences in the Examples as
"p").
[0099] In certain embodiments, one strand serves also as a primer,
and its 3' terminus is not blocked. In certain other embodiments,
one strand serves as a detection probe, in which case its 3' end
can be blocked, for example by a terminal modifying group, a
terminal fluorophore, or a terminal phosphate group. For primer
embodiments, a single-stranded amplification primer can be
converted into an additive by including a single-stranded
oligonucleotide that is complementary to the primer, which we call
the reverse complement sequence, so that it forms a double-stranded
hybrid with the primer. The hybrid can function as an additive when
it is double-stranded. The hybrid can include three modifiers, such
as Dabcyl groups. The Tm of the reverse complement sequence to the
primer strand can be designed to be 5-30.degree. C., preferably
15-25.degree. C., lower than the Tm of the primer strand to its
amplification target sequence. To achieve the difference in Tm's,
the reverse complement sequence may be rendered partially
complementary to the primer strand by making it either shorter or
mismatched at one or more nucleotide, or both. For probe
embodiments, a labeled, single-stranded hybridization probe can be
converted to an additive similarly to the conversion of a primer
and has a Tm that is similarly lower than the Tm of the
probe-target hybrid. Preferred probe embodiments include a probe
strand having a fluorophore and a quencher and a reverse complement
sequence having two terminal quenchers.
[0100] Primer-dependent amplification reaction mixtures for
amplifying at least one DNA or cDNA target can be included. The
reaction mixtures include at least one of the foregoing additives
as well as target nucleic acid and amplification reagents that
include primers, a DNA polymerase, dNTP's and, generally,
amplification buffer. If the amplification mixture is for an
amplification assay that includes both amplification and
homogeneous detection of double-stranded amplification products,
single-stranded amplification products, or both, the reaction
mixture can include at least one reagent for product detection,
preferably fluorescence detection. Preferred reagents for detecting
double-stranded amplification products are DNA dyes, such as SYBR
Green. Preferred reagents for detecting single-stranded products
are fluorescently labeled detection probes whose hybridization to
single-stranded products causes a detectable fluorescent signal
change or whose hybridization to single-stranded products during
amplification leads to a detectable fluorescent signal change.
Numerous homogeneous detection reagents are known in the art, and
any suitable detection reagent or reagents can be used. Other
reagents can also be used. If target nucleic acid that is included
is an RNA target sequence, the reaction mixture will include
reverse transcriptase.
[0101] Reaction mixtures can include multiple primer pairs for
multiple targets for multiplex amplifications and assays. Example 5
illustrates a reaction mixture for a duplex LATE-PCR assay for two
target sequences that includes two primer pairs and a fluorescent
probe for each amplified product. Example 8 illustrates a reaction
mixture for a highly multiplexed amplification, a twelve-plex that
contains twelve primer pairs for twelve different targets. If an
additive includes one of the primer strands, the reaction mixture
can further include the appropriate reverse complement sequence.
Reaction mixtures can be PCR reaction mixtures, and in some
embodiments LATE-PCR reaction mixtures. Reaction mixtures may
include a combination, or mixture, of two additives. Such a mixture
may comprise four strands or, if two additives share a common
strand, three strands. Reaction mixtures can include at least one
modified, double-stranded additive at a total concentration of up
to 2000 nM, preferably up to 1000 nM and more preferably up to 600
nM. If the reaction mixture includes a mixture of additives, the
total concentration of additives can remain as stated.
[0102] Methods for primer-dependent amplification of one or more
DNA or cDNA target sequences and primer-dependent amplification of
one or more DNA or cDNA target sequences with homogeneous detection
of amplification products (that is, amplification assays with
homogeneous detection) utilizing reaction mixtures described above
are provided. Amplification methods and amplification assay methods
may include isothermal amplification reactions or thermal cycling
amplification reactions. In one embodiment, the amplification
method can PCR and in some embodiments, LATE-PCR. The additive or
combination of additives selected to be used in a particular
amplification or amplification assay, and its or their amount(s),
depends on the effect desired and on the temperatures to be
utilized during amplification. Isothermal amplifications may
include only a reaction mixture preparation temperature, typically
room temperature, followed by an isothermal amplification reaction
at a single reaction temperature, for example, 37.degree. C. PCR
and other thermal cycling amplification methods include a reaction
mixture preparation temperature followed by numerous thermal cycles
that include a primer annealing temperature (annealing
temperature), a primer extension temperature (extension
temperature), and a strand denaturation temperature (melting
temperature). Although the annealing temperature and the extension
temperature may be the same, it is more common for the annealing
temperature to be 5-20 degrees Celsius (.degree. C.) below the
extension temperature. LATE-PCR assays may further include a
low-temperature detection step in some or all of the thermal
cycles, during which the temperature of the reaction mixture is
reduced below the annealing temperature to permit low-temperature
probes to bind to their target sequences. Amplification reactions
may be interrupted at an intermediate point for performing some
operation that may include low temperature (below the annealing
temperature), after which the amplification reaction can be
resumed. Amplifications may take advantage of other ways of
reducing mispriming. For example, the DNA polymerase that is used
may be a hot-start polymerase. Further, the primers that are used
may be designed to have AT-rich 5' ends, including where necessary
by adding extensions. Additionally or alternatively, the 3' ends of
primers can be designed to be either GC-rich or AT-rich so as to
alter polymerase inhibition in amplifications and amplification
assays. Products of amplification reactions can be suitable for
sequencing, including but not limited to dideoxy sequencing.
[0103] Amplification assays may include real-time homogeneous
detection of single-stranded products, double-stranded products, or
both, at multiple times during amplification of DNA target
sequences, for example, during some or all cycles of a PCR
amplification reaction. As stated above, fluorescence detection can
be used. Alternatively, amplification assays may include
homogeneous detection at end-point following completion of an
amplification reaction. Detection may include melting amplification
products and detecting fluorescence change as a function of
temperature. Detection may be qualitative or quantitative. For
targets that are RNA, assays can include reverse transcription.
[0104] Reagent kits for performing amplifications and amplification
assays are provided. Such kits can include reagents needed to
prepare reaction mixtures, including primers for at least one
target sequence, dNTPs, a DNA polymerase, and at least one modified
double-stranded additive, as described above. Kits for
amplification assays can also include at least one detection
reagent, such as, a DNA fluorescent dye or a fluorescently labeled
hybridization probe. Amplification kits and amplification assay
kits may also include reagents for sample preparation, for example,
cell lysing reagents, reagents for nucleic acid isolation, and
reverse transcriptase. Amplification assay kits may include control
target sequences and primers for their amplification.
[0105] Selection of an additive or mixture of additives can take
into account their properties of DNA polymerase inhibition,
selectivity against 3' terminal primer mismatches, selectivity
against AT-rich primer 3' terminal regions, inhibition of
polymerase exonuclease activity, mispriming suppression, and
reduction of scatter among replicates. An additive's effect
depends, in turn, on the inherent properties of the additive, its
concentration, its melting temperature, and its concentration. For
example, inherent polymerase inhibition tends to increase with the
number of modifiers included in the additive, and the effective
inhibition of an additive increases with its concentration.
Selectivity against a 3' terminal primer mismatch has been found to
correlate with blocking exonuclease activity of DNA polymerases
that have that activity or at least have an exonuclease site. This
may be due to blocking the exonuclease site of the enzyme by the
additive.
[0106] Additives can be added to amplification reaction mixtures in
concentrations that are effective for one or more of the functions
of suppressing mispriming, increasing polymerase selectivity
against hybrids having recessed 3' terminal sequences that are not
perfectly complementary, increasing polymerase selectivity against
hybrids having recessed 3' terminal sequences that are AT-rich,
reducing scatter among replicate reactions, inhibiting polymerase
5' exonuclease activity, and inhibiting polymerase activity.
Because additives interact with DNA polymerases, the concentration
required will vary with the concentration of DNA polymerase that is
included in an amplification reaction mixture. Determination of the
additive concentration required to be effective for one or more of
the foregoing functions, as well a determination of an optimum
concentration, can be determined routinely by trying several
concentrations in the amplification reaction or amplification assay
for which an additive is intended, as demonstrated in the Examples
below. Example 3, for instance, reports empirical trials of several
additives at several concentrations to determine the effects of the
additives at various concentrations to aid in selection of a
preferred additive, to ascertain the effective concentration, and
to determine an optimum concentration for a particular purpose in a
particular LATE-PCR assay. For Taq DNA polymerases, which are the
most commonly used polymerases for amplification reactions and
assays, a typical polymerase concentration can be 1.25 units in 25
microliters (.mu.l0r ul) of reaction mixture. In some embodiments,
no more than 2000 nanomolar (nM) of additive is required, in some
embodiments, no more than 1000 nM, and in some embodiments, not
more than 600 nM. For Tfi DNA polymerases, which can be included in
reaction mixtures at higher concentrations than Taq DNA
polymerases, the same concentrations of additives are generally
effective.
[0107] For an additive to act as a "hot start" reagent, it is
preferred that the additive nearly or completely inhibit the
polymerase activity of the polymerase being used, for example, Taq
DNA polymerase, at temperatures below the reaction temperature of
an isothermal amplification and below the annealing temperature of
a thermal cycling reaction such as PCR. For this purpose, the
additive can have a high inhibitory effect on polymerase activity
and a melting temperature (Tm) that is at least 32.degree. C. and
equal to or below, preferably, 1-15.degree. C. below, more
preferably 1-5.degree. C. below, the isothermal reaction
temperature or the PCR, and at a concentration sufficiently high to
completely or at least substantially inhibit the polymerase
activity. As additives are not irreversibly denatured by being
melted apart at temperatures above their Tm, the additives will
function during the isothermal reaction of PCR thermal cycling
every time the temperature is lowered sufficiently for the additive
to become double-stranded, for example, during a low-temperature
detection step, as is sometimes used in a LATE-PCR assay.
[0108] An additive can also act to reduce mispriming and increase
polymerase selectivity at the reaction temperature of an isothermal
amplification or at temperatures above the annealing temperature of
a PCR amplification, particularly at the extension temperature. For
this purpose, an additive can have low to modest inhibitory effect
on polymerase activity and a melting temperature that is not more
than 2.degree. C. below, preferably at least equal to, and more
preferably above, the isothermal reaction temperature or the PCR
extension temperature, and at a concentration that is only as high
as necessary to achieve the desired effect without unduly
inhibiting the efficiency of the reaction. Here again, because the
additives are not irreversibly denatured during the strand-melting
step of PCR cycles, the additives can function to increase
polymerase selectivity during every PCR cycle as the temperature is
lowered for the strand-melting temperature to the annealing
temperature or below.
[0109] Additives may be used singly or in combination. A mixture of
two modified double-stranded oligonucleotides may include four
strands or, if the two additives share a common strand, three
strands. Three-strand mixtures insert one less strand into a
reaction mixture, which can be advantageous in embodiments wherein
the additive is neither a primer nor a probe for any target
sequence in an amplification reaction mixture. Using additives in
combination imparts flexibility of design. For example, to suppress
Type I mispriming, one may include a first additive that, by its
inherent nature, Tm and concentration, is very inhibitory of
polymerase activity below the primer annealing temperature of an
amplification reaction, but that is single-stranded during
amplification so as not to inhibit the polymerization reaction. In
combination with such an additive, to suppress Type II mispriming
and where applicable, Type III mispriming during amplification, one
may include an additive that is double-stranded during primer
annealing but that minimally inhibits polymerase activity during
primer extension.
[0110] Oligonucleotide reagents that interact directly with a DNA
polymerase enzyme used in either an isothermal DNA amplification
reaction or a thermal cycling DNA amplification reaction, such as a
PCR reaction, are provided. Oligonucleotide reagents can act in
amplification reactions during all steps in which they are
double-stranded. They can have the effect of both suppressing
mispriming and increasing polymerase selectivity, including the
preference of the DNA polymerase to extend recessed 3' ends that
are perfectly complementary to the strands to which they hybridize
in comparison to recessed 3' ends that are imperfectly
complementary to the strands to which they hybridize. Mispriming
may be considered according to different types. Type I is
mispriming that occurs whenever the temperature of the reaction
mixture is below the primer annealing temperature. It occurs during
preparation of reaction mixtures prior to the start of
amplification. It may also occur during amplification, if the
temperature is reduced below the primer annealing temperature. Type
II is mispriming that occurs during amplification whenever the
temperature of the reaction mixture is at or above the primer
annealing temperature but below the melting temperature of a primer
that is present. Type III is mispriming that occurs during
amplification that continues after a high concentration of
amplification product (amplicon) has been made. Yet another
manifestation of mispriming is primer-dimer formation, wherein one
primer hybridizes to another primer or to itself and then undergoes
extension to generate a short double-stranded amplicon, which can
then amplify further or even multimerize and amplify further. It is
useful to divide an amplification reaction into stages to consider
mispriming possibilities. Mispriming creates an amplifiable
product, so a mispriming event that occurs early in an
amplification reaction will be amplified almost as if it were a
target molecule. The following general description is for PCR
reactions, but persons skilled in the art will appreciate its
application to other amplification reactions. This general
description of PCR is for illustration purposes only and is not
intended to limit the types of amplification reactions that can be
used.
[0111] Pre-Stage: Reagents are prepared and mixed at 25.degree. C.
or lower (for example, on-ice). The concentration of primers is
highest during the Pre-Stage, which typically lasts for minutes.
Usually, the number of targets is low or very low during Pre-Stage,
and some or all of those targets may be single-stranded, depending
on how the sample was prepared and whether or not it is a cDNA.
Indeed, synthesis of cDNA using an enzyme such as reverse
transcriptase is also a part of Pre-Stage when the reaction mixture
used for cDNA synthesis also contains primers and a DNA polymerase,
since these components of the reaction mixture can misprime under
the conditions required cDNA synthesis, typically 5-30 minutes at
temperatures in the range of 40-60.degree. C. The Pre-Stage is
terminated by heating to high temperature, for example, 95.degree.
C., to denature all double-stranded DNA in the reaction mixture. If
the DNA polymerase has been added in an inactivated form, for
example, antibody-bound DNA polymerase, this heating step activates
the polymerase, a process known as "hot start."
[0112] Type I mispriming occurs during the Pre-Stage. Chances of
Type I mispriming are enhanced, if the DNA polymerase is not a
hot-start enzyme and if no other inhibitor of polymerase activity
is included in the reaction mixture. Also, Type I mispriming
occurs, if the hot-start modification of the polymerase or added
inhibitors used to block polymerase activity fail to do so
completely. Both primer-dimer formation and Type I mispriming are
favored during the Pre-Stage because the temperature is low.
Products of Pre-Stage mispriming will be amplified.
[0113] Early-Stage: This stage of the reaction is typically 10-15
thermal cycles of a PCR amplification. The thermal profile of each
cycle of 3-step PCR includes a strand-melting temperature, a primer
annealing temperature, and primer extension temperature. For 2-step
PCR, primer annealing and primer extension are performed at the
same temperature. The amount of time allotted for each step in the
thermal cycles is typically seconds long. During the first and
second thermal cycles primers first anneal to their target
sequences within the full-length target and are intended to
selectively extend only when on fully complementary target
sequences. Primers anneal to and extend on both strands of the
target and, if all goes perfectly, generate and then exponentially
amplify two complementary strands of defined length. The tendency
of product strands to hybridize to each other is low, because their
concentrations are low.
[0114] Type II mispriming can occur during the Early-Stage if
primers extend on allelic targets to which they are not fully
complementary. It is not atypical for primers to have Tms several
degrees or even more above the annealing temperature, which invites
Type II mispriming. Shorter annealing times and higher annealing
temperatures (relative to the primer Tms) are more stringent than
longer annealing times and lower annealing temperatures and
therefore decrease Type II mispriming and increase polymerase
selectivity. Products of Type II mispriming can be amplified during
the remainder of amplification. Hot-start polymerase modifications
do not apply here, because the first heating to high temperature
irreversibly inactivates the hot-start antibody or enzyme
alkylation. Thermally stable inhibitors, including those described
here, will be functional during the first and subsequent annealing
steps, because they are not irreversibly denatured by high
temperature.
[0115] Middle-Stage: This stage of a PCR reaction is typically
comprised of 10-25 thermal cycles and includes melting, primer
annealing, and primer extension. The amount of time allotted for
each step in the thermal cycle is typically seconds long. Primers
anneal to and extend on both strands of the target and, under
optimal conditions generate and then exponentially amplify two
complementary strands of defined length that is determined by
primer pairs.
[0116] In the case of real-time symmetric PCR assays, Middle-Stage
typically includes product detection during either the annealing
step or the extension step of the reaction. In the case of LATE-PCR
reactions, the Middle-Stage may include product detection at a
temperature that is lower than the annealing temperature and occurs
after the extension step. Fluorescent signals using a hybridization
probe typically become detectable late in the exponential phase of
both symmetric and LATE-PCR.
[0117] Toward the end of the Middle-Stage in symmetric PCR, the
concentration of the exponentially accumulating product strands
grows high enough for hybridization of product strands during the
primer-annealing step. Exponential amplification slows down and
plateaus, because, it is believed, the polymerase binds to the
double-stranded product of the reaction. In the case of LATE-PCR,
the limiting primer runs out and terminates the exponential phase
of the reaction before the concentration of the product strands
becomes high enough to slow the reaction.
[0118] In LATE-PCR amplifications that include a low-temperature
detection step, Type I and Type II mispriming can occur in the
Middle-Stage, just as in the Early Stage. This is particularly a
risk during the low temperature detection step in real-time
LATE-PCR. Type III mispriming can also occur during the Middle
Stage as the concentration of product strands increases. Mispriming
of any type, whether during Pre-Stage, Early-Stage or Middle-Stage
results in scatter among replicate reactions, which is particularly
manifest as exponential amplification slows down.
[0119] Late-Stage: The Late-Stage of amplification is generally
found only in LATE-PCR because symmetric PCR has reached plateau
and been terminated by this stage. This stage of a LATE-PCR
amplification is typically comprised of 10-25 thermal cycles that
include steps of melting, primer annealing (excess primer only),
and primer extension (excess primer only). The amount of time
allotted for each step in the thermal cycle is typically seconds
long. Each excess primer anneals to and extends on the extension
product made by extension of its corresponding limiting primer (its
Limiting-Primer Strand) and, if all goes perfectly, efficiently
generates the Excess-Primer Strand, which accumulates linearly
until it begins to out-compete the excess primer itself. Thus,
LATE-PCR reactions slow down but do not plateau as do symmetric PCR
reactions.
[0120] In the case of real-time LATE-PCR assays, this stage may
include product detection at the primer annealing temperature or at
a temperature that is lower than the annealing temperature and
occurs after the extension phase. Fluorescent signals using a
hybridization probe typically increase with approximately linear
kinetics during this stage.
[0121] Type III mispriming can occur during the Late-Stage after a
number of linear cycles, because the 3' end of the Excess Primer
strand can misprime anywhere along another molecule of the Excess
Primer strand. Thus, the probability of Type III mispriming
increases as: 1) the concentration of single-stranded product
increases; 2) the number of different single-stranded products in a
multiplex reaction increases; 3) the temperature of the reaction is
lowered; 4) the 3' ends, or bases near the 3' ends of the Excess
Primer Strands are GC-rich and hybridize (misprime) more readily.
Type III mispriming results in conversion of single-stranded DNA
back into double-stranded DNA, which we refer to as "product
evolution" (although products are incomplete or abnormal). Product
evolution is manifest as a sudden late increase in the fluorescence
using dyes that detect double-stranded products (an increase in
slope after plateau), or a sudden decrease in fluorescence from
probes that detect single-stranded DNA. Thus, Type III mispriming
is similar to Type II mispriming in that the error can occur above
the annealing temperature, but Type III mispriming is also similar
to Type I mispriming in that the error can occur below the
annealing temperature. Type II mispriming can, of course, occur
during this stage as well, as can Type I mispriming, if a
low-temperature step is included.
[0122] End-Stage: End-Stage in LATE-PCR does not involve additional
amplification because double-stranded products are no longer melted
apart. End-Stage is a post-amplification stage in which some
operation is carried out. Most commonly the temperature is lowered
below the annealing temperature to permit probe target
hybridization (signal generation=anneal signal) and then the
temperature is raised over time to melt probe-target complexes
apart (loss of signal=melting). We refer to this as "Probe
Anneal-Melt Analysis". Probe Anneal-Melt Analysis at End-Stage can
be carried with or without real-time analysis during LATE-PCR
amplification. Typically Probe Anneal-Melt Analysis after a
Late-Stage of 10-15 cycles generates quantitative information about
the number of target copies present at the start of the
reaction.
[0123] Typically, mispriming does not occur during End-Stage or, if
it does, it is not followed by additional amplification needed to
make products of mispriming visible. And, as shown in Example 10,
it is possible using the "ColdStop" protocol to carry out Probe
Anneal-Melt Analysis during Late-Stage, then to resume
amplification for additional cycles until End-Stage is reached, at
which time Probe Anneal-Melt Analysis can be repeated. As shown in
Example 10, there is less scatter among replicates when real-time
analysis is not used before Probe Anneal Melt Analysis, because the
frequency of Type III mispriming is reduced by omission of a
detection step in each thermal cycle.
[0124] Although not intending to be bound by any theory, we
theorize that modified double-stranded oligonucleotides, as
described herein, interact directly with DNA polymerases to
suppress all types of mispriming, that is, Type I, Type II, Type
III and primer-dimers. We believe that the additives, when
double-stranded, preferentially bind to the 5' exonuclease domains
of DNA polymerases but also bind to the polymerase domains of DNA
polymerases, if added in sufficient concentration to more than
saturate the 5' exonuclease domains. Empirically, 300-600 nM
concentration of additive per 1.25 Units of Taq DNA polymerase in a
25 .mu.L reaction volume can be sufficient to saturate both the 5'
nuclease domain and the polymerase domain.
[0125] Although not intending to be bound by any theory, we
theorize that by saturating both domains at temperatures below the
primer annealing temperature, additives, as described herein,
prevent Type I mispriming by effectively shutting down the
polymerase by a combination of mass action and binding due to the
modifying groups. At temperatures above the primer annealing
temperature, additives can be used in concentrations which do not
saturate both the 5' exonuclease domain and the polymerase domain.
At these temperatures, additives preferentially bind to and
selectively inhibit the activity of the 5' exonuclease domain while
leaving the polymerase domain largely free to carry out extension
of correctly hybridized primers. By selectively binding to the 5'
exonuclease domain, additives increase the selectivity of the
polymerase domain by an allosteric effect.
[0126] Although not intending to be bound by any theory, we
theorize that modifying groups, for example Dabcyl groups,
contribute to the functioning of additives in ways that can be used
in selecting one or more additives for a particular purpose. Even
one 3' terminal modifying group can suppress mispriming that is
potentially caused by the additive itself. However, 3' terminal
modifying groups, whether one or two on a double-stranded
oligonucleotide, do not function to increase polymerase selectivity
against a mismatch at the 3' terminus of a primer. On the other
hand, 5' terminal modifying groups, particularly two 5' modifying
groups, can significantly enhance that polymerase selectivity.
Inclusion of modifiers on both strands at one end of the
double-stranded oligonucleotide (that is, one 5' modifier and one
3' modifier) can significantly enhance that selectivity even if the
double-stranded oligonucleotide is not blunt-ended. Having two
modifiers on both ends of a double-stranded oligonucleotide can be
better for selectivity enhancement than having two modifiers on
just one end, but double-stranded oligonucleotides with four
modifying groups tend to lower the efficiency of the polymerization
reaction more than do double-stranded oligonucleotides with one,
two or three modifying groups. We theorize that the cause for this
is that additives with four modifying groups bind more efficiently
to polymerase domains than do additives with fewer modifying
groups.
Suppression of Type I Mispriming
[0127] Additives include double-stranded oligonucleotides that are
modified by the addition of 1, 2, 3 or 4 modifying groups, for
example Dabcyl modifying groups, at or near the termini of the
strands, that is, in the terminal regions of the strands. In some
embodiments, there are 2-4 such groups, and in some embodiments,
the groups are covalently attached to terminal nucleotides. In the
Examples, additives as described herein, whether single additives
or mixtures, are denoted by the prefix "EP" to distinguish them
from other additives described for purposes of comparison. Example
1 demonstrates that additives suppress Type I mispriming without
causing additional mispriming. In this example, a LATE-PCR
amplification that produced incorrect product (product other than
that defined by the primer pair, as determined by melt analysis)
was used. Production of the wrong product indicates Type I
mispriming. Two different additives comprising unmodified
double-stranded oligonucleotides having the same length (16
nucleotides) but different sequences were tried as control
additives in this amplification. One, 16merA, added at a
concentration of at least 300 nM caused the reaction to produce the
correct product (FIG. 1). The other, 16merB, did not (FIG. 2), even
when added at concentrations of 600 nM or 1000 nM, and in fact
caused mispriming. This inconsistency was in accord with the
teaching of Kainz et al. that double-stranded oligonucleotides
could suppress mispriming or could cause mispriming. The assay was
repeated with additives that were modifications of the
mispriming-causing oligonucleotide, 16merB, the modifications being
the inclusion of either one or two terminal Dabcyl modifiers.
Inclusion of a single Dabcyl modifier, additive EP048 (FIG. 3) or
additive EO049 at 600 nM concentration, suppressed mispriming as
compared to 16merB (FIG. 2), including mispriming caused by the
unmodified oligomer. Inclusion of two Dabcyl modifiers, additive
EP027, did so at only 300 nM concentration and gave quite an
improvement when added at only 100 nM concentration (FIG. 4). As
shown by the kinetic analysis of reactions containing additive
EP027 at different concentrations (FIG. 5), additive EP027 at 300
nM concentration eliminated scatter among replicates, and 300 nM
was judged to be the optimum concentration in this assay.
[0128] The assay of Example 1 was repeated with several other
unmodified double-stranded oligonucleotides having lengths from 12
to 30 nucleotides. Results, reported in Example 1, confirmed that
unmodified oligonucleotides were inconsistent regarding suppressing
or causing Type I mispriming. As reported in Example 1, the assay
was also repeated with a number of double-stranded oligonucleotides
having lengths in the range of 8-22 nucleotides and having two
modifiers that were Dabcyl, two modifiers that were digoxigenin,
four modifiers that were Dabcyl, or four modifiers that were
digoxigenin. Results confirmed that additives, as described herein,
suppressed Type I mispriming. These results also demonstrate the
influence of Tm for additives. (In this application the Tm of an
additive means the calculated Tm of its unmodified double-stranded
sequence, as defined above. Modifiers tend to increase actual Tm
slightly, perhaps 1-2.degree. C., which the reader can take into
account). To suppress Type I mispriming, it is preferred that
additives remain double-stranded up to, or nearly up to, the primer
annealing temperature and the primer Tm's. In Example 1, the primer
annealing temperature for the first 10 cycles was 55.degree. C.
While good results were obtained in all cases at 600 nM
concentration with additives having Tms ranging from 37.degree. C.
to 63.degree. C. in Example 1, it was only additive EP021, the
additive with the lowest Tm, that did not also give good results at
300 nM. The additives that performed best at concentrations of 100
nM and 50 nM had Tm's of at least 60.degree. C. For suppression of
Type I mispriming in PCR amplification reactions, additives can
have Tms of at least 32.degree. C., more typically at least
50.degree. C., and more preferably at least 60.degree. C.
[0129] As a further check on the consistency with which additives
as described herein suppress Type I mispriming, we performed a
LATE-PCR assay for a different target sequence using different
primers. In this assay, as reported in Example 2, we compared
twelve additives to the unmodified double-stranded oligonucleotide,
oligonucleotide 22merA, that performed well in the assay of the
first part of Example 1. The additives all had lengths of 22
nucleotides, several different sequences, and several different
configurations of two, three or four terminal Dabcyl modifiers. All
were at least as good as additive 22mer A in suppressing mispriming
at 300 nM concentration, and nearly half did so at a lower
concentration of only 100 nM. FIG. 6 is melt curves for additive
EP003 and additive 22merA, showing that only the additive
suppressed mispriming at 100 nM concentration.
[0130] Example 9 illustrates a quantitative LATE-PCR assay to
measure polymerase activity of a DNA polymerase prior to the first
thermal cycle. This same assay can be used to quantify and compare
the DNA polymerase inhibitory capacities of additives, which can be
assayed over a broad range of concentrations, temperatures, and
incubation times. The initial reaction mixture includes a high
concentration of two oligonucleotides (62 and 75 base pairs,
respectively) capable of annealing to each other at their 3' ends
to form a hybrid that is 27 base pairs long and has a calculated Tm
of 60.degree. C. They also have priming sites at their 5' ends.
Amplification primers are not included in the initial reaction
mixture. The thermal profile of the reaction begins with an
isothermal soak at 50.degree. C. for 10 minutes. During this step
the overlapping oligonucleotides can prime themselves, that is,
hybridize and be extended by active DNA polymerase. To the extent
that this occurs, there will be created copies of a double-stranded
target for the primers, which are added to the reaction mixture
prior to thermal cycling. Inhibition of the activity of the
polymerase activity during the long incubation at 50.degree. C.
will reduce the number of copies of target formed during this
step.
[0131] After the long 50.degree. C. incubation, high Tm primers are
added, and a 2-step LATE-PCR amplification is performed to amplify
whatever targets had been made. The primer annealing temperature
use for amplification (72.degree. C.) is well above the Tm of the
overlapping nucleotides so that additional double-stranded targets
are not generated. In this assay, the number of cycles required to
generate a detectable level of product (observed with either SYBR
Green or a probe to the Excess-Primer-Strand) depends on how many
full length strands were generated during the initial isothermal
incubation of the partially complementary oligomers. This, in turn,
depends on how active the DNA polymerase was during isothermal
incubation due to the presence/absence of any potential enzyme
inhibitor(s), such inhibitors, of known composition and
concentration, having been added to the reaction mixture when it
was first assembled on ice and prior to addition of the overlapping
oligonucleotides.
[0132] We tested additives in this quantitative assay, including
additives having Tm's at or below the 50.degree. C. incubation
temperature (EP020, Tm 50.degree. C.; EP022, Tm 45.degree. C.) and
an additive having a Tm substantially above the incubation
temperature (EP046, Tm 67.degree. C.). The additives having the
lower Tm's would have been at least substantially single-stranded
during the 50.degree. C. incubation, while high-Tm additive EP046
would have been double-stranded. Incorporation of the low-Tm
additives into the reaction mixture resulted in no delay of the
C.sub.T, but incorporation of EP046 at a concentration of 600 nM
did delay the C.sub.T, whether the polymerase was Taq or
Taq-plus-antibody. Kinetic curves for additive EP046 are shown in
FIG. 13. FIG. 13 reveals that in the absence of any DNA polymerase
inhibitor the 3' ends of the overlapping oligonucleotides
hybridized to each other and extended. Addition of the antibody
with the polymerase for hot-start partially inhibited Type I
mispriming, by about 1000-fold, but further addition of 600 nM
EP046 inhibited Type I mispriming an additional 10-fold.
[0133] Example 16 reports similar tests with additives having
single-stranded overhangs six nucleotides in length and a
double-stranded region of 22 base pairs. The additives all
contained the same strand sequences but differed in the number and
placement of modifiers, which were Dabcyl groups in the example.
Both individual strands were hairpin-forming as depicted in FIG.
18C. The method of the tests included and isothermal soak at
50.degree. C. for one minute (rather than for 10 minutes as in
Example 9), followed by incubation on ice and then the LATE-PCR
amplification. Melt-curve analysis showed that additives with two
modifiers (FIG. 19A) and three modifiers (FIGS. 19B, 19C) reduced
generation of incorrect product, and the additive with four
modifiers (FIG. 19D) completely suppressed its generation.
[0134] Example 20 reports a test according to Example 9 that more
strictly isolates Type I mispriming during the Pre-Stage. By using
an additive that becomes single-stranded at the PCR
annealing/extension temperature, possible Type II mispriming is
eliminated. Based on the results reported in Example 20, we
conclude that: a) hot-start antibody does not suppress DNA
synthesis completely and that most products generated in the
presence of the antibody result from Type I mispriming; b) products
synthesized during incubation on ice are largely the result of Type
I mispriming; c) additive EP010 acts to increase the specificity of
product extension on ice, and because most products generated on
ice are the result of Type I mispriming, EP010 inhibits most primer
extension events on ice. Because melt curves of the amplified
product containing additive EP010 (FIG. 23E) show that the
double-stranded form is no longer present at 72.degree. C., the
temperature at which primer annealing and extension was carried out
during amplification, the effects of EP010 observed in Example 20
are entirely due to the activity of EP010 during incubation at
50.degree. C. and on ice, prior to the start of amplification. The
same analysis of the additives used in Example 9 revealed that they
have melt peaks (not shown) that are higher than that of EP010 and,
therefore, the effects of the additives in Example 9 are due not
strictly to steps prior to amplification, but also to steps during
amplification.
Suppression of Type II Mispriming and Increasing Polymerase
Selectivity in PCR Reactions
[0135] Additives can suppress Type II mispriming and increase the
selectivity of DNA polymerase for hybridized 3' terminal
nucleotides of primers. To determine the selectivity against a
mismatch at the 3' terminal nucleotide of the limiting primer
during amplification in a LATE-PCR assay, we amplify a target that
is perfectly complementary to both primers (matched target), and we
separately amplify a target that is perfectly complementary to the
excess primer but that contains a single mismatch to the 3'
terminal nucleotide of the limiting primer. Alternately, as
described below and demonstrated in Example 19, a 3' terminal
mismatch can be created by use of a blocker oligonucleotide. We
detect double-stranded product by DNA dye. "Selectivity" is the
difference (.DELTA.C.sub.T) between the C.sub.T of the signal from
amplification of the mismatched target and the C.sub.T of the
signal from amplification of the matched target. When performed on
a sample containing no additive, this assay can demonstrate the
basic selectivity of the polymerase for the primer/matched-target
over primer/mismatched target, as well as the basic efficiency of
amplification of the primer/matched target. For Taq DNA polymerase,
the .DELTA.C.sub.T can be less than two amplification cycles.
Improvement in selectivity caused by an additive is the gain in
.DELTA.C.sub.T resulting from the inclusion of the additive in the
amplification reaction mixture.
[0136] We tested unmodified double-stranded oligonucleotide and a
number of additives in this selectivity assay. Results of assays
run in triplicate are reported in Example 3. The C.sub.T
differences (.DELTA.C.sub.T) that are reported are the improvement
in selectivity based on averages of the three replicates.
Unmodified double-stranded oligonucleotide 22merA, despite having a
Tm slightly above the primer annealing temperature of the assay,
improved the basic selectivity of the Taq DNA polymerase itself by
fewer than two C.sub.T units at concentrations up to 300 nM. We
tested numerous additives having the same length, 22 nucleotides,
with various configurations of two, three, or four Dabcyl
modifiers. As reported in Example 3, most configurations of two,
three, or four Dabcyl modifiers improved the selectivity of the
polymerase substantially, thereby reducing its tendency for Type II
mispriming. As further reported in Example 3, we also tested three
other modifiers useful in additives and fluorescein (FAM), not
useful as a modifying group in additives. In at least some
double-stranded oligonucleotides, each of the modifiers
digoxigenin, coumarin and the quencher QSY 21 significantly
improved selectivity as compared to additive 22merA and as compared
to a 22 nucleotide-long oligonucleotide with four FAM
modifiers.
[0137] As reported in Example 17, we similarly tested amplification
with various amounts of three additives having a double-stranded
region of 22 base pairs and single-stranded overhangs six
nucleotides in length. The sequences of the additives are given in
Example 16. The additives comprised two strands that were
hairpin-forming, as shown in FIG. 18C. Such additives with two and
three Dabcyl groups as modifiers showed moderate improvement in
selectivity (.DELTA.C.sub.T) of greater than three C.sub.T units.
The largest gain in selectivity was achieved with the additive
having four Dabcyl groups as modifiers, namely, greater than six
C.sub.T units.
[0138] Additives can also suppress Type II mispriming and increase
polymerase selectivity in conventional symmetric PCR
amplifications. Example 11 reports a symmetric PCR assay for two
target sequences, one that was perfectly complementary to both
primers and one that was perfectly complementary to one primer but
contained a mismatch opposite the 3' terminal nucleotide of the
other primer. The assay was run with no additive in the reaction
mixture and also with a combination of two additives in the
reaction mixture. That combination, designated EP043, included two
double-stranded oligonucleotides with Dabcyl modifiers at combined
concentration of 300 nM. In the assay of Example 11 the combination
of Platinum Taq DNA polymerase, a hot-start DNA polymerase, and a
highly discriminating allele-specific primer pair preferentially
amplified the matched target by 7.84 C.sub.T values relative to the
mismatched target. This detection specificity would be equivalent
to detection of 1 matched target in an excess of 229 mismatched
targets (i.e., 0.43% intended target) in a theoretical mixed
population of both DNA targets. In comparison, addition of additive
EP043 to the same symmetric PCR assay increased the specificity in
favor of the matched target by another 4.75 C.sub.T values to 12.59
C.sub.T values, which would be equivalent to detection of 1 matched
target in an excess of 6,615 mismatched targets (i.e., 0.02%),
corresponding to a 26.7-fold increase in detection specificity.
[0139] In the experiment reported in Example 5, we performed a
series of LATE-PCR amplifications with no additive, with a low-Tm
additive, EP020 (Tm 51.degree. C.), and with a higher-Tm additive,
EP013 (Tm 62.degree. C.). The experiment included the use of
different primer annealing temperatures to test the amplification
reaction under highly stringent conditions (high annealing
temperature), moderately stringent conditions, and rather
unstringent conditions (low annealing temperature as compared to
the primer Tm's). Mispriming problems typically worsen as
stringency is reduced. The assays were duplex assays for two target
sequences, each having its own primer pair and its own detection
probe.
[0140] The probes were molecular beacon probes that fluoresced upon
hybridization to correct amplicons. Kinetic curves of probe
fluorescences over the first 50 cycles are reported in FIGS.
9A-9F.
[0141] FIG. 9A shows that in this amplification reaction, Platinum
Taq DNA polymerase, a hot-start polymerase, was not able to
suppress Type I and Type II mispriming even under stringent
conditions: 65.degree. C. annealing temperature for all cycles. In
contrast, both additives were able to do so (FIGS. 9B and 9D) at
the concentrations used. With low stringency during the first 20
cycles (annealing temperature 60.7.degree. C.), low-Tm additive
EP020, which was not double-stranded at the annealing temperature,
did not suppress Type II mispriming during amplification (FIG. 9C),
but higher-Tm additive EP013 did (FIG. 9F). This shows that to
suppress a type of mispriming occurring at a particular
temperature, the additive should be double-stranded at that
temperature. Comparison of FIGS. 9D-9F shows that with additive
EP013 the least scatter among replicates was achieved using a
stringent annealing condition for the first 20 cycles (66.5.degree.
C.), and that scatter was less at the least stringent condition
(60.7.degree. C.) than at an intermediate stringency (64.2.degree.
C.). This latter result is explained by the fact that the
concentration of double strands, that is the functional
concentration of the additive, was higher at the lower annealing
temperature, illustrating the interrelationship between additive
concentration and primer annealing temperature. It will be noted
from FIGS. 9D-9F that with additive EP013, one target sequence
amplified significantly less efficiently in the reaction than the
other product sequence. We found that the difference could be much
reduced by increasing the limiting primer concentration for the
less efficient amplification from 50 nM to 100 nM.
Suppression of Type III Mispriming
[0142] Additives can suppress Type III mispriming. Example 13
reports an experiment in which a LATE-PCR reaction was carried out
to 65 cycles, long enough for Type III mispriming to occur and
generate long double-stranded products resulting from the priming
of one amplicon strand by another amplicon strand. We tested
amplification with no additive; amplification with an additive
having a Tm very close to the 58.degree. C. primer annealing
temperature (additive EP047, Tm 59.1.degree. C.); and with a
mixture of additives in which we replaced a minor amount, only
about one-tenth, of additive EP047 with an additive that is
double-stranded at temperatures above the annealing temperature. In
this example, we used a higher Tm additive having a Tm
(67.4.degree. C.) substantially above the annealing temperature. A
melt curve for three replicate amplifications with no additive
showed that after 65 cycles of amplification the detected products
had higher Tm's than the intended product, indicating that product
evolution occurred. Kinetic curves showed that during the plateau
phase there occurred a rise in the SYBR signal, also indicating
that product evolution occurred. When the 5' end of the limiting
primer was modified by the addition of a pair of A-nucleotides, the
result remained the same: the melt curves showed products having
higher Tm's than the desired amplicon. Inclusion of EP047 at 600 nM
concentration with the unmodified limiting primer helped a little:
it delayed product evolution by several cycles, and some detected
products in two of three replicates had the correct Tm. Inclusion
of EP047 at 600 nM and the use of the modified limiting primer
decreased product evolution significantly and prevented it entirely
in one of three replicates. Inclusion of additive mixture EP043 at
600 nM total concentration when used with the unmodified limiting
primer decreased product evolution significantly and prevented it
entirely in one of three replicates. Inclusion of EP043 at 600 nM
and use of the modified limiting primer significantly decreased
product evolution and prevented it entirely in two of three
replicates. Thus, low concentrations of additives that are designed
to have a Tm above the primer annealing temperature can suppress
Type III mispriming. Further, the effect can be enhanced, if the 3'
ends of amplicon strands are rendered AT-nucleotide rich, which can
be accomplished, where necessary, by modification of the 5' ends of
limiting primers.
[0143] Example 15 includes a no-additive control amplification
assay for an RNA target sequence that showed severe Type III
mispriming. It also shows that inclusion of additives, both
double-stranded oligonucleotides and four-strand mixtures of
double-stranded oligonucleotides, can suppress the Type III
mispriming seen in the control. Example 15 demonstrates that
additives, reaction mixtures, and methods do not inhibit reverse
transcriptase used to convert RNA target into cDNA target.
Multiplexing
[0144] Additives can enable highly multiplexed reaction for
numerous target sequences with numerous primer pairs. Example 8
reports a 12-plex reaction, that is, multiplexed amplification of
twelve target sequences using twelve primer pairs in a single
reaction mixture. The amplification reaction was a LATE-PCR
amplification of 65 cycles. The target sequences were included as
human mitochondrial genomic DNA, which was included in the reaction
mixtures with starting copy numbers of 1000, 100 and 10. In
addition to a control amplification with no additive, additive
EP011 was included in the reaction mixtures at concentrations of
300 nM and 600 nM. Following amplification, the reaction mixture
was subjected to electorphoretic separation to ascertain whether or
not the twelve intended products were made. In addition, dideoxy
sequencing was performed to evaluate the amplicons. A photograph of
the electrophoretic gel, FIG. 12, shows that amplification starting
with 1000 copies, but with no additive, failed to produce the
intended set of twelve products, but amplification starting with
1000 copies plus additive EP011 at 300 nM and 600 nM concentrations
did produce the twelve products. The gel revealed that in this
reaction EP011 at 300 nM concentration did not completely suppress
mispriming, as evidenced by a band of lightweight product.
Mispriming products were not seen in the gel when additive EP011
was included in the reaction mixture at 600 nM concentration. As a
further analysis on this last product, it was sequenced. Sequencing
results showed that a sufficient amount of each of the twelve
amplicons had been generated to permit dideoxy sequencing by the
simplified Dilute'N'Go protocol. That was found not to be the case
when the starting numbers of target were reduced to 100 and 10
copies. The results with 1000 copies of mitochondrial DNA show that
mispriming was suppressed successfully both prior to amplification
and during amplification.
Additive Mixtures
[0145] A mixture of additives, additive mixture EP043, is discussed
above in connection with Example 13. A reason to use a mixture can
be understood by reference to Example 1, for example. The results
show that suppression of Type I mispriming typically requires a
moderately high concentration of additives. The kinetic curves in
FIG. 5 show, however, that efficiency of the polymerization
reaction tends to decrease as one increases the concentration of an
additive having a Tm significantly above the primer annealing
temperature. Yet Example 13 shows that a high-Tm additive can be
needed to suppress Type III mispriming. A mixture of additives can
be designed to suppress both types of mispriming while minimizing
the reduction in amplification efficiency. In one embodiment, use a
mixture that includes a higher concentration (300 nM to 1000 nM) of
an additive that has a Tm close to the annealing temperature and a
lower concentration (25 nM to 300 nM) of an additive that is
double-stranded at temperatures above the annealing temperature,
specifically, an additive that has a Tm several degrees above the
annealing temperature (or the higher annealing temperature, if two
are used in the reaction) can be used to suppress both types of
mispriming. A mixture of additives may comprise four different
strands, that is, two double-stranded additives that do not share a
common strand. Alternatively, a mixture of additives may comprise
three strands, that is, two double-stranded additives that share a
common strand. The latter approach reduces the number of different
strands included in an amplification mixture.
[0146] We tested mixtures of additives in the polymerase
selectivity assay described in Example 3, both mixtures of
unmodified double-stranded oligonucleotides and mixtures of
additives. Experimental results are reported in Example 4. The
mixtures tested were all three-strand mixtures in which two
additives share a common strand. The mixtures all included a
high-Tm additive having a Tm of 67.4.degree. C., several degrees
above the primer annealing temperature, which in this experiment
was 62.degree. C., and a low-Tm additive having a Tm in the range
of 57.4-59.1.degree. C., that is, slightly below the annealing
temperature. Two of the mixtures, additive 041 and additive 042,
contained unmodified double-stranded oligonucleotides. Both
mixtures with unmodified oligonucleotides improved selectivity of
the polymerase only relatively slightly, less than two
amplification cycles, when added at concentrations of 75 nM for the
higher Tm hybrid and 325 nM for the lower Tm hybrid. We also tested
four mixtures of additives. In two (EP041, EP042), both
double-stranded oligonucleotides contained three Dabcyl modifiers;
in one (EP043), the higher Tm oligonucleotide contained three
Dabcyls, while the lower Tm oligonucleotide contained four Dabcyls;
and in one (EP045), both oligonucleotides contained four Dabcyls.
All four mixtures improved selectivity more than did additives 041
and 042. FIGS. 7A-7D and 8A-8D are kinetic curves for mixtures
EP043 and EP045, respectively, at the same total concentration of
600 nM but with the amount of the higher Tm hybrid varying from 25
nM to 100 nM. These curves reveal inhibition caused by additives
and also scatter among replicates. The .DELTA.C.sub.T results and
the kinetic curves taken together show that for each mixture there
may be an optimum amount of the higher Tm hybrid in the mixture.
For mixture EP043, (a) even the lowest concentration (25 nM) of the
high-Tm component increases polymerase selectivity, (b) polymerase
selectivity is not increased more by increasing the proportion of
the high-Tm component up to 100 nM, and (c) none of the
formulations significantly inhibits the efficiency of amplification
of the primer to its matched target. For mixture EP045, (a) even
the lowest concentration (25 nM) of the high-Tm component increases
polymerase selectivity to a greater extent than EP043, (b)
polymerase selectivity increases in proportion of the concentration
of the high-Tm component, (c) all of the formulations inhibit the
efficiency of amplification of the primer to its matched target,
and (d) the extent of inhibition increases with the proportion of
the high-Tm component. We judged the optimal formulation of mixture
EP043 to be 75/600/525 nM, and we judged the optimal formulation of
mixture EP045 to be 50/600/550 nM, as these formulations had low
scatter among replicates.
[0147] We also tested, in Example 19, additive mixture EP043 in an
assay in which a 3' terminal mismatch is created by use of a
blocker oligonucleotide. The scheme for that assay is illustrated
generally in FIG. 21A and FIG. 21B. FIGS. 21A, 21B depict two
double-stranded targets 231, 232, which differ by one base pair
(either a G or an A in the excess-primer strand) shortly downstream
from the binding site for limiting primer, arrow 233. The binding
site for the excess primer, arrow 234, is also conserved between
the two targets. Oligonucleotide blocker 235 is complementary to,
and binds to, target 231 (FIG. 21A), which is the "mismatched"
target to be selected against. Blocker 235 is allele-discriminating
and mismatched against target 232 (FIG. 21B) and does not bind to
it. Accordingly, primer 233 binds fully to target 232 and is
extended, but the 3' terminus of primer 233 cannot bind to target
231, preventing extension. In FIG. 21A dashed line 242 is the
limiting primer strand that would be created were primer 233
extended. In FIG. 21B dashed line 243 is the limiting primer strand
created by extension of primer 233. Blocker 235 is shown with a
terminal fluorophore 236 and a terminal quencher 237, but all that
is required is that blocker 235 have a blocked 3' terminal
nucleotide so as not to be extendable by a DNA polymerase during
amplification. In the particular embodiment shown in FIGS. 21A,
21B, targets 231, 232 are shown to differ by another base pair
(either a G in excess primer strand 241 in FIG. 21A or a C in
excess primer strand primer strand 244 in FIG. 21B) downstream from
blocker 235 and downstream from excess primer 234. A
sequence-specific probe 238, labeled with fluorophore 239 and
quencher 240, binds to the product of amplification of target 231
(the "mismatched" target) but not to the product of amplification
of target 232, and signals upon hybridization. Probe 238 is
optional in the sense that it is not used to enhance polymerase
selectivity. It can be used, for example, for a melt analysis of
the amplification product. Example 19 shows that in the case of
induced-Type II mis-priming, when the additive reduces
amplification efficiency, amplification is delayed in a
thermal-cycle-dependent manner, and when the magnitude of the
enhancement of selectivity due to the presence of an additive is
also thermal-cycle dependent, the apparent enhancement of
selectivity needs to be corrected for the thermal-cycle-dependent
decrease in efficiency. A way to make that correction using a
series of target dilution reactions in the presence of the blocker
plus the presence/absence of the additive is demonstrated in
Example 19.
[0148] We utilized additive mixture EP043 in the 12-plex of Example
8, discussed above, to see if sufficient amounts of all twelve
products could be generated for sequencing. For these experiments
we modified the limiting primer by adding AT-rich tails, and we
extended the amplification reaction from 65 cycles to 80-90 cycles.
With these modifications, all twelve intended products were
successfully made in amounts needed for sequencing when additive
mixture EP043 was included at strand concentrations of 50/600/550
nM and the starting amount of genomic mitochondrial DNA was only
100 copies or 10 copies. These results show that mispriming was
prevented successfully prior to and during amplification, despite
the fact that the extended length of the amplification presented a
severe test for suppression of Type III mispriming.
[0149] In Example 12 we tested mixture EP043 at 600 nM total
concentration in LATE-PCR amplification reactions that differed in
the 3' end of the limiting primers. One reaction included a
limiting primer having a GC-rich 3' end (GGC). The other reaction
included a limiting primer having at AT-rich 3' end (AAG). As
compared to a no-additive control, inclusion of additive EP013
(three Dabcyl modifiers, Tm 60.degree. C.) in the amplification
with the primer having the GC-rich 3' end resulted in relatively
little reduction in efficiency of polymerization (C.sub.T delay of
4 cycles). As compared to a no-additive control, however, inclusion
of the same additive at the same concentration with the primer
having the AT-rich 3' end resulted in a significantly greater
reduction in efficiency (C.sub.T delay of 11 cycles). In both
reactions, which were continued for 70 cycles, additive EP013
significantly reduced scatter among four replicates as compared to
the no-additive control.
ColdStop Protocol and all Types of Mispriming
[0150] The likelihood of Type II mispriming is enhanced by the
inclusion of a low-temperature detection step in PCR cycles for
real-time detection. Type III mispriming is enhanced by lengthening
a LATE-PCR amplification to generate single-stranded product. We
have tested a protocol that we refer to as "ColdStop" in which, as
a replacement for real-time, low-temperature detection, the
amplification reaction is interrupted at one or several
intermediate points in order to perform an operation that may
include a low-temperature step. Example 10 illustrates a "ColdStop"
protocol in which that operation is a melt analysis. The
amplification in Example 10 is a 2-step LATE-PCR amplification of
70 cycles using a hybridization probe for fluorescence detection.
Additive EP010 was tested at a concentration of 600 nM. For
purposes of comparison, an amplification was performed with
real-time detection. For real-time detection a low-temperature
detection step (60.degree. C.) was added following each
annealing/extension step of the amplification cycles. Probe
fluorescence as a function of thermal cycles is shown in FIG. 14A,
which shows a moderate scatter among replicates for the
amplifications starting with 1000, 100, and 10 copies of the target
sequence. FIG. 14A also shows the curves for the three amounts of
initial target beginning to converge by cycle 70. The inclusion of
real-time, low temperature detection increased the chance for Type
II mispriming. We repeated the amplification for all three starting
copy numbers with no real-time low-temperature detection but with
an interruption after 40 cycles to perform a melt beginning at
45.degree. C. Then we resumed amplification to conclusion after 70
cycles, at which time a second melt was performed. The melt curves
for the first melt are presented in FIG. 14B. The replicates for
the three different starting amounts of target are clearly
distinguishable and show little scatter. The melt curves for the
second melt are presented in FIG. 14C. By cycle 70 the curves for
the three levels of initial target amount have converged, and
little scatter is detected.
[0151] To interpret the results shown in FIGS. 14B and 14C, the
following are noted. If mispriming takes place due to a
low-temperature interruption, single-stranded DNA will be converted
into double-stranded DNA, and the amount of single-stranded product
will decrease between cycles 40 and 70. That did not happen. If
mispriming occurs during the interruption after 40 cycles, scatter
among the replicates will increase between cycle 40 and 70. That
did not happen. If mispriming occurs during the interruption, the
amount of single-stranded product generated from the differing
amounts of initial target would fail to equalize after 70 cycles.
That did not happen. Comparison of FIG. 14A, FIG. 14B and FIG. 14C
indicates that additive EP046 completely suppressed all types of
mispriming in this "ColdStop" amplification. The "ColdStop"
protocol with a single interruption eliminates any low-temperature
step prior to cycle 40 and after cycle 41. This reduces the chances
for Type II and Type III mispriming during all but cycle 41. The
first melt includes a lengthy time at a temperature below the
primer annealing temperature (in this example, about 15 minutes),
and so increased the likelihood of mispriming during the melt
(which would include one extension of misprimed 3' ends), in
exchange for eliminating a low-temperature step in other cycles.
That trade-off may help to reduce scatter among replicates. It will
be appreciated a "ColdStop" protocol can be used to screen additive
compositions and concentrations for their effects on
mispriming.
Inhibition of 5' Exonuclease Activity of DNA Polymerase
[0152] Additives can be effective to inhibit the 5' exonuclease
activity of DNA polymerases that possess that activity, for example
Taq DNA polymerase and Tfi (+) DNA polymerase. (This effect is not
applicable to DNA polymerases not having that activity, such as the
Klenow fragment, which does not possess a 5' exonuclease domain,
and Tfi(-) DNA polymerase, which contains a 5' exonuclease domain
that is modified to render it inactive.) We developed the assay
reported in Example 6 as a primer-independent means to gage the
inhibitory effects of additives on the 5' exonuclease activity of
DNA polymerases. In that assay, a non-extendable probe that is dual
labeled with a fluorophore and a quencher is hybridized to a target
without primers being included in the reaction mixture. The
reaction mixture is then subjected to thermal oscillation in which
the temperature is cycled between 45.degree. C. and 60.degree. C.
forty-five times, during which probe fluorescence is detected in
real time. Probe cleavage leads to increased fluorescence
indicative of 5' exonuclease activity of the polymerase. Several
additives were tested in this assay at a concentration of 300 nM
and compared to a control assay that included probe but no target.
In the control assay no hybrid was formed, and the probe was not
cleaved. In an assay containing probe and target but no additive, a
large increase in fluorescence resulted. In assays containing
probe, target and an additive, fluorescence increase was markedly
reduced compared to the assay with target but no additive, showing
substantial inhibition of 5' nuclease activity. Additives EP004 and
EP001, that have three and four covalently linked Dabcyl groups
respectively, completely inhibited primer-independent 5'exonuclease
cleavage of the probe. Additive EP008, that has a covalently linked
Dabcyl group on each of its 5'nucleotides, also completely
inhibited primer-independent 5'exonuclease activity in this assay.
In comparison, additive EP009, that has a covalently linked Dabcyl
group on each of its 3'nucleotides, only partially inhibited
primer-independent 5'exonuclease activity in this assay. The
results show that the Dabcyl modifier groups on double-stranded
oligonucleotides can enhance inhibition of the 5'exonuclease
activity in a position-dependent manner. Dabcyl groups on both
5'ends of the additive are preferred, and three and four Dabcyl
groups are preferred over two Dabcyl groups. Addition experiments
demonstrated consistent results for Tfi(+) DNA polymerase.
[0153] As reported in Example 18, we performed the
temperature-oscillation assay of Example 6 with various amounts of
three additives having a single-stranded region of 22 base pairs
and single-stranded overhangs six nucleotides in length. The
sequences of the additives are given in Example 16. The additives
comprised two strands that were hairpin-forming, as shown in FIG.
18C. Such additives included two, three or four Dabcyl groups as
modifiers. As shown in FIG. 20, the additive with two Dabcyl
modifiers inhibited primer-independent 5' exonuclease activity of
Taq DNA polymerase in a concentration-dependent manner, with
concentrations of 200 nM and 400 nM largely inhibiting activity and
a concentration of 600 nM nearly completely inhibiting activity.
The tested additives with three and four modifiers also inhibited
primer-independent 5' exonuclease activity of the polymerase in a
concentration-dependent manner but to a somewhat lesser degree than
the results shown in FIG. 20.
[0154] To gage inhibition of 5' nuclease activity during PCR
amplification, we subjected probes and amplicons resulting from the
LATE-PCR amplification described in Example 5 to hybridizing
conditions followed by melt analysis. A reaction mixture of probe
alone was also subjected to melt analysis. The experiment is
reported in Example 7, and melt curves are presented in FIGS. 11A
and 11B. Comparison of fluorescence from the probe alone and the
amplification with no additive in FIG. 11A shows some probe
molecules were cleaved: fluorescence from the amplification
reaction did not fall to the level of probe fluorescence after
melting was completed. FIG. 11B shows probe cleavage due to 5'
nuclease activity of the polymerase (in this case Taq DNA
polymerase) was inhibited when the amplification reaction mixture
included additive EP013 at a concentration of 600 nM: fluorescence
from the amplification reaction fell to the level of probe
fluorescence after melting was completed.
Additive as a PCR Primer
[0155] Example 14 demonstrates an additive in the form of a PCR
primer. To convert a typical excess primer for a LATE-PCR
amplification into an additive that suppresses Type I mispriming,
two things were done: first, a modifying group, in this case a
Dabcyl group, was added to the 5' terminus of the primer; and
second, a reverse complement strand that was partially
complementary to the excess primer and that had both a 5' terminal
Dabcyl group and a 3' terminal Dabcyl group was included in the
reaction mixture at a concentration of 100, 200 or 300 nM. The Tm
of the hybrid formed by the excess primer and the reverse
complement strand was reduced relative to the Tm of the hybrid
formed by the excess primer and the target sequence by introducing
several mismatches into the reverse complement strand
(alternatively, the length of the reverse complement strand could
have been reduced). The hybrid formed by the excess primer and the
reverse complement strand included three modifying groups. Melt
analysis of double-stranded amplification products showed that
inclusion of the reverse complement sequence in the reaction
mixture at a concentration of 200 nM or 300 nM resulted in the
expected amplicon with little-to-no other products, and the melt
curves showed little scatter among replicates. In contrast,
amplification without the reverse complement sequence in the
reaction mixture resulted in a mixture of intended amplicon and
lower Tm products, and the melt curves showed scatter among
replicates.
[0156] The foregoing examples are meant to illustrate certain
preferred embodiments of additives, reaction mixtures, and methods
according and should not be construed as exhaustive or limiting.
Numerous variations are possible and would be apparent to one of
skill in the art. For example, amplification methods other than PCR
may be utilized, and additives may be modified versions of
molecules other than double-stranded DNA molecules. Other
variations will be apparent to persons skilled in the art.
EXAMPLES
Example 1. Suppression of Type I Mispriming
[0157] LATE-PCR assays were performed using a single pair of
primers and a single target to generate double-stranded and
single-stranded amplicons. Double-stranded products were
characterized by melting analysis at the end of amplification.
Reaction components other than double-stranded oligonucleotides,
and reaction conditions were as follows.
TABLE-US-00001 Limiting Primer. (SEQ ID No. 1) 5'
CCTGGATTATGCCTGGCACCAT Excess Primer. (SEQ ID No. 2) 5'
CCTTGATGACGCTTCTGTATCTA Target. (SEQ ID No. 3) 5'
CCTGGATTATGCCTGGCACCATTAAAGAAAATATCATCTTTGGT
GTTTCCTATGATGAATATAGATACAGAAGCGTCATCAAAG
[0158] LATE-PCR amplifications were carried out in 25 ul volume
consisting of 1.times.PCR buffer (Invitrogen, Carlsbad, Calif.), 3
mM MgCl.sub.2, 250 nM dNTPs, 50 nM of limiting primer, 1000 nM of
excess primer, 0.24.times.SYBR Green (Invitrogen, Carlsbad,
Calif.), 1.25 units of Taq DNA polymerase (Invitrogen, Carlsbad,
Calif.) with approximately 1000 genomes of human genomic DNA
(Sigma-Aldrich, St. Louis, Mo.). Amplification reactions were run
in a triplicate set for each additive, utilizing the additive at
concentrations of 50, 100, 300, 600, and 1000 nM, along with a
no-additive reaction.
[0159] The thermal profile conditions for these reactions were as
follows: 95.degree. C./10 s-55.degree. C./30 s-70.degree. C./30 s
for 10 cycles followed by 95.degree. C./10 s-50.degree. C./30
s-70.degree. C./30 s for 40 cycles followed by a melt starting at
55.degree. C. with 1.degree. C. increments at 30 s intervals to
97.degree. C.
[0160] Reactions were analyzed at the end of 50 cycles by a melt
curve analysis using the first derivative of SYBR Green
fluorescence (-dF/dT, SYBR) of double-stranded DNA product. In
addition, the kinetics of production of double-stranded product
(SYBR intensity reading as a function of thermal cycles) was
analyzed for certain reactions.
A. 16mers
[0161] Each of the following additives that were 16 nucleotides
long was included in the starting reaction mixture (terminal
blocker C.sub.3 is a three-carbon linker chain):
TABLE-US-00002 16merA. (SEQ ID No. 4) 5' CACGACCTCGCCGACC (C.sub.3)
(C.sub.3) GTGCTGGAGCGGCTGG 5' 16merB. (SEQ ID No. 5) 5'
CACGACCTCGCTGACC (C.sub.3) (C.sub.3)GTGCTGGAGCGACTGG 5'
EP048: 16merB with one Dabcyl at 3' end of top strand (SEQ. ID No.
6) EP049: 16merB with one Dabcyl at 3' end of bottom strand (SEQ ID
No. 7) EP027: 16merB with two Dabcyls one at 3' end of each strand
(SEQ ID No. 8)
[0162] With no additive, the amplification generated products other
than the "correct" product, that is, other than the double-stranded
product (amplicon) defined by the primers. The melt curves for the
three replicate amplification reactions containing additive 16merA
at 300 nM concentration is shown in FIG. 1, with the intended
product identified by the downward-pointing arrow. Circle 11 is the
curves for the three replicates. This amplification was judged to
be very good, because (1) the correct product was made to the
general exclusion of incorrect products, and (2) the three
replicates were quite consistent (overlapping curves). The same
result was obtained with higher concentrations of 16merA. At lower
concentrations (50 nM, 100 nM), large amounts of incorrect products
were found, and the three replicates were inconsistent.
[0163] The melt curve for additive 16merB at 300 nM concentration
is shown in FIG. 2. Circle 21 is the curves for the three
replicates. This amplification was judged quite unacceptable,
because large amounts of incorrect products were found, and the
three replicates were inconsistent. At none of the concentrations
utilized was the amplification found to generate correct product to
the general exclusion of incorrect products, and in none were the
replicates highly consistent. The incorrect products differed
significantly from the incorrect products obtained with no
additive, indicating that additive 16merB caused mispriming.
[0164] The melt curve for additive EP049 at 600 nM concentration is
shown in FIG. 3, with the intended product identified by the
downward-pointing arrow. Circle 31 is the curves for the three
replicates. This amplification was judged to be very good, because
(1) the correct product was made to the general exclusion of
incorrect products, and (2) the three replicates were quite
consistent (overlapping curves). The same result was obtained with
higher concentrations, but lower concentrations were not consistent
among the replicates and yielded incorrect products. Additive EP048
showed more consistent product at concentrations of 100 and 600 nM,
indicating that both strands were capable of mispriming.
[0165] The melt curve for additive EP027 at 100 nM concentration is
shown in FIG. 4, with the intended product identified by the
downward-pointing arrow. Circle 41 is the curves for the three
replicates. This amplification was judged to be good rather than
very good, because (1) the correct product was made to the general
exclusion of incorrect products, and (2) the three replicates were
reasonably consistent, with minor variability among the curves. At
higher concentration of this additive, the results were judged very
good, because the three replicates were quite consistent. At 50 nM,
however, significant incorrect products were made, and the
replicates were not consistent.
[0166] Kinetic analysis of amplifications with EP027 are shown in
FIG. 5. Circle 51 is the three replicates at a concentration of 100
nM; circle 52 is the three replicates at a concentration of 300 nM;
circle 53 is the three replicates at a concentration of 600 nM; and
circle 54 is the three replicates at a concentration of 1000 nM. At
100 nM concentration, there was scatter among the three replicates
in the plateau region. The three reactions containing 300 nM had
entirely overlapping kinetics and higher efficiency than reactions
containing 600 or 1000 nM. Therefore, 300 nM of EP027 was the
optimal amount in this assay.
B. Other Additives
[0167] Several additives consisting of double-stranded
oligonucleotides without added modifiers, and having lengths of 12,
18, 20, 22 and 24 nucleotides were tested in the assay of this
example at concentrations of 50, 100, 300, 600 and 1000 nM. As with
the 16mers discussed in Part A, results were inconsistent. Of three
different 12mer's tested, for example, one failed to produce the
correct product at all concentrations, one produced the correct
product only at 1000 nM concentration, and one produced correct
product at concentrations of 600 nM and higher. Of eight longer
oligonucleotides tested, half produced significant amounts of
incorrect products even at the highest concentrations of 600 and
1000 nM. Only three produced the correct product to the general
exclusion of incorrect products at 300 nM concentration, and none
did so at lower concentrations. We judged additive 22merA to be the
best in this assay (terminal blocker p is a phosphate):
TABLE-US-00003 22merA. (SEQ ID No. 9) 5' GGAGCAAAATAGCAATGAGGTAp
pCCTCGTTTTATCGTTACTCCAT 5'
[0168] Several additives consisting of double-stranded
oligonucleotides that included either two or four terminal
modifiers and had lengths of 8, 11 and 22 nucleotides were also
tested. The modifiers were either Dabcyl or digoxigenin (DIG):
TABLE-US-00004 Additive EP010. (SEQ ID No. 10) 5' Dabcyl
GGTCAGATGAAAATGATACGTG Dabcyl Dabcyl CCAGTCTACTTTTACTATGCAC Dabcyl
5' Additive EP018. (SEQ ID No. 11) 5' GGTCAGATGAAAATGATACGTG Dabcyl
Dabcyl CCAGTCTACTTTTACTATGCAC 5' Additive EP020. (SEQ ID No. 12) 5'
Dabcyl GAAATAAAATAAAAATAAAATA Dabcyl Dabcyl CTTTATTTTATTTTTATTTTAT
Dabcyl 5' Additive EP021. (SEQ ID No. 13) 5' Dabcyl CAGCCGGC Dabcyl
Dabcyl GTCGGCCG Dabcyl 5' Additive EP022. (SEQ ID No. 14) 5' Dabcyl
CCGCCGGC Dabcyl Dabcyl GGCGGCCG Dabcyl 5' Additive EP023 (SEQ ID
No. 15) 5' Dabcyl GCGTACGCAGG Dabcyl Dabcyl CGCATGCGTCC Dabcyl 5'
Additive EP024. (SEQ ID No. 16) 5' Dabcyl GCGTACGAAGG Dabcyl Dabcyl
CGCATGCTTCC Dabcyl 5' Additive EP026. (SEQ ID No. 17) 5' DIG
GGAGCAAAATAGCAATGAGGTA DIG DIG CCTCGTTTTATCGTTACTCCAT DIG 5'
Additive EP028. (SEQ ID No. 18) 5' Dabcyl TGAGAGATGAAAATGATCGAGT
Dabcyl Dabcyl ACTCTCTACTTTTACTAGCTCA Dabcyl 5' Additive EP029. (SEQ
ID No. 19) 5' GGTCAGATGAAAATGATACGTG DIG DIG CCAGTCTACTTTTACTATGCAC
5'
[0169] All of this group of additives produced the correct product
to the general exclusion of other products at a concentration equal
to or less than 600 nM. All but one (EP021) did so at a
concentration of 300 nM or less. Additive EP028 did so at a
concentration of 100 nM, and additive EP010 did so at a
concentration of 50 nM.
Example 2. Suppression of Type I Mispriming
[0170] Unmodified double-stranded oligonucleotide 22merA, which was
judged to be the best unmodified additive in Example 1, and several
Dabcyl-modified oligonucleotides were used in an assay for a
different target with different primers. Each additive was
separately added to a LATE-PCR amplification reaction mixture prior
to the start of amplification at concentrations of 100 and 300 nM.
Reactions were analyzed at the end of 50 cycles by a melt curve
analysis using the first derivative of SYBR Green fluorescence
(-dF/dT, Sybr) of double-stranded DNA product. In addition, the
kinetics of production of double-stranded product (Sybr intensity
reading as a function of thermal cycles) was analyzed for certain
reactions. Reaction components other than double-stranded
oligonucleotides, and reaction conditions were as follows.
TABLE-US-00005 Limiting Primer. (SEQ ID No. 20) 5'
AAATTGCGTCATTGTTTCACAGGGCCA Excess Primer. (SEQ ID No. 21) 5'
AATCTGGGTGGTGGTCATAC Target. (SEQ ID No. 22) 5'
AATCTGGGTGGTGGTCATACAGGTCATCACTGTAAAATTCTTTGA
ACTTTTCTGTATATATCTTTGAAAATTTTGGAAAAAAAATGTTGG
AAAACTTAAAAGGCTGTTGCTTTGCTCATATTGGCGGTACATAT
ACAAAAGTGGAAAGGATGAGATTGATTGGCATGGCCCTGTGAA ACAATGACGCAATTT
[0171] LATE-PCR amplifications were carried out in 25 ul volume
consisting of 1.times. Invitrogen PCR buffer (Invitrogen, Carlsbad,
Calif.), 3 mM MgCl.sub.2, 250 nM dNTPs, 50 nM of limiting primer,
1000 nM of excess primer, 0.24.times.SYBR Green (Invitrogen,
Carlsbad, Calif.), 1.25 units of Taq DNA polymerase (Invitrogen,
Carlsbad, Calif.) with approximately 1000 genomes of human genomic
DNA (Sigma-Aldrich, St. Louis, Mo.). The thermal profile conditions
for these reactions were as follows: 25.degree. C. for 30 minutes
followed by 95.degree. C./10 s-62.degree. C./20 s-70.degree. C./20
s for 50 cycles followed by a melt starting at 55.degree. C./30 s
with 1.degree. C. increments for 42 cycles. (The abbreviation "s",
as in 20 s, is "seconds".) All reactions analyzed at the end of 50
cycles using the first derivative of SYBR Green fluorescence (melt
curve analysis) of double-stranded DNA product.
[0172] The following additives were tested:
TABLE-US-00006 Additive 22merA. (SEQ ID No. 9) 5'
GGAGCAAAATAGCAATGAGGTAp pCCTCGTTTTATCGTTACTCCAT 5' Additive EP001.
(SEQ ID NO. 23) 5' Dabcyl GGAGCAAAATAGCAATGAGGTA Dabcyl Dabcyl
CCTCGTTTTATCGTTACTCCAT Dabcyl 5' Additive EP002. (SEQ ID No. 24) 5'
Dabcyl GGAGCAAAATAGCAATGAGGTA Dabcyl pCCTCGTTTTATCGTTACTCCAT Dabcyl
5' Additive EP003. (SEQ ID No. 25) 5' GGAGCAAAATAGCAATGAGGTA Dabcyl
Dabcyl CCTCGTTTTATCGTTACTCCAT Dabcyl 5' Additive EP004. (SEQ ID No.
26) 5' Dabcyl GGAGCAAAATAGCAATGAGGTAp Dabcyl CCTCGTTTTATCGTTACTCCAT
Dabcyl 5' Additive EP005. (SEQ ID No. 27) 5' Dabcyl
GGAGCAAAATAGCAATGAGGTA Dabcyl Dabcyl CCTCGTTTTATCGTTACTCCAT 5'
Additive EP006. (SEQ ID No. 28) 5' Dabcyl GGAGCAAAATAGCAATGAGGTAp
Dabcyl CCTCGTTTTATCGTTACTCCAT 5' Additive EP007. (SEQ ID No. 29) 5'
GGAGCAAAATAGCAATGAGGTA Dabcyl pCCTCGTTTTATCGTTACTCCAT Dabcyl 5'
Additive EP008. (SEQ ID No. 30) 5' Dabcyl GGAGCAAAATAGCAATGAGGTAp
pCCTCGTTTTATCGTTACTCCAT Dabcyl 5' Additive EP009. (SEQ ID No. 31)
5' GGAGCAAAATAGCAATGAGGTA Dabcyl Dabcyl CCTCGTTTTATCGTTACTCCAT 5'
Additive EP020. (SEQ ID No. 12) 5' Dabcyl GAAATAAAATAAAAATAAAATA
Dabcyl Dabcyl CTTTATTTTATTTTTATTTTAT Dabcyl 5' Additive EP052. (SEQ
ID No. 32) 5' Dabcyl GGAGCAAAATAGCAATGAGGTA Dabcyl
pCCTCGTTTTATCGTTACTCCAT 5' Additive EPO53. (SEQ ID No. 33) 5'
GGAGCAAAATAGCAATGAGGTAp Dabcyl CCTCGTTTTATCGTTACTCCAT Dabcyl 5'
[0173] The double-stranded oligonucleotide 22merA at 300 nM
concentration was judged to be very good, because (1) the correct
product was made to the general exclusion of incorrect products,
and (2) the three replicates were quite consistent (overlapping
curves). That was not the case for 22merA at 100 nM concentration,
however, because one of the replicates did not generally exclude
incorrect products. All of the Dabcyl-containing additives were
judged to be very good at 300 nM as well. Five of them (EP001,
EP002, EP003, EP004 and EP005) were also judged to be very good at
100 nM concentration. FIG. 6 shows the melt curves for the three
replicate reactions with additive EP003 and with additive 22merA at
100 nM concentration. Circle 61 is the three replicates of additive
22merA. Circle 62 is the three replicates of additive EP003.
Example 3. Type II Mispriming and Polymerase Selectivity
[0174] We performed a LATE-PCR assay in which we amplified a target
that was complementary to both primers (matched target), and in
which we separately amplified a target that was complementary to
the excess primer but that contained a single mismatch to the 3'
terminal nucleotide of the limiting primer. We detected
double-stranded product in real time, that is, during the primer
annealing portion of every PCR cycle, by a DNA dye, in this case
SYBR Green. Selectivity against a 3' terminal mismatch in the
presence of an additive at any concentration is the difference
between the threshold cycle (C.sub.T) of the signal from
amplification of the mismatched target and the C.sub.T of the
signal from amplification of the matched target (.DELTA. C.sub.T).
Amplification reactions were run in triplicate. The C.sub.T
differences are calculated using averages of the three replicates.
The effectiveness of an additive for improving selectivity of a DNA
polymerase is the C.sub.T difference with the additive minus the
C.sub.T difference without any additive. Under the heading
"Selectivity" in this and subsequent Examples, we report the
improvement in the C.sub.T difference resulting from the use of an
additive, in C.sub.T units, that is, as a .DELTA.C.sub.T.
[0175] The sequences of the primers and single-stranded targets are
as follows:
TABLE-US-00007 Limiting Primer. (SEQ ID NO. 34)
5'CGTAAGATTACAATGGCAGGCTCCAGT Excess Primer. (SEQ ID NO. 35)
5'GCCCAAGTTTTATCGTTCTTCTCA Matched Target (A). (SEQ ID No. 36)
5'CGTAAGATTACAATGGCAGGCTCCAGAAGGTTCTAA
GTGCCATGATACAAGCTTCCCAATTACTAAGTATGC TGAGAA GAACGATAAAACTTGGG
Mismatched Target (T). (SEQ ID No. 37)
5'CGTAAGATTACAATGGCAGGCTCCAGTAGGTTCTA
AGTGCCATGATACAAGCTTCCCAATTACTAAGTATGCTG
AGAAGAACGATAAAACTTGGGCAA
[0176] The underlined and bolded nucleotide is the nucleotide whose
complement in the excess primer strand will either match or
mismatch the 3' terminal nucleotide of the limiting primer.
[0177] The LATE-PCR amplifications were carried out in triplicate
(three replicate assays) in 25 ul volume consisting of 1.times.
Invitrogen PCR buffer (Invitrogen, Carlsbad, Calif.), 3 mM
MgCl.sub.2, 250 nM dNTPs, 50 nM of limiting primer, 1000 nM of
excess primer, 0.24.times.SYBR Green (Invitrogen, Carlsbad,
Calif.), 1.25 units of Platinum Taq DNA polymerase (Invitrogen,
Carlsbad, Calif.) with approximately 1000 single-stranded target A
(matched) or T (mismatched). The thermal profile conditions for
these reactions were: 95.degree. C. for 3 minutes followed by
95.degree. C./5 s-62.degree. C./20 s-72.degree. C./30 s for 60
cycles. For this and other assays containing two targets, we run a
control amplifications using the excess primer, which is perfectly
complementary to both targets, and a control limiting primer that
is also perfectly complementary to both targets, to ensure that the
starting copy numbers of both targets are the same, in which case
the C.sub.T's for both targets is the same. (If the control
amplifications reveal that the starting copy numbers are not the
same, one has two choices: either reformulate or, if the C.sub.T
difference is slight--as was the case in all Examples reported
here, correct the observed C.sub.T values to adjust for the
difference.)
[0178] Where Tm is reported, that is the calculated melting
temperature of the double-stranded additive without modifiers. Tm's
of double-stranded additives presented in this specification were
calculated according to Markhan and Zuker (2005) DINAMELT web
server for nucleic acid melting prediction, Nucleic Acids Res.
33:W577-W581, and Markham and Zuker (2008) UNAFOLD: software for
nucleic acid folding and hybridization. In Keith, J. M., ed.,
BIOINFORMATICS, vol. II, Structure, Functions and Applications, No.
453 in Methods in Molecular Biology, Ch. 1, pages 3-31 (Humana
Press, Totowa, N.J. ISBN 978-1-60327-428-9.
A. No Additive
[0179] This assay was run with no additive. SYBR Green signals were
detected in real time, that is, during the primer annealing portion
of all PCR cycles. The fluorescence intensity readings as a
function of amplification cycle number show that the enzyme has a
modest inherent selectivity for the matched target. When additives
were tested in this assay, a no-additive control was also included,
and the C.sub.T difference between matched and mismatched target
sequences for the no-additive control was subtracted from the
C.sub.T difference between matched and mismatched target sequences
for the additive to arrive at the selectivity improvement numbers
(.DELTA. C.sub.T) presented.
B. Double-Stranded Additive with No Modifier.
[0180] The following 22-nucleotide long double-stranded
oligonucleotide, denominated "22merA", in which the 3' terminus of
each strand was capped with a phosphate (p) to prevent extension by
the DNA polymerase, was utilized as the additive at three different
concentrations:
TABLE-US-00008 22mer A. (SEQ ID NO. 9) 5' GGAGCAAAATAGCAATGAGGTAp
pCCTCGTTTTATCGTTACTCCAT 5'
[0181] The results for selectivity (C.sub.T for mismatched target
minus C.sub.T for matched target) are shown in Table 1.
TABLE-US-00009 TABLE 1 Length Concentration, Additive (NT's) Tm,
.degree. C. nM Selectivity, .DELTA. C.sub.T 22merA 22 63.1 100 0.1
200 1.2 300 1.8
C. Double-Stranded Additives with Two Dabcyl Modifiers.
[0182] The double-stranded oligonucleotide 16mer B described in
Example 1 (SEQ ID No. 5) was modified with two Dabcyls by placing a
Dabcyl at the 5' end of the top strand and a Dabcyl at the 3' end
of the bottom strand (additive EP050, SEQ ID No. 38); and by
placing a Dabcyl at the 3' end of the top strand and a Dabcyl at
the 5' end of the bottom strand (additive EP051, SEQ ID No. 39).
The double-stranded oligonucleotide 22merA described in part B
above (SEQ ID No. 9) was modified by placing a Dabcyl on the 5' end
of the top strand and a Dabcyl on the 3' end of the bottom strand
(additive EP006, SEQ ID No. 28); by placing a Dabcyl on the 3' end
of the top strand and a Dabcyl on the 5'end of the bottom strand
(additive EP007, SEQ ID No. 29); by placing a Dabcyl on the 5' end
of each strand (additive EP008, SEQ ID No. 30); by placing a Dabcyl
on the 3' end of each strand (additive EP009, SEQ ID No. 31); by
placing a Dabcyl on each end of the top strand (additive EP052, SEQ
ID No. 32); and by placing a Dabcyl on each end of the bottom
strand (additive EP053, SEQ ID No. 33). Sequences of these
additives are given below, and results for selectivity are
presented in Table 2.
TABLE-US-00010 Aditive EP050. (SEQ ID No. 38) 5' Dabcyl
CACGACCTCGCTGACC (C.sub.3) Dabcyl GTGCTGGAGCGACTGG 5' Additive
EP051. (SEQ ID No. 39) 5' CACGACCTCGCTGACC Dabcyl pGTGCTGGAGCGACTGG
Dabcyl 5' Additive EP006. (SEQ ID No. 28) 5' Dabcyl
GGAGCAAAATAGCAATGAGGTAp Dabcyl CCTCGTTTTATCGTTACTCCAT 5' Additive
EP007. (SEQ ID No. 29) 5' GGAGCAAAATAGCAATGAGGTA Dabcyl
pCCTCGTTTTATCGTTACTCCAT Dabcyl 5' Additive EP008. (SEQ ID No. 30)
5' Dabcyl GGAGCAAAATAGCAATGAGGTAp pCCTCGTTTTATCGTTACTCCAT Dabcyl 5'
Additive EP009. (SEQ ID No. 31) 5' GGAGCAAAATAGCAATGAGGTA Dabcyl
Dabcyl CCTCGTTTTATCGTTACTCCAT 5' Additive EP052. (SEQ ID No. 32) 5'
Dabcyl GGAGCAAAATAGCAATGAGGTA Dabcyl pCCTCGTTTTATCGTTACTCCAT 5'
Additive EP053. (SEQ ID No. 33) 5' GGAGCAAAATAGCAATGAGGTAp Dabcyl
CCTCGTTTTATCGTTACTCCAT Dabcyl
TABLE-US-00011 TABLE 2 Length Concentration, Additive (NT's) Tm,
.degree. C. nM Selectivity, .DELTA. C.sub.T EP050 16 62.8 200 1.6
300 2.9 400 5.5 EP051 16 62.8 200 1.1 300 2.7 400 1.8 EP006 22 63.1
100 3.5 300 8.3 600 12.0 EP007 22 63.1 100 3.5 300 7.3 600 11.5
EP008 22 63.1 100 1.7 300 5.8 600 9.7
D. Additives with Three Dabcyl Modifiers.
[0183] The double-stranded oligonucleotide 22merA described in part
B above (SEQ ID No. 9) was modified by placing a Dabcyl on each end
of the top strand and on the 5' end of the bottom strand (additive
EP002, SEQ ID No. 24); by placing a Dabcyl on the 3' end of the top
strand and on each end of the bottom strand (additive EP003, SEQ ID
No. 25); by placing a Dabcyl on the 5' end of the top strand and on
each end of the bottom strand (additive EP004, SEQ ID No. 26); and
by placing a Dabcyl on each end of the top strand and on the 3' end
of the bottom strand (additive EP005, SEQ ID No. 27). Sequences of
the additives are given below and results are presented in Table
3.
TABLE-US-00012 Additive EP002. (SEQ ID No. 24) 5' Dabcyl
GGAGCAAAATAGCAATGAGGTA Dabcyl pCCTCGTTTTATCGTTACTCCAT Dabcyl 5'
Additive EP003. (SEQ ID No. 25) 5' GGAGCAAAATAGCAATGAGGTA Dabcyl
Dabcyl CCTCGTTTTATCGTTACTCCAT Dabcyl 5' Additive EP004. (SEQ ID No.
26) 5' Dabcyl GGAGCAAAATAGCAATGAGGTAp Dabcyl CCTCGTTTTATCGTTACTCCAT
Dabcyl 5' Additive EP005. (SEQ ID No. 27) 5' Dabcyl
GGAGCAAAATAGCAATGAGGTA Dabcyl Dabcyl CCTCGTTTTATCGTTACTCCAT 5'
TABLE-US-00013 TABLE 3 Length Concentration, Additive (NT's) Tm,
.degree. C. nM Selectivity, .DELTA. C.sub.T EP002 22 63.1 100 4.2
200 7.1 300 9.2 EP003 22 63.1 100 2.1 200 5.6 300 8.2 EP004 22 63.1
100 5.0 200 6.6 300 11.9 EP005 22 63.1 100 5.9 200 9.3 300 7.8
E. Additives with Four Dabcyl Modifiers.
[0184] Several double-stranded oligonucleotides were modified with
four terminal Dabcyl modifiers:
TABLE-US-00014 Additive EP022. (SEQ ID No. 153) 5' Dabcyl CGCCGCGC
Dabcyl Dabcyl GCGGCGCG Dabcyl 5' Additive EP020. (SEQ ID No. 12) 5'
Dabcyl GAAATAAAATAAAAATAAAATA Dabcyl Dabcyl CTTTATTTTATTTTTATTTTAT
Dabcyl 5' Additive EP001. (SEQ ID NO. 23) 5' Dabcyl
GGAGCAAAATAGCAATGAGGTA Dabcyl Dabcyl CCTCGTTTTATCGTTACTCCAT Dabcyl
5' Additive EP028. (SEQ ID Nos 154 and 155) 5' Dabcyl
TGAGAGATGAAAATCATCGAGT Dabcyl Dabcyl ACTCTCACTTTTTACTAGCTCA Dabcyl
5'
[0185] Results are shown in Table 4.
TABLE-US-00015 TABLE 4 Length Concentration, Additive (NT's) Tm,
.degree. C. nM Selectivity, .DELTA. C.sub.T EP0022 8 42.8 600 1.2
EP0020 22 47.7 600 0.9 EP001 22 63.1 100 7.1 200 9.5 EP028 22 60.6
300 10.0
F. Additives with Different Modifiers.
[0186] Several double-stranded oligonucleotides were modified with
modifiers other than Dabcyl. Three modifiers, digoxigenin (DIG),
coumarin (CMN), QSY 21 (QSY), were shown to be useful in additives,
and one, fluorescein (FAM), was not. Sequences of the
oligonucleotides were as follows:
TABLE-US-00016 Additive EP026. (SEQ ID No. 17) 5' DIG
GGAGCAAAATAGCAATGAGGTA DIG DIG CCTCGTTTTATCGTTACTCCAT DIG 5'
Additive EP029. (SEQ ID No. 40) 5' GGTCAGATGAAAATGATACGTG DIG DIG
CCAGTCTACTTTTACTATGCAC 5' Additive EP031. (SEQ ID No. 41) 5' CMN
GGTCAGATGAAAATGATACGTG CMN CMN CCAGTCTACTTTTACTATGCAC CMN 5'
Additive EP033. (SEQ ID No. 42) 5' QSY GGTCAGATGAAAATGATACGTG QSY
QSY CCAGTCTACTTTTACTATGCAC QSY 5' Additive F032. (SEQ ID No. 43) 5'
FAM GGTCAGATGAAAATGATACGTG FAM FAM CCAGTCTACTTTTACTATGCAC FAM
5'
[0187] Results are shown in Table 5.
TABLE-US-00017 TABLE 5 Length Concentration, Additive (NT's) Tm,
.degree. C. nM Selectivity, .DELTA. C.sub.T EP026 22 63.1 300 3.8
EP029 22 63.1 300 0.9 EP031 22 63.1 200 3.2 EP033 22 63.1 200 3.4
F032 22 63.1 200 0.9
Example 4. Type II Mispriming and Polymerase Selectivity with
Additive Mixtures
[0188] Combinations of two additives can be added to the reaction
mixture as four strands, that is, as a mixture of two different
double-stranded oligonucleotides. Alternatively, two additives can
share a common strand and, thus, be added to the reaction mixture
as three strands. This example reports results obtained in the
assay reported in Example 3 using three-strand versions of
mixtures, including a control mixture having no modifiers. For two
additives that share a common strand, we write the common strand in
the middle, the strand whose hybrid with the middle strand has the
higher melting temperature on top, and the strand whose hybrid with
the middle strand has the lower melting temperature on the bottom.
We write the strand concentrations, in nM, as top/middle/bottom. We
write the Tm's of the two hybrids (.degree. C.) as upper/lower.
Melting temperatures were adjusted either by shortening the bottom
strand or introducing mismatches into the bottom strand (mismatched
nucleotides are underlined). The additives tested were:
TABLE-US-00018 Additive 041. (SEQ ID No. 44)
pCCTCGTCTGATCGTGACTCCAT 5' 5' GGAGCAGACTAGCACTGAGGTAp
pTCTGATCGTGACTCCAT 5' Additive EP041. (SEQ ID No. 45) Dabcyl
CCTCGTCTGATCGTGACTCCAT Dabcyl 5' 5' GGAGCAGACTAGCACTGAGGTA Dabcyl
Dabcyl TCTGATCGTGACTCCAT Dabcyl 5' Additive 042. (SEQ ID Nos 46 and
156) pCCTCGTCTGATCGTGACTCCAT 5' 5' GGAGCAGACTAGCACTGAGGTAp
pCCTGGTCTGATTGTGACTCCAT 5' Additive EP042. (SEQ ID Nos 47 and 157)
Dabcyl CCTCGTCTGATCGTGACTCCAT Dabcyl 5' 5' GGAGCAGACTAGCACTGAGGTA
Dabcyl Dabcyl CCTGGTCTGATTGTGACTCCAT Dabcyl 5' Additive EP043. (SEQ
ID No. 48) 5' GGAGCAGACTAGCACTGAGGTA Dabcyl Dabcyl
CCTCGTCTGATCGTGACTCCAT Dabcyl 5' 5' Dabcyl AGACTAGCACTGAGGTA Dabcyl
Additive EP045. (SEQ ID No. 49) 5' Dabcyl GGAGCAGACTAGCACTGAGGTA
Dabcyl Dabcyl CCTCGTCTGATCGTGACTCCAT Dabcyl 5' 5' Dabcyl
AGACTAGCACTGAGGTA Dabcyl
[0189] Results are shown in Table 6, along with the strand
concentrations and the Tm's of the unmodified hybrid of the upper
two strands and the lower two strands. Numbers for improvement in
selectivity over a no-additive control (.DELTA.C.sub.T) were
calculated as described in Example 3.
TABLE-US-00019 TABLE 6 Selectivity, Additive Tm (Ubper/Lower,
(.degree. C.) Concentrations, nM .DELTA.C.sub.T 041 67.4/59.0 Top
75 1.7 Mid. 400 Bot. 325 EP041 67.4/59.0 Top 75 4.8 Mid. 400 Bot.
325 042 67.4/57.4 Top 75 1.9 Mid. 400 Bot. 325 EP042 67.4/57.4 Top
75 6.8 Mid. 400 Bot. 325 EP043 67.4/59.1 Top 25 2.4 Mid. 600 Bot.
575 Top 50 2.9 Mid. 600 Bot. 550 Top 75 2.2 Mid. 600 Bot. 525 Top
100 3.3 Mid. 600 Bot. 500 EP045 67.4/59.1 Top 25 5.0 Mid. 600 Bot.
575 Top 50 6.9 Mid. 600 Bot. 550 Top 75 7.7 Mid. 600 Bot. 525 Top
100 10.8 Mid. 600 Bot. 500
[0190] Kinetic analysis of amplification reactions with additives
EP043 and EP045 are shown in FIGS. 7A-7D and FIGS. 8A-8D,
respectively. These figures present fluorescence intensity readings
from SYBR Green dye as a function of LATE-PCR cycle number for
different concentrations of additive. FIG. 7A presents the results
with additive EP043 having strand concentrations
(upper/middle/lower strands) of 25/600/575 nM. In FIG. 7A, circle
71 is the three replicates for the matched target, and circle 72 is
the three replicates for the mismatched target. FIG. 7B presents
the results with additive EP043 having strand concentrations
(upper/middle/lower strands) of 50/600/550 nM. In FIG. 7B, circle
73 is the three replicates for the matched target, and circle 74 is
the three replicates for the mismatched target. FIG. 7C presents
the results with additive EP043 having strand concentrations
(upper/middle/lower strands) of 75/600/525 nM. In FIG. 7C, circle
75 is the three replicates for the matched target, and circle 76 is
the three replicates for the mismatched target. FIG. 7D presents
the results with additive EP043 having strand concentrations
(upper/middle/lower strands) of 100/600/500 nM. In FIG. 7D, circle
77 is the three replicates for the matched target, and circle 78 is
the three replicates for the mismatched target.
[0191] FIG. 8A presents the results with additive EP045 having
strand concentrations (upper/middle/lower strands) of 25/600/575
nM. In FIG. 8A, circle 81 is the three replicates for the matched
target, and circle 82 is the three replicates for the mismatched
target. FIG. 8B presents the results with additive EP045 having
strand concentrations (upper/middle/lower strands) of 50/600/550
nM. In FIG. 8B, circle 83 is the three replicates for the matched
target, and circle 84 is the three replicates for the mismatched
target. FIG. 8C presents the results with additive EP045 having
strand concentrations (upper/middle/lower strands) of 75/600/525
nM. In FIG. 8C, circle 85 is the three replicates for the matched
target, and circle 86 is the three replicates for the mismatched
target. FIG. 8D presents the results with additive EP045 having
strand concentrations (upper/middle/lower strands) of 100/600/500
nM. In FIG. 8D, circle 87 is the three replicates for the matched
target, and circle 88 is the three replicates for the mismatched
target.
Example 5. Suppression of Type I and Type III Mispriming in a
Duplex Reaction
[0192] A duplex LATE-PCR reaction was run in triplicate with two
DNA targets, a primer pair for each target, and a molecular beacon
hybridization probe for each target. Each reaction mixture
contained the following primers and probes.
For First Target Sequence:
TABLE-US-00020 [0193] Excess primer. (SEQ ID No. 50) 5'
TGTCATCTTCTGTCCCTTCCCAGAAA Limiting primer. (SEQ ID No. 51) 5'
ACTGTCCCAGAATGCAAGAAGCCCAGACG Probe for First Amplicon. (SEQ ID No.
52) 5' BHQ-1 CCGTAGCTGCCCTGG' Cal Red 610
For Second Target Sequence:
TABLE-US-00021 [0194] Excess primer. (SEQ ID No. 53) 5'
GCACAGTTACAGTATTCCAGCAGACTCA Limiting primer. (SEQ ID No. 54) 5'
TCAGTGGTGGCAGTGGTAGTGGTGGC Probe for Second Amplicon. (SEQ ID No.
55) 5' BHQ-2 TCAGTGGTGGCAGTGGTAGA Quasar 670
[0195] LATE-PCR reaction mixtures included 1.times. Platinum Taq
buffer (Invitrogen, Carlsbad, Calif.), 3 mM MgCl2, 0.25 nM dNTPs,
50 nM each limiting primer, 1000 nM each excess primer, and 500 nM
each detection probe, 1.25 units Platinum Taq polymerase
(Invitrogen, Carlsbad, Calif.) and 1000 genomes equivalents of
human DNA in a volume of 25 ul. Different reaction mixtures
contained no additive, additive EP020 at 400 nM concentration, or
additive EP013 at 300 nM concentration.
[0196] The LATE-PCR amplification reaction thermal profile
conditions were 20 cycles of 95.degree. C./10 s, annealing at the
temperature specified below for 10 s, and 72.degree. C./10 s;
followed by 50 cycles at 95.degree. C./10 s, 65.degree. C./10 s,
72.degree. C./10 s, and fluorescent signal detection at 54.degree.
C./20 s. Amplification was carried out in a Bio-Rad IQ-5 Multicolor
Real-Time PCR Detection System (Bio-Rad, Hercules, Calif.) using
the temperature gradient function that permits multiple
amplification temperature profiles with different annealing
temperatures to be run in the same instrument.
TABLE-US-00022 Additive EP020. (SEQ ID No. 12) 5' Dabcyl
GAAATAAAATAAAAATAAAATA Dabcyl Dabcyl CTTTATTTTATTTTTATTTTAT Dabcyl
5' Additive EP013. (SEQ ID No. 56) 5' Dabcyl
GGTCAGATGAAAATGATACGTGp Dabcyl CCAGTCTACTTTTACTATGCAC Dabcyl 5'
[0197] Six assays were run. They had the following additives and
initial annealing temperature (first 20 cycles):
Reaction 1: No additive, annealing temperature: 65.degree. C.
Reaction 2: additive EP020, annealing temperature 65.degree. C.
Reaction 3: additive EP020, annealing temperature 60.7.degree. C.
Reaction 4: additive EP013, annealing temperature 66.5.degree. C.
Reaction 5: additive EP013, annealing temperature 64.2.degree. C.
Reaction 6: additive EP013, annealing temperature 60.7.degree.
C.
[0198] FIG. 9 presents the fluorescence readings from the probes as
a function of the LATE-PCR thermal cycle number. FIG. 9A shows the
readings from Reaction 1, wherein circle 911 is the readings from
the first probe in the four replicates of amplification of the
first target, and circle 912 is the readings from the second probe
in the four replicates of amplification of the second target. FIG.
9B shows the readings from Reaction 2, wherein circle 913 is the
readings from the first probe in the four replicates of
amplification of the first target, and circle 914 is the readings
from the second probe in the four replicates of amplification of
the second target. FIG. 9C shows the readings from Reaction 3,
wherein circle 915 is the readings from the first probe in the four
replicates of amplification of the first target, and circle 916 is
the readings from the second probe in the four replicates of
amplification of the second target. FIG. 9D shows the readings from
Reaction 4, wherein circle 917 is the readings from the first probe
in the four replicates of amplification of the first target, and
circle 918 is the readings from the second probe in the four
replicates of amplification of the second target. FIG. 9E shows the
readings from Reaction 5, wherein circle 919 is the readings from
the first probe in the four replicates of amplification of the
first target, and circle 920 is the readings from the second probe
in the four replicates of amplification of the second target. FIG.
9F shows the readings from Reaction 6, wherein circle 921 is the
readings from the first probe in the four replicates of
amplification of the first target, and circle 922 is the readings
from the second probe in the four replicates of amplification of
the second target.
Example 6. A Primer-Independent Oscillating-Temperature Assay for
Evaluating Inhibition of 5'Exonuclease Activity
[0199] Many DNA polymerases, including Taq and Tfi(+) have the
capacity to cleave the fluorescently labeled nucleotide on the 5'
end of an oligonucleotide probe that is hybridized to its target
strand. This 5'exonuclease cleavage even occurs under isothermal
conditions in the absence of extension of an upstream primer. It is
therefore primer-independent cleavage in contrast to
primer-dependent cleavage that takes place in standard 5' nuclease
amplification reactions. The rate of primer-independent
5'exonuclease cleavage can be increased by oscillating the
temperature of the reaction mixture over a limited temperature
range above and below the Tm of the probe/target hybrid.
[0200] Oscillation reactions were carried out in 25 ul volume
consisting of 1.times.PCR buffer (Invitrogen, Carlsbad, Calif.), 3
mM MgCl.sub.2, 200 nM dNTPs, 1.25 units of Taq DNA polymerase
(Invitrogen, Carlsbad, Calif.), 200 nM of a probe having a 5'FAM
and a 3' Black Hole Quencher 1 (BHQ1), and 100 nM of a
complementary 41 nucleotide target. This reaction mixture was used
with and without any additive and with each of the additives
identified below at a concentration of 300 nM. A control reaction
was run with the probe as the only oligonucleotide in the reaction
mixture. The additives included PS060, a single-stranded additive
that forms a stem-loop structure (complementary nucleotides forming
the stem are underlined), as well as double-stranded additives.
Reaction mixtures were oscillated using the following thermal
profile: 45.degree. C./20 s, 60.degree. C./10 s for 45 cycles,
followed by a melt starting at 45.degree. C./30 secs with 1.degree.
C. increments for 30 cycles. The FAM fluorescence was acquired
during the 45.degree. C./10 s segment of the thermal profile.
Sequences for the probe, target and additives were:
TABLE-US-00023 Probe. (SEQ ID No. 57) 5' FAM CCATGATACAAGCTTCC BHQ1
Target. (SEQ ID No. 58) 5'
ACTTAGTAATTGGGAAGCTTGTATCATGGCACTTAGAACCT Additive EP001. (SEQ ID
No. 23) 5' Dabcyl GGAGCAAAATAGCAATGAGGTA Dabcyl Dabcyl
CCTCGTTTTATCGTTACTCCAT Dabcyl 5' Additive EP004. (SEQ ID No. 26) 5'
Dabcyl GGAGCAAAATAGCAATGAGGTAp Dabcyl CCTCGTTTTATCGTTACTCCAT Dabcyl
5' Additive EP008. (SEQ ID No. 30) 5' Dabcyl
GGAGCAAAATAGCAATGAGGTAp pCCTCGTTTTATCGTTACTCCAT Dabcyl 5' Additive
EP009. (SEQ ID No. 31) 5' GGAGCAAAATAGCAATGAGGTA Dabcyl Dabcyl
CCTCGTTTTATCGTTACTCCAT 5' Additive PS060. (SEQ ID No. 59) 5'
CGCGGCGTCAGGCATATAGGATACCGGGACAGAC GCCGCG
[0201] Exonuclease cleavage activity separates the probe's
fluorophore from the probe, thereby resulting in an increase in
fluorescence (FAM). Results are reported in FIG. 10. In FIG. 10,
curve 101 for the probe-only reaction shows that in the absence of
target, the probe is not cleaved. Curve 102 for the reaction
containing probe and target but no additive, shows the highest
probe cleavage. Curve 103 for PS060 shows higher probe cleavage
than the curves for additives; that is, curve 104, EP009; curve
105, the same curve for EP004 and for EP008; and curve 106,
EP001.
Example 7. Inhibitor of 5'Exonuclease Activity During PCR
[0202] After the LATE-PCR amplification as described in Example 5,
the detection probe for the first target was hybridized to its
complementary amplification products at 50.degree. C. for 1 minute.
The probe-target hybrids were then subjected to melting curve
analysis by monitoring probe fluorescent intensities at 1.degree.
C. intervals of 30 seconds each between 50.degree. C. and
80.degree. C. as the probe was being melted from the amplicon. A
no-template control containing only the probe was also subjected to
melting regimen (fluorescence increases slightly with temperature
in the absence of probe cleavage, because fluorescence intensity
from the fluorophore is temperature dependent). Two samples were
subjected to melting: one containing no additive and one containing
additive EP013 (SEQ ID Nos 47 and 157) at 600 nM concentration.
[0203] Results are presented in FIGS. 11A and 11B. In FIG. 11A,
curve 111 is for the probe alone, and curve 112 is for the
amplification product of the reaction containing no additive. In
FIG. 11B, curve 113 is for the probe alone, and curve 114 is for
the amplification product containing the additive EP013. Inhibition
of primer-dependent Taq DNA polymerase 5' exonuclease activity is
evidenced by fluorescence signals from the probe melted off the
amplification targets matching the fluorescence signals of control
samples containing the probe alone when melting is completed.
Example 8. Large Multiplexed Reactions
[0204] Twelve pairs of primers, each for a different sequence
within genes of the human mitochondrial genome, were combined into
a single multiplex amplification mixture for a multiplex
amplification of twelve different target sequences. The 25 ul
reaction mixtures contained 1.times.PCR Buffer, 400 nM dNTPs, 3 mM
MgCl.sub.2, 0.24.times.SYBR Green, 50 nM Limiting Primer, 1000 nM
Excess Primer, and 3.75 units of Tfi(-) DNA polymerase, with either
no additive, additive EP011 at 300 nM concentration, or additive
EP011 at 600 nM concentration.
[0205] Reaction mixtures were subjected to the following LATE-PCR
thermal cycling protocol: 95.degree. C. for 3 minutes followed by
65 cycles of 95.degree. C./5 s, 58.degree. C./20 s, and 68.degree.
C./2 m; followed by a melt starting at 45.degree. C. with 1.degree.
C. increments at 30 s intervals to 95.degree. C. Reactions were
analyzed at the end of 65 cycles by a melt curve analysis using the
first derivative of SYBR Green fluorescence (-dF/dT, SYBR) of
double-stranded DNA product. In addition, the kinetics of
production of double-stranded product (SYBR Green intensity reading
as a function of thermal cycles) was analyzed for reactions.
[0206] The sequence of additive EP011, and the sequences of the 12
targets and the primers used to amplify each were are as
follows:
TABLE-US-00024 Additive EP011. (SEQ ID No. 60) 5'
DabcylGGTCAGATGAAAATGATACGTG Dabcyl pCCAGTCTACTTTTACTATGCAC Dabcyl
5' Target HV1. (SEQ ID No. 61) 5'
GCCCGGAGCGAGGAGAGTAGCACTCTTGTGCGGGATATTGA
TTTCACGGAGGATGGTGGTCAAGGGACCCCTATCTGAGGGG
GGTCATCCATGGGGACGAGAAGGGATTTGACTGTAAT GTGC
TATGTACGGTAAATGGCTTTATGTACTATGTACTGTTAAGGG
TGGGTAGGTTTGTTGGTATCCTAGTGGGTGAGGGGTGGCTT
TGGAGTTGCAGTTGATGTGTGATAGTTGAGGGTTGATTGCT
GTACTTGCTTGTAAGCATGGGGAGGGGGTTTTGATGTG GAT
TGGGTTTTTATGTACTACAGGTGGTCAAGTATTTATGGTAC
CGTACAATATTCATGGTGGCTGGCAGTAATGTACGAAATA
CATAGCGGTTGTTGATGGGTGAGTCAATACTTGGGTGGTAC
CCAAATCTGCTTCCCCATGAAAGAACAGAGAATAGTTTAA
ATTAGAATCTTAGCTTTGGGTGCTAATGGTGGAGTTAAAGACT
TTTTCTCTGATTTGTCCTTGGAAAAAGGTTTTCATCTCCGGT TTACAAGACTGGTG Limiting
Primer. (SEQ ID No. 62) 5' GCCCGGAGCGAGGAGAGTAGCACTCTTG Excess
Primer. (SEQ ID No. 63) 5' CACCAGTCTTGTAAACCGGAGATGAA Target HV2.
(SEQ ID No. 64) 5' ACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCC
ATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGC
ATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTAT
CTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTA
CGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA
ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT
GTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAA
ATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCA
CTTAAACACATCTCTGCCAAACCCCAAAAACAAAGAACCC
TAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCG
GTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATT
TTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAAC
CCCCGCCCATCCTACCCAGCACACACACACCGCTG Limiting Primer. (SEQ ID No.
65) 5' AGCGGTGTGTGTGTGCTGGGTAGGAT Excess Primer. (SEQ ID No. 66) 5'
ACAGGTCTATCACCCTATTAACCACTCA Target CO1-1. (SEQ ID No. 67) 5'
AGGTTGCGGTCTGTTAGTAGTATAGTGATGCCAGCAGCT
AGGACTGGGAGAGATAGGAGAAGTAGGACTGCTGTGATT
AGGACGGATCAGACGAAGAGGGGCGTTTGGTATTGGGTTA
TGGCAGGGGGTTTTATATTGATAATTGTTGTGATGAAATTG
ATGGCCCCTAAGATAGAGGAGACACCTGCTAGGTGTAAGG
AGAAGATGGTTAGGTCTACGGAGGCTCCAGGGTGGGAGT
AGTTCCCTGCTAAGGGAGGGTAGACTGTTCAACCTGTTCCT
GCTCCGGCCTCCACTATAGCAGATGCGAGCAGGAGTAGG
AGAGAGGGAGGTAAGAGTCAGAAGCTTATGTTGTTTATGC
GGGGAAACGCCATATCGGGGGCACCGATTATTAGGGGAAC
TAGTCAGTTGCCAAAGCCTCCGATTATGATGGGTATTACT
ATGAAGAAGATTATTACAAATGCATGGGCTGTGACGATAA
CGTTGTAGATGTGGTCGTTACCTAGAAGGTTGCCTGGCTGG
CCCAGCTCGGCTCGAATAAGGAGGCTTAGAGCTGTGCCTA
GGACTCCAGCTCATGCGCCGAATAATAGGTATAGTGTTCCA
ATGTCTTTGTGGTTTGTAGAGAATAGTCAACGGT Limiting Primer. (SEQ ID No. 68)
5' AGGTTGCGGTCTGTTAGTAGTATAGTGATGCCAGCA Excess Primer. (SEQ ID No.
69) 5' ACCGTTGACTATTCTCTACAAACCACA Target CO1-2. (SEQ ID No. 70) 5'
ATGGAGGGTTCTTCTACTATTAGGACTTTTCGCTTCGAAG
CGAAGGCTTCTCAAATCATGAAAATTATTAATATTACTGCT
GTTAGAGAAATGAATGAGCCTACAGATGATAGGATGTTTC
ATGTGGTGTATGCATCGGGGTAGTCCGAGTAACGTCGGGG
CATTCCGGATAGGCCGAGAAAGTGTTGTGGGAAGAAAGTT
AGATTTACGCCGATGAATATGATAGTGAAATGGATTTTGGC
GTAGGTTTGGTCTAGGGTGTAGCCTGAGAATAGGGGAAATC
AGTGAATGAAGCCTCCTATGATGGCAAATACAGCTCCTAT
TGATAGGACATAGTGGAAGTGGGCTACAACGTAGTACGTG
TCGTGTAGTACGATGTCTAGTGATGAGTTTGCTAATACAAT
GCCAGTCAGGCCACCTACGGTGAAAAGAAAGATGAATCC
TAGGGCTCAGAGCACTGCAGCAGATCATTTCATATTGCTTC
CGTGGAGTGTGGCGAGTCAGCTAAATACTTTGACGCCGGT
GGGGATAGCGATGATTATGGTAGCGGAGGTGAAATATGCT
CGTGTGTCTACGTCTATTCCTACTGTAAATATATGGTGTGC
TCACACGATAAACCCTAGGAAGCCAATTGATATCATAGCT
CAGACCATACCTATGTATCCAAATGGTTCTTTTTTTCCGGA
GTAGTAAGTTACAATATGGGAGATTATTCCGAAGCCTGG TAGGAT Limiting Primer.
(SEQ ID No. 71) 5' ATGGAGGGTTCTTCTACTATTAGGACTTTTCGCT Excess
Primer. (SEQ ID No. 72) 5' ATCCTACCAGGCTTCGGAATAATCTC Target CO2.
(SEQ ID No. 73) 5' AGGGTAAATACGGGCCCTATTTCAAAGATTTTTAGGGG
AATTAATTCTAGGACGATGGGCATGAAACTGTGGTTTGCTC
CACAGATTTCAGAGCATTGACCGTAGTATACCCCCGGTCG
TGTAGCGGTGAAAGTGGTTTGGTTTAGACGTCCGGGAATTG
CATCTGTTTTTAAGCCTAATGTGGGGACAGCTCATGAGTGCA
AGACGTCTTGTGATGTAATTATTATACGAATGGGGGCTTCA
ATCGGGAGTACTACTCGATTGTCAACGTCAAGGAGTCGCA
GGTCGCCTGGTTCTAGGAATAATGGGGGAAGTATGTAGGA
GTTGAAGATTAGTCCGCCGTAGTCGGTGTACTCGTAGGTTC
AGTACCATTGGTGGCCAATTGATTTGATGGTAAGGGAGGG
ATCGTTGACCTCGTCTGTTATGTAAAGGATGCGTAGGGAT
GGGAGGGCGATGAGGACTAGGATGATGGCGGGCAGGATA
GTTCAGACGGTTTCTATTTCCTGAGCGTCTGAGATGTTAGTA
TTAGTTAGTTTTGTTGTGAGTGTTAGGAAAAGGGCATACA GGACTAGGAAGCAGATAAGGA
Limiting Primer. (SEQ ID No. 74) 5'
AGGGTAAATACGGGCCCTATTTCAAAGATTTTTAGGGGA Excess Primer. (SEQ ID No.
75) 5' TCCTTATCTGCTTCCTAGTCCTGTATGC Target 12srRNA. (SEQ ID No. 76)
5' CCTCTAAATCACCACGATCAAAAGGAACAAGCATCAA
GCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCA
CACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATA
AACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTT
GGTCAATTTCGTGCCAGCCACCGCGGTCACACGATTA
ACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGAT
CACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGT
AAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGG
CTTTAACATATCTGAACACACAATAGCTAAGACCCAAAC
TGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAA
CAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAG
CCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATA
TCCCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGA
TCAACCTCACCACCTCTTGCTCAGCCTATATACCGCCATC
TTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAG
TACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAG
GTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACT
ACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATT
TAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGG
CCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTCAAG
TATACTTCAAAGGACATTTAACTAAAACCCCTACGCATT
TATATAGAGGAGACAAGTCGTAACATGGTAAGTGT ACTGGA Limiting Primer. (SEQ ID
No. 77) 5' TCCAGTACACTTACCATGTTACGACTTGTCTCCTCTA Excess Primer.
(SEQ ID No. 78) 5' CCTCTAAATCACCACGATCAAAAGGAAC Target Cytb-1. (SEQ
ID No. 79) 5' TGTGAGGGTGGGACTGTCTACTGAGTAGCCTCCTCAGAT
TCATTGAACTAGGTCTGTCCCAATGTATGGGATGGCGGATA
GTAAGTTTGTAATTACTGTGGCCCCTCAGAATGATATTTGG
CCTCACGGGAGGACATAGCCTATGAAGGCTGTTGCTATAG
TTGCAAGCAGGAGGATAATGCCGATGTTTCAGGTTTCTGA
GTAGAGAAATGATCCGTAATATAGGCCTCGCCCGATGTGT
AGGAAGAGGCAGATAAAGAATATTGAGGCGCCATTGGCG
TGAAGGTAGCGGATGATTCAGCCATAATTTACGTCTCGAG
TGATGTGGGCGATTGATGAAAAGGCGGTTGAGGCGTCTGG
TGAGTAGTGCATGGCTAGGAATAGTCCTGTGGTGATTTGG
AGGATCAGGCAGGCGCCAAGGAGTGAGCCGAAGTTTC ATCATGCGGA Limiting Primer.
(SEQ ID No. 80) 5' TGTGAGGGTGGGACTGTCTACTGAGTAGCC Excess Primer.
(SEQ ID No. 81) 5' TCCGCATGATGAAACTTCGGCTC Target Cytb-2. (SEQ ID
No. 82) 5' ACTCCACCTCCTATTCTTGCACGAAACGGGATCAAACAA
CCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCC
ACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCT
TCCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGAC
CTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCT
TAAACACCCCTCCCCACATCAAGCCCGAATGATATTTCCT
ATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTAG
GAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCA
ATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAAT
ATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCG
CAGACCTCCTCATTCTAACCTGAATCG Limiting Primer. (SEQ ID No. 83) 5'
CGATTCAGGTTAGAATGAGGAGGTCTGCGGCTAG Excess Primer. (SEQ ID No. 84)
5' ACTCCACCTCCTATTCTTGCACGA Target ND1. (SEQ ID No. 85) 5'
CATAAGAACAGGGAGGTTAGAAGTAGGGTCTTGGTGACAA
AATATGTTGTGTAGAGTTCAGGGGAGAGTGCGTCATATGT
TGTTCCTAGGAAGATTGTAGTGGTGAGGGTGTTTATTATAA
TAATGTTTGTGTATTCGGCTATGAAGAATAGGGCGAAGGG
GCCTGCGGCGTATTCGATGTTGAAGCCTGAGACTAGTTCGG
ACTCCCCTTCGGCAAGGTCGAAGGGGGTTCGGTTGGTCTC
TGCTAGTGTGGAGATAAATCATATTATGGCCAAGGGTCAT
GATGGCAGGAGTAATCAGAGGTGTTCTTGTGTTGTGATAA
GGGTGGAGAGGTTAAAGGAGCCACTTATTAGTAATGTTGA
TAGTAGAATGATGGCTAGGGTGACTTCATATGAGATTGTTT
GGGCTACTGCTCGCAGTGCGCCGATCAGGGCGTAGTTTGAG
TTTGATGCTCACCCTGATCAGAGGATTGAGTAAACGGCTA
GGCTAGAGGTGGCTAGAATAAATAGGAGGCCTAGGTTGA
GGTTGACCAGGGGGTTGGGTATGGGGAGGGGGGTTCATA
GTAGAAGAGCGATGGTGAGAGCTAAGGTCGGGGCGGTGA
TGTAGAGGGTGATGGTAGATGTGGCGGGTTTTAGGGG Limiting Primer. (SEQ ID No.
86) 5' CATAAGAACAGGGAGGTTAGAAGTAGGGTCTTGGT Excess Primer. (SEQ ID
No. 87) 5' CCCCTAAAACCCGCCACAT Target ND2. (SEQ ID No. 88) 5'
AGTGTGATTGAGGTGGAGTAGATTAGGCGTAGGTAGAA
GTAGAGGTTAAGGAGGGTGATGGTGGCTATGATGGTGGGG
ATGATGAGGCTATTGTTTTTTGTGAATTCTTCGATAATGGC
CCATTTGGGCAAAAAGCCGGTTAGCGGGGGCAGGCCTCC
TAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCAT
GTTAGCTTGTTTCAGGTGCGAGATAGTAGTAGGGTCGTGGT
GCTGGAGTTTAAGTTGAGTAGTAGGAATGCGGTAGTAGTT
AGGATAATATAAATAGTTAAATTAAGAATGGTTATGTTAG
GGTTGTACGGTAGAACTGCTATTATTCATCCTATGTGGGTA
ATTGAGGAGTATGCTAAGATTTTGCGTAGCTGGGTTTGGTT
TAATCCACCTCAACTGCCTGCTATGATGGATAAGATTGAG
AGAGTGAGGAGAAGGCTTACGTTTAGTGAGGGAGAGATTT
GGTATATGATTGAGATGGGGGCTAGTTTTTGTCATGTGAG
AAGAAGCAGGCCGGATGTCAGAGGGGTGCCTTGGGTAACC
TCTGGGACTCAGAAGTGAAAGGGGGCTATTCCTAGTTTTAT
TGCTATAGCTATTATGATTATTAATGATGAGTATTGATTGG
TAGTATTGGTTATGGTTCATTGTCCGGAGAGTATATTGTTG
AAGAGGATAGCTATTAGAAGGATTATGGATGCGGTTGCTT
GCGTGAGGAAATACTTGATGGCAGCTTCTGTGGAACGAGGG
TTTATTTTTTTGGTTAGAACTGGAATAAAAGCTAGCATGTTT
ATTTCTAGGCCTACTCAGGTAAAAAATCAGTGCGAGCTTA GCGCTGTGATGAGTGTGCCTGCA
Limiting Primer (SEQ ID No. 89) 5'
AGTGTGATTGAGGTGGAGTAGATTAGGCGTAGGT AGAAGT Excess Primer. (SEQ ID
No. 90) 5' TGCAGGCACACTCATCACAGCGCTAAGCT Target ND4-1. (SEQ ID No.
91) 5' AACACAACCACCCACAGCCTAATTATTAGCATCATCCCTC
TACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTT
CCCCAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTA
ATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAG
CCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAA
CTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATT
ATAACATTCACAGCCACAGAACTAATCATATTTTATATCTT
CTTCGAAACCACACTTATCCCCACCTTGGCTATCATCACCC
GATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATA
CTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCAT
CGCACTAATTTACACTCACAACACCCTAGGCTCACTAAACA
TTCTACTACTCACTCTCACTGCCCAAGAACTATCAA ACTCCTGAGC Limiting Primer.
(SEQ ID No. 92) 5' GCTCAGGAGTTTGATAGTTCTTGGGCAGTGAGAG Excess
Primer. (SEQ ID No. 93) 5' AACACAACCACCCACAGCCTAATTATTAG Target
ND4-2. (SEQ ID No. 94) 5' GTGGTGGGTGAGTGAGCCCCATTGTGTTGTGGTAAATAT
GTAGAGGGAGTATAGGGCTGTGACTAGTATGTTGAGTCCT
GTAAGTAGGAGAGTGATATTTGATCAGGAGAACGTGGTTA
CTAGCACAGAGAGTTCTCCCAGTAGGTTAATAGTGGGGGG
TAAGGCGAGGTTAGCGAGGCTTGCTAGAAGTCATCAAAAA
GCTATTAGTGGGAGTAGAGTTTGAAGTCCTTGAGAGAGGA
TTATGATGCGACTGTGAGTGCGTTCGTAGTTTGAGTTTGCT
AGGCAGAATAGTAATGAGGATGTAAGCCCGTGGGCGATTA
TGAGAATGACTGCGCCGGTGAAGCTTCAGGGGGTTTGGAT
GAGAATGGCTGTTACTACGAGGGCTATGTGGCTGATTGAA
GAGTATGCAATGAGCGATTTTAGGTCTGTTTGTCGTAGGCA
GATGGAGCTTGTTATAATTATGCCTCATAGGGATAGTACA AGGAAGGGGTAG Limiting
Primer. (SEQ ID No. 95) 5' GTGGTGGGTGAGTGAGCCCCATTGTGT Excess
Primer. (SEQ ID No. 96) 5' CTACCCCTTCCTTGTACTATCCCTATGAG
[0207] The amplified products were then analyzed using a 5%
Polyacrylamide gel, loaded with 1 ul of PCR product combined with 1
ul of loading dye. The gel was run for eight hours at 30 volts at
4.degree. C. The gel was developed for ten minutes using SYBR Gold.
A photograph of the gel is presented in FIG. 12. The first lane is
the reaction with no additive. The second lane is the reaction with
additive EP011 at 300 nM concentration. The third lane is the
reaction with additive EP011 at 600 nM concentration. As can be
seen from FIG. 12, the reaction without additive failed to generate
the expected set of twelve products. From lane 2 it can be seen
that 300 nM of additive EP011 suppressed most mispriming (one band
of light weight product can be seen at the bottom). From lane 3 it
can be seen that additive EP011 at 600 nM concentration suppressed
all mispriming.
[0208] The reaction containing 600 nM additive EP011 was subjected
to the sequencing sample preparation known as the Dilute-'N'-Go
method. See, Rice, J. E. et al. (2007), Monoplex/Multiplex
Linear-After-The-Exponential PCR Assay Combined with PrimeSafe and
Dilute-'N'-Go Sequencing, Nature Protocols 2: 2429-2438. The
prepared sample was divided into twelve aliquots, and each aliquot
was subjected to dideoxy sequencing utilizing one of the twelve
limiting primers as the sequencing primer. Sequencing results
demonstrated that the amplification reaction generated a sufficient
single-stranded DNA for each amplicon to permit sequencing of each
of the 12 different Limiting Primer strands from a single reaction
via the Dilute'N'Go dideoxy sequencing protocol.
[0209] The above results were obtained using 1000 copies of
mitochondrial genomic DNA in each reaction. Additional samples in
this experiment (results not shown) demonstrated that complete
amplification of all 12 products was not obtained when each
reaction contained only 100 or 10 copies of mitochondrial genomic
DNA. This is consistent with the fact that Type 1 and Type 3
mispriming increase with decreasing numbers of targets.
[0210] But, 100 and 10 copies of mitochondrial genomic DNA can be
successfully amplified with the multiplex reaction described above
after making the following adjustments: 1) use EP043 with a
combination of strands at 50/600/550 nM; 2) increase the number of
amplification cycles to 80-90; and 3) in accord with Example 14
alter the limiting primers for the following targets by addition of
at least two mismatched A's or T's to their 5' ends (indicated by
underlining).
TABLE-US-00025 For target HV1: Limiting Primer. (SEQ ID No. 97) 5'
TAAAGCCCGGAGCGAGGAGAGTAGCACTCTTG For target HV2: Limiting Primer.
(SEQ ID No. 98) 5' AAAGCGGTGTGTGTGTGCTGGGTAGGAT For target CO1-1:
Limiting Primer. (SEQ ID No. 99) 5'
AAAGGTTGCGGTCTGTTAGTAGTATAGTGATGCCAGCA For target CO1-2: Limiting
Primer. (SEQ ID No. 100) 5' AAATGGAGGGTTCTTCTACTATTAGGACTTTTCGCT
For target CO2: Limiting Primer. (SEQ ID No. 101) 5'
TAAGGGTAAATACGGGCCCTATTTCAAAGATTTTT AGGGGA For target 12srRNA:
Limiting Primer. (SEQ ID No. 102) 5'
AATCCAGTACACTTACCATGTTACGACTTGTCTCCTCTA For target Cytb-1: Limiting
Primer. (SEQ ID No. 103) 5' AATGTGAGGGTGGGACTGTCTACTGAGTAGCC For
target Cytb-2: Limiting Primer. (SEQ ID No. 104) 5'
AACGATTCAGGTTAGAATGAGGAGGTCTGCGGCTAG For target ND1: Limiting: (SEQ
ID No. 105) 5' AACATAAGAACAGGGAGGTTAGAAGTAGGGTCTTGGT For target
ND2: Limiting Primer. (SEQ ID No. 106) 5'
AAAGTGTGATTGAGGTGGAGTAGATTAGGCGT AGGTAGAAGT For target ND4-1:
Limiting Primer. (SEQ ID No. 107) 5'
AAGCTCAGGAGTTTGATAGTTCTTGGGCAGTGAGAG For target ND4-2: Limiting
Primer. (SEQ ID No. 108) 5' TAGTGGTGGGTGAGTGAGCCCCATTGTGT
Example 9. Direct Quantitative Measure of Suppression of Type 1
Mispriming
[0211] The assay reported in this example was developed to measure
Type I mispriming and the effect of additives and hot-start
reagents in suppressing Type I mispriming. In this assay, two
overlapping oligonucleotides that can anneal and extend are first
incubated at a temperature (50.degree. C.) below a LATE-PCR
annealing temperature for an extended period (10 minutes). If
extension occurs, priming sites for a pair of LATE-PCR primers are
created, that is, the extended overlapping nucleotides include the
priming sites but the oligonucleotides themselves contain only the
complements of the priming sites. The reaction mixture is then
subjected to LATE-PCR amplification using the primer pair. Under
these conditions, the number of cycles required to generate a
detectable level of product (observed with either SYBR Green or a
probe to the Excess-Primer-Strand) will depend on how many extended
(or full length) strands are generated during the initial
isothermal incubation of the partially complementary oligomers.
This, in turn, will depend on how active the DNA polymerase is
during isothermal incubation. By comparing the threshold cycles
(C.sub.T) of a reaction with an inhibitor to a reaction with no
inhibitor, one obtains a quantitative measure of the effect of the
inhibitor in suppressing the initial, isothermal extension, which
is considered to be a mispriming event in this assay. The lowest
C.sub.T value is observed when all oligomers present initially are
fully extended prior to the first round of amplification. Higher
and higher C.sub.T values are observed with greater and greater
inhibition of DNA polymerase. After the respective combinations of
reactions were mixed and prior to the isothermal incubation at
50.degree. C. all reactions had the overlap oligonucleotides 1 and
2 added at approximately 100,000 copies each.
[0212] The following oligonucleotides were used. For the
overlapping oligonucleotides, the sequences complementary to
priming sites are underlined, and overlapping sequences are
italicized.
TABLE-US-00026 Overlapping oligonucleotide 1: (SEQ ID No. 109)
5'TTGCACGAGAGCCAGCTCGTCAGGTAGTCACCAGTACAGTCCGCT TGTGTCAAGACAGCACG
Overlapping oligonucleotide 2 (SEQ ID No. 110)
5'CAGCAGCAGACAGTGCACTCGTCACTCACTAACCGCTATTCGAGTT
CGCGTGCTGTCTTGACACAAGCGGACTGT Limiting Primer: (SEQ ID No. 111)
5'TTGCACGAGAGCCAGCTCGTCAGGTAGTCACCAGT Excess Primer: (SEQ ID No.
112) 5'CAGCAGCAGACAGTGCACTCGTCAC Additive EP046. (SEQ ID No. 113)
5' Dabcyl GGAGCAGACTAGCACTGAGGTA Dabcyl Dabcyl
CCTCGTCTGATCGTGACTCCAT Dabcyl 5' Additive EP020. (SEQ ID No. 12) 5'
Dabcyl GAAATAAAATAAAAATAAAATA Dabcyl Dabcyl CTTTATTTTATTTTTATTTTAT
Dabcyl 5' Additive EP022. (SEQ ID No. 14) 5' Dabcyl CCGCCGGC Dabcyl
Dabcyl GGCGGCCG Dabcyl 5'
[0213] Each reaction was carried out in triplicate in a 25 ul
reaction. Each reaction mixture contained 1.times.PCR buffer
(Invitrogen, Carlsbad, Calif.), 3 mM MgCl.sub.2, 250 nM dNTPs,
0.24.times.SYBR Green (Invitrogen, Carlsbad, Calif.), and 1.25
units of Taq DNA polymerase (Invitrogen, Carlsbad, Calif.). One
reaction mixture contained only Taq DNA polymerase. A second
reaction mixture contained Taq DNA polymerase and additive EP046 at
600 nM concentration. A third reaction mixture contained "hot
start" Taq DNA polymerase with antibody (Invitrogen, Carlsbad,
Calif.). A fourth reaction mixture contained Taq DNA polymerase
with antibody and additive EP046 at 600 nM concentration. After the
respective combinations of reaction ingredients were mixed and
prior to the isothermal incubation at 50.degree. C., all reactions
had the overlapping oligonucleotides 1 and 2 added at approximately
100,000 copies each.
[0214] The thermal profile conditions for these reactions were as
follows: 50.degree. C. for 10 minutes followed by incubation on ice
for long enough to add the primers, followed by rapid heating to
98.degree. C., then 60 cycles at 98.degree. C./10 s and 72.degree.
C./40 s. The melting temperature of the hybrid formed by the
overlapping oligonucleotides was about 60.degree. C., that is, well
above the temperature of the initial 10-minute incubation. The
annealing/extension temperature of the two-step PCR protocol was
below the concentration-adjusted melting temperatures of the
limiting and excess primers, which were 75.1.degree. C. and
73.6.degree. C., respectively, calculated according to the method
given in Example 1. Each of the samples was analyzed by SYBR Green
fluorescence in real-time, and at the end of the run each was
subjected to melt curve analysis to confirm that the reaction
generated a single product peak of 88.degree. C. as expected for
the double-stranded product of the amplification reaction (not
shown).
[0215] SYBR Green fluorescence as a function of amplification cycle
is shown in FIG. 13, where circle 131 identifies the replicates
from the sample with Taq DNA polymerase only, circle 132 identifies
the replicates from the sample with Taq DNA polymerase and the
additive EP046, circle 133 identifies the replicates from the
sample with Taq DNA polymerase-plus-antibody and circle 134
identifies the replicates from the sample with Taq DNA
polymerase-plus-antibody and additive EP046.
Example 10. Mispriming and "ColdStop" Detection
[0216] To determine whether or not it is possible to interrupt a
PCR amplification to perform some low-temperature operation.
Mispriming effects of doing so need to be determined. We have
developed the assay reported in this example for that purpose. The
assay is a LATE-PCR amplification assay in which we have utilized
the following target strand, primers and hybridization probe
(labeled on one end with the fluorophore Quasar670 (Biosearch
Technologies, Novato, Calif.) and on the other end with the
quencher BHQ2 (Biosearch Technologies, Novato, Calif.):
TABLE-US-00027 Limiting Primer. (SEQ ID No. 114) 5'
CTCCAGCCCGGCACGCTCACGTGACAGACCG Excess Primer. (SEQ ID No. 115) 5'
CCGGTGGTCGCCGCGATCAAGGAG Probe. (SEQ ID No. 116) 5' Quasar670
GCGGGTTGTTCTGGTCCATGA BHQ2 Target. (SEQ ID No. 117) 5'
CCGGTGGTCGCCGCGATCAAGGAGTTCTTCGGCACCAGCCA
GCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGG
TTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCG
GTCTGTCACGTGAGCGTGCCGGGCTGGAG
[0217] The reaction mixture included 1.times.PCR buffer
(Invitrogen, Carlsbad, Calif.), 2 mM MgCl.sub.2, 200 nM dNTPs, 50
nM of limiting primer, 1000 nM of excess primer, 200 nM of probe,
1.25 units of Taq DNA polymerase (Invitrogen, Carlsbad, Calif.),
and an additive to be tested, in this case additive EP010 at 600 nM
concentration. In addition, each reaction contained 10 million
copies of human genomic DNA (Sigma-Aldrich, St. Louis, Mo.). The
sequence of the tested additive was:
TABLE-US-00028 Additive EP010. (SEQ ID No. 10) 5' Dabcyl
GGTCAGATGAAAATGATACGTG Dabcyl Dabcyl CCAGTCTACTTTTACTATGCAC Dabcyl
5'
[0218] Three control assays were first performed with the test
additive included in the reaction mixture but without any
interruption of the thermal cycling protocol to establish that the
uninterrupted protocol was both sensitive and robust. The control
assays were begun with 1000, 100 and 10 copies of the target strand
in the amplification reaction mixture. Thermal cycling regimen was
98.degree. C. for 3 minutes, followed by 70 cycles of 98.degree.
C./10 s. 75.degree. C./40 s. 60.degree. C./30 s, with fluorescence
reading at 60.degree. C. FIG. 14A presents the fluorescence
readings from the probe as a function of PCR cycle number, with
circle 141 being the readings from the four replicate
amplifications of the sample with 1000 copies of target, circle 142
(dashed lines) being the readings from the replicates of the sample
with 100 copies of target, and circle 143 being from the replicates
of the sample with 10 copies of target.
[0219] A separate reaction mixture was subjected to a thermal
cycling protocol that was interrupted. The thermal profile was 1
minute at 98.degree. C. followed by 40 cycles of 98.degree. C./10
s, 75.degree. C./40 s, then a melt starting at 45.degree. C. and
increasing in 1.degree. C. steps every 30 seconds (data acquisition
for each step) for 40 steps, followed by 30 more cycles of
98.degree. C./10 s, 75.degree. C./40 s, at the conclusion of which
the melt was repeated.
[0220] Results from the two melts are presented in FIG. 14B and
FIG. 14C. These figures present melt curves in which the
fluorescent values at each temperature are normalized by being
divided by the fluorescent value at 75.degree. C., a temperature at
which the probe is not bound to the single-stranded product.
Normalized melts were determined after 40 amplification cycles
(FIG. 14B) and after 70 cycles, following the conclusion of
amplification (FIG. 14C). In FIG. 14B, circle 144 is the replicates
for 1000 copies of the target, circle 145 is the replicates of the
sample with 100 copies of target, and circle 146 is the replicates
of the sample with 10 copies of target. Similarly, in FIG. 14C,
circle 147 (solid black lines) is the three replicate
amplifications of the sample with 1000 copies of target, circle 148
(dashed lines) is the replicates of the sample with 100 copies of
target, and circle 149 (solid gray lines) is the replicates of the
sample with 10 copies of target.
Example 11. Type II Mispriming in Symmetric PCR Reactions
[0221] To demonstrate the effect of additives on the specificity of
conventional symmetric PCR, allele-discriminating primers, the
following assay was performed. Equal concentrations of two DNA
target sequences differing at a single nucleotide position were
amplified in parallel under symmetric PCR conditions in the
presence or absence of additive EP043 (SEQ ID No. 45) using a
primer pair in which one primer is specific (allele-specific
primer) for one those DNA targets DNA (designated as the "matched
target"). As suggested in the literature (Newton et al., Analysis
of any point mutation in DNA. The amplification refractory mutation
system (ARMS). 1989, Nucleic Acids Res. 17:2503-2516), a pair of
symmetric PCR primers for preferential amplification of the matched
target was constructed such that 3' end of one of the primers is
complementary to the nucleotide unique to the intended DNA target
and the penultimate 3' end position is mismatched to both the
intended and the unintended DNA targets. Thus, the primer specific
for the intended target is mismatched only once at its 3' end to
the intended DNA target, but it is mismatched twice at its 3' end
to the mismatched target. This primer design results in
preferential amplification of the matched target. Prior to this
experiment, genomic DNA samples containing the matched and
mismatched targets were quantified with primers fully complementary
to both targets to normalize the data for differences in target
genome concentration. In this instance, the C.sub.T for the
mismatched target was lower than the C.sub.T for the matched target
by 1.52, so for assays using the allele-specific primer, any noted
delay in the C.sub.T of the mismatched target had to be corrected
by adding 1.52 to the observed .DELTA.C.sub.T to account for target
concentration difference.
[0222] The target and primer sequences for preferential
amplification, and the additive sequence were:
TABLE-US-00029 Allele-Specific Primer. (SEQ ID No. 118) 5'
TATCGTCAAGGCACTCTTGCCTACGCCTT Common Primer. (SEQ ID No. 119) 5'
GTACTGGTGGAGTATTTGATAGTGTATTAACC Matched Target. (SEQ ID No. 120)
5' GTACTGGTGGAGTATTTGATAGTGTATTAACCTTATGTGT
GACATGTTCTAATATAGTCACATTTTCATTATTTTTATTATA
AGGCCTGCTGAAAATGACTGAATATAAACTTGTGGTAGTT
GGAGCTGATGGCGTAGGCAAGAGTGCCTTGACGATA Mismatehed Target. (SEQ ID No.
121) 5' GTACTGGTGGAGTATTTGATAGTGTATTAACCTTATGT
GTGACATGTTCTAATATAGTCACATTTTCATTATTTTT
ATTATAAGGCCTGCTGAAAATGACTGAATATAAACTT
GTGGTAGTTGGAGCTGGTGGCGTAGGCAAGAGTGC CTTGACGATA Additive EP043. (SEQ
ID No. 48) 5' GGAGCAGACTAGCACTGAGGTA Dabcyl Dabcyl
CCTCGTCTGATCGTGACTCCAT Dabcyl 5' 5' Dabcyl AGACTAGCACTGAGGTA
Dabcyl
[0223] Symmetric PCR amplification were carried out in 1.times.
Platinum Taq buffer (Invitrogen, Carlsbad, Calif.), 3 mM
MgCl.sub.2, 0.2 mM dNTP, 1 uM of primer pair, 0.24.times. SYBR
Green (Invitrogen, Carlsbad, Calif.), 1 unit Platinum Taq DNA
polymerase (Invitrogen, Carlsbad, Calif.) and 1000 genomes
equivalents of human DNA containing either the matched or the
mismatched target sequence in a final reaction volume of 25 ul. The
reaction mixture either contained no additive or contained additive
EP043 at a total concentration of 300 nM, with the top strand at
100 nM, the middle strand at 300 nM, and the bottom strand at 200
nM concentration.
[0224] The amplification conditions were 94.degree. C. for 5
minutes; followed by 60 cycles of 94.degree. C./1 minute (m),
64.degree. C./1 m, 72.degree. C./1 m, with data acquisition at the
72.degree. C. step; and a final extension step of 72.degree. C./10
m. Amplification was carried out in a Bio-Rad IQ-5 Multicolor
Real-Time PCR Detection System (Bio-Rad, Hercules, Calif.).
[0225] From SYBR green real-time fluorescence signals it was
determined that in the assay containing no additive, signal from
the mismatched target was delayed relative to signal from the
matched target, giving a corrected .DELTA.C.sub.T of 7.84.
Similarly, in the assay containing additive EP043 at a total of 300
nM concentration signal from the mismatched target was even more
delayed relative to signal from the matched target, giving a
corrected .DELTA.C.sub.T of 12.59. Accordingly, increased
polymerase specificity due to the presence of EP043 was 4.75
cycles.
Example 12. Inhibition of Taq DNA Polymerase Activity and AT
Content of Limiting Primer 3' End
[0226] LATE-PCR assays utilizing a limiting primer GC rich at its
3' end and a limiting primer AT rich at its 3' end were compared as
to the delay caused by the presence of an additive as described
herein. Four amplification reactions were performed: one using the
primer having the GC rich 3' end and no additive, a second using
the same primer and additive EP013; a third using the primer having
the AT rich 3' end and no additive; and a fourth using the same
primer and additive EP013.
[0227] Each 25 ul amplification reaction mixture included 1.times.
Platinum Taq buffer (Invitrogen, Carlsbad, Calif.), 3 mM
MgCl.sub.2, 250 nM dNTP, 1.25 units Platinum Taq polymerase
(Invitrogen, Carlsbad, Calif.), 1000 genomes equivalents of human
DNA, excess primer at 1000 nM concentration, limiting primer at 50
nM concentration, and detection probe at 500 nM concentration. For
the two assays that included additive EP013 (SEQ ID Nos 47 and 157)
was included in the reaction mixture at 600 nM concentration.
[0228] The thermal cycling regimen was 95.degree. C. for 10
seconds., 66.5.degree. C. for 10 seconds, and 72.degree. C. for 10
seconds for 20 cycles, followed by 50 cycles at 95.degree. C. for
10 seconds, 65.degree. C. for 10 seconds, 72.degree. C. for 10
seconds, and fluorescent signal detection at 54.degree. C. for 20
seconds. Fluorescence detection from each probe when bound to its
target was measured during the annealing phase of the PCR
cycles.
[0229] Sequences of target, primers and probe utilized in assays
with limiting primer having GC rich 3' end were:
TABLE-US-00030 Excess primer. (SEQ ID No. 122) 5'
GCACAGTTACAGTATTCCAGCAGACTCA Limiting primer. (SEQ ID No. 123) 5'
TCAGTGGTGGCAGTGGTAGTGGTGGC Target for GC rich primer. (SEQ ID No.
124) 5' GCACAGTTACAGTATTCCAGCAGACTCAAAT
ACAAGAACCTACTGCTAATGCCACCACTAC CACTGCCACCACTGA Detection probe.
(SEQ ID No. 125) 5' BHQ-2 TCAGTGGTGGCAGTGGTAGA Quasar 670
[0230] Sequences for target, primers, and probe utilized in assays
with limiting primer having AT rich 3' end were:
TABLE-US-00031 Excess primer. (SEQ ID No. 126) 5'
CTTTGGCACCAGAGGTGAGC Limiting primer. (SEQ ID No. 127) 5'
GGTGCGTGGGTCCCAGTCTGCAGTTAAG Target for AT rich primer. (SEQ ID No.
128) 5' GGTGCGTGGGTCCCAGTCTGCAGTTAAGGG GGCAGGAGTGGCGCTGCTCACCTCTGG
TGCCAAAG Detection probe. (SEQ ID No. 129) 5' BHQ-2 GCAGGAGTGGCGCT
Quasar 670
[0231] Sequence of additive EP013 was as follows:
TABLE-US-00032 Additive EP013. (SEQ ID No. 56) 5' Dabcyl
GGTCAGATGAAAATGATACGTGp Dabcyl CCAGTCTACTTTTACTATGCAC Dabcyl 5'
[0232] In the assays using the limiting primer having the GC rich
3' end, addition of additive EP013 to the reaction mixture at 600
nM concentration resulted in a delay in the threshold cycle
(C.sub.T) of 4 cycles as compared to amplification with no
additive. In the assays using the limiting primer having the AT
rich 3' end, addition of additive EP013 to the reaction mixture at
600 nM concentration resulted in a C.sub.T delay of 11 cycles.
Example 13. Modification of 5' End of Primers and Type III
Mispriming
[0233] We used additional nucleotides to form a non-complementary
tail on the 5'end of one of the PCR amplification primers. In this
example we used LATE-PCR amplification, and we modified the
limiting primer. We compared modified and unmodified primers to
discriminate between fully bound and partially bound 3'ends. Two
adenines were added to the 5'-end of the limiting primer used to
amplify the human mitochondrial cytochrome b gene (denoted by the
underlined bases). We tested two additives: additive EP047, target,
primer, and additive sequences were as follows:
TABLE-US-00033 Target Cytb-1. (SEQ ID No. 79) 5'
TGTGAGGGTGGGACTGTCTACTGAGTAGCCTCCTCAGAT
TCATTGAACTAGGTCTGTCCCAATGTATGGGATGGCGGATA
GTAAGTTTGTAATTACTGTGGCCCCTCAGAATGATATTTGG
CCTCACGGGAGGACATAGCCTATGAAGGCTGTTGCTATAG
TTGCAAGCAGGAGGATAATGCCGATGTTTCAGGTTTCTGA
GTAGAGAAATGATCCGTAATATAGGCCTCGCCCGATGTGT
AGGAAGAGGCAGATAAAGAATATTGAGGCGCCATTGGCG
TGAAGGTAGCGGATGATTCAGCCATAATTTACGTCTCGAG
TGATGTGGGCGATTGATGAAAAGGCGGTTGAGGCGTCTGG
TGAGTAGTGCATGGCTAGGAATAGTCCTGTGGTGATTTGG
AGGATCAGGCAGGCGCCAAGGAGTGAGCCGAAGTTTC ATCATGCGGA Limiting Primer.
(SEQ ID No. 80) 5' TGTGAGGGTGGGACTGTCTACTGAGTAGCC Excess Primer.
(SEQ ID No. 81) 5' TCCGCATGATGAAACTTCGGCTC Modified Limiting
Primer. (SEQ ID No. 130) 5' AATGTGAGGGTGGGACTGTCTACTGAGTAGCC
Additive EP047. (SEQ ID No. 131) Dabcyl CCTCGTCTGATCGTGACTCCAT
Dabcyl 5' 5' Dabcyl AGACTAGCACTGAGGTA Additive EP043. (SEQ ID No.
48) 5' GGAGCAGACTAGCACTGAGGTA Dabcyl Dabcyl CCTCGTCTGATCGTGACTCCAT
Dabcyl 5' 5' Dabcyl AGACTAGCACTGAGGTA Dabcyl
[0234] Additive EP047 includes a strand 22 nucleotides long and a
strand 17 nucleotides long that form a double-stranded region that
is 17 nucleotides long, and it has four terminal Dabcyl modifiers.
The Tm of additive EP047 is 59.1.degree. C. Additive EP043 is a
mixture of additives. It includes as one component additive EP047
(which comprises the two bottom strands), which was included in
this test at a concentration of 550 nM. Mixture EP043 also includes
another double-stranded oligonucleotide shown as the top two
strands. This second oligomer includes two complementary strands
that are 22 nucleotides long, and it has three terminal Dabcyl
modifiers. It has a Tm of 67.4.degree. C., and it was included in
this test at a concentration of 50 nM. Because the two additives in
the mixture share a common strand, the strand concentrations were
50/600/550 for the top/middle//bottom strands.
[0235] LATE-PCR reaction mixtures included 1.times.PCR buffer, 250
nM dNTPs, 3 mM MgCl.sub.2, 0.24.times.SYBR Green, 50 nM limiting
primer, 1000 nM excess primer, 1000 copies of human mitochondrial
DNA, and 2.5 units of TFi(-) DNA polymerase, an antibody-bound, 5'
exonuclease (-) polymerase (Invitrogen, Carlsbad Calif.) in 25 ul
volume. Six assays were performed, with additives and limiting
primers in the reaction mixture as follows: [0236] (1) no additive,
untailed limiting primer (SEQ ID No. 80) [0237] (2) no additive,
tailed limiting primer (SEQ ID No. 133) [0238] (3) additive EP047
at 600 nM concentration, untailed limiting primer [0239] (4)
additive EP047 at 600 nM concentration, tailed primer [0240] (5)
three-strand additive mixture EP043 at strand concentrations of
50/600/550, untailed primer [0241] (6) three-strand additive
mixture EP043 at strand concentrations of 50/600/550, tailed
primer
[0242] The six reaction mixtures were amplified under the following
conditions: 95.degree. C. for 3 minutes followed by 65 cycles of
95.degree./5 s, 58.degree. C./20 s, and 68.degree. C./2 m. Melt
analysis of the products was then conducted, starting at 45.degree.
C. with 1.degree. C. increments at 30 s intervals to 95.degree. C.
PCR amplification as well as the melt analysis was monitored by the
use of SYBR Green.
[0243] For the reactions with no additive, product evolution
resulted in an amplicon having a Tm above the Tm of the desired
product, no matter which limiting primer was used. Including
additive EP047 in the reaction mixture delayed the onset of
detectable product evolution by several amplification cycles and
resulted in a portion of the amplification product being the
correct product. With additive EP047, more correct product was made
using the tailed primer than was made using the untailed primer.
Additive EP047 has a calculated Tm based on its unmodified strands
of 59.1.degree. C. Including additive EP043 in the reaction mixture
also delayed the onset of detectable product evolution and resulted
in the most correct product being generated. With additive EP043,
more correct product was made using the tailed primer than was made
using the untailed primer. Additive EP043 is a mixture having
calculated Tm's base on the unmodified strands of 67.4.degree. C.
and 59.1.degree. C.
[0244] Real-time kinetic curves the six replicates with additive
EP043, tailed limiting primer and untailed limiting primer, are
shown in FIG. 15A. In FIG. 15A circle 151 (gray lines) identifies
the curves for the three replicates with the untailed primer, and
circle 152 (black lines) identifies the curves for the replicates
with the tailed primer. Melt curves of the six amplification
products with additive EP043 are shown in FIG. 15B, where the
downward pointing arrow indicates the melting temperature,
86.degree. C., of the correct double-stranded DNA product. In FIG.
15B circle 153 identifies the one replicate with untailed primer
that showed the correct peak with no product evolution (flat
plateau) in FIG. 15A, and circle 154 identifies the two replicates
with tailed primer also showed no product evolution (flat plateau)
in FIG. 15A.
Example 14: Additive as Primer for Suppressing Mispriming
[0245] A primer that is an additive is a double-stranded
oligonucleotide in which one strand is an amplification primer
having an extendable 3' end. Its 5' end has a modifier substituent.
The other strand, which we refer to as the reverse complement
sequence has two, and its 3' end is non-extendable. Because the
amplification assay of this example is a LATE-PCR assay in which
the limiting primer is included in the reaction mixture a very low
concentration, only the excess primer is made an additive. The
strand having the free 3' end serves as an amplification primer
when it hybridizes to and extends on its target strand, and it
serves as an inhibitor of mispriming when it hybridizes to its
modified complementary strand. In this example, the primer-reverse
complement sequence additive has three terminal Dabcyl modifiers.
The primer strand is modified by covalent linkage of a modifying
group, here a Dabcyl group, to its 5' terminal nucleotide. The
reverse complement sequence is modified by covalent linkage of a
modifying group, here a Dabcyl group, to each of its 5' and 3'
ends. The Tm of the reverse complement sequence to the primer
strand is designed to be 5-30.degree. C., preferably 15-25.degree.
C., lower than the Tm of the primer strand to its amplification
target sequence. To achieve the difference in Tm's, the reverse
complement sequence may be rendered partially complementary to the
primer strand by making it either shorter or mismatched at one or
more nucleotides. In this example, several mismatched nucleotides
were included. In multiplex reactions having more than one pair of
primers at least one primer is converted to an additive with its
corresponding partially complementary reverse complement sequence.
In both monoplex and multiplex reactions the concentration of said
at least one oligonucleotide is titrated and optimized empirically
to achieve suppression of mispriming together with the lowest
scatter among replicate reactions. Typically, said optimum
concentration is close to that of a double-stranded additive that
is not a primer added to the same reaction to suppress mispriming.
As one skilled in the art will understand, reactions utilizing an
additive-primer can be further supplemented with an additive that
is not a primer, provided the latter does not cross hybridize with
the former.
[0246] LATE-PCR reactions were carried out in triplicate using the
following sequences:
TABLE-US-00034 Limiting Primer. (SEQ ID No. 132) 5'
TCCAGTACACTTACCATGTTACGACTTGTCTCCTCTA Excess Primer. (SEQ ID No.
133) 5' Dabcyl AGTTCACCCTCTAAATCACCACGAT Reverse Complement
Sequence. (SEQ ID No. 134) 5' Dabcyl
ATCGTTGTGGTATAGAGGGTGAACT-Dabcyl Target. (SEQ ID No. 135) 5'
AGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGC
ATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCA
CACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAAC
GAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCG
TGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAATAGAAGC
CGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTA
AAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGA
CTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGA
CCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCT
CAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGC
CACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTC
TAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCAC
CACCTCTTGCTCAGCCTATATACCGCCATCTTCAGCAAACCCTGA
TGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAG
GTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTC
TACCCCAGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGA
AGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAAC
AGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTCAAGT
ATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATA
GAGGAGACAAGTCGTAACATGGTAAGTGTACTGG
[0247] LATE PCR amplifications were carried out in 25 ul volume
consisting of 1.times. Platinum Tfi(-) buffer (Invitrogen,
Carlsbad, Calif.), 3 mM MgCl.sub.2, 250 nM dNTPs, 50 nM of limiting
primer, 1000 nM of excess primer, 0.24.times.SYBR Green
(Invitrogen, Carlsbad, Calif.), 2.5 units of Platinum Tfi(-) DNA
polymerase (Invitrogen, Carlsbad, Calif.) with approximately 1000
mitochondrial genomes from human genomic DNA. The concentrations of
the reverse complement that created the additive were 100, 200 and
300 nM. In this instance we lowered the Tm of the primer-reverse
complement hybrid relative to the primer-target hybrid by
introducing mismatches into the reverse complement strand
(mismatched nucleotides are underlined).
[0248] The thermal profile conditions for these reactions were as
follows: 95.degree. C. for 3 minutes followed by 95.degree. C./5
s-58.degree. C./20 s-68.degree. C./2 m for 60 cycles, followed by a
melt starting at 45.degree. C./45 s with 1.degree. C. increments
for 51 cycles. All reactions were analyzed in real time during the
extension phase (68.degree. C.) of thermal cycles. At the end of 60
cycles the amplification products were analyzed using the first
derivative of SYBR Green fluorescence (melt curve analysis) of
double-stranded DNA product.
[0249] The melt curves are presented in FIGS. 16A-16D. FIG. 16A is
the melt curves for the three replicates with no reverse complement
sequence. Curves 161 show that in the absence of the complementary
oligonucleotide only one of three reactions generated the expected
product having a melting temperature of 86.degree. C. (arrow). FIG.
16B is the melt curves for the three replicates that included the
reverse complement sequence at 100 nM concentration. Curves 162
show that two of three reactions generated the expected product.
FIGS. 16C and 16D are the melt curves for the replicates with the
reverse complement sequence at concentrations of 200 nM and 300 nM,
respectively. Curves 163 and 164 show that all three replicates in
each set of reactions generated the correct product (as judged by
the presence of a melting peak of 86.degree. C.).
Example 15: Mispriming with RNA Target
[0250] This example describes a series of LATE-PCR assays in which
the starting target sequence was RNA rather than DNA, so the
initial reaction mixtures included reverse transcriptase, and the
protocol included an initial incubation to convert RNA to cDNA
prior to amplification of the cDNA. The RNA utilized in this series
was a sequence within an Enterovirus Armored RNA (EV, Catalog
#42050 from Asuragen, Austin, Tex., USA) containing the a portion
of the 5' untranslated region (UTR) from the Enterovirus RNA.
Samples include primer pairs for both EV and Foot and Mouth Disease
Virus (FMDV), but no FMDV targets are included in this example.
Amplification reactions were followed in real time by the use of a
molecular beacon probe having a fluorophore (Cal Red 610) and a
quencher (Black Hole Quencher No. 2). All sets of all reactions
were run in triplicate, and products were analyzed via melt curve
analysis at end-point.
[0251] Several additives, including mixtures, were compared to a
no-additive control. Sequences of the EV primers, EV probe and
additives were as follows:
TABLE-US-00035 EV Limiting Primer. (SEQ ID No. 136) 5'
GACTTGCGCGTTACGACAGGCCAATC EV Excess Primer. (SEQ ID No. 137) 5'
TGAATGCGGCTAATCCCAAC EV Probe. (SEQ ID No. 138) 5' Cal Red
610-AACCACCTGCCCCTT-BHQ2 Additive EP020. (SEQ ID No. 12) 5' Dabcyl
GAAATAAAATAAAAATAAAATA Dabcyl Dabcyl CTTTATTTTATTTTTATTTTAT Dabcyl
5' Additive EP010. (SEQ ID No. 10) 5' Dabcyl GGTCAGATGAAAATGATACGTG
Dabcyl Dabcyl CCAGTCTACTTTTACTATGCAC Dabcyl 5' Additive EP003. (SEQ
ID No. 25) 5' GGAGCAAAATAGCAATGAGGTA Dabcyl Dabcyl
CCTCGTTTTATCGTTACTCCAT Dabcyl 5'
[0252] EV Armored RNA was diluted in 10 mM TRIS, pH 8.3 to about
25,000 particles per .mu.l and heated at 75.degree. C. for 3
minutes to denature the coat protein and release the RNA. The RNA
(2 .mu.l per sample) was mixed with a solution containing the
concentrated primers (3 .mu.l per sample) and was incubated at room
temperature for 5 minutes, then a concentrated reagent mix was
added to yield the following concentrations in a final volume of 25
.mu.l per sample: 3 mM magnesium chloride, 400 nM each
deoxynucleotide, 500 nM each probe, 50 nM each limiting primer, 500
nM each excess primer, 1.times. Tfi (exo-) reaction buffer, 2 Units
Tfi (exo-) polymerase per sample (Invitrogen, Cat. No. 60684-050),
and 100 Units per sample SuperScript III Reverse Transcriptase
(Invitrogen, Cat. No. 18080-044). EV RNA was at about 50,000 copies
per sample. Additives were included at the following
concentrations:
[0253] Reaction A--Additive EP020 at 2000 nM
[0254] Reaction B--Additive EP010 at 200 nM
[0255] Reaction C--Additive EP003 at 400 nM
[0256] Reaction D--Additive EP010 at 400 nM and Additive EP020 at
1000 nM
[0257] Reaction E--Additive EP003 at 400 nM and Additive EP020 at
1000 nM
[0258] Reaction F--no additive control
[0259] Samples were placed in a Stratagene MX3005P thermal cycler
and incubated at 50.degree. C. for 6 minutes, 95.degree. C. for 1
minute, then 25 cycles of 95.degree. C./10 s, 64.degree. C./10 s,
and 68.degree. C./20 s, followed by 35 cycles of 95.degree. C./10
s, 64.degree. C./10 s, 68.degree. C./20 s, and 50.degree. C./30 s
with fluorescence detection for probe at 50.degree. C.
[0260] FIGS. 17A-17F show the real-time results for probe
fluorescence during the low-temperature (50.degree. C.) detection
step in cycles 26-60. In FIG. 17A, circle 171 is the curves for the
three replicates for Reaction A. In FIG. 17B, circle 172 is the
curves for the three replicates for Reaction B. In FIG. 17C, circle
173 is the curves for the three replicates for Reaction C. In FIG.
17D, circle 174 is the curves for the three replicates for Reaction
D. In FIG. 17E, circle 175 is the curves for the three replicates
for Reaction E. In FIG. 17F, circle 176 is the curves for the three
replicates for Reaction F.
[0261] The curves of circle 176 show that the no-additive control
exhibited Type III mispriming (severe product evolution), shown by
the reduction of single-stranded product in later amplification
cycles (roughly cycles 42-60). The curves of circle 171 for
Reaction A, which contained a low-Tm additive (Tm 47.7.degree. C.,
which was some 16.degree. C. below the annealing temperature and
2.3.degree. C. below the low-temperature detection temperature) in
very high concentration, showed suppression of Type 1 mispriming
but only partial suppression of Type III mispriming, with high
scatter among replicates by cycle 60. The curves of circle 172 for
Reaction B, which contained an additive having a somewhat higher Tm
(Tm 60.degree. C., which was 4.degree. C. below the annealing
temperature but above the low-temperature detection temperature) at
very low concentration totally suppressed Type I mispriming and
only partially suppressed Type III mispriming (two of three
replicates showed some reduction in probe signal by cycle 60), but
significantly reduced scatter at cycle 60 nonetheless. Reactions C,
D, and E, all of which contained additives showed no reduction in
probe signal through cycle 60. Because curves of circle 174 show
suppression of Type III mispriming with high signal, indicating
minimal reduction in efficiency of the reaction, Reaction D was
judged to be optimal for this set of reactions.
Example 16. Direct Quantitative Measure of Suppression of Type I
Mispriming by Additives with Overhangs
[0262] The assay reported here was carried out as described in
Example 9 with the following exceptions: (a) a Taq polymerase
antibody was present in all samples during the 50.degree. C.
incubation step; (b) the incubation step at 50.degree. C. was for 1
minute.
[0263] Each additive was comprised of the same two hairpin-forming
34-nucleotide long single-stranded oligomers having the structure
of oligomers 194,195 depicted in FIG. 18C, with 1, 2, 3 or 4 ends
modified by addition of a Dabcyl moiety. All oligos in which the 3'
ends were not blocked by a quencher were blocked by either a
phosphate (P) or a three-carbon modifier (C.sub.3) to prevent
extension. The six nucleotides on the 5' and 3' ends of each
single-stranded oligomer were complementary, such that when these
ends hybridized to each other they formed a 6-base-pair stem and a
22-nucleotide loop structure. With reference to FIG. 18C, the two
22-nucleotide loops of said additive were complementary, such that
when hybridized to each other formed an additive 196 having a
22-base-pair long double-stranded portion 197 with four
non-complementary single-stranded 6-base-pair long ends 198, 199,
200, 201. The sequences of the single-stranded oligomers were not
randomly assigned but required careful consideration due to the
inherent complementarity in the design. The consideration is not to
allow the oligomers to form other structures at the temperature in
which the loops are engaged, in particular to prevent the arm
sequences to remain disengaged from each other as well as not
binding to any of the complementary loop sequences of either
oligonucleotide. These additive sequences have the ability to
remain in a predesigned conformation over a range of
temperatures.
[0264] In the case of additives in which one or both of the
component oligonucleotide strands has the capacity to form a
stem-loop structure (see FIGS. 18B, 18C) it is desirable that the
melting temperature (Tm) of said stem be higher than the melting
temperature of the double-strand of the additive, but not so much
higher as to prevent formation of the double-stranded conformation
of the additive in a reasonable period of time when the temperature
of the reaction is decreased. In this case the calculated Tm of the
double-stranded portion of the additives was 59.degree. C., and the
calculated Tm of the stem nucleotides was 65.degree. C. These
calculations are based on reagent concentrations of 70 mM Na+, 3 mM
Mg++ at 50.degree. C. For the double-stranded portion the website
(http://dinamelt.bioinfo.rpi.edu/twostate.php) was used, and for
the stem the website
(http://frontend.bioinfo.rpi.edu/applications/mfold/cgi-bin/dna-form1.cgi-
) was used. In practice the actual Tm depends on the number of
interacting Dabcyls and can increase from the calculated Tm by
approximately 4.degree. C.
[0265] The following additives were used and sequences that are
complementary are underlined.
TABLE-US-00036 Additive SL02. (SEQ ID Nos 139 and 158) 5'
GCGCCTCACGTATCATTTTCATCTGACCAGGCGC (P) 3' Dabcyl
GCCTCCGTGCATAGTAAAAGTAGACTGGGGAGGC Additive SL03. (SEQ ID Nos 140
and 159) 5' GCGCCTCACGTATCATTTTCATCTGACCAGGCGC (P) 3' (P)
GCCTCCGTGCATAGTAAAAGTAGACTGGGGAGGC Dabcyl Additive SL04. (SEQ ID
Nos 141 and 160) 5' Dabcyl GCGCCTCACGTATCATTTTCATCTGACCAGGCGC (P)
3' (P) GCCTCCGTGCATAGTAAAAGTAGACTGGGGAGGC Dabcyl Additive SL05.
(SEQ ID Nos 142 and 161) 5' GCGCCTCACGTATCATTTTCATCTGACCAGGCGC
Dabcyl 3' Dabcyl GCCTCCGTGCATAGTAAAAGTAGACTGGGGAGGC Additive SL06.
(SEQ ID Nos 143 and 162) 5' Dabcyl
GCGCCTCACGTATCATTTTCATCTGACCAGGCGC (P) 3' Dabcyl
GCCTCCGTGCATAGTAAAAGTAGACTGGGGAGGC Additive SL07. (SEQ ID Nos 144
and 163) 5' Dabcyl GCGCCTCACGTATCATTTTCATCTGACCAGGCGC Dabcyl 3'
Dabcyl GCCTCCGTGCATAGTAAAAGTAGACTGGGGAGGC Additive SL08. (SEQ ID
Nos 145 and 164) 5' Dabcyl GCGCCTCACGTATCATTTTCATCTGACCAGGCGC
(C.sub.3) 3' Dabcyl GCCTCCGTGCATAGTAAAAGTAGACTGGGGAGGC Dabcyl
Additive SL09. (SEQ ID Nos 146 and 165) 5' Dabcyl
GCGCCTCACGTATCATTTTCATCTGACCAGGCGC Dabcyl 3' Dabcyl
GCCTCCGTGCATAGTAAAAGTAGACTGGGGAGGC Dabcyl
[0266] Each reaction was carried out in 25 .mu.l volume in
triplicate. The final reaction mixture contained 1.times.PCR buffer
(Invitrogen, Carlsbad, Calif.), 3 mM MgCl.sub.2, 250 nM dNTPs,
0.24.times.SYBR Green (Invitrogen, Carlsbad, Calif.), 1.25 units of
both Taq DNA polymerase and Taq DNA polymerase antibody
(Invitrogen, Carlsbad, Calif.). Separate reaction mixtures
contained 300 nM of each additive and no additive. After the
respective combinations of reaction ingredients were mixed and
prior to the isothermal incubation at 50.degree. C., all reactions
had the overlapping oligonucleotides 1 and 2 (Example 9) added at
approximately 100,000 copies each.
[0267] The thermal profile conditions for these reactions were as
follows: 50.degree. C. for 1 minute followed by incubation on ice
then the addition of primers to all reaction mixtures for final
concentrations of 50 nM limiting primer and 1 .mu.M excess primer.
This was followed by rapid heating to 95.degree. C. for 3 min, then
50 cycles at 98.degree. C./10 s and 72.degree. C./40 s. Each of the
samples was analyzed by SYBR Green fluorescence in real-time, and
at the end of the run each was subjected to melt curve analysis to
confirm that the reaction generated a single product peak of
88.degree. C. as expected for the double-stranded product of the
amplification reaction.
[0268] The melt-curve analysis with additives SL04, SL07, SL08 and
SL09 is shown in FIGS. 19A-19D. The lines identified by circle 210
in each figure are the replicates from the sample with Taq DNA
polymerase-plus-antibody. The lines identified by circles 211, 212,
213 and 214 are the replicates with additive SL04, SL07, SL08 and
SL09, respectively.
[0269] The results (see FIG. 19A) confirm that the antibody (circle
210) did not reduce mispriming, because of the presence of two
peaks, a low melting peak (i.e., incorrect product, 85.degree. C.)
and the correct product at higher peak (88.degree. C.). The results
with additives SL04, SL05, SL07 and SL08 show that each additive
greatly reduced the amount of incorrect product but did not
completely suppress it. FIG. 19D shows that additive SL09, which
has 4 Dabcyls, was able to completely suppress the production of
the incorrect product.
Example 17. Type II Mispriming and Polymerase Selectivity with
Additives Having Overhangs
[0270] We performed a LATE-PCR assay described in Example 3 using
the additives SL06, SL07, and SL09 (Example 16) at 200 nM, 400 nM,
and 600 nM concentrations. These additives contain two, three or
four Dabcyl modifiers, respectively.
[0271] The LATE-PCR amplifications were carried out in triplicate
in 25 .mu.l volume consisting of 1.times. Invitrogen PCR buffer
(Invitrogen, Carlsbad, Calif.), 3 mM MgCl.sub.2, 250 nM dNTPs, 50
nM limiting primer, 1000 nM excess primer, 0.24.times.SYBR Green
(Invitrogen, Carlsbad, Calif.), 1.25 units Platinum Taq DNA
polymerase (Invitrogen, Carlsbad, Calif.) with approximately 10000
single-stranded target A (matched) or T (mismatched). The thermal
profile conditions for these reactions were: 95.degree. C. for 3
minutes followed by 95.degree. C./5 s-62.degree. C./20 s-72.degree.
C./30 s for 60 cycles. For this and other assays containing two
targets, a control amplification is done using the excess primer,
which is perfectly complementary to both targets, and a control
limiting primer that is also perfectly complementary to both
targets, to ensure that the starting copy numbers of both targets
are the same, in which case the C.sub.T for both targets is the
same. (If the control amplifications reveal that the starting copy
numbers are not the same, one has two choices: either reformulate
or, if the C.sub.T difference is slight--as was the case in all
examples reported here, correct the observed C.sub.T values to
adjust for the difference.)
[0272] The results for selectivity (.DELTA. C.sub.T equals C.sub.T
for mismatched target minus C.sub.T for matched target) are shown
in Table 7.
TABLE-US-00037 TABLE 7 Additive Concentration, nM Selectivity,
.DELTA. C.sub.T SL06 (two Dabcyls) 200 1.3 400 0.8 600 3.2 SL07
(three Dabcyls) 200 0.8 400 2.4 600 2.6 SL09 (four Dabcyls) 200 2.8
400 4.2 600 6.8
Example 18. Inhibition of Primer-Independent 5' Exonuclease
Activity by Additives with Overhangs
[0273] We performed a LATE-PCR assay as described in detail in
Example 6 to determine the efficacy of inhibition of
primer-independent 5' exonuclease activity of DNA Taq polymerase
using additives with single-stranded overhangs of the type shown in
FIG. 18C.
[0274] Oscillation reactions were carried out in 25 .mu.l volume
consisting of 1.times.PCR buffer (Invitrogen, Carlsbad, Calif.), 3
mM MgCl.sub.2, 200 nM dNTPs, 1.25 units of Taq DNA polymerase
(Invitrogen, Carlsbad, Calif.), 200 nM of probe (Example 6), and
100 nM of target (Example 6). This reaction mixture was used
without any additive and with each additive at 200 nM, 400 nM, and
600 nM concentrations. A control reaction was run with the probe as
the only oligonucleotide in the reaction mixture. The additives
(see Example 16) included SL06, which has two Dabcyls; SL07, which
has 3 Dabcyls; and SL09, which has 4 Dabcyls. Reaction mixtures
were oscillated using the following thermal profile: 45.degree.
C./20 s, 60.degree. C./10 s for 45 cycles, followed by a melt
starting at 45.degree. C./30 secs with 1.degree. C. increments for
25 cycles. During cycling FAM fluorescence was acquired during the
60.degree. C./10 s segment of the thermal profile.
[0275] Exonuclease cleavage activity separates the probe's
fluorophore from the probe, thereby resulting in an increase in
fluorescence (FAM). Results with additive SL06 are reported in FIG.
20, wherein circle 220 identifies the probe-only control; circle
221 identifies the samples with probe and target but no additive;
circle 222 identifies the samples with probe, target and additive
SL06 at 200 nM concentration; circle 223 identifies the samples
with probe, target and additive SL06 at 400 nM concentration; and
circle 224 identifies the samples with probe, target and additive
SL06 at 600 nM concentration.
Example 19. Use of a Blocker to Create a 3' Terminal Mismatch
[0276] Example 4 above demonstrates the effect of additive mixtures
on Type II mispriming and polymerase selectivity in LATE-PCR
amplification for a target sequence that is perfectly complementary
to the limiting primer as opposed to a mismatched target containing
a single base-pair mismatch at the 3' terminal nucleotide of the
limiting primer. The present example demonstrates the use of an
oligonucleotide, referred to as a "blocker", to prevent the 3'
terminus of the limiting primer from hybridizing to a target that
is considered to be the mismatched target, that is, the one to be
selected against, when the mismatched nucleotide or nucleotides are
downstream from the limiting primer binding site. Targets, primers
and blocker for the type of assay are depicted generally in FIGS.
21A, 21B.
[0277] LATE-PCR amplifications were performed using a limiting
primer and an excess primer that were perfectly complementary to
the strands of a double-stranded first target and also perfectly
complementary to the strands of a double-stranded second target. It
was desired that the second target be amplified selectively
relative to the first target. The second target contained two
base-pair differences from the first target. The first base-pair
difference was downstream of the limiting primer binding site and
was included in the binding site for a blocker oligonucleotide that
was utilized to create a 3' terminal mismatch. The second base-pair
difference was downstream of both the limiting primer binding site
and the blocker binding site, and the downstream of the excess
primer binding site, and was used for probing. The blocker binding
site overlapped the limiting primer binding site at the 3' end of
the limiting primer, as shown in FIG. 21A.
[0278] The blocker used in the LATE-PCR assays was allele-specific
so that, due to the first base-pair difference between the targets,
it preferentially hybridized to the strand of the first target to
which the limiting primer hybridized (see FIG. 21A) rather than the
second target (see FIG. 21B). The 5' end of the blocker and the 3'
end of the limiting primer were both complementary to the same
bases on the first-target strand, but the melting temperature of
the blocker, Tm(B), to said strand was higher so that it would bind
first as the reaction temperature was lowered during amplification,
preventing the 3' terminus of the primer from hybridizing to the
first target, creating a 3' terminal mismatch with a perfectly
complementary primer. The 3' end of the blocker was itself blocked
to prevent extension during amplification. In this instance, the
blocker was dual labeled with a fluorophore (Cal Orange 560) on its
5' end and a Dabcyl quencher on its 3' end.
[0279] Both LATE-PCR assays also contained an allele-specific probe
that hybridizes to the excess primer strand generated from said
first target (to the extent that such strands are generated) at a
higher melting temperature, Tm(P1), than when hybridized to the
excess primer stranded generated from said second target Tm(P2). In
this instance the probe was a molecular beacon probe labeled on its
5' end with a Black Hole Quencher 2 (BHQ2) and on its 3' end with a
fluorophore (Quasar 670).
[0280] The binding of the limiting primer, the allele-specific
blocker, and the allele-specific probe to both said first and
second targets is illustrated generally in FIGS. 21A and 21B. To
effectively block the binding and extension of the limiting primer,
the blocker must overlap with the 3' end of the primer at least one
nucleotide. The 5' end of the blocker does not have to be a perfect
match to the target as long as the blocker binds at a higher
temperature than the limiting primer.
[0281] Reaction components and reaction conditions were as
follows:
TABLE-US-00038 Limiting Primer: (SEQ ID NO. 147) 5'
GCACTCTTGCCTACGCC Excess Primer: (SEQ ID NO. 148) 5'
CTGGTGGAGTATTTGATAGTG Allele-Specific Blocker: (SEQ ID NO. 149) 5'
Cal Org 560-GCCTACGCCACCAGCTCC-Dabcyl Molecular Beacon Probe: (SEQ
ID NO. 150) 5' BHQ2-CAAGAACATGTCACACATAATG-Quasar 670
Excess Primer Strand of Said First Target:
TABLE-US-00039 [0282] (SEQ ID NO. 151) 5'
CTGGTGGAGTATTTGATAGTGTATTAACCTTATGTGTGACAT
GTTCTAATATAGTCACATTTTCATTATTTTTATTATAAGGCCTGCTGAAA
ATGACTGAATATAAACTTGTGGTAGTTGGAGCTGGTGGCGTAGGCAAGAG TGC
Excess Primer Strand of Said Second Target (the first base pair
change, the change in the blocker binding site, is underlined; the
second base pair change, the change in the probe binding site,
bolded:
TABLE-US-00040 (SEQ ID NO. 152) 5'
CTGGTGGAGTATTTGATAGTGTATTAACCTTATGTGTCACAT
GTTCTAATATAGTCACATTTTCATTATTTTTATTATAAGGCCTGCTGAAAA
TGACTGAATATAAACTTGTGGTAGTTGGAGCTGATGGCGTAGGCAAGAGTG C
[0283] LATE-PCR amplifications were carried out in 25 ul volume
consisting of 1.times.PCR buffer (Invitrogen, Carlsbad, Calif.), 3
mM MgCl.sub.2, 200 nM dNTPs, 50 nM limiting primer, 1000 nM excess
primer, 0.24.times.SYBR Green (Invitrogen, Carlsbad, Calif.), 200
nM probe, 2 units of Taq DNA polymerase (Invitrogen, Carlsbad,
Calif.) with different concentrations of plasmid DNA (Epoch
Biolabs, Inc, Sugar Land, Tex.) that gave starting copy numbers in
the range of 10.sup.0 to 10.sup.6, obtained by serial dilution.
Amplification reactions were run in a duplicate set for each
condition in the presence or absence of 500 nM blocker and either
with no additive or with additive EP043 (Example 4) whose strand
concentrations (top/middle/bottom) were 33.3 nM, 200 nM and 166.7
nM.
[0284] The thermal profile conditions for these reactions were as
follows: 95.degree. C. for 3 min followed by 70 cycles of
95.degree. C./10 s, 70.degree. C./30 s, 62.degree. C./10 s,
72.degree. C./20 s, followed by a melt starting at 30.degree. C.
with 1.degree. C. increments at 30 s intervals to 90.degree. C.
SYBR Green signals were detected in real time during the primer
extension portion of all PCR cycles. and the C.sub.T values were
determined. As the assays were run in duplicate, the two C.sub.T
values at each concentration of target were averaged. FIG. 22A
presents C.sub.T values as a function of target concentration for
assays performed without the blocker, both with and without the
EP043 additive. FIG. 22B presents C.sub.T values as a function of
target concentration for assays performed with the blocker, both
with and without the additive.
[0285] Turning to FIG. 22A, filled squares are C.sub.T values of
samples with the first target (to be discriminated against through
operation of the blocker) at various amounts of starting target
(copy number), no blocker and no additive, and the C.sub.T values
are connected by line 250; and filled triangles are C.sub.T values
of samples with the second target (to be preferentially amplified,
because it is mismatched to the blocker), no blocker and no
additive, and the C.sub.T values are connected by line 251. Also in
FIG. 22A, open squared are C.sub.T values of samples with the first
target and additive but no blocker, and the C.sub.T values are
connected by line 252; and open triangles are C.sub.T values of
samples with the first target and additive but no blocker, and the
C.sub.T values are connected by line 253.
[0286] Turning to FIG. 22B, filled squares are C.sub.T values of
samples with the first target and blocker but no additive, and the
C.sub.T values are connected by line 254 (which is extrapolated to
low copy numbers); and open squares are C.sub.T values of samples
with the second target and blocker but no additive, and the C.sub.T
values are connected by line 255 (which is extrapolated to low copy
numbers). Also in FIG. 22B, filled circles are C.sub.T values of
samples with the first target, blocker and additive, and the
C.sub.T values are connected by line 256 (which is extrapolated);
and open circles are C.sub.T values of samples with the second
target, blocker and additive, and the C.sub.T values are connected
by line 257 (which is extrapolated).
[0287] Selectivity against the created 3' terminal mismatch in the
absence of additive, in this case additive EP043, is the difference
between the threshold cycle (C.sub.T) of the signal from
amplification of said first target at a first concentration and the
C.sub.T of the signal from amplification of said second target at
said first concentration, and is designated (.DELTA.C.sub.TB).
Selectivity due to additive EP043 is the double-C.sub.T difference,
designated (A.DELTA.C.sub.T), calculated as
.DELTA.C.sub.TA-.DELTA.C.sub.TB, where .DELTA.C.sub.TA is measured
as the difference between the C.sub.T values of said first target
and said second target at a second concentration in the presence of
both the additive and the blocker, wherein the C.sub.T value of
said second target is the same for the reaction containing just the
blocker at said first concentration and the reaction containing
both the blocker and the additive at said second concentration.
[0288] FIG. 22A shows that without the blocker there was no
selectivity for either target, as we expected due to the lack of a
3' terminal mismatch between the limiting primer and either target.
The data show that without additive EP043, the assay is efficient,
as lines 250 and 251 both have slopes of about 3.5. With additive
EP043, however, the slopes of lines 252 and 253 are both about 3.9,
thereby demonstrating that EP043 decreased PCR amplification for
both targets.
[0289] For the effect of the additive on selectivity, one turns to
FIG. 22B. With the allele-specific blocker but no additive, a
mismatched 3' end of the limiting primer is created to said first
target, which gives a first selectivity that shows as a
.DELTA.C.sub.T between the C.sub.T of said first target and the
C.sub.T of said second target. As shown by lines 254, 255, this
.DELTA.C.sub.T is a function of the concentration of target. With
both the blocker and additive EP043, there is another selectivity
due to the additive. Because of the inhibition of the PCR
amplification reaction by EP043, the C.sub.T difference between the
first target and the second target in the presence of EP043
actually includes two factors: 1) the selectivity due to the
allele-specific blocker compounded with selectivity due to EP043;
and 2) the progressive decrease in efficiency due to EP043
inhibition of PCR.
[0290] In order to distinguish and quantify the contribution of
these two factors, we did the following with the information in
FIG. 22B. At a certain target concentration (copy number), the
C.sub.T of a sample with second target, blocker and additive has
the value of point A on line 257, and the C.sub.T of a sample with
first target, blocker and additive has the value of point D on line
256. These C.sub.T values are 35 and 62, respectively, giving
sample a .DELTA.C.sub.TA of 27. However, the C.sub.T value of point
A is the C.sub.T value of point B on line 255 (same target, that
is, second target, without additive EP043). The concentration of
second target at point B is the effective target concentration in
the presence of EP043 because of its inhibition of amplification.
At the concentration of point B, the .DELTA.C.sub.TB is the segment
BC, which is 17. Without additive EP043, this selectivity between
said first target and said second target is due to the
allele-specific blocker. In order to remove the inhibitory effect
of the additive EP043 from .DELTA.C.sub.TA, the .DELTA.C.sub.TB at
said first concentration of target, 17, is subtracted from the
.DELTA.C.sub.TA at the said second concentration of target, 27.
This gives the .DELTA..DELTA.CT of 10. The .DELTA..DELTA.CT of 10
is the selectivity effect of additive EP043 in the presence of
induced-Type II mis-priming at the target concentration of point A.
As can be seen from the FIG. 22B, the magnitude of the selectivity
effect of additive EP043 depends on the target concentration,
because lines 254, 255, 256, 257 are not parallel to one another.
The lower the target concentration, the greater is the selectivity
effect of the additive. This is the case, because more thermal
cycles are required to detect the product.
Example 20. Suppression of Type I Mispriming on Ice Prior to
Amplification
[0291] The assay reported here was carried out as described in
Example 9 with the following exceptions: (a) the incubation step at
50.degree. C. was for 1 minute; (b) the number of amplifications
cycles was reduced to 50; (c) EP010, described in Example 10, was
used as the additive; (d) the concentration of the additive was 300
nM.
[0292] SYBR Green fluorescence of the double-stranded products
generated in these amplification reactions is shown in FIG. 23A,
where circle 260 identifies the replicates from the sample with Taq
DNA polymerase only, circle 261 identifies the replicates from the
sample with Taq DNA polymerase and antibody added immediately after
the isothermal extension step, circle 262 identifies the replicates
from the sample with Taq DNA polymerase-plus-antibody present
during the isothermal extension step.
[0293] FIG. 23A shows the effect of antibody on extension of the
overlapping oligonucleotides. The replicate samples without any
antibody (circle 260) had a C.sub.T value of 22, and, therefore,
extension of the overlapping templates was efficient. In contrast,
extension of the overlapping templates is extensively inhibited
when the antibody is added prior to the 50.degree. C. incubation
step (circle 262). When addition of the antibody is delayed until
the end of the 50.degree. C. incubation (circle 261), the C.sub.T
is higher than in the no-antibody case (circle 260). This means
that most, but not all, of the possible overlapping templates were
extended during the 1-minute incubation at 50.degree. C. Additional
overlapping templates are extended during the subsequent incubation
on ice.
[0294] FIG. 23B shows the effect of additive EP010 on extension of
the overlapping oligonucleotides. Replicates with EP10 (circle 263)
received additive EP010 either prior to incubation at 50.degree. C.
or after incubation at 50.degree. C. The results (combined as
circle 263) show no difference in amplification when EP010 is added
before or after the incubation step. This demonstrates that EP010
does not inhibit polymerization during the incubation at the
50.degree. C. step. However, the C.sub.T values are slightly higher
than C.sub.T replicates that received the antibody at the end of
the 50.degree. C. step (circle 261). This demonstrates that
addition of additive EP010 is slightly more effective than the
antibody in inhibiting the extension of the overlapping
oligonucleotides on ice.
[0295] FIG. 23C shows the SYBR Green melt curves of the
double-strand product generated in replicates with Taq DNA
polymerase only (circle 264) and in replicates with Taq DNA
polymerase and antibody added immediately after the extension step
(circle 265). FIG. 23D shows the SYBR Green melt curve of the
double-stranded product generated in replicates with Taq DNA
polymerase-plus-antibody during extension step (circle 266). FIG.
23E shows the SYBR Green melt curves (circle 267) of the
double-stranded product generated in replicates that received
additive EP010 either prior to incubation at 50.degree. C. (circle
267) or after incubation at 50.degree. C. (circle 268, only two
replicates, as one was lost).
[0296] FIG. 23C demonstrates that omission of the antibody entirely
(circle 264) or omission of the antibody during incubation of the
templates at 50.degree. C. (circle 265) results in extension and
subsequent amplification of a fairly clean product that melts at
88.degree. C. FIG. 23D demonstrates, in contrast, that inclusion of
the antibody during the incubation at 50.degree. C. (circle 266)
results in a mixture of products with peaks at 88.degree. C. and
85.degree. C. FIG. 23E demonstrates that addition of the EP010
additive either before or after the 50.degree. C. step results
amplification of a clean double-stranded product with a sharp
melting peak at 88.degree. C. The melt curves in FIG. 23E also show
the presence of a small broad peak at 67-71.degree. C. This peak is
due to melting of the double-stranded form of EP010. It shows that
the double-stranded form is no longer present at 72.degree. C., the
temperature at which extension was carried out during the
amplification phase of these reactions and in Example 9. In
contrast, the additives used in Example 9 were found to have melt
peaks (not shown) that are higher than that of EP010.
[0297] The specific embodiments described above are not exhaustive
and should not be construed as limiting the claims. Various
modifications of these embodiments can be made without departing
from the concepts described herein. Such modifications are intended
to fall within the scope of the claims.
Sequence CWU 1
1
165122DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 1cctggattat gcctggcacc at
22223DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 2ccttgatgac gcttctgtat cta
23384DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 3cctggattat gcctggcacc attaaagaaa atatcatctt
tggtgtttcc tatgatgaat 60atagatacag aagcgtcatc aaag
84416DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 4cacgacctcg ccgacc
16516DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 5cacgacctcg ctgacc
16616DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 6cacgacctcg ctgacc
16716DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 7cacgacctcg ctgacc
16816DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 8cacgacctcg ctgacc
16922DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 9ggagcaaaat agcaatgagg ta
221022DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 10ggtcagatga aaatgatacg tg
221122DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 11ggtcagatga aaatgatacg tg
221222DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 12gaaataaaat aaaaataaaa ta
22138DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 13cagccggc 8148DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 14ccgccggc 81511DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 15gcgtacgcag g 111611DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 16gcgtacgaag g 111722DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 17ggagcaaaat agcaatgagg ta 221822DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 18tgagagatga aaatgatcga gt 221922DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 19ggtcagatga aaatgatacg tg 222027DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 20aaattgcgtc attgtttcac agggcca 272120DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 21aatctgggtg gtggtcatac
2022192DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 22aatctgggtg gtggtcatac aggtcatcac tgtaaaattc
tttgaacttt tctgtatata 60tctttgaaaa ttttggaaaa aaaatgttgg aaaacttaaa
aggctgttgc tttgctcata 120ttggcggtac atatacaaaa gtggaaagga
tgagattgat tggcatggcc ctgtgaaaca 180atgacgcaat tt
1922322DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 23ggagcaaaat agcaatgagg ta
222422DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 24ggagcaaaat agcaatgagg ta
222522DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 25ggagcaaaat agcaatgagg ta
222622DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 26ggagcaaaat agcaatgagg ta
222722DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 27ggagcaaaat agcaatgagg ta
222822DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 28ggagcaaaat agcaatgagg ta
222922DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 29ggagcaaaat agcaatgagg ta
223022DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 30ggagcaaaat agcaatgagg ta
223122DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 31ggagcaaaat agcaatgagg ta
223222DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 32ggagcaaaat agcaatgagg ta
223322DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 33ggagcaaaat agcaatgagg ta
223427DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 34cgtaagatta caatggcagg ctccagt
273524DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 35gcccaagttt tatcgttctt ctca
243695DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 36cgtaagatta caatggcagg ctccagaagg ttctaagtgc
catgatacaa gcttcccaat 60tactaagtat gctgagaaga acgataaaac ttggg
953798DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 37cgtaagatta caatggcagg ctccagtagg ttctaagtgc
catgatacaa gcttcccaat 60tactaagtat gctgagaaga acgataaaac ttgggcaa
983816DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 38cacgacctcg ctgacc
163916DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 39cacgacctcg ctgacc
164022DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 40ggtcagatga aaatgatacg tg
224122DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 41ggtcagatga aaatgatacg tg
224222DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 42ggtcagatga aaatgatacg tg
224322DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 43ggtcagatga aaatgatacg tg
224422DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 44cctcgtctga tcgtgactcc at
224522DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 45cctcgtctga tcgtgactcc at
224622DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 46cctcgtctga tcgtgactcc at
224722DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 47cctcgtctga tcgtgactcc at
224822DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 48ggagcagact agcactgagg ta
224922DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 49ggagcagact agcactgagg ta
225026DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 50tgtcatcttc tgtcccttcc cagaaa
265129DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 51actgtcccag aatgcaagaa gcccagacg
295215DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic probe" 52ccgtagctgc cctgg 155328DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 53gcacagttac agtattccag cagactca 285426DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 54tcagtggtgg cagtggtagt ggtggc 265520DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
probe" 55tcagtggtgg cagtggtaga 205622DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 56ggtcagatga aaatgatacg tg 225717DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
probe" 57ccatgataca agcttcc
175841DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 58acttagtaat tgggaagctt gtatcatggc acttagaacc t
415940DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 59cgcggcgtca ggcatatagg
ataccgggac agacgccgcg 406022DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 60ggtcagatga aaatgatacg tg
2261549DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 61gcccggagcg aggagagtag cactcttgtg cgggatattg
atttcacgga ggatggtggt 60caagggaccc ctatctgagg ggggtcatcc atggggacga
gaagggattt gactgtaatg 120tgctatgtac ggtaaatggc tttatgtact
atgtactgtt aagggtgggt aggtttgttg 180gtatcctagt gggtgagggg
tggctttgga gttgcagttg atgtgtgata gttgagggtt 240gattgctgta
cttgcttgta agcatgggga gggggttttg atgtggattg ggtttttatg
300tactacaggt ggtcaagtat ttatggtacc gtacaatatt catggtggct
ggcagtaatg 360tacgaaatac atagcggttg ttgatgggtg agtcaatact
tgggtggtac ccaaatctgc 420ttccccatga aagaacagag aatagtttaa
attagaatct tagctttggg tgctaatggt 480ggagttaaag actttttctc
tgatttgtcc ttggaaaaag gttttcatct ccggtttaca 540agactggtg
5496228DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 62gcccggagcg aggagagtag cactcttg
286326DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 63caccagtctt gtaaaccgga gatgaa
2664525DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 64acaggtctat caccctatta accactcacg ggagctctcc
atgcatttgg tattttcgtc 60tggggggtat gcacgcgata gcattgcgag acgctggagc
cggagcaccc tatgtcgcag 120tatctgtctt tgattcctgc ctcatcctat
tatttatcgc acctacgttc aatattacag 180gcgaacatac ttactaaagt
gtgttaatta attaatgctt gtaggacata ataataacaa 240ttgaatgtct
gcacagccac tttccacaca gacatcataa caaaaaattt ccaccaaacc
300ccccctcccc cgcttctggc cacagcactt aaacacatct ctgccaaacc
ccaaaaacaa 360agaaccctaa caccagccta accagatttc aaattttatc
ttttggcggt atgcactttt 420aacagtcacc ccccaactaa cacattattt
tcccctccca ctcccatact actaatctca 480tcaatacaac ccccgcccat
cctacccagc acacacacac cgctg 5256526DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 65agcggtgtgt gtgtgctggg taggat 266628DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 66acaggtctat caccctatta accactca
2867634DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 67aggttgcggt ctgttagtag tatagtgatg ccagcagcta
ggactgggag agataggaga 60agtaggactg ctgtgattag gacggatcag acgaagaggg
gcgtttggta ttgggttatg 120gcagggggtt ttatattgat aattgttgtg
atgaaattga tggcccctaa gatagaggag 180acacctgcta ggtgtaagga
gaagatggtt aggtctacgg aggctccagg gtgggagtag 240ttccctgcta
agggagggta gactgttcaa cctgttcctg ctccggcctc cactatagca
300gatgcgagca ggagtaggag agagggaggt aagagtcaga agcttatgtt
gtttatgcgg 360ggaaacgcca tatcgggggc accgattatt aggggaacta
gtcagttgcc aaagcctccg 420attatgatgg gtattactat gaagaagatt
attacaaatg catgggctgt gacgataacg 480ttgtagatgt ggtcgttacc
tagaaggttg cctggctggc ccagctcggc tcgaataagg 540aggcttagag
ctgtgcctag gactccagct catgcgccga ataataggta tagtgttcca
600atgtctttgt ggtttgtaga gaatagtcaa cggt 6346836DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 68aggttgcggt ctgttagtag tatagtgatg ccagca
366927DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 69accgttgact attctctaca aaccaca
2770731DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 70atggagggtt cttctactat taggactttt cgcttcgaag
cgaaggcttc tcaaatcatg 60aaaattatta atattactgc tgttagagaa atgaatgagc
ctacagatga taggatgttt 120catgtggtgt atgcatcggg gtagtccgag
taacgtcggg gcattccgga taggccgaga 180aagtgttgtg ggaagaaagt
tagatttacg ccgatgaata tgatagtgaa atggattttg 240gcgtaggttt
ggtctagggt gtagcctgag aataggggaa atcagtgaat gaagcctcct
300atgatggcaa atacagctcc tattgatagg acatagtgga agtgggctac
aacgtagtac 360gtgtcgtgta gtacgatgtc tagtgatgag tttgctaata
caatgccagt caggccacct 420acggtgaaaa gaaagatgaa tcctagggct
cagagcactg cagcagatca tttcatattg 480cttccgtgga gtgtggcgag
tcagctaaat actttgacgc cggtggggat agcgatgatt 540atggtagcgg
aggtgaaata tgctcgtgtg tctacgtcta ttcctactgt aaatatatgg
600tgtgctcaca cgataaaccc taggaagcca attgatatca tagctcagac
catacctatg 660tatccaaatg gttctttttt tccggagtag taagttacaa
tatgggagat tattccgaag 720cctggtagga t 7317134DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 71atggagggtt cttctactat taggactttt cgct 347226DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 72atcctaccag gcttcggaat aatctc
2673586DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 73agggtaaata cgggccctat ttcaaagatt tttaggggaa
ttaattctag gacgatgggc 60atgaaactgt ggtttgctcc acagatttca gagcattgac
cgtagtatac ccccggtcgt 120gtagcggtga aagtggtttg gtttagacgt
ccgggaattg catctgtttt taagcctaat 180gtggggacag ctcatgagtg
caagacgtct tgtgatgtaa ttattatacg aatgggggct 240tcaatcggga
gtactactcg attgtcaacg tcaaggagtc gcaggtcgcc tggttctagg
300aataatgggg gaagtatgta ggagttgaag attagtccgc cgtagtcggt
gtactcgtag 360gttcagtacc attggtggcc aattgatttg atggtaaggg
agggatcgtt gacctcgtct 420gttatgtaaa ggatgcgtag ggatgggagg
gcgatgagga ctaggatgat ggcgggcagg 480atagttcaga cggtttctat
ttcctgagcg tctgagatgt tagtattagt tagttttgtt 540gtgagtgtta
ggaaaagggc atacaggact aggaagcaga taagga 5867439DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 74agggtaaata cgggccctat ttcaaagatt tttagggga
397528DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 75tccttatctg cttcctagtc ctgtatgc
2876859DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 76cctctaaatc accacgatca aaaggaacaa gcatcaagca
cgcagcaatg cagctcaaaa 60cgcttagcct agccacaccc ccacgggaaa cagcagtgat
taacctttag caataaacga 120aagtttaact aagctatact aaccccaggg
ttggtcaatt tcgtgccagc caccgcggtc 180acacgattaa cccaagtcaa
tagaagccgg cgtaaagagt gttttagatc accccctccc 240caataaagct
aaaactcacc tgagttgtaa aaaactccag ttgacacaaa atagactacg
300aaagtggctt taacatatct gaacacacaa tagctaagac ccaaactggg
attagatacc 360ccactatgct tagccctaaa cctcaacagt taaatcaaca
aaactgctcg
ccagaacact 420acgagccaca gcttaaaact caaaggacct ggcggtgctt
catatccctc tagaggagcc 480tgttctgtaa tcgataaacc ccgatcaacc
tcaccacctc ttgctcagcc tatataccgc 540catcttcagc aaaccctgat
gaaggctaca aagtaagcgc aagtacccac gtaaagacgt 600taggtcaagg
tgtagcccat gaggtggcaa gaaatgggct acattttcta ccccagaaaa
660ctacgatagc ccttatgaaa cttaagggtc gaaggtggat ttagcagtaa
actaagagta 720gagtgcttag ttgaacaggg ccctgaagcg cgtacacacc
gcccgtcacc ctcctcaagt 780atacttcaaa ggacatttaa ctaaaacccc
tacgcattta tatagaggag acaagtcgta 840acatggtaag tgtactgga
8597737DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 77tccagtacac ttaccatgtt acgacttgtc
tcctcta 377828DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 78cctctaaatc accacgatca
aaaggaac 2879447DNAUnknownsource/note="Description of Unknown
Target polynucleotide" 79tgtgagggtg ggactgtcta ctgagtagcc
tcctcagatt cattgaacta ggtctgtccc 60aatgtatggg atggcggata gtaagtttgt
aattactgtg gcccctcaga atgatatttg 120gcctcacggg aggacatagc
ctatgaaggc tgttgctata gttgcaagca ggaggataat 180gccgatgttt
caggtttctg agtagagaaa tgatccgtaa tataggcctc gcccgatgtg
240taggaagagg cagataaaga atattgaggc gccattggcg tgaaggtagc
ggatgattca 300gccataattt acgtctcgag tgatgtgggc gattgatgaa
aaggcggttg aggcgtctgg 360tgagtagtgc atggctagga atagtcctgt
ggtgatttgg aggatcaggc aggcgccaag 420gagtgagccg aagtttcatc atgcgga
4478030DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 80tgtgagggtg ggactgtcta ctgagtagcc
308123DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 81tccgcatgat gaaacttcgg ctc
2382434DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 82actccacctc ctattcttgc acgaaacggg atcaaacaac
cccctaggaa tcacctccca 60ttccgataaa atcaccttcc acccttacta cacaatcaaa
gacgccctcg gcttacttct 120cttccttctc tccttaatga cattaacact
attctcacca gacctcctag gcgacccaga 180caattatacc ctagccaacc
ccttaaacac ccctccccac atcaagcccg aatgatattt 240cctattcgcc
tacacaattc tccgatccgt ccctaacaaa ctaggaggcg tccttgccct
300attactatcc atcctcatcc tagcaataat ccccatcctc catatatcca
aacaacaaag 360cataatattt cgcccactaa gccaatcact ttattgactc
ctagccgcag acctcctcat 420tctaacctga atcg 4348334DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 83cgattcaggt tagaatgagg aggtctgcgg ctag 348424DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 84actccacctc ctattcttgc acga
2485638DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 85cataagaaca gggaggttag aagtagggtc ttggtgacaa
aatatgttgt gtagagttca 60ggggagagtg cgtcatatgt tgttcctagg aagattgtag
tggtgagggt gtttattata 120ataatgtttg tgtattcggc tatgaagaat
agggcgaagg ggcctgcggc gtattcgatg 180ttgaagcctg agactagttc
ggactcccct tcggcaaggt cgaagggggt tcggttggtc 240tctgctagtg
tggagataaa tcatattatg gccaagggtc atgatggcag gagtaatcag
300aggtgttctt gtgttgtgat aagggtggag aggttaaagg agccacttat
tagtaatgtt 360gatagtagaa tgatggctag ggtgacttca tatgagattg
tttgggctac tgctcgcagt 420gcgccgatca gggcgtagtt tgagtttgat
gctcaccctg atcagaggat tgagtaaacg 480gctaggctag aggtggctag
aataaatagg aggcctaggt tgaggttgac cagggggttg 540ggtatgggga
ggggggttca tagtagaaga gcgatggtga gagctaaggt cggggcggtg
600atgtagaggg tgatggtaga tgtggcgggt tttagggg 6388635DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 86cataagaaca gggaggttag aagtagggtc ttggt
358719DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 87cccctaaaac ccgccacat
1988870DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 88agtgtgattg aggtggagta gattaggcgt aggtagaagt
agaggttaag gagggtgatg 60gtggctatga tggtggggat gatgaggcta ttgttttttg
tgaattcttc gataatggcc 120catttgggca aaaagccggt tagcgggggc
aggcctccta gggagaggag ggtggatgga 180attaagggtg ttagtcatgt
tagcttgttt caggtgcgag atagtagtag ggtcgtggtg 240ctggagttta
agttgagtag taggaatgcg gtagtagtta ggataatata aatagttaaa
300ttaagaatgg ttatgttagg gttgtacggt agaactgcta ttattcatcc
tatgtgggta 360attgaggagt atgctaagat tttgcgtagc tgggtttggt
ttaatccacc tcaactgcct 420gctatgatgg ataagattga gagagtgagg
agaaggctta cgtttagtga gggagagatt 480tggtatatga ttgagatggg
ggctagtttt tgtcatgtga gaagaagcag gccggatgtc 540agaggggtgc
cttgggtaac ctctgggact cagaagtgaa agggggctat tcctagtttt
600attgctatag ctattatgat tattaatgat gagtattgat tggtagtatt
ggttatggtt 660cattgtccgg agagtatatt gttgaagagg atagctatta
gaaggattat ggatgcggtt 720gcttgcgtga ggaaatactt gatggcagct
tctgtggaac gagggtttat ttttttggtt 780agaactggaa taaaagctag
catgtttatt tctaggccta ctcaggtaaa aaatcagtgc 840gagcttagcg
ctgtgatgag tgtgcctgca 8708940DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 89agtgtgattg aggtggagta gattaggcgt aggtagaagt
409029DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 90tgcaggcaca ctcatcacag cgctaagct
2991497DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 91aacacaacca cccacagcct aattattagc atcatccctc
tactattttt taaccaaatc 60aacaacaacc tatttagctg ttccccaacc ttttcctccg
accccctaac aacccccctc 120ctaatactaa ctacctgact cctacccctc
acaatcatgg caagccaacg ccacttatcc 180agtgaaccac tatcacgaaa
aaaactctac ctctctatac taatctccct acaaatctcc 240ttaattataa
cattcacagc cacagaacta atcatatttt atatcttctt cgaaaccaca
300cttatcccca ccttggctat catcacccga tgaggcaacc agccagaacg
cctgaacgca 360ggcacatact tcctattcta caccctagta ggctcccttc
ccctactcat cgcactaatt 420tacactcaca acaccctagg ctcactaaac
attctactac tcactctcac tgcccaagaa 480ctatcaaact cctgagc
4979234DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 92gctcaggagt ttgatagttc ttgggcagtg agag
349329DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 93aacacaacca cccacagcct aattattag
2994493DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 94gtggtgggtg agtgagcccc attgtgttgt ggtaaatatg
tagagggagt atagggctgt 60gactagtatg ttgagtcctg taagtaggag agtgatattt
gatcaggaga acgtggttac 120tagcacagag agttctccca gtaggttaat
agtggggggt aaggcgaggt tagcgaggct 180tgctagaagt catcaaaaag
ctattagtgg gagtagagtt tgaagtcctt gagagaggat 240tatgatgcga
ctgtgagtgc gttcgtagtt tgagtttgct aggcagaata gtaatgagga
300tgtaagcccg tgggcgatta tgagaatgac tgcgccggtg aagcttcagg
gggtttggat 360gagaatggct gttactacga gggctatgtg gctgattgaa
gagtatgcaa tgagcgattt 420taggtctgtt tgtcgtaggc agatggagct
tgttataatt atgcctcata gggatagtac 480aaggaagggg tag
4939527DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 95gtggtgggtg agtgagcccc attgtgt
279629DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 96ctaccccttc cttgtactat ccctatgag
299732DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 97taaagcccgg agcgaggaga gtagcactct tg
329828DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 98aaagcggtgt gtgtgtgctg ggtaggat
289938DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 99aaaggttgcg gtctgttagt agtatagtga
tgccagca 3810036DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 100aaatggaggg ttcttctact
attaggactt ttcgct 3610141DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 101taagggtaaa tacgggccct atttcaaaga tttttagggg a
4110239DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 102aatccagtac acttaccatg ttacgacttg
tctcctcta 3910332DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 103aatgtgaggg tgggactgtc
tactgagtag cc 3210436DNAArtificial Sequencesource/note="Description
of Artificial Sequence Synthetic primer" 104aacgattcag gttagaatga
ggaggtctgc ggctag 3610537DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 105aacataagaa cagggaggtt agaagtaggg tcttggt
3710642DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 106aaagtgtgat tgaggtggag tagattaggc
gtaggtagaa gt 4210736DNAArtificial Sequencesource/note="Description
of Artificial Sequence Synthetic primer" 107aagctcagga gtttgatagt
tcttgggcag tgagag 3610829DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 108tagtggtggg tgagtgagcc ccattgtgt 2910962DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 109ttgcacgaga gccagctcgt caggtagtca ccagtacagt
ccgcttgtgt caagacagca 60cg 6211075DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 110cagcagcaga cagtgcactc gtcactcact aaccgctatt
cgagttcgcg tgctgtcttg 60acacaagcgg actgt 7511135DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 111ttgcacgaga gccagctcgt caggtagtca ccagt
3511225DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 112cagcagcaga cagtgcactc gtcac
2511322DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 113ggagcagact agcactgagg ta
2211431DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 114ctccagcccg gcacgctcac gtgacagacc g
3111524DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 115ccggtggtcg ccgcgatcaa ggag
2411621DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic probe" 116gcgggttgtt ctggtccatg a
21117150DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 117ccggtggtcg ccgcgatcaa ggagttcttc ggcaccagcc
agctgagcca attcatggac 60cagaacaacc cgctgtcggg gttgacccac aagcgccgac
tgtcggcgct ggggcccggc 120ggtctgtcac gtgagcgtgc cgggctggag
15011829DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 118tatcgtcaag gcactcttgc
ctacgcctt 2911932DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 119gtactggtgg agtatttgat
agtgtattaa cc 32120158DNAUnknownsource/note="Description of Unknown
Target polynucleotide" 120gtactggtgg agtatttgat agtgtattaa
ccttatgtgt gacatgttct aatatagtca 60cattttcatt atttttatta taaggcctgc
tgaaaatgac tgaatataaa cttgtggtag 120ttggagctga tggcgtaggc
aagagtgcct tgacgata 158121158DNAUnknownsource/note="Description of
Unknown Target polynucleotide" 121gtactggtgg agtatttgat agtgtattaa
ccttatgtgt gacatgttct aatatagtca 60cattttcatt atttttatta taaggcctgc
tgaaaatgac tgaatataaa cttgtggtag 120ttggagctgg tggcgtaggc
aagagtgcct tgacgata 15812228DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 122gcacagttac agtattccag cagactca 2812326DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 123tcagtggtgg cagtggtagt ggtggc
2612476DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 124gcacagttac agtattccag cagactcaaa tacaagaacc
tactgctaat gccaccacta 60ccactgccac cactga 7612520DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
probe" 125tcagtggtgg cagtggtaga 2012620DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 126ctttggcacc agaggtgagc 2012728DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 127ggtgcgtggg tcccagtctg cagttaag
2812865DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 128ggtgcgtggg tcccagtctg cagttaaggg ggcaggagtg
gcgctgctca cctctggtgc 60caaag 6512914DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
probe" 129gcaggagtgg cgct 1413032DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 130aatgtgaggg tgggactgtc tactgagtag cc 3213122DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 131tacctcagtg ctagtctgct cc 2213237DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 132tccagtacac ttaccatgtt acgacttgtc tcctcta
3713325DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 133agttcaccct ctaaatcacc acgat
2513425DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 134atcgttgtgg tatagagggt gaact
25135865DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 135agttcaccct ctaaatcacc acgatcaaaa ggaacaagca
tcaagcacgc agcaatgcag 60ctcaaaacgc ttagcctagc cacaccccca cgggaaacag
cagtgattaa cctttagcaa 120taaacgaaag tttaactaag ctatactaac
cccagggttg gtcaatttcg tgccagccac 180cgcggtcaca cgattaaccc
aagtcaatag aagccggcgt aaagagtgtt ttagatcacc 240ccctccccaa
taaagctaaa actcacctga gttgtaaaaa actccagttg acacaaaata
300gactacgaaa gtggctttaa catatctgaa cacacaatag ctaagaccca
aactgggatt 360agatacccca ctatgcttag ccctaaacct caacagttaa
atcaacaaaa ctgctcgcca 420gaacactacg agccacagct taaaactcaa
aggacctggc ggtgcttcat atccctctag 480aggagcctgt tctgtaatcg
ataaaccccg atcaacctca ccacctcttg ctcagcctat 540ataccgccat
cttcagcaaa ccctgatgaa ggctacaaag taagcgcaag tacccacgta
600aagacgttag gtcaaggtgt agcccatgag gtggcaagaa atgggctaca
ttttctaccc 660cagaaaacta cgatagccct tatgaaactt aagggtcgaa
ggtggattta gcagtaaact 720aagagtagag tgcttagttg aacagggccc
tgaagcgcgt acacaccgcc cgtcaccctc 780ctcaagtata cttcaaagga
catttaacta aaacccctac gcatttatat agaggagaca 840agtcgtaaca
tggtaagtgt actgg 86513626DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 136gacttgcgcg ttacgacagg ccaatc 2613720DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 137tgaatgcggc taatcccaac 2013815DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
probe" 138aaccacctgc ccctt 1513934DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 139gcgcctcacg tatcattttc atctgaccag gcgc
3414034DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 140gcgcctcacg tatcattttc
atctgaccag gcgc 3414134DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 141gcgcctcacg tatcattttc atctgaccag gcgc
3414234DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 142gcgcctcacg tatcattttc
atctgaccag gcgc 3414334DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 143gcgcctcacg
tatcattttc atctgaccag gcgc 3414434DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 144gcgcctcacg tatcattttc atctgaccag gcgc
3414534DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 145gcgcctcacg tatcattttc
atctgaccag gcgc 3414634DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 146gcgcctcacg tatcattttc atctgaccag gcgc
3414717DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 147gcactcttgc ctacgcc
1714821DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 148ctggtggagt atttgatagt g
2114918DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 149gcctacgcca ccagctcc
1815022DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic probe" 150caagaacatg tcacacataa tg
22151145DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 151ctggtggagt atttgatagt gtattaacct tatgtgtgac
atgttctaat atagtcacat 60tttcattatt tttattataa ggcctgctga aaatgactga
atataaactt gtggtagttg 120gagctggtgg cgtaggcaag agtgc
145152145DNAUnknownsource/note="Description of Unknown Target
polynucleotide" 152ctggtggagt atttgatagt gtattaacct tatgtgtcac
atgttctaat atagtcacat 60tttcattatt tttattataa ggcctgctga aaatgactga
atataaactt gtggtagttg 120gagctgatgg cgtaggcaag agtgc
1451538DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 153cgccgcgc 815422DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 154tgagagatga aaatcatcga gt 2215522DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 155actcgatcat ttttcactct ca 2215622DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 156tacctcagtg ttagtctggt cc 2215722DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 157tacctcagtg ttagtctggt cc 2215834DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 158cggaggggtc agatgaaaat gatacgtgcc tccg
3415934DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 159cggaggggtc agatgaaaat
gatacgtgcc tccg 3416034DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 160cggaggggtc agatgaaaat gatacgtgcc tccg
3416134DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 161cggaggggtc agatgaaaat
gatacgtgcc tccg 3416234DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 162cggaggggtc agatgaaaat gatacgtgcc tccg
3416334DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 163cggaggggtc agatgaaaat
gatacgtgcc tccg 3416434DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 164cggaggggtc agatgaaaat gatacgtgcc tccg
3416534DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 165cggaggggtc agatgaaaat
gatacgtgcc tccg 34
* * * * *
References