U.S. patent application number 15/384168 was filed with the patent office on 2017-08-17 for methods and compositions for pcr using blocked and universal primers.
The applicant listed for this patent is UniTaq Bio. Invention is credited to Karl Guegler, Eugene Spier.
Application Number | 20170233791 15/384168 |
Document ID | / |
Family ID | 51167430 |
Filed Date | 2017-08-17 |
United States Patent
Application |
20170233791 |
Kind Code |
A1 |
Spier; Eugene ; et
al. |
August 17, 2017 |
METHODS AND COMPOSITIONS FOR PCR USING BLOCKED AND UNIVERSAL
PRIMERS
Abstract
Provided herein are methods and compositions for performing PCR
with primers with blocked 3'-ends that are unblocked when these
primers anneal to the template. The multiplexed PCR can be used as
real-time qPCR, for end-point detection or as enrichment method for
next generation sequencing (NGS). Also described herein are methods
and compositions to improve sensitivity of mutation-specific PCR
when targeting closely-spaced mutations.
Inventors: |
Spier; Eugene; (Los Altos,
CA) ; Guegler; Karl; (Menlo Park, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
UniTaq Bio |
Los Altos |
CA |
US |
|
|
Family ID: |
51167430 |
Appl. No.: |
15/384168 |
Filed: |
December 19, 2016 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14154117 |
Jan 13, 2014 |
9523121 |
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15384168 |
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61751869 |
Jan 13, 2013 |
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Current U.S.
Class: |
506/9 |
Current CPC
Class: |
C12Q 1/686 20130101;
C12Q 1/686 20130101; C12Q 1/6848 20130101; C12Q 2525/186 20130101;
C12Q 1/6858 20130101; C12Q 1/686 20130101; C12Q 1/6853 20130101;
C12Q 2547/101 20130101; C12Q 2537/143 20130101; C12Q 2525/15
20130101; C12Q 2521/327 20130101; C12Q 2525/161 20130101; C12Q
2537/163 20130101; C12Q 2537/143 20130101; C12Q 2521/301
20130101 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68 |
Claims
1-10. (canceled)
11. A blocked PCR primer and an enhancer 3'-blocked oligo that
anneals downstream from the blocked primer, forming no gap or a
single base gap between the primer and the oligo when both are
annealed to the target in a PCR or isothermal amplification mixture
comprising an endonuclease that cleaves off a cleavable group at
the single base gap and enables primer extension.
12-13. (canceled)
14. A multiplex allele (mutation) specific PCR reaction mixture
used to detect two or more closely spaced mutations, comprising:
(a) mutation (allele) specific primers for each mutation to be
detected, wherein the primers comprise the same target-specific
3'-regions, except for different 3'-ends; and (b) the primers of
(a) further comprising different non-target-specific 5' tags; such
that after the first two PCR cycles the first allele-specific
primer that was extended in the first PCR cycle continues PCR by
annealing to the amplicons that are 100% complementary to the whole
first primer, but other allele-specific primers with 5'-tags not
matching the amplicons generated by the first primer do not anneal
at the annealing temperature used in PCR.
15. The PCR reaction mixture of claim 14, wherein the allele
(mutation) and target-specific primers of (a) and (b) further
comprise universal 5'-tags and the different non-target specific
tags of (b) are situated between the 3'-target-specific region and
the universal 5' tags of the allele specific primers; and wherein
the reaction mixture further comprises (c) at least one pair of
universal primers that can prime on the universal 5' tags.
16. The reaction mixture of claim 14, where at least one of the
allele or locus specific primers is blocked.
17. A method of using PCR to detect two or more closely-spaced
mutations with increased sensitivity, comprising the use of
mutation-specific primers for each mutation with 5'-non target tags
different for each primer, such that after first two PCR cycles, an
increased annealing temperature is used to decrease completion
between different mutation-specific primers, thus increasing assay
sensitivity.
18. A PCR amplification method comprising the use of at least one
blocked PCR primer with a 3'-end complementary to the template,
such that unblocking is performed by a 3'-exonuclease activity and
extension by a polymerase activity, respectively, and wherein the
two enzymatic activities are performed by a single enzyme or two
separate enzymes.
19. A PCR reaction mixture comprising at least one 3'-blocked
primer comprising a 3'-end having a nucleotide sequence 100%
complementary to a template; and either a polymerase with
3'-exonuclease activity, or a separate 3'-exonuclease and a
polymerase; such that after the 3'-blocked primer anneals to the
template the exonuclease unblocks the primer(s) and the polymerase
extends the unblocked primer(s) during PCR.
Description
CROSS-REFERENCE TO RELATED APPLICATION
[0001] This application is a non-provisional utility patent
application claiming priority to and benefit of the following prior
provisional patent application: U.S. Ser. No. 61/751,869 filed on
Jan. 13, 2013, entitled "Methods and compositions for PCR using
blocked and universal primers" by Eugene Spier. This provisional
application is incorporated herein by reference in its entirety for
all purposes.
BACKGROUND OF THE INVENTION
[0002] PCR-based nucleic acid detection typically employs two
primers that anneal to opposite strands of a DNA target. PCR can be
multiplexed to amplify several targets in a well or droplet. One of
the challenges of PCR is that primers can prime non-specifically on
themselves forming primer dimers or on DNA targets that are similar
to intended targets. This non-specific priming can occur during
single-plex PCR, but is markedly more likely in multiplex PCR. For
example, 10-plex PCR requires 10 primer pairs (20 primers) that can
form 19+18+ . . . 1=19*10=190 different pairs, each potentially
causing a non-specific amplification product such as a primer
dimer.
[0003] Various methods have been described for overcoming
non-specific PCR amplification caused by non-specific priming. The
U.S. Pat. No. 5,792,607 (Backman et al) describes a method using
EndolV to unblock primers for PCR and ligation reaction. But
because the activation of primers using EndolV is very slow
(minutes instead of seconds), it is impractical to use this method
to amplify DNA exponentially. Also, the Backman patent only
describes EndolV derived from E. coli and only mentions that the
method should work better if using thermostable EndolV. The method
described by Backman et al. has not been commercialized.
[0004] Recently IDT (Integrated DNA Technologies) published methods
and made reagents available for RNAse H-dependent PCR (rhPCR,
patent application U.S. 2009/0325169; Dobosy et al., BMC
Biotechnology 2011, 11:80). The authors describe a method using
primers with blocked 3'-ends and containing a single RNA base close
to the 3'-end. Primer activation occurs if a thermostable RNAseH
enzyme cleaves the annealed primer at the RNA base, generating a
3'-OH, thereby making the primer extendable by polymerase. The
rhPCR makes PCR more complex as it requires an additional
thermostable enzyme, RNAse H, that is currently commercially
available only from IDT and Epicentre. Also, an RNA base in the
primer requires a more complex manufacturing and can double the
cost of primer compared to a regular DNA oligo. For example, a list
price per base at the 100 nmolar scale is $0.55 and $6.50 per base
for DNA and RNA bases, respectively (IDT Technologies).
[0005] Next generation sequencing (NGS) often requires enrichment
of regions of interest in the genome or transcriptome. PCR,
single-plex or multiplex, is one of the methods frequently used for
enrichment, for example, AmpliSeq from Life Technologies. There are
three major challenges in multiplex PCR enrichment for NGS: 1)
formation of primer-dimers; 2) carry over contamination; and 3)
PCR-errors. [0006] 1. Primer Dimers: Primer dimers can consume a
lot of reagents as short primer dimer amplicons tend to be
amplified very efficiently and dominate the PCR reaction. [0007] 2.
Carry over Contaimination: The high cost and sequencing throughput
of NGS, where millions of sequences are generated in a single run,
results frequently in multiple samples with different bar-codes
being combined and processed together on the same plate or strip.
Opening reaction tubes after PCR can result in a few amplicons
being transferred through aerosols into other reaction tubes; this
is called carry over contamination. [0008] 3. PCR Errors:
Polymerases tend to make errors during PCR (most frequently
mis-incorporation of nucleotides) and, if these errors occur during
early cycles they appear as "mutations" in NGS. Molecular bar-codes
called degenerate base regions (DBR; see J. Casbon, S. Brenner et.
al "Increasing confidence of allele calls with molecular counting,"
U.S. Pat. No. 8,481,292, and U.S. patent application Ser. No.
13/853,981 "Method for accurately counting starting molecules") are
random sequence tags that are attached to molecules that are
present in the sample. These tags allow one to distinguish PCR
errors during sample preparation from mutations that were
originally present in the sample.
[0009] Previously Bi and Stambrook, ["Detection of known mutation
by proof-reading PCR"; Bi and Stambrook, Nucleic Acids Research,
1998, Vol. 26, No. 12 3073-3075] and Lin-Ling et al. ["Single-base
discrimination mediated by proofreading inert allele specific
primers"; Lin-Ling et al., J Biochem Mol Biol. 2005 Jan. 31;
38(1):24-7] described how exo+ polymerases remove mismatched bases
at the 3'-end. They specifically teach this as a genotyping or
mutation detection method. Mutations are amplified by wild type
specific primers that have a non-Watson-Crick base pair at the 3'
ends that are cleaved and extended; primers that perfectly match
wild type are not cleaved and thus not extended. Similarly,
PCT/US2005/010782 "Quantitative amplification with a labeled probe
and 3' to 5' exonuclease activity" by Bin Li et. al. specifically
teaches that the 3' most "N residue represents a mismatch to the
target nucleic acid sequence". Also, patent EP 2324124
"Proofreading primer extension" by Fiss and Myers teaches that
extension during PCR happens "if the 3' portion of the
oligonucleotide is not 100% complementary to the template nucleic
acid". The "proof-reading PCR" is rarely used in practice as seen
by its low citations number: 36 citations for Bi and Stambrook and
5 for Lin-Ling (Google Scholar, January 2014).
[0010] The idea of combining tagged target specific and universal
primers is known; see, for example, application PCT/US2010/029854
by May et al. "Multi-primer amplification method for bar-coding of
target nucleic acids". The "four primer amplicon tagging" method
developed by Fluidigm uses closed tube amplification to incorporate
sample bar codes for next generation sequencing (NGS) enrichment.
But the method works only for singleplex PCR: each well has a pair
of target-specific primers and a pair of universal, thus the name
"four primer". Fluidigm also offers 10-plex PCR enrichment, but it
is an open tube protocol: bar coded primers are added after
multiplex PCR. Recently, similar methods were published for NGS
enrichment using 60-plex 4 nM 5'-taged primers for 6 PCR cycles and
then 2 .mu.M universal primers are added (Nguyen-Dumont et, "A
high-plex PCR approach for massively parallel sequencing,"
Biotechniques, 55, pp 69-74, 2013). Nguyen-Dumont et al. also
review different methods for NGS enrichment.
[0011] The primer concentrations are 50 to 1,000.times. lower than
the 50 nM-1 .mu.M used in traditional PCR. Low primer
concentrations decrease the chance of primer dimer formation
proportionally to the square of primer concentrations. However,
concentrations of 5 nM and below generally do not generate a
sufficient amount of PCR products to observe a signal in qPCR or a
band on a gel.
[0012] Due to the above-noted drawbacks of current strategies to
prevent non-specific amplification during PCR, e.g., specificity,
cost, manufacturing logistics, and the like, there is a need for
more specific, flexible, and cost-effective methods of PCR nucleic
acid detection. The present invention meets these and a variety of
other needs.
SUMMARY OF THE INVENTION
[0013] The present invention generally provides methods and
compositions for overcoming non-specific PCR amplification caused
by non-specific priming. Methods of the present invention include
the use of tagged, target-specific primers that are blocked, in
combination with universal primers. A variety of strategies for
activating blocked primers are provided. The present invention is
broadly applicable to any PCR, but is more important when PCR is
multiplexed: more than one DNA target is amplified in the same
reaction. The methods and compositions described here can be used
for both qPCR (aka real-time PCR) or end-point PCR when the
products of PCR are further analyzed by sequencing, fragment sizing
and other methods known in the art. The primary use of the present
invention is for PCR based detection methods, but can also be used
for ligation-based detection methods.
[0014] The present invention combines the idea of using blocked
primers that are unblocked during PCR after they anneal to their
templates. Described herein are novel methods to unblock the
primers. In one aspect of the invention, one method to activate
blocked primers is using a polymerase with 3'-exonuclease (exo+)
activity to remove a blocking moiety at the 3'-end of primers. The
results demonstrate that Endonuclease IV can cleave 5' from an
internal C3 spacer and that 3'-exonuclease activity of a
thermostable polymerase can cleave off a 3'-C3 blocker when 3'ends
of primers form a perfect Watson-Crick pairing with the templates.
The methods of the invention combine the use of blocked primers
(extendable after activation as described above) with the idea of
using tagged target specific and universal primers in a closed tube
reaction. It is very difficult to perform highly multiplexed
reactions in a closed tube when regular unblocked primers are used:
these primers form primer dimers that tend to dominate the
amplification. Blocked primers are extremely resistant to primer
dimer formation, thus enabling high multiplex PCR.
[0015] In another aspect of the invention, to overcome the low
activity of EndolV, the methods employ a two-step four-primer PCR:
this approach requires EndolV activity only for the first one or
two cycles; in subsequent cycles unblocked universal primers
continue PCR.
[0016] Described herein are methods and compositions that utilize
3'-blocked primers that cannot be extended by a polymerase activity
only during PCR. Primers with the blocked 3'-end cannot be extended
before an enzyme cleaves off the blocked 3'-end. The enzymes used
to activate primers have dsDNA specificity: they require that
primers are stably annealed to the complementary DNA. Thus it is
unlikely that activation occurs during very brief non-specific
primer annealing to each other or non-target sequences. This should
dramatically decrease the chance of primer dimer formation and
non-specific amplifications. Interactions between primers (that
cause primer dimers) and potential mispriming sites are too brief
for two enzymatic steps to occur: 1) blocking group removal and 2)
polymerase extension. These blocked primers enable higher PCR
multiplex as primer dimer formation is greatly diminished. In
addition, these primers have a lower chance of non-specific
priming.
[0017] These blocked primers can be activated sufficiently (time
and quantity) to yield the desired amounts of amplicons during a
regular PCR reaction using two target-specific primer for each
locus (no universal primers), typically 20-45 or more cycles.
However, our main emphasis is on applications where the blocked
primers are comprised of two or more specific portions. For example
primers may consist of a target-specific sequence at the 3'-end and
one or more universal sequences at the 5'-end (5' tags). The
target-specific sequence will amplify the desired target during the
first few cycles. The amplicons generated in the first few cycles
will then be further amplified in all subsequent cycles with
universal primers matching the 5-tags of the primers. Two cycles
are required, if both target specific primers are blocked, but only
one single cycle is needed if only one primer is blocked. Universal
primers that prime on these universal tags drive the PCR after one
or two cycles, respectively.
[0018] Herein described are methods comprising the use of blocked
primers comprising an abasic site, e.g., 3' 1',2'-Dideoxyribose
(aka dSpacer or tetrahydrofuran) or C3 spacer. The annealed primers
are cleaved at the 5'-side of the abasic site by commercially
available thermostable Tth EndolV from NEB (New England Biolabs)
leaving a 3'-OH group which can be extended by polymerase. In
addition, the inventors demonstrate that DNA polymerases that have
3'-exonuclease activity can activate and extend blocked primers by
removing the 3'-blocking group, e.g., C3-spacer. In this case a
single enzyme with 3'exonuclease and polymerase activity is
sufficient to generate a PCR product. Alternatively, a separate
enzyme with 3'-exonuclease activity and a polymerase can be
used.
[0019] One can also use a separate "enhancer" oligo downstream from
the 3'-blocked primer, so that there is a stretch of dsDNA on both
sides of the blocking site; a preferred substrate for endonuclease
IV. In still another aspect of the invention, methods and
compositions to decrease primer dimers and non-specific
amplifications are employed, using decreasing primer concentrations
to 5 nM and below, e.g., 1 nM. Low primer concentrations decrease
the chance of primer dimer formation proportionally to the square
of primer concentrations. Concentrations of 5 nM and below
generally do not generate a sufficient amount of PCR products to
observe a signal in qPCR or a band on a gel. Therefore, 5' tags are
added to the target-specific primers and regular universal PCR
primers matching these tags are added to the PCR reaction. These
universal primers are present in concentrations traditionally used
in PCR typically ranging between 100 nM to 1 mM, typically
>40-fold higher than the target specific primers. During the
early PCR cycles with relatively long annealing time, low
concentration target-specific primers initiate amplification.
Alternatively, the methods of the invention use several PCR cycles
with high annealing temperature, e.g., 68-72.degree. C. that favors
annealing and extension of long target-specific primers that have
5'-tags (tails). Then, the annealing time is shortened and
optionally the annealing temperature is lowered to a more typical
range of 58-64 C, where universal primers present at high
concentrations (0.1-1.0 .mu.M) drive the reaction and generate
sufficient amplification to observe a qPCR signal or use amplified
product for an end-point read out including sequencing using
NGS.
[0020] Described herein are examples of using blocked primers for
regular qPCR, multiplexed mutation detection using qPCR and PCR for
NGS enrichment. Two examples of qPCR detection are shown using
universal hairpin 5'-nuclease assays: single-plex for Enterococcus
and multiplex for model EML4-ALK gene fusions. For closed tube
EML4-ALK, 60.times. lower concentration of target-specific (5 nM)
than universal primers (300 nM) were used. Described herein is a
closed tube NGS enrichment method that can incorporate both unique
molecular bar-codes (DBR) and sample bar-codes in a closed tube
PCR. This method is not only quick and simple, but also minimizes
the chance of carry over contamination between samples. Further
described herein is a method to normalize (make similar) the
amounts of different amplicons in a PCR reaction by slowing down
cooling at late PCR cycles.
[0021] In another aspect of the invention, a method is used to
design and use 5'-tailed target-specific primers that detect
closely spaced mutations. The PCR cycling protocol uses high
annealing temperatures, typically from cycle 3 onward, so that the
mutation-specific primers that were extended during the first cycle
and were complemented during the second cycle will preferentially
anneal to those amplicons based on their increased melting
temperature (Tm): both target-specific part of the primer and the
5'-tail contribute to primer annealing. Primers that were not
extended in the first cycle will have a lower chance to
anneal/extend starting cycle three because amplicons do not match
their 5'-tails. One can then increase annealing temperature
beginning with cycle 3 so that the temperature is too high for the
allele-specific primers that did not extend at cycle 1.
Alternatively, one can employ a high annealing temperature during
the first two cycles, so that the allele specific primers are
barely priming, and the same high annealing temperature is used
after cycle two, so that tagged primers that extended at cycle 1
prime efficiently using 100% of their lengths, including tags, but
competing allele-specific primers do not.
[0022] In a still further aspect of the invention, methods are
described herein to improve sensitivity of detection of closely
spaced mutation using rhPCR/qPCR with several blocked
mutation-specific primers. Each mutation-specific primer carries a
different tag next to its target-specific 3'-region, so that the
primer that was extended in the first PCR cycle gains a
thermodynamic advantage (higher Tm) starting cycle three over other
mutation-specific primers specific for adjacent mutations. This
approach is demonstrated using the methods to detect six mutations
in codon 526 of rpoB gene in Mycobacterium tuberculosis (MTB): all
six mutations cause resistance to rifampicin. The inventors used
two sets of universal tags: one for six drug resistance mutations,
so that FAM-dye signal in qPCR will indicate that at least one of
these mutations is present in the sample, thus detecting all six
mutations together. The second set of universal tags detects
control region of MTB using HEX dye, so that the difference between
FAM and HEX signals is used to make resistance or "no resistance"
call.
[0023] The enrichment for sequencing, including NGS, for regions of
interest, usually targets areas known for polymorphisms and
mutations in human genes, is a rapidly growing application that is
used for genetics and cancer diagnostics. Polymorphisms in
BRAC1/BRCA2 genes are the most well-known example of germline
(inherited) changes that have clinical significance. Somatic
mutations in EGFR, BRAF, KRAS, and other genes are used for
targeted cancer treatment (companion diagnostics). Advances in NGS
technologies and its broad use in clinical research will rapidly
expand both genetic and somatic mutation testing. The methods we
describe will make both applications more robust and simpler to
implement for clinical research and diagnostics use, including
laboratory developed testing (LDT).
[0024] In one aspect of the invention, a PCR reaction mixture is
provided comprising: (a) at least one pair of target-specific
primers comprising universal 5' tags, where at least one
target-specific primer cannot be extended by polymerase (3'-blocked
primer); (b) at least one pair of universal primers that can prime
on the universal 5' tags; (c) an enzyme that unblocks the
3'-blocked primer after it anneals to the target DNA generating a
3'-OH end; and (d) a polymerase that extends unblocked primers
during one or more initial PCR cycles; and subsequently extends
universal primers driving amplification in a closed tube reaction.
Preferably, multiple blocked target-specific primers in the PCR
reaction mixture amplify multiple targets (multiplex PCR), and
target-specific primers for targets that are to be detected
together comprise the same universal tags, and optionally blocked
target-specific primers for targets to be detected separately
comprise different universal tags; more preferably, universal
primers and optionally universal probes are labeled and different
universal primers and optionally probes are used to detect targets
by priming on the different universal tags of the amplicons
generated by the blocked primers. Said reaction mixture may be used
for PCR enrichment for sequencing, wherein at least one of the
universal primers comprises a sample bar-code that enables sample
pooling for sequencing; and optionally wherein the blocked
target-specific primers comprise random molecular barcodes allowing
identification of individual DNA strands amplified in PCR, such
that the first two PCR cycles incorporate random molecular
bar-codes for each DNA strand present in the sample.
[0025] Preferably, the concentration of the target-specific primers
in the reaction mixture is at least 40-fold less than the
concentration of the universal primers; and/or the one or more 3'
blocked primer(s) comprise(s) a C3 spacer(s) or another 3'-blocking
modification. Preferably, the reaction mixture comprises a DNA
polymerase with 3'-exonuclease activity or an endonuclease to
unblock the primers. Optionally, the reaction mixture comprises a
blocked primer comprising an abasic site to anneal to the target on
both sides of the abasic site, and an endonuclease IV to cleave 5'
from the abasic site, unblocking the primer; or comprises a primer
comprising at least one RNA base, and further comprises an RNase H
enzyme for unblocking the primer.
[0026] In a second aspect of the invention, a multiplex allele
(mutation) specific PCR reaction mixture is provided to detect two
or more closely spaced mutations, comprising: (a) mutation (allele)
specific primers for each mutation to be detected, wherein the
primers comprise the same target-specific 3'-regions, except for
different 3'-ends; and (b) the primers of (a) further comprising
different non-target-specific 5' tags; such that after the first
two PCR cycles the first allele-specific primer that was extended
in the first PCR cycle continues PCR by annealing to the amplicons
that are 100% complementary to the whole first primer, but other
allele-specific primers with 5'-tags not matching the amplicons
generated by the first primer do not anneal at the annealing
temperature used in PCR. Preferably, the allele (mutation) and
target-specific primers of (a) and (b) further comprise universal
5'-tags and the different non-target specific tags of (b) are
situated between the 3'-target-specific region and the universal 5'
tags of the allele specific primers; and the reaction mixture
further comprises (c) at least one pair of universal primers that
can prime on the universal 5' tags; more preferably, at least one
of the allele or locus specific primers is blocked.
[0027] In additional embodiments of the invention, a PCR reaction
mixture comprises at least one 3'-blocked primer comprising a
3'-end having a nucleotide sequence 100% complementary to a
template; and either a polymerase with 3'-exonuclease activity, or
a separate 3'-exonuclease and a polymerase; such that after the
3'-blocked primer anneals to the template the exonuclease unblocks
the primer(s) and the polymerase extends the unblocked primer(s)
during PCR.
[0028] The invention further provides a blocked PCR primer and an
enhancer 3'-blocked oligo that anneals downstream from the blocked
primer, forming no gap or a single base gap between the primer and
the oligo when both are annealed to the target in a PCR or
isothermal amplification mixture comprising an endonuclease that
cleaves off a cleavable group at the single base gap and enables
primer extension.
[0029] In a further aspect of the invention, methods are provided
to detect or enrich target nucleic acids in a sample in a closed
tube reaction, comprising the use of PCR with one or more 5' tagged
target-specific primer(s) with a blocked 3'-end and universal
primers that optionally comprise blocked 3' ends; that can prime on
these universal tags, and optionally probes; such that during
initial PCR cycles, the target-specific primer anneal, get
unblocked and extend on target DNA, and in subsequent PCR cycles,
the universal primers drive PCR. Optionally, the PCR reaction is
normalized by slowing down cooling from melting to annealing
temperature during late PCR cycles, such that the majority of
abundant target amplicons reanneal and do not amplify, but rare
ones continue their amplification. Preferably, the read-out for the
detection of nucleic acids is real-time or end-point PCR for
sequencing, NGS enrichment, fragment sizing using electrophoresis,
surface hybridization, amplicon melting, molecular weight
determination via electrophoresis or mass spectrometry.
[0030] Preferably, the one or more 3' blocked primer(s) comprise(s)
a C3 spacer(s) or another 3'-blocking modification; more
preferably, the method comprises the use of a DNA polymerase with
3'-exonuclease activity or an endonuclease to unblock the primers;
or comprises the use of a blocked primer comprising an abasic site
to anneal to the target on both sides of the abasic site, and an
endonuclease IV to cleave 5' from the abasic site, unblocking the
primer. In one embodiment, the method comprises the use of a primer
comprising at least one RNA base, and further comprises the use of
RNase H enzyme for unblocking the primer.
[0031] The methods can be used for PCR enrichment for sequencing,
wherein at least one of the universal primers comprises a sample
bar-code that enables sample pooling for sequencing; and optionally
wherein the blocked target-specific primers comprise random
molecular barcodes allowing identification of individual DNA
strands amplified in PCR, such that the first two PCR cycles
incorporate random molecular bar-codes for each DNA strand present
in the sample.
[0032] In a further aspect of the invention, methods are provided
for using PCR to detect two or more closely-spaced mutations with
increased sensitivity, comprising the use of mutation-specific
primers for each mutation with 5'-non target tags different for
each primer, such that after first two PCR cycles, an increased
annealing temperature is used to decrease completion between
different mutation-specific primers, thus increasing assay
sensitivity.
[0033] In a still further aspect of the invention, PCR
amplification methods are provided comprising the use of at least
one blocked PCR primer with a 3'-end complementary to the template,
such that unblocking is performed by a 3'-exonuclease activity and
extension by a polymerase activity, respectively, and wherein the
two enzymatic activities are performed by a single enzyme or two
separate enzymes
[0034] The methods and compositions summarized above are described
in detail hereinbelow.
BRIEF DESCRIPTION OF THE DRAWINGS
[0035] FIG. 1. PCR/qPCR closed tube schema. (a) Multiplex PCR
encodes for targets by incorporating universal tags for each
nucleic acid target: Ai, Bi and Ci where i=1 to M are used for N
targets; N.gtoreq.M. (b) Tagged amplicons. Detection using (c)
universal hairpin (e) circle and (d) 5' nuclease (TaqMan.TM.)
assays. If no probe is used, the PCR reaction can be used for NGS
enrichment and Bi tags can be molecular bar codes. Target-specific
3' ends of primers are shown as black arrows. "Primes" indicate
complements: e.g., B'.sub.1, is complement of B.sub.1.
[0036] FIG. 2. An example of a closed tube UniTaq qPCR to detect
varying amounts of Enterococcus gDNA. Four primer pairs including
two Enterococcus specific primers (5 nM) and UniTaq detection
primers (600 nM). Amplification curves for 700, 70 and 7 copies of
Enterococcus and NTCs are shown. The delta Ct between 10.times.
dilutions approximates 3.3, the expected optimal theoretical
amplification efficiency. PCR amplification buffer was 1.times. PCR
Environmental Master Mix (Life Technologies).
[0037] An example of a closed tube reaction detecting artificial
template (oligonucleotide) representing the ELM4-ALK fusion gene
using rhPCR. (FIG. 3A) Amplification curves; (FIG. 3B) melt
curves.
[0038] FIG. 4. PCR closed tube using blocked primers. (a) Multiplex
PCR encodes targets by incorporating universal tags for each
nucleic acid target: Ai, Bi and Ci where i=1 to M are used for N
targets; N.gtoreq.M. "X" indicates blocked primers(b) Tagged
amplicons are generated by a combination of cleaving agent and a
polymerase. Detection using (c,e) UniTaq and (d) 5'nuclease assays.
In the absence of any probes the PCR reaction can be used for NGS
enrichment; in this case M=1 and N can be any number between one
and many thousands.
[0039] FIG. 5. Using 3'-phoshorylated blocked primers (a) and
endonuclease IV to remove blocking 3'-phosphates; (b) After
unblocking 5'-tailed target-specific primers are extended; (c)
polymerase extends universal primers (thick and dashed arrows); and
(d) Similar approach that uses THF or C3 spacer ("X") that is
cleaved off by the endonuclease.
[0040] FIG. 6. Exonuclease-dependent PCR amplification curves. The
three curves that show signal (lower Ct values) are for regular
(#1), THF (#2) and C3 (#3) blocked primers with the same reverse
primer #4 (at 5 nM). NTC (gDNA-) using regular primers and
gDNA+/Endo-(wells with gDNA, but no endonuclease IV) using THF/C3
blocked primers give much lower signal. UniTaq method was used to
generate signal.
[0041] Blocked and unblocked primer PCR of human gDNA. EvaGreen
signal in qPCR (FIG. 7A) and melt curves after PCR (FIG. 7B)
demonstrate that blocked primers are unblocked by the
3'-exonuclease activity of Q5 thermostable DNA polymerase from NEB
but not by a DNA polymerase lacking 3-exonuclease activity (Qiagen
Quantifast Multiplex PCR Kit). Also in the absence of any target
DNA (NTC) no primer-dimer formation was observed in reactions with
blocked primers (FIG. 7B), whereas reactions with regular primers
show low Tm primer dimer peak (FIG. 7B) in the melt curve.
[0042] FIG. 8. The schematics of a closed tube NGS enrichment
experiment. One primer pair is shown as an example of a multiplex.
The target-specific primers consist of the following parts,
starting at the 5'-end: (a) universal tag, (b) degenerate base
region (DBR, optional), (c) locus/target-specific region, (d)
blocked 3'-end and (e) optionally an additional cleavable site (not
shown). Universal primers have these parts, starting at the 5'-end:
(f) P5/P7 tags (Illumina surface tags; any tag supported by
sequencing instrument can be used), (g) index/sample bar codes
(optional) and (a) universal tags.
[0043] Schema for increasing sensitivity of detection for
mutation-specific primers targeting closely spaced mutations using
different 5'-tags. "R" and "X" are examples of an RNA base in locus
and mutation-specific primers, respectively. (FIG. 9A) Three allele
(mutation) specific primers targeting three closely-spaced
mutations, shown as "X" have different M.sub.1, M.sub.2 and M.sub.3
tags. (FIG. 9B) Encoding allele-specific primers (as in A) with
universal Ai tag and locus-specific primer with Bi and Ci tags used
for detection reaction. (FIG. 9C) Example of temperature cycling
program.
[0044] rhPCR using RNase H blocked primers for MTB (tuberculosis)
drug resistance mutations for rifampicin (RIF) in codon 526 (aka
445). Any one of six mutation in the codon #526 of rpoB gene
generate FAM signal, HEX signal is control. (FIG. 10A)
amplification curves; (FIG. 10B) cycling program.
DETAILED DESCRIPTION
[0045] Multiplex PCR or ligation can be used for multiplex encoding
reaction for detection that we described previously (U.S. patent
application Ser. No. 12/931,803). Here we describe a closed tube
PCR using blocked primers. It is generally run as a multiplex PCR
that includes 5' tailed target-specific primers at low
concentrations and universal amplification or detection primers
[probes] at regular concentrations. One can also add universal
primers after, say 2 cycles of PCR with target specific primers,
but this is less advantageous because this extra step requires
opening a tube and active polymerase present in the reaction
mixture can quickly generate non-specific amplicons if the
temperature drops below the annealing temperature used in PCR.
[0046] Multiplex PCR is also used for so called "pre-amplification"
to amplify targets from small samples, e.g., single cells, or for
qPCR detection in very small volumes in droplets or nanowells.
Multiplex PCR is also used as a target enrichment method for NGS.
For example, AmpliSeq from Life Technologies uses 1,536-plex PCR or
even .about.20,000 plex for enrichment. Conventional wisdom
indicates it is impossible to avoid primer dimer formation and
indeed the protocol for AmpliSeq requires a step to separate long
target-specific amplicons from short primer dimers. This additional
clean-up step makes the NGS sample prep workflow more complex; in
addition non-target amplifications, e.g., primer dimers, consume
PCR reagents reducing the yield of target specific amplicons.
Described herein is a multiplex PCR method using primer
concentrations of 50 nM, 5 nM, 1 nM or less . The schematics are
shown in FIG. 1. Each 5'-tailed target specific primer in FIG. 1 is
present at concentrations of 5 nM, 1 nM or less . During the first
2 to 6 cycles, the disclosed methods use relatively long annealing
times (typically 2-15 minutes) so that these low concentration
primers have sufficient time to anneal to their targets. After two
cycles, PCR will generate amplicons that have universal tags at
both ends. Now, one can use regular PCR conditions with short
annealing times, e.g., 1 minute or less. Short annealing times
decrease the likelihood that low concentration target-specific
primers will have sufficient time to anneal to the amplicons; the
higher concentration universal primers (FIG. 1c, d) have a kinetic
advantage and dominate detection at later stages of the PCR
amplification. One can also help to shift the balance towards the
universal high concentration primers by using the maximum ramp
speed of the thermo cycler to cool from 95.degree. C. to the
annealing temperature. This closed tube multiplex tag-PCR
amplification has several advantages over traditional multiplex PCR
including [0047] 1. Very low primer concentrations allow high
multiplex; [0048] 2. A lower chance of primer dimer formation that
is proportional to the square of primer concentration; [0049] 3.
Amplicons that are to be detected together, e.g., sequences by an
NGS, can use the same tags, but those that are to be detected
separately can use different tags. For example, in case of qPCR
detection (FIG. 1c, d) different dyes measure the cumulative
presence for each set of targets that use the same tags. [0050] 4.
1-step tag-PCR permits UDG contamination control that is
traditionally used in diagnostics and other PCR applications
avoiding sample cross contamination issues associated with
preamplified DNA.
EXAMPLE
[0051] The inventors have used a closed tube qPCR to detect
Enterococcus gDNA from water samples. In the case of Enterococcus a
16S DNA-specific assay at 5 nM was used. FIG. 2 shows amplification
curves for 700, 70 and 7 copies of Enterococcus and NTCs. Each qPCR
reaction contained four primers: two target-specific primers for
16S gDNA with 5' tails and two universal UniTaq primers as shown in
FIG. 1c. The delta Ct between 10.times. dilutions is close to 3.3,
the expected optimal theoretical amplification efficiency. The non
template control (NTC) reaction is also shown.
[0052] FIG. 3 shows a 1-step closed tube reaction where the sample
consisted of 10.sup.3, 10.sup.4 and 10.sup.5 copies of an
artificial template representing the ELM4-ALK fusion gene using
rhPCR. Seven EML4 fusion specific rhPCR primers and exon 20 ALK
rhPCR primers @ 5 nM (all primers had a single RNA base and 3'-C3
block) were multiplexed with universal FAM labeled and regular
primers @300 nM (FIG. 4c). Amplification curves (a) and melt curves
(b) are shown for 3 dilutions of EML4-ALK ATs and NTC.
Amplification curves demonstrate a deltaCt -3.33 is close to the
theoretical PCR amplification efficiency (doubling in every cycle).
The NTC signal has a lower Tm than the target amplicon.
[0053] FIG. 4 shows schematics for multiplexing using blocked
primers (FIG. 4a, "X" indicates a cleavable modification and lack
of an arrow a blocked 3' end) that after unblocking and extension
generate tagged (encoded) products (FIG. 4b). This encoding PCR can
use the same (M=1) or different (M>1) universal tags (FIG. 4a).
The encoded products can be detected using universal hairpin (FIG.
4c) or "circle" (FIG. 4e) methods described in the U.S. patent
application Ser. No. 12/931,803. Alternatively, an optional
universal probe can be used (FIG. 4d) to generate signal using
universal primers with or without 5' tags (FIG. 4d shows both an
optional probe and 5'-tags on universal primers). The two stages of
PCR: 1. unblocking and extension of tagged target-specific primers
and 2. amplification by universal primers can be performed in a
closed tube reaction. Alternatively one can employ two separate
steps: after at least two cycles of encoding the reaction can be
optionally split into multiple reactions, universal primers/probes
are added, and PCR is continued.
[0054] FIG. 5 shows schematics of using endonuclease IV (EndolV)
for unblocking 3'-phosphates (FIG. 5a) or an internal abasic site,
e.g., C3 or THF for multiplex PCR, e.g., for NGS enrichment. After
unblocking (FIG. 5b) a polymerase first generates tagged amplicons
that are amplified by universal primers (FIG. 5c).
[0055] With no primer dimers competing for PCR reagents, one can
run more cycles of multiplex PCR and use a technique known as
"C.sub.0t" (DNA reassociation kinetics) at later cycles to
normalize the amounts of PCR amplicons. The C.sub.0t method uses an
additional temperature holding step when cooling from 95.degree. C.
to the annealing temperature at late cycles of the PCR. , The
holding temperature (between 75.degree. C. and 80.degree. C. for 10
sec to 2 min) is chosen to be much higher than the Tm of the
primers, but lower than the melting temperature of the amplicons,
so that the complementary strands of the more abundant PCR products
reanneal and stop being amplified whereas lower abundance products
continue to be generated.
[0056] In principle, two PCR cycles that use encoding primer are
sufficient to incorporate the universal tags; starting with cycle 3
universal primers can take over the amplification. However in some
cases it is desirable to continue amplification using the
target-specific encoding primers for additional cycles. For example
when performing rhPCR/qPCR (using RNaseH for cleavage) additional
cycles of rhPCR (target-specific) exponentially increase mutation
detection specificity. In this case, we propose to use high
annealing temperatures and long annealing times during early PCR
cycles, e.g., 3-18. High annealing temperatures prevent the short
universal primers from annealing, resulting in the tailed target
specific primer to continue driving the reaction. For example, we
used the following cycling protocol: (95.degree. C. 5 min);
(95.degree. C.-155, 62.degree. C.-2 min).times.2 cycles;
(95.degree. C.-15 s-70.degree. C.-2 min).times.12 cycles;
(95.degree. C.-15 s-62.degree. C.-455).times.40 cycles.
[0057] As used herein, "endonuclease-dependent PCR" is PCR that
contains Endonuclease to cleave primers. The inventors found that
C3 spacers can be effectively cleaved by endonuclease IV (a DNA
repair enzyme) leaving an OH-group at the 3'-end so the unblocked
primer can be extended by a DNA polymerase. The inventors used
thermostable Tth EndolV from NEB. Thus, endonuclease-dependent PCR
can not only use blocked primers with canonical abasic sites, e.g.,
tetrahydrofuran (THF), but also a C3 spacer. The C3 spacer is less
expensive than THF and is used by IDT for rhPCR as a polymerase
extension blockers, either at the 3'-end (GEN1 rhPCR primer design)
or close to the 3'-end (GEN2 rhPCR primer designs).
[0058] FIG. 6. shows results for endonuclease-dependent PCR (with
and without Tth Endo IV enzyme) comparing regular and blocked
primers that contain a single THF or C3 spacer. The signal is
similar for regular primers and THF/C3 endonuclease-dependent PCR.
The NTC signal is also similar for regular primers and Endo-minus
reaction that contains target DNA indicating that EndolV cleavage
is required for reaction. Tth EndolV has a relatively low activity:
1 unit cleaves 1 ug (0.5 pMol) of partially depurinated plasmid DNA
in 30 min, whereas 1 mU of RNaseH is sufficient to amplify 1 ng of
plasmid in rhPCR using cycle times of 30 sec. Therefore we used 10
units in a 10 uL reaction and long extension times (20 min) during
the first 2 cycles followed by fast cycling: 95.degree. C. 5 min;
(95.degree. C.-15 s, 55.degree. C.-10 min, 62.degree. C.-10
min).times.2 cycles; (95.degree. C.-15 s-62.degree. C.-30 s;
70.degree. C.-155).times.40 cycles. After EndolV cleaves the
blocked primers during the first 2 cycles the reaction is driven by
universal primers in subsequent cycles. All target-specific primers
were at 5 nM, the two universal primers were at 300 nM. It may be
possible to shorten the annealing time for the first two cycles
using higher activity endonuclease.
[0059] The experiments used one of the first 3 oligos as a forward
primer: 1. control regular non-modified primer, 2. THF /idSp/, aka
dSpacer and 3. C3 /iSpC3/ with a regular reverse primer (#4) at 5
nM in a close tube reaction with the universal detection primers
(#5 and #6). The last oligo (#7) is an artificial template that was
detected; all oligos are shown in Table 1.
TABLE-US-00001 TABLE 1 1. c1_RS133_RM2204-1
TGTGCCGAACGTGTACCAAtCCAATATGCCAGGTGCCATGGTGCTTCC GGCGGTAC (SEQ ID
NO: 1) 2. c1_RS133_RM2204-152
TGTGCCGAACGTGTACCAAtCCAATATGCCAGGTGCcatggcttgcag
ctccTGGTG/idSp/TTCCGGCGGTACA/3SpC3/ (SEQ ID NO: 2) 3.
c1_RS133_RM2204-155
TGTGCCGAACGTGTACCAAtCCAATATGCCAGGTGCCATGGTGCTTCC
GGCGGTAC/iSpC3/ctttaggtcctttcc/3SpC3/ (SEQ ID NO: 3) 4.
EML4_1725_46_RM2204-4 TTGTCTCTGCGACCCATCAAGTGGAGTCATGCTTATATGGAGCAA
(SEQ ID NO: 4) 5. R5600-RM2204Fz-87
/56-FAM/TCCAATATG/ZEN/CCAGGTGCCA/ ZEN/TTGTCTCTGCGACCCATCAA (SEQ ID
NO: 5) 6. RS133_RM2204I-40 cgTGTGCCGAACGTGTACCAAt (SEQ ID NO: 6) 7.
EML4_1725_at_c1I-153~10{circumflex over ( )}5 copies of artificial
template GTGGAGTCATGCTTATATGGAGCAAAACTACtGTAGAGCCCACACCtG
GGAAAGGACCTAAAGTGTACCGCCGGAAGCACCAggagctgcaagcca tgca/3SpC3 (SEQ ID
NO: 7)
[0060] Endonuclease-dependent PCR is similar to rhPCR developed by
IDT, except using a different base modification (C3/THF vs. RNA)
and a different cleavage enzyme: EndolV vs. RNase H. One difference
is that rhPCR is using only target-specific primers and therefore
sufficiently active RNase H must be present during late cycles to
drive the reaction when there is a very large number of amplicons
being generated. When using Endo IV, enzymatic cleavage is required
only during the first (if using only one blocked primer per target)
or the first two cycles (if using both forward and reverse blocked
primers). One can also use rhPCR with a very small amount of RNAase
H enzyme, as its activity is only needed during early PCR cycles to
cleave a small number of amplicons. Tth EndolV has a low activity
that is not sufficient to drive PCR at late stages, though
endonucleases from different thermophilic bacteria, e.g., Pfu, may
have a higher activity.
[0061] Endonuclease IV does not cleave single stranded DNA. Thus, a
mismatch next to the cleavage site that causes a disruption in
Watson-Crick base-pairing slows down cleavage. This can be used to
detect mutations and SNPs. For example, one can use a mutation
specific primer where the base next to the cleavage site targets a
mutation. In case when the mutation-specific base is upstream of
the cleavage site, there would be a mismatch at the newly generated
3'OH end of the primer. The specificity of the PCR will depend on
two enzymatic steps: Endo IV cleavage at a mismatch and polymerase
extension at the same mismatch; traditional allele-specific PCR
depends only on the specificity of polymerase. In this case the
specificity is determined by the first cycle; after mismatch
extension the amplicon caries the "mutated" base from the primer.
Cleavage next to a 3'-terminal phosphate (due to diesterase
activity) with the 3'-base of the primer being specific to the
mutation would be an example of the specificity of the assay being
determined by two independent enzymatic steps in the first PCR
cycle. It should be noted that the efficiency of endonuclease
cleavage at the 3' end of a primer can be significantly increased
by using an enhancer oligo downstream from the blocked primer, see
Kutyavin et al., Nucleic Acids Research, 2006, 34, No. 19 e128. One
can also use an enhancer oligo for endonuclease dependent PCR. In
case 3'-blocked primer has 3'-phosphate the enhancer oligo can be
abut with the 3'-blocked primer. In case a 3'-C3 block is used,
there may be a single base gap between the 3'-end of the blocked
primer and the 5'-end of the enhancer oligo. In both cases EndolV
is presented with dsDNA template and can cleave off the blocking
moiety. Having mutation-specific base in the primer downstream from
the cleavage site has single enzyme (endonuclease) specificity, but
this specificity is exponential when blocked target specific
primers drive the PCR: e.g., a 20% mispriming over 10 cycles
generates a marginal amplification: (1.2).sup.10 is much smaller
than 2.sup.10.
[0062] The inventors found that 3'-exonuclease (AKA proof reading)
activity of polymerase by itself is sufficient to remove the
3'-blocking from primers even if the 3'-end is matching the
template. In addition, this exo+ activity is sufficient to drive
PCR at late cycles, so that one can run [multiplex] PCR without
universal primers; blocked target-specific primers are cleaved
efficiently enough to generate a detectable signal. FIG. 7 shows
the performance of C3-blocked compared to regular primer pairs for
the human gDNA GNAS complex on chromosome 20: EvaGreen signal in
qPCR (FIG. 7a) shows amplification and melt curves of dsDNA PCR
amplicons (FIG. 7b) indicate if desired gDNA (high Tm) or primer
dimers were amplified (low Tm). As expected, polymerase with the
3'-exonuclease activity (Q5 from NEB was used), but not regular
polymerase that lacks 3'-exonuclease activity generated signal
using C3-blocked primers. In this experiment the C3-blocked primers
were perfectly complementary to human gDNA. There is a small loss
of PCR efficiency for blocked primers that have 1.5 cycles higher
Ct than unblocked ones. The inventors observed that non-template
control (NTC, no human gDNA, -gDNA) reactions do not form primer
dimers (flat line in FIG. 7b), if blocked primers are used, but
regular primer do generate low Tm.about.81 C melt curve indicating
primer dimer formation. This experiment demonstrates that one can
run regular two primers per locus PCR amplification (without
universal primers) using blocked primers perfectly matching the
target DNA using 3'-exo+ DNA polymerase.
[0063] FIG. 8 shows the schema for the closed tube PCR enrichment
for NGS using blocked primers. Multiple blocked primers at low 1
nM-50 nM concentrations are multiplexed together with universal
primers. The target (locus) specific primers have universal tags
and the 5' end and optionally DBR (see Casbon et. al)--random
molecular tags. During the first two PCR cycles with long annealing
times, typically between 1 and 15 minutes, primers at low
concentrations have enough time to anneal to the target regions.
The exonuclease unblocks the annealed primers and polymerase
extends them. High fidelity polymerases (to minimize PCR errors)
that have 3'-exonuclease activity are typically used for NGS PCR;
so a single enzyme can perform both steps: primer unblocking and
extension. Universal primers cannot anneal during the first two
cycles because amplicons with regions complementary to universal
tags are generated only at cycle 2. In case DBRs are used, each
strand of DNA present in the sample acquires a pair of two unique
molecular bar-codes at both ends of the amplicon. After 2 cycles
the primer annealing conditions are shifted to a short annealing at
a lower temperature, e.g., 10-60 seconds at 55-64.degree. C. These
conditions favor the annealing of the universal primers (present at
high concentrations) over the target-specific blocked primers.
Optionally, the universal primers can also be blocked. Depending on
the number of amplicons in the multiplex and the desired sequencing
depth, usually 4 to 96 (or more) samples can be pooled and
sequenced together in a single lane. In this case universal primers
may contain so called indexes or sample bar codes (SBCs), to
identify each sample in the pool. Occasionally target-specific
primers anneal and extend in later cycles (after cycle 2)
incorporating a new DBR at one end of the amplicon. But it is
unlikely that this would occur at both ends of the amplicon; one
will still be able to match individual strands that were present in
the original sample to reads using one of the two DBRs in each
read. Small differences in efficiencies for different amplicons in
multiplex PCR after exponential amplification can generate vastly
different number of molecules for each amplicon (and different NGS
coverage). The inventors propose a simple method to normalize PCR
by slowing down the cooling from the melting to the annealing
temperature at late PCR cycles. Starting cycle 20 (the starting
cycle depends on the initial amount of amplifiable DNA) a
80.degree. C. degree step typically between 15-sec and 2 minutes is
introduced between melting and annealing steps. This way, the
opposite strands of abundant amplicons would mostly reanneal and
not amplify in subsequent cycles; the rate of reannealing is
proportional to square of their concentration. The temperature for
this intermediate step is much higher than the Tm for primers, but
lower than the Tm for the amplicons; typically this C.sub.0t
temperature is between 70.degree. C. and 85.degree. C. During the
C.sub.0t step, the less abundant amplicons do not reanneal much and
continue amplification. Essentially we are lowering the PCR plateau
for the abundant amplicons that are mostly melting and reannealing
at late cycles and not consume the PCR reagents, so that slower
amplicons have more PCR cycles to catch up. The total number of PCR
cycles can also be increased to 40-55.
[0064] In a typical experiment DNA from each sample is mixed with
universal primers containing sample barcodes, pooled blocked
primers and the PCR mix. After PCR all wells are pooled together
and cleanup is usually performed, e.g., using SPRI (solid phase
reversible immobilized) beads. The key advantage of this "closed
tube" protocol is that wells are opened after sample bar codes
(indexes) were attached to the amplicons eliminating the risk of
carry over contamination between samples. In addition to minimize a
chance of carry over contamination between different experiments
one can employ a regular dUTP/UDG (uracil DNA glycosylase) method
(Longo et. al. Gene, 93 pp125-8, 1990). Finally, we would like to
note here that it is possible to run 2 cycles of PCR first and
then, after an optional clean-up, add universal sample bar-coded
primers to the reaction and continue PCR. The chance of carry over
contamination after two cycles is low, but this workflow is less
convenient than the closed tube approach we describe above.
[0065] Previously, investigators (Bi and Stambrook, "Detection of
known mutation by proof-reading PCR", Nucleic Acids Research, 1998,
26, pp 3073-3075 and Lin-Ling et al. "Single-base discrimination
mediated by proofreading inert allele specific primers", J Biochem
Mol Biol. 2005, 38, pp24-7) used primers with a mismatch at the
3'-end (it can also be up to 6 bases away) in PCR with exo+
polymerases. Blocked primers with intentional mismatches at or near
the 3' end can also be used for the NGS enrichment, e.g., when
using 3'-NH2 or 3'-dideoxy base. This "intentional mismatch" method
would be useful to amplify several mutations in the same position
or same codon or in some cases even adjacent codons using a single
wild-type (normal) primers: predominantly mutated molecules that
have a mismatch will amplify.
[0066] Commercially-available thermostable DNA polymerases
generally have either 5' or 3' exonuclease activities, but not
both. Therefore, to use DNA detection using 5'-nuclease (TaqMan, or
methods described in U.S. patent application Ser. No. 12/931,803)
and 3'-blocked primers one can use a mixture of polymerase with
5'-exonuclease activity and either a separate enzyme with the
3'-exonuclease activity or a polymerase with 3'exonuclease
activity. Mixtures of 3'-exo+ and Taq polymerase (5'-exo+ and
3'-exo-) are often used for long range PCR: most of extensions are
performed by the more processive Taq, but if it incorporates a
mismatch and dissociates from the template the 3'-exo+ enzyme can
correct the mismatch. Thus 3'-blocked primers can be employed to
generate 5'-nuclease signal in qPCR using a mixture of 3'-exo+ and
5'-exo+ polymerases.
[0067] In many genes several mutations in the same or adjacent
codons result in a similar phenotype. Examples include multiple
activating somatic mutations in cancer in KRAS codons 12 and 13:
12ALA, 12ASP, 12ARG, 12CYS, 12SER, 12VAL and 13ASP. Activating
somatic mutations in BRAF gene codon 600: V600E and V600K is
another example. Similarly, many drug resistance mutation in
bacteria and viruses occur in the same or nearby codons, e.g., HIV
becomes resistant to neverapine (NVP) if any one of these amino
acid changes in codons 188 or 190 has occurred: Y188[LHC] or
G190[ASE]. Mycobacterium tuberculosis (MTB) becomes resistant to
rifampicin, if codon 526 in rpoB gene is mutated to encode one of 5
amino acids: H526[LRYDN]. When using multiplexed mutation-specific
PCR and detecting all nearby mutations, the target-specific primers
share similar sequences; they "overlap" in the target region they
anneal to. This may cause a loss of sensitivity as these primers
are competing with each other. For example, if six
mutation-specific primers target mutations in the same codon only
one primer is a perfect match for a given mutation, but other five
primers have a small thermodynamic disadvantage: they have only one
or two mismatches when binding to the same mutated target region.
FIG. 9 shows an example of three primers that target three closely
spaced mutations, shown as "X": they anneal to the shared region in
the target DNA. The loss of sensitivity should be less than
3.times. in the first cycle and it is, generally, not detrimental
to PCR, as less than 2 (2.sup.2=4) additional cycles will be
required to overcome a 3x loss in sensitivity. But if this
competition between primers continues to the end of PCR, the loss
of sensitivity would be substantial. The 5' M.sub.1-3-tags in FIG.
9a help to minimize primer competition starting cycle 3. At cycle 1
one of the M-tags that matches the mutation is incorporated into
the amplicon. At cycle 2 this M-tag is copied. Starting cycle 3 the
mutation-specific primer that has extended at cycle 1 has a
significant thermodynamic advantage over the competing primers: it
forms dsDNA over 100% of its length, including the M-tag; the
competing primers have a mismatched M-tags and much lower Tm. One
can increase the annealing temperature starting cycle 3 or use high
annealing temperature (relative to the predicted Tm of
allele-specific parts of the primers) starting from cycle 1.
[0068] In case of allele-specific PCR with mutation-specific and
universal primers, after the first two cycles that incorporate
universal tags, the universal primers continue amplification to
generate signal with little competition from low concentration
target-specific primers. But in some cases, e.g., rhPCR, the
specificity of mutation detection increases exponentially, if
target-specific rhPCR primers, rather than the universal ones
continue amplification beyond the first two cycles. To achieve
this, we propose using additional 5'-tags in mutation-specific
primers, tags M.sub.1-3 in FIG. 9. Each mutation-specific primer
will be incorporates a different M tag in the first cycle and
complements or this tag at the 2nd cycle. We then use a high
annealing temperature, e.g., 68-74.degree. C. (FIG. 9c shows an
example), so that the matching mutation-specific primers that were
extended in the first two cycles anneal and hybridize with their
5'-tag and thus have a significant thermodynamic advantage over
mismatched mutation-specific primers. At high annealing temperature
the matching mutation-specific primers that "won" the competition
during the first cycle gains an advantage over competing
mutation-specific primers that have mismatched universal tags.
Thus, we prevent the exponential loss of sensitivity, but preserve
the exponential gain in specificity for mutation-specific
rhPCR.
[0069] FIG. 9b shows how this method can be combined with encoding
detection reaction, described above. In this case mutation-specific
M.sub.1-3 tags become middle tags between the target-specific
3'-regions and universal 5'-tags. The high annealing temperature
after cycle two, also helps to prevent priming by universal primers
in early cycling that we described above, exponentially increasing
specificity of rhPCR or exonuclease-dependent PCR with mutated base
downstream from the cleavage site. FIG. 9c shows cycling protocol
used: 2 cycles with 62.degree. C. annealing, followed by 8 cycles
with 70.degree. C. annealing, both using long 2 minutes
anneal-extend time and followed by fast 40 cycles with 30 sec
@62.degree. C. and 15 sec @70.degree. C.
[0070] FIG. 10 shows multiplex rhPCR/qPCR detection of six
mutations in codon 526 (445) of Mycobacterium tuberculosis (MTB)
rpoB gene that cause resistance to rifampicin (RIF). Closed tube
multiplex PCR contained: (a) six mutation-specific primers (Table
2), (b) a single shared reverse primer; (c) a separate primer pair
for control MTB region with different universal tags (so that this
control region is detected by HEX signal); (d) two labeled primers
with FAM/HEX dye and quencher (see oligo #5 in Table 1 as an
example) and (e) a regular primer as shown in FIG. 4c (dashed
line), see U.S. patent application Ser. No. 12/931,803. Blocked
mutation specific primers with additional competition tags and Ct
values for mutated and wild-type MTB are shown in Table 2. The
mutation-specific primers contain several functional parts from 5'
to 3': same universal tags to generate the same dye signal,
different for each mutation-specific primer non-template
"competition" tags (underlined), MTB-specific region: DNA, an RNA
base ("rN" in italics) and C3-blocked 3'-end that has either 3' C3
or two internal C3 spacers (underlined).
TABLE-US-00002 TABLE 2 Use of blocked primers with "completion"
tags for mutation detection. Mutat- ion Primer Sequences FAM HEX
.DELTA.Ct H526D- CAAGCTGATCCGTACAACGCTGACGT 10.24 14.44 4.2 445gAC
CCCGCTGTCGGGGTTGACCrGA/ iSpC3//iSpC3/A (SEQ ID NO: 8) H526Y-
CAAGCTGATCCGTACAGTCGTGCACA 9.78 16.13 6.35 445tAC
CGCTGTCGGGGTTGACCrUACAA/ 3SpC3/ (SEQ ID NO: 9) H526L-
CAAGCTGATCCGTACAGAGGACCATG 9.01 17.01 8 445CtC
CTGTCGGGGTTGACCCrUCAAG/ 3SpC3/ (SEQ ID NO: 10) H526N-
CAAGCTGATCCGTACAGAGCTGtAGT 10.17 16.25 6.08 445aAC
CCGCTGTCGGGGTTGACCrAA/ iSpC3//iSpC3/A (SEQ ID NO: 11) H526S-
CAAGCTGATCCGTACATCCAATAACG 12.98 14.97 1.99 445agC
TGTCGGGGTTGACCrAGCAAA/ 3SpC3/ (SEQ ID NO: 12) H526R-
CAAGCTGATCCGTACAACCACAGTGT 10.31 13.78 3.48 445CgC
CGCTGTCGGGGTTGACCCrGC/ iSpC3//iSpC3/G (SEQ ID NO: 13) MTB- 12.94
13.6 0.66 WT gDNA
[0071] The qPCR cycling (FIG. 9b) has four stages: [0072] 1.
Denaturation: 95.degree. C., 2:00 Min [0073] 2. Stage 2: 2 cycles:
(95.degree. C., 15 sec, 58.degree. C. 1:00 Min, 71.degree. C. 40
sec [0074] 3. Stage 3: 20 cycles: (95.degree. C., 10 sec,
76.degree. C., 20 sec, 74.degree. C., 40 sec) [0075] 4. Stage 4: 30
cycles: (95.degree. C., 10 sec+Plate Read, 52.degree. C., 40 sec,
70.degree. C., 1:00 Min+Plate Read)
[0076] During the first 2 cycles there is competition between the
six primers: if a primer that does not match the mutation in the
template anneals, it may stay annealed long enough and not let the
matching primer to anneal, causing a loss of sensitivity. At cycle
2 the 5' "competition" tag on the primer than extended at cycle 1
is copied. At stage 3, starting cycle 3, we use a high annealing
temperature, so that the matching primer that extended at cycle 1
has a perfectly matching competition tag and much higher Tm than
the five primers specific for the other five mutations. Also at
high annealing temperatures, the PCR is driven by long rhPCR
primers (FIG. 1a), rather than the short universal primer in FIG.
1c. At stage 4, at a lower annealing temperature, the annealing of
the universal primers present at high concentrations is favored and
fluorescent signal is being generated.
[0077] The method and compositions described above can be used for
highly multiplexed PCR followed by sequencing (NGS), array
hybridization, electro-chemical surface detection or
electrophoresis (CE). In case of NGS, one can envision multiplexing
a large number of blocked target-specific primers with two
universal primers that have sequencing tags, e.g., so called P5 and
P7 in case of Illumina and optional bar-codes that are used to
identify different samples. This would be a simple sample prep
protocol that does not require complex additional ligation and
other steps that require opening tubes after PCR and risk carry
over contamination. Multiplex PCR inevitably generates a lot of
primer dimers, but blocked primers diminish this side reaction.
Additionally, the C.sub.ot method described above can be used at
late cycles to normalize the amount of different amplicons in
multiplex PCR.
Definitions
[0078] As used herein, "Target nucleic acids"or "target" are
DNA/RNA molecules present in a sample prior to any changes in the
nucleic acid sequence composition during sample processing. A
certain location target DNA/RNA is called locus.
[0079] As used herein, a "primer" or "unblocked primer" is an oligo
with its 3' termini extendable by a polymerase after it anneals to
the template. In some embodiments, primers can have one or several
labels.
[0080] As used herein, a "3'-blocked (blocked) primer" cannot be
extended by a polymerase: a 3'-OH is missing or a chemical moiety
is used to block polymerase extension. For example, primer may have
3'-phosphate, C3 spacer (3' Propyl), Spacer 9/18 either at the 3'
end or close to it (see Table 2 for examples), 1',2'-Dideoxyribose
(dSpacer), 3' Hexanediol, 2'-3'-Dideoxy, 3'-deoxy bases, inverted
dT (see modified bases and spacers by IDT), 3'-amine or any other
moiety that disables polymerase extension, see for example Table 2
in Lin-Ling et al. Single-base discrimination mediated by
proofreading inert allele specific primers. Lin-Ling et al., J
Biochem Mol Biol. 2005 Jan. 31; 38(1):24-7
[0081] As used herein, a "mutation (allele) specific primer" has
the 3'-end specific for the target mutations, rather the normal
(wild type) bases and optionally additional intentional mismatches
of modified bases near the 3'-end.
[0082] As used herein, a "probe" is an oligo that carries at least
one label that is used to generate a detectable signal. Probes have
a blocked 3' end to prevent their extension by a polymerase.
[0083] As used herein, "qPCR" is quantitative Polymerase Chain
Reaction, where signal is measured during and/or at the end of
PCR.
[0084] As used herein, a "universal tag" is a part of the primer or
amplicon with an artificial sequence that does not match the target
nucleic acid, with exception of very short tags that either
intentionally or accidentally match target nucleic acid.
[0085] As used herein, a "universal primer/probe" is a primer
and/or probe that comprises one or more universal tags that do not
match the target nucleic acid and by chance or intentionally may
comprise a very short stretch of target nucleic acid that occurs at
the locus that is detected.
[0086] As used herein, "encoding or linking reaction" is a step
within the target nucleic acid detection that generates "encoded
DNA molecules with universal tags". PCR pre-amplification with 5'
tailed (tagged) primers is an example of an encoding or linking
reaction.
[0087] As used herein, a "template" is a nucleic acid to which
primers, probes, or amplicons anneal; the sequence of the template
can be either target or complementary to universal tags.
[0088] As used herein, "first PCR cycles" are 1, 2 or more cycles
when polymerase extends target-specific primers.
[0089] As used herein, a "closed tube PCR or reaction" is a
reaction that generates signal or incorporates sample bar-codes for
NGS without the need to open a well/tube after PCR, thus
eliminating possibility of carry over contamination in an
experiment that processes several samples in parallel.
[0090] As used herein, "cleavage or unblocking" is an enzymatic
step that modifies a blocked primer opening up a 3'-OH group that
can be extended by polymerase after this blocked primer forms a
double-stranded DNA annealing to the template. Different enzymes
can be used for the unblocking: Endonuclease IV (EndolV), Human
apurinic/apyrimidinic (AP) endonuclease, APE 1, other
3'-exonucleases, and DNA polymerases with 3'-exonuclease (exo+)
activity. RNase H cleaves RNA bases and several DNA repair enzymes
can cleave at a modified base leaving an extendable 3'-OH.
Target Nucleic Acid Sources and Molecular Biology Reagents and
Techniques
[0091] As will be appreciated, target nucleic acids that find use
in the invention can be obtained from a wide variety of sources.
For example, target nucleic acids can be obtained from biological
or laboratory samples including cells, tissues, lysates, and the
like. In certain aspects, the source of target nucleic acids
includes cells or tissues from an individual with a disease, e.g.,
cancer or any other disease of particular interest to the user.
[0092] A plethora of kits are commercially available for the
purification of target nucleic acids from cells or tissues, if
desired (see, e.g., EASYPREP.TM., FLEXIPREP.TM., both from
Pharmacia Biotech; STRATACLEAN.TM. from Stratagene; QIAPREP.TM.
from Qiagen). In addition, essentially any target nucleic acid can
be custom or standard ordered from any of a variety of commercial
sources.
[0093] General texts which describe molecular biological techniques
for the isolation and manipulation of nucleic acids include Berger
and Kimmel, Guide to Molecular Cloning Techniques, Methods in
Enzymology volume 152 Academic Press, Inc., San Diego, Calif.
(Berger); Sambrook et al., Molecular Cloning: A Laboratory Manual
(3rd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring
Harbor, N.Y., 2001 ("Sambrook") and Current Protocols in Molecular
Biology, F. M. Ausubel et al., eds., Current Protocols, a joint
venture between Greene Publishing Associates, Inc. and John Wiley
& Sons, Inc., (supplemented through the current date)
("Ausubel")).
[0094] Labeling strategies for labeling nucleic acids and
corresponding detection strategies can be found, e.g., in Haugland
(1996) Handbook of Fluorescent Probes and Research Chemicals Sixth
Edition by Molecular Probes, Inc. (Eugene Oreg.); or Haugland
(2001) Handbook of Fluorescent Probes and Research Chemicals Eighth
Edition by Molecular Probes, Inc. (Eugene Oreg.) (Available on CD
ROM).
[0095] A number of embodiments of the present invention utilize the
principles of polymerase chain reaction (PCR). PCR methods and
reagents, as well as optimization of PCR reaction conditions (e.g.,
annealing temperatures, extension times, buffer components, metal
cofactor concentrations, etc.) are well known in the art. Details
regarding PCR and its uses are described, e.g., in Van Pelt-Verkuil
et al. (2010) Principles and Technical Aspects of PCR Amplification
Springer; 1st Edition ISBN-10: 9048175798, ISBN-13: 978-9048175796;
Bustin (Ed) (2009) The PCR Revolution: Basic Technologies and
Applications Cambridge University Press; 1st edition ISBN-10:
0521882311, ISBN-13: 978-0521882316; PCR Protocols: A Guide to
Methods and Applications (Innis et al. eds) Academic Press Inc. San
Diego, Calif. (1990) (Innis); Chen et al. (ed) PCR Cloning
Protocols, Second Edition (Methods in Molecular Biology, Volume
192) Humana Press; and in Viljoen et al. (2005) Molecular
Diagnostic PCR Handbook Springer, ISBN 1402034032.
[0096] As noted herein, the universal detection steps of the
present invention can be performed in real-time, e.g., where one or
more detectable signals (if any) corresponding to the presence or
amount of one or more target nucleic acids are detected at the
conclusion of one or more PCR cycles prior to completion of thermal
cycling. Real-time/quantitative PCR techniques are known in the
art. Detailed guidance can be found in, e.g., Clementi M. et al
(1993) PCR Methods Appl, 2:191-196; Freeman W. M. et al (1999)
Biotechniques, 26:112-122, 124-125; Lutfalla G. and Uze G. (2006)
Methods Enzymol, 410: 386-400; Diviacco S. et al (1992) Gene, 122:
313-320 Gu Z. et al (2003)/. Clin. Microbiol, 41: 4636-4641.
Real-time (e.g., quantitative) PCR detection chemistries are also
known and have been reviewed in, e.g. Mackay J., Landt O. (2007)
Methods Mol. Biol, 353: 237-262; Didenko V. V. (2001)
BioTechniques, 31, 1106-1121; and Mackay L M. et al (2002) Nucleic
Acids Res., 30: 1292-1305, which are incorporated herein by
reference in their entireties for all purposes.
[0097] While the foregoing invention has been described in some
detail for purposes of clarity and understanding, it will be clear
to one skilled in the art from a reading of this disclosure that
various changes in form and detail can be made without departing
from the true scope of the invention. For example, all the
techniques and apparatus described above can be used in various
combinations. All publications, patents, patent applications,
and/or other documents cited in this application are incorporated
by reference in their entirety for all purposes to the same extent
as if each individual publication, patent, patent application,
and/or other document were individually indicated to be
incorporated by reference for all purposes.
Sequence CWU 1
1
13156DNAArtificial Sequencesynthetic oligonucleotide primer
1tgtgccgaac gtgtaccaat ccaatatgcc aggtgccatg gtgcttccgg cggtac
56272DNAArtificial Sequencesynthetic oligonucleotide
primermisc_feature(58)..(58)N is dSpacer (abasic site
mimic)misc_feature(72)..(72)N is C3 spacer (abasic site mimic)
2tgtgccgaac gtgtaccaat ccaatatgcc aggtgccatg gcttgcagct cctggtgntt
60ccggcggtac an 72373DNAArtificial Sequencesynthetic
oligonucleotide primermisc_feature(57)..(57)N is C3 spacer (abasic
site mimic)misc_feature(73)..(73)N is C3 spacer (abasic site mimic)
3tgtgccgaac gtgtaccaat ccaatatgcc aggtgccatg gtgcttccgg cggtacnctt
60taggtccttt ccn 73445DNAArtificial Sequencesynthetic
oligonucleotide primer 4ttgtctctgc gacccatcaa gtggagtcat gcttatatgg
agcaa 45539DNAArtificial Sequencesynthetic oligonucleotide primer
5tccaatatgc caggtgccat tgtctctgcg acccatcaa 39622DNAArtificial
Sequencesynthetic oligonucleotide primer 6cgtgtgccga acgtgtacca at
227101DNAArtificial Sequencesynthetic oligonucleotide
templatemisc_feature(101)..(101)N is C3 spacer (abasic site mimic)
7gtggagtcat gcttatatgg agcaaaacta ctgtagagcc cacacctggg aaaggaccta
60aagtgtaccg ccggaagcac caggagctgc aagccatgca n 101850DNAArtificial
Sequencesynthetic oligonucleotide primermisc_feature(46)..(46)N is
ribo-Gmisc_feature(48)..(49)N is C3 spacer (abasic site mimic)
8caagctgatc cgtacaacgc tgacgtcccg ctgtcggggt tgaccnanna
50949DNAArtificial Sequencesynthetic oligonucleotide
primermisc_feature(44)..(44)N is ribo-Umisc_feature(49)..(49)N is
C3 spacer (abasic site mimic) 9caagctgatc cgtacagtcg tgcacacgct
gtcggggttg accnacaan 491048DNAArtificial Sequencesynthetic
oligonucleotide primermisc_feature(43)..(43)N is
ribo-Umisc_feature(48)..(48)N is C3 spacer (abasic site mimic)
10caagctgatc cgtacagagg accatgctgt cggggttgac ccncaagn
481149DNAArtificial Sequencesynthetic oligonucleotide
primermisc_feature(45)..(45)N is ribo-Amisc_feature(47)..(48)N is
C3 spacer (abasic site mimic) 11caagctgatc cgtacagagc tgtagtccgc
tgtcggggtt gaccnanna 491247DNAArtificial Sequencesynthetic
oligonucleotide primermisc_feature(41)..(41)N is
ribo-Amisc_feature(47)..(47)N is C3 spacer (abasic site mimic)
12caagctgatc cgtacatcca ataacgtgtc ggggttgacc ngcaaan
471349DNAArtificial Sequencesynthetic oligonucleotide
primermisc_feature(45)..(45)N is ribo-Gmisc_feature(47)..(48)N is
C3 spacer (abasic site mimic) 13caagctgatc cgtacaacca cagtgtcgct
gtcggggttg acccncnng 49
* * * * *