U.S. patent application number 17/392531 was filed with the patent office on 2021-11-25 for isothermal methods for amplifying nucleic acid samples.
This patent application is currently assigned to Tangen Biosciences, Inc.. The applicant listed for this patent is Tangen Biosciences, Inc.. Invention is credited to John Davidson, John R. Nobile.
Application Number | 20210363575 17/392531 |
Document ID | / |
Family ID | 1000005754865 |
Filed Date | 2021-11-25 |
United States Patent
Application |
20210363575 |
Kind Code |
A1 |
Nobile; John R. ; et
al. |
November 25, 2021 |
ISOTHERMAL METHODS FOR AMPLIFYING NUCLEIC ACID SAMPLES
Abstract
The description provides two-stage methods of nucleic acid
amplification and detection reactions, which are useful for rapid
pathogen detection or disease diagnosis. In particular, the
description provides a method comprising a first-stage slow rate
amplification reaction followed by a plurality of second-stage fast
rate amplification reactions that are simultaneously monitored in
real-time, and wherein a rapid rate of amplification is indicative
of the presence of a site of interest.
Inventors: |
Nobile; John R.; (Guilford,
CT) ; Davidson; John; (Guilford, CT) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Tangen Biosciences, Inc. |
Branford |
CT |
US |
|
|
Assignee: |
Tangen Biosciences, Inc.
Branford
CT
|
Family ID: |
1000005754865 |
Appl. No.: |
17/392531 |
Filed: |
August 3, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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16509452 |
Jul 11, 2019 |
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17392531 |
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16509447 |
Jul 11, 2019 |
11111531 |
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16509452 |
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15326604 |
Jan 16, 2017 |
10364458 |
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PCT/US2015/040792 |
Jul 16, 2015 |
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16509452 |
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62025345 |
Jul 16, 2014 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
B01L 7/52 20130101; B01L
7/525 20130101; C12Q 1/6858 20130101 |
International
Class: |
C12Q 1/6858 20060101
C12Q001/6858; B01L 7/00 20060101 B01L007/00 |
Claims
1-34. (canceled)
35. A method of detecting a pathogenic organism from a biological
sample comprising a. providing a composition comprising a target
nucleic acid template from a pathogenic organism and a combination
of site-specific primers that anneal to the target nucleic acid
template near a region of interest to be amplified; b. performing a
first isothermal reaction to amplify the region of interest,
thereby forming a primary amplicon; c. dividing (b) into at least
two secondary reactions, and including in at least one of the
reactions one or more site-specific secondary primer that is
complementary to a site-specific primer binding site that may be
present within the primary amplicon and defines a site of interest
within the region of interest; d. performing a second isothermal
reaction (second-stage reaction) thereby accelerating the
amplification of the region of interest only if the site-specific
primer binding site is complementary to the site-specific primer;
and e. detecting and comparing the amplification rates of the at
least two secondary reactions, wherein an enhanced relative rate of
amplification in the reaction with the secondary primer indicates
the presence of the site of interest in a pathogenic organism.
36. The method of claim 35, wherein in step e), the detecting and
comparing is in real time.
37. The method of claim 35, wherein the pathogenic organism
detected is a virus, bacteria, archae, protozoa or multicellular
organism.
38. The method of claim 35, wherein the pathogenic organism
detected is a virus.
39. The method of claim 35, wherein the pathogenic organism
detected is a bacteria.
40. The method of claim 35, wherein the pathogenic organism
detected is a coronavirus.
41. The method of claim 36, wherein the amplification reaction
mixture comprises fluorescently labeled dNTPs, a fluorescent DNA
intercalating dye, bioluminescent, chemiluminescent,
electrochemical or other reporter system as a means to follow the
extent of amplification in real-time.
42. The method of claim 35, wherein the isothermal nucleic acid
amplification method is selected from Nucleic Acid Sequence Based
Amplification (NASBA), Transcription Mediated Amplification (TMA),
Helicase Dependent Amplification (HDA), Recombinase polymerase
amplification (RPA), Strand Displacement Amplification (SDA),
Loop-mediated Isothermal Amplification (LAMP), Chimera Displacement
Reaction (RDC), Isothermal Chimeric Amplification of Nucleic Acids
(ICAN), SMart Amplification Process (SMAP), Linear Isothermal
Multimerization Amplification (LIMA), or Self Extending
Amplification (SEA).
43. The method of claim 35, wherein the first nucleic acid
amplification is Loop-mediated Isothermal Amplification (LAMP).
44. The method of claim 35, wherein step (a) includes a forward and
reverse loop-forming primer.
45. The method of claim 44, wherein step (a) includes a forward and
reverse displacement primer.
46. The method of claim 35, wherein the second isothermal nucleic
acid amplification reaction is LAMP-STEM.
47. The method of claim 35, wherein the method comprises dividing
(b) into at least an additional secondary reaction, wherein the
additional secondary reaction includes a mismatch secondary
primer.
48. The method of claim 45, wherein the mismatch primer comprises a
3' end nucleotide mismatch or 3' end nucleotide complementary to an
allele, mutation or polymorphism different from the site-specific
primer.
49. The method of claim 35, wherein step (e) comprises detecting
and comparing in real-time the amplification rates of all secondary
reactions, wherein an enhanced relative rate of amplification as
compared to the other two reactions indicates the presence of the
site of interest that is complementary to the secondary primer.
50. The method of claim 35, wherein the step of performing the
second nucleic acid amplification reaction includes amplification
in the presence of a fluorescent label or dye, thereby labeling the
amplification products.
51. The method of claim 50, wherein the step of detecting and
comparing in real-time the amplification rates includes detecting
and comparing a fluorescent signal from each of the reactions.
52. The method of claim 35, wherein a slow-rate isothermal
pre-amplification is performed in the first-stage followed by
multiple, discrete second-stage amplification and detection
reactions performed in parallel directly on the products from the
first-stage primary amplicon amplification product.
53. The method of claim 35, wherein the first-stage amplification
reaction comprises site-specific primers such that a first-stage
pre-amplification reaction is selective for a particular site of
interest, and only if that site or region exists in the sample will
rapid amplification of the template proceed at the second stage
amplification reaction.
54. The method of claim 35, wherein the second-stage amplification
reaction comprises multiple site-specific primers.
55. The method of claim 35, wherein an amount or volume of the
first-stage reaction is introduced directly into a plurality of
second reaction chambers.
56. The method of claim 35, further comprising the steps of
providing a first reaction chamber; performing a first-stage
pre-amplification reaction in the first reaction chamber;
introducing an amount or volume of the first-stage pre-amp reaction
directly into a plurality of second reaction chambers, wherein at
least one second reaction chamber comprises a site-specific primer,
and at least one second reaction chamber comprises a mismatched
primer; and performing in each second reaction chamber a
second-stage amplification reaction.
57. The method of claim 35, wherein the first-stage and
second-stage amplification reactions are performed sequentially in
the same reaction container or chamber.
58. The method of claim 35, wherein the target nucleic acid
template is nested within a larger amplified region.
59. The method of claim 35, wherein the first-stage amplification
reaction comprises site-specific primers such that the first-stage
amplification reaction is selective for a particular site of
interest, and wherein only if that site or region exists in the
sample will rapid amplification of the template proceed at the
second-stage amplification reaction.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of, and priority to,
U.S. Provisional Application Ser. No. 62,025,345 filed Jul. 16,
2014, entitled "Isothermal Methods for Amplifying Nucleic Acid
Samples", which is incorporated herein by reference in its
entirety.
BACKGROUND
1. Field of the Discovery
[0002] The description provides methods of nucleic acid
amplification and detection reactions, which are useful for rapid
pathogen detection or disease diagnosis.
2. Background Information
[0003] Nucleic acid analysis methods based on the complementarity
of nucleic acid nucleotide sequences can analyze genetic traits
directly. Accordingly, these methods are a very powerful means for
identification of genetic diseases, cancer, microorganisms etc.
Nevertheless, the detection of a target gene or nucleic acid
present in a very small amount in a sample is not easy, and
therefore, amplification of the target gene or its detection signal
is necessary. As such, in vitro nucleic acid amplification
technologies (NAATs) are an invaluable and powerful tool for
detection and analysis of small amounts of nucleic acid in many
areas of research and diagnosis.
[0004] NAAT techniques allow detection and quantification of a
nucleic acid in a sample with high sensitivity and specificity.
NAAT techniques may be used to determine the presence of a
particular template nucleic acid in a sample, as indicated by the
presence of an amplification product (i.e., amplicon) following the
implementation of a particular NAAT. Conversely, the absence of any
amplification product indicates the absence of template nucleic
acid in the sample. Such techniques are of great importance in
diagnostic applications, for example, for determining whether a
pathogen is present in a sample. Thus, NAAT techniques are useful
for detection and quantification of specific nucleic acids for
diagnosis of infectious and genetic diseases.
[0005] NAATs can be grouped according to the temperature
requirements of the procedure. For example, the polymerase chain
reaction (PCR) is the most popular method as a technique of
amplifying nucleic acid in vitro. This method was established
firmly as an excellent detection method by virtue of high
sensitivity based on the effect of exponential amplification.
Further, since the amplification product can be recovered as DNA,
this method is applied widely as an important tool supporting
genetic engineering techniques such as gene cloning and structural
determination. In the PCR method, however, temperature cycling or a
special temperature controller is necessary for practice; the
exponential progress of the amplification reaction causes a problem
in quantification; and samples and reaction solutions are easily
contaminated from the outside to permit nucleic acid mixed in error
to function as a template (See R. K. Saiki, et al. 1985. Science
230, 1350-1354). Other PCR-based amplification techniques, for
example, transcription-based amplification (D. Y. Kwoh, et at.
1989. Proc. Natl. Acad Sci. USA 86, 1173-1177), ligase chain
reaction (LCR; D. Y. Wu, et al. 1989. Genomics 4, 560-569; K.
Barringer, et al. 1990. Gene 89, 117-122; F. Barany. 1991. Proc.
Natl. Acad. Sci. USA 88, 189-193), and restriction amplification
(U.S. Pat. No. 5,102,784) similarly require temperature
cycling.
[0006] More recently, a number of isothermal nucleic acid
amplification techniques (iNAATs) have been developed. That is,
these techniques do not rely on thermocycling to drive the
amplification reaction. Isothermal amplification techniques
typically utilize DNA polymerases with strand-displacement
activity, thus eliminating the high temperature melt cycle that is
required for PCR. This allows isothermal techniques to be faster
and more energy efficient than PCR, and also allows for more simple
and thus lower cost instrumentation since rapid temperature cycling
is not required. For example, methods such as Strand Displacement
Amplification (SDA; G. T. Walker, et at. 1992. Proc. Natl. Acad.
Sci. USA 89, 392-396; G. T. Walker, et al. 1992. Nuc. Acids. Res.
20, 1691-1696; U.S. Pat. No. 5,648,211and EP 0 497 272, all
disclosures being incorporated herein by reference); self-sustained
sequence replication (3SR; J. C. Guatelli, et al. 1990. Proc. Natl.
Acad. Sci. USA 87, 1874-1878, which is incorporated herein by
reference); and Q.beta. replicase system (P. M. Lizardi, et al.
1988. BioTechnology 6, 1197-1202, which is incorporated herein by
reference) are isothermal reactions (See also, Nucleic Acid
Isothermal Amplification Technologies--A Review. Nucleosides,
Nucleotides and Nucleic Acids, 2008. v27(3):224-243, which is
incorporated herein by reference).
[0007] In the SDA method, a special DNA polymerase is used to
synthesize a complementary chain starting from an amplification
primer complementary to the 3'-side of a certain nucleotide
sequence template, and including one or more bumper primers
upstream of the amplification primer to displace the
double-stranded chain if any at the 5'-side of the sequence
template. Because a double-stranded chain at the 5'-side is
displaced by a newly synthesized complementary chain, this
technique is called the SDA method. The temperature-changing step
essential in the PCR method can be eliminated in the SDA method by
previously inserting a-restriction enzyme recognition sequence into
an annealed sequence as a primer. That is, a nick generated by a
restriction enzyme gives a 3'-OH group acting as the origin of
synthesis of complementary chain, and the previously synthesized
complementary chain is released as a single-stranded chain by
strand displacement synthesis and then utilized again as a template
for subsequent synthesis of complementary chain. In this manner,
the complicated control of temperature essential in the PCR method
is not required in the SDA method.
[0008] In the SDA method, however, the restriction enzyme
generating a nick should be used in addition to the strand
displacement-type DNA polymerase. This requirement for the
additional enzyme is a major cause for higher cost. Further,
because the restriction enzyme is to be used not for cleavage of
both double-stranded chains but for introduction of a nick (that
is, cleavage of only one of the chains), a dNTP derivative such as
alpha-thio dNTP should be used as a substrate for synthesis to
render the other chain resistant to digestion with the enzyme.
Accordingly, the amplification product by SDA has a different
structure from that of natural nucleic acid, and there is a limit
to cleavage with restriction enzymes or application of the
amplification product to gene cloning. In this respect too, there
is a major cause for higher cost. In addition, when the SDA method
is applied to an unknown sequence, there is the possibility that
the same nucleotide sequence as the restriction enzyme recognition
sequence used for introducing a nick may be present in a region to
be synthesized. In this case, it is possible that a complete
complementary chain is prevented from being synthesized.
[0009] Loop-Mediated Isothermal Amplification (LAMP) is another
isothermal nucleic acid amplification technique. In LAMP, the
target sequence is amplified at a constant temperature of 60 - 65
.degree. C. using either two or three primer sets, and a polymerase
with high strand displacement activity in addition to a replication
activity. (See Nagamine K, Hase T, Notomi T (2002). "Accelerated
reaction by loop-mediated isothermal amplification using loop
primers". Mol. Cell. Probes 16 (3): 223-9; and U.S. Pat. No.
6,410,278, which is incorporated herein by reference).
[0010] LAMP was originally invented and formulated as an isothermal
amplification with the strict requirement for four primers: two
loop-generating primers (FIP and BIP comprising F1, F2 and B1, B2
priming sites, correspondingly) and two "Displacement primers" (F3
and B3) (FIG. 1). However, in this manifestation the LAMP
technology was far too slow for the majority of practical
applications. In order to increase the speed of LAMP-based assays
the inventors of LAMP came up with additional "Loop primers" which,
when added in conjunction with the other primers used in LAMP,
resulted in significantly faster assays. Currently, the commonly
used manifestation of LAMP requires a total of six primers: two
loop-generating primers, two displacement primers and two "Loop
primers" (L.sub.B and L.sub.F).
[0011] Due to the specific nature of the action of these primers,
the amount of DNA produced in LAMP is considerably higher than PCR
based amplification. The reaction can be followed in real-time
either by measuring the turbidity or by fluorescence using
intercalating dyes. Dye molecules intercalate or directly label the
DNA, and in turn can be correlated to the number of copies
initially present. Hence, LAMP can also be quantitative. Thus, LAMP
provides major advantages due to its simplicity, ruggedness, and
low cost, and has the potential to be used as a simple screening
assay in the field or at the point of care by clinicians.
[0012] Primer design for LAMP assays thus requires the selection of
eight separate regions of a target nucleic acid sequence (the FIP
and BIP primers encompass two primer binding sites each), with the
BIP/FIP and Loop primers having significant restrictions on their
positioning respective to each other. "Loop primers" must be
positioned strictly between the B2 and B1 sites and the F2 and F1
sites, respectively, and must be orientated in one particular
direction. Further, significant care must be taken in primer design
to avoid primer-dimers between the six primers needed (especially
difficult as the FIP and BIP primers are generally greater than 40
nucleotides long). As a consequence, LAMP primer design is
extremely challenging, especially when targeting highly polymorphic
markers and sequences containing complex secondary structure. Also,
because LAMP uses 4 (or 6) primers targeting 6 (or 8) regions
within a fairly small segment of the genome, and because primer
design is subject to numerous constraints, it is difficult to
design primer sets for LAMP "by eye". Software is generally used to
assist with LAMP primer design, although the primer design
constraints mean there is less freedom to choose the target site
than with PCR. In a diagnostic application, this must be balanced
against the need to choose an appropriate target (e.g., a conserved
site in a highly variable viral genome, or a target that is
specific for a particular strain of pathogen).
[0013] LAMP has been observed to be less sensitive than PCR to
inhibitors in complex samples such as blood, likely due to use of a
different DNA polymerase (typically Bst DNA polymerase rather than
Taq polymerase as in PCR). LAMP is useful primarily as a diagnostic
or detection technique, but is not useful for cloning or myriad
other molecular biology applications enabled by PCR.
[0014] Also, multiplexing approaches for LAMP are relatively
undeveloped. The larger number of primers per target in LAMP
increases the likelihood of primer-primer interactions for
multiplexed target sets. The product of LAMP is a series of
concatemers of the target region, giving rise to a characteristic
"ladder" or banding pattern on a gel, rather than a single band as
with PCR. Although this is not a problem when detecting single
targets with LAMP, "traditional" (endpoint) multiplex PCR
applications wherein identity of a target is confirmed by size of a
band on a gel are not feasible with LAMP. Multiplexing in LAMP has
been achieved by choosing a target region with a restriction site,
and digesting prior to running on a gel, such that each product
gives rise to a distinct size of fragment, although this approach
adds complexity to the experimental design and protocol. The use of
a strand-displacing DNA polymerase in LAMP also precludes the use
of hydrolysis probes, e.g. TaqMan probes, which rely upon the 5'-3'
exonuclease activity of Taq polymerase.
[0015] More recently, investigators have developed a modified LAMP
technique called, STEM. The LAMP-STEM system utilizes "Stem
primers," which are directed to the stem portion of the LAMP
amplicon (or "dumbbell"). Stem primers can be used as an
alternative to LAMP "Loop primers" (See FIG. 2). When used in
addition to loop-generating and displacement primers, Stem primers
offer similar benefits in speed and sensitivity to the Loop
primers. (See Gandelman et al., Loop-Mediated Amplificaiton
Accelerated by Stem Primers. Int. J. Mol. Sci. 2011, v12:9108-9124,
and US 2012/0157326, which are both incorporated herein by
reference). This beneficial effect of Stem primers is surprising as
they do not bind to the single-stranded DNA loops, which define the
very nature of the LAMP technology. Stem primers can be employed in
either orientation, do not require either the B2/B1 or F2/F1 sites
to be a specific distance apart, can be multiplexed, and allow the
F1 and B1 sites to be positioned further from each other than in
LAMP.
[0016] STEM primers significantly accelerate LAMP comprised of
loop-generating and displacement primers only. They can be used on
their own or synergistically with other STEM primers or even Loop
primers. Addition of Stem primers into LAMP has a positive effect
on both speed and sensitivity. In some cases they improve
reproducibility at low copy number. The action of Stem primers can
be rationalized via the proposed mechanism of LAMP. They anneal to
transiently single-stranded regions of the amplicon and recopy the
entire binding sites for the BIP/FIP primers. An additional unique
feature is the extra strong intra-molecular self-priming when Stem
primers delimit amplicon.
[0017] In general, positioning of Stem primers is less constrained
than that of Loop primers. A rather challenging primer design
involving selection of at least eight binding sites is thus
simplified. Furthermore, Stem primers impose fewer limitations on
the primer design in terms of stem length, orientation and
distances between B1-B2 and F1-F2 sites. In contradiction to the
postulated LAMP mechanism that relies on the involvement of
displacement primers Stem primers can occasionally allow
displacement primers not to be used at all, though it is not clear
why this is so. This has a major implication for primer design, as
it allows the ability to omit one displacement primer or even both,
if necessary.
[0018] In many circumstances, such as point of care diagnostics, it
is advantageous to be able to simultaneously amplify and detect
multiple targets in a single sample using a single assay. This is
typically done by combining the amplification of multiple targets
in the same tube using different dyes attached to each different
target primer set or probe. This very common method has two
significant drawbacks. One, since all the primers are together in
one solution, there is a very high chance of them cross-reacting
with each other and creating dimers and other spurious products
that would interfere with the results. This is overcome by
laboriously screening many combinations of primer sets to find ones
that to not cross-react.
[0019] The second major limitation of this method is that there are
a limited number of dyes that can be separately detected when in
the same solution. Since the wavelength of the emitted light from
the dye has some bandwidth to it, each dye's emission spectrum must
be adequately separated from the others in order for specific and
reliable detection. In practice, this limits each amplification
reaction to the detection of 5 or 6 different targets.
[0020] A technique that could detect a higher number of targets
from the same sample without compromising sensitivity would be a
huge improvement for many applications, such as a respiratory
infection screening panel, where about 20 different targets are
required for a thorough test. Another example is Tuberculosis,
where about 20 different alleles must be screened in order to
accurately and specifically determine the presence of resistance to
either a the two front-line drugs.
SUMMARY
[0021] The present description provides an improved nucleic acid
amplification technique (NAAT), which is robust, cost-effective,
provides for flexibility in primer placement and design, and also
demonstrates increased rate, sensitivity, and reproducibility at
low copy number. The methods as described herein are advantageous
for detecting, in real-time, a nucleic acid region of interest,
e.g., for the diagnosis of a disease or infection.
[0022] The methods as described herein provide for a first-stage,
slow-rate isothermal pre-amplification followed by multiple,
discrete second-stage amplification and detection reactions
performed in parallel directly on the products from the first-stage
primary amplicon amplification product. At least one of the
second-stage reactions includes a site or sequence-specific
secondary primer ("site-specific primer"), wherein if the template
comprises a complementary site for the site-specific primer, the
site-specific primer amplification reaction proceeds at a faster
rate relative to both the first-stage reaction and second-stage
reaction in which no secondary primer is added. In certain
embodiments, at least one of the second-stage reactions includes a
secondary primer having a base pair mismatch ("mismatch primer"),
e.g., 3' mismatch nucleotide ("3' mismatch primer"), wherein the
site-specific primer amplification reaction proceeds at a faster
rate relative to the first-stage reaction, second-stage reactions
in which no secondary primer is added, and the second-stage
mismatch primer reaction.
[0023] For example, a first-stage region-specific pre-amplification
step is done then the reaction is split into multiple reaction
chambers, where in each chamber a different set of secondary
primers, e.g., loop or stem primers, are introduced that are
site-specific sensitive by virtue of, e.g., a 3' end
match/mismatch, or annealing temperature difference, so that a much
higher speed exponential reaction only occurs if the secondary
primers are correctly matched to the sample sequence. The
significant difference in amplification rate can be detected by
real-time fluorescent measurement of, e.g., an intercalating dye,
and thus multiple site-specific reactions within the same region of
interest can be individually identified with a single assay.
[0024] Thus, in one aspect, the description provides two-stage
nucleic acid amplification reaction comprising: providing a target
nucleic acid template and at least one primer that anneals to the
target nucleic acid template near a region of interest to be
amplified; performing a first-stage nucleic acid amplification (or
"pre-amp") reaction to amplify the region of interest (amplicon).
In certain embodiments, a forward and reverse primer are provided
and used to synthesize and amplify the region of interest or
amplicon of interest.
[0025] Subsequently, the pre-amp reaction product ("amplified
region of interest") is utilized in one or more second-stage
amplification reactions wherein at leaset one of the reactions
includes a site-specific secondary primer, such that rapid
amplification occurs only if a complementary sequence for the
site-specific primer (i.e., a site-specific region of interest)
exists in the amplified region of interest from stage-one (i.e.,
the nucleic acid region of interest from stage-one is positive for
the site of interest). As described herein, the appearance of
amplification products in each second-stage reaction can be
detected and compared simultaneously and in real-time, wherein a
fast rate of amplification relative to the first-stage reaction, a
second-stage reaction in which no secondary primer is added, and a
second-stage mismatch primer reaction is indicative of the presence
of the site-specific region of interest.
[0026] In certain embodiments, the site-specific primer comprises a
nucleotide mismatch at a site other than the 3' terminus.
[0027] In certain embodiments, multiple second-stage nucleic acid
amplification reactions are performed in parallel. In a preferred
embodiment, the site-specific primer reaction is performed and
monitored in parallel with a separate reaction in which similar
site-specific primers are used but that comprise a mismatch in its
nucleic acid sequence.
[0028] In another aspect, a method is described comprising
performing multiple, separate or discrete second-stage
amplification reactions utilizing the first-stage amplification
product or primary amplicon in which the rate of the second-stage
amplification reaction is detected and compared as between at least
one reaction having a site-specific primer complementary to a site
or sequence of interest on the primary amplicon template, and a
reaction having a secondary primer that anneals to the same site
but comprises a base-pair mismatch (herein, "a mismatch primer"),
wherein a faster reaction rate relative to the other is indicative
of the presence or absence of the specific site or region of
interest. In still additional embodiments, the rate of the
second-stage amplification reaction is detected and compared as
between at least one reaction having a site-specific primer
complementary to a site or sequence of interest on the primary
amplicon template, a reaction having a mismatch primer, and a
reaction that has no secondary primer, wherein a faster reaction
rate relative to the other reactions is indicative of the presence
or absence of the specific site or region of interest.
[0029] In certain embodiments, the mismatch primer is a mismatch
Stem primer. In any of the embodiments described herein, the
mismatch primer comprises at least one mismatched nucleotide (i.e.,
a nucleotide that is not complementary to the template). In certain
embodiments, the mismatched nucleotide is at the 3' end of the
mismatch primer ("3' mismatch primer).
[0030] In certain embodiments, the site-specific primer and the
mismatch primer comprise at their 3' ends a nucleotide that is
specific or complementary for a multi-allelic or polymorphic site
such that, depending on which allele or polymorphism the nucleic
acid template comprises, the site-specific primer could comprise a
3' end nucleotide mismatch, and the mismatch primer could contain
the 3' end complementary nucleotide. In other words, in certain
embodiments, the method comprises performing a plurality of
second-stage amplification reactions, wherein each reaction
comprises a site-specific primer. However, as described herein,
only those amplification reactions comprising a primer that is
complementary at its 3' end to the site of interest will proceed at
an increased rate relative to the first-stage reaction, and
relative to the second-stage reaction comprising a 3' mismatch.
[0031] In certain embodiments, the method comprises performing a
plurality of second-stage amplification reactions, wherein each
respective reaction comprises a site-specific primer. In certain
embodiments, the site-specific primer is specific for a different
multi-allelic or polymporphic site. In such a configuration, the
methods provide for a multiplexing method of determining the
presence or absence of multiple polymorphisms simultaneously.
[0032] In certain embodiments, the method includes performing at
least one additional second-stage amplification reaction in
parallel in which no additional primers are added, and monitoring
and comparing in real-time the rate of the second-stage
amplification reaction as between the reaction comprising the
site-specific primer, the reaction comprising the mismatch primer,
and the reaction comprising no primer, wherein an enhanced reaction
rate relative to the others is indicative of the presence of the
specific site or region of interest.
[0033] In certain embodiments, the method comprises performing a
plurality of separate or discrete second-stage amplification
reactions approximately simultaneously. In certain additional
embodiments, the discrete reactions comprise the same or different
site-specific primers. In certain embodiments, the discrete
reactions comprise a plurality or combination of site-specific
primers (i.e., "multiplexing reaction").
[0034] Although several of the aspects and embodiments refer to a
two-staged amplification scheme, the invention is not so limited.
Indeed, the methods described herein are predicated upon the
surprising discovery that the presence of a specific site or
sequence of interest in a target nucleic acid region can be
detected by the enhanced rate of amplification with a site-specific
or sequence-specific (i.e., complementary) primer relative to the
slower rate of an amplification reaction with mismatch primer that,
but-for the mismatched base, anneals to the same target region. As
such, any number of additional amplification steps can be
performed, e.g., 3, 4, 5, 6, 7, 8, 9, etc., and therefore, any
number of sites, regions or sequences of interest can be detected.
Similarly, for each of the respective site-specific primer
reactions to be performed, a parallel mismatch primer reaction can
be performed and the rate of amplification of the two reactions
monitored.
[0035] In any of the aspects or embodiments described herein, the
first-stage amplification reaction can comprise site-specific
primers such that the first-stage pre-amplification reaction is
selective for a particular site of interest, and only if that site
or region exists in the sample will rapid amplification of the
template proceed at the second or later stage amplification
reaction.
[0036] In any of the aspects or embodiments described herein, the
second-stage (or later stage) amplification reaction can comprise
multiple site-specific primers (i.e., "multiplex reaction"). By
using differentially labeled site-specific oligonucleotides
different amplification products can be detected and compared
(i.e., multiplexed) within the same reaction.
[0037] In another aspect, the description provides a method for
detecting and comparing nucleic acid amplification comprising
providing a first reaction chamber; performing a first-stage
pre-amplification reaction as described herein in the first
reaction chamber; introducing an amount or volume of the
first-stage pre-amp reaction directly into a plurality of second
reaction chambers, wherein at least one second reaction chamber
comprises a site-specific primer, and at least one second reaction
chamber comprises a mismatched primer; and performing in each
second reaction chamber a second-stage amplification reaction as
descried herein; and detecting and comparing the rate of
amplification of each reaction simultaneously, wherein a faster
rate of amplification in the site-specific primer reaction versus
the mismatch primer reaction is indicative of the presence of the
site of interest.
[0038] In any of the embodiments described herein, the
amplification reactions of stage-one and stage-two are performed
sequentially in the same reaction container or chamber. In certain
embodiments, the amplification reactions are performed sequentially
but in different reaction containers or chambers. In a preferred
embodiment, the second-stage reaction is performed in parallel in a
plurality of containers or chambers, and detected and compared.
[0039] In any of the embodiments described herein, the target
nucleic acid template is comprised in a suitable buffer and
introduced into a container comprising loop-forming primers. In
still additional embodiments, the mixture from the first-stage
amplification reaction is introduced into a container comprising
site-specific or mismatch primers.
[0040] In additional embodiments, the first-stage amplification
reaction is performed in a container or chamber comprising a
channel that is in fluid communication with one or more additional
containers or chambers comprising primers for performing the
second-stage amplification reaction (i.e., site-specific primer,
site-specific Stem primer; mismatch primer, mismatch Stem primer,
etc). In still additional embodiments, the first-stage reaction
chamber comprises a channel that is in one-way fluid communication
with one or more additional containers or chambers comprising
primers for performing the second-stage amplification reaction.
[0041] In any of the aspects or embodiments described herein, the
first-stage amplification reaction is an isothermal nucleic acid
amplification reaction. In certain embodiments, the second-stage
amplification reaction is an isothermal nucleic acid amplification
reaction. In additional embodiments, both the first-stage
amplification reaction, and the second-stage amplification reaction
are isothermal nucleic acid amplification reactions. In certain
embodiments, the first-stage and/or second-stage amplification
reaction is a LAMP-based isothermal amplification reaction. In a
preferred embodiment, the first-stage amplification is a LAMP-based
isothermal amplification reaction and the second-stage is a
LAMP-STEM-based isothermal amplification reaction.
[0042] In any of the aspects or embodiments described herein, the
mismatch primer comprises a 3' end terminal nucleotide mismatch. In
certain embodiments, a site-specific primer as described herein
comprises on the 3' terminal end a nucleotide complementary to a
nucleotide of interest in the target nucleic acid template.
[0043] In another aspect the description provides a two-stage
method of diagnosing a genetic disease, SNP, viral or microbial
infection wherein said method comprises providing a nucleic acid
sample from subject to be tested, performing the two-stage
amplification reaction as described herein, wherein the
site-specific primer is specific for a region or nucleotide(s) of
interest associated with at least one of a genetic disease,
mutation, SNP, virus, or bacteria, and wherein an increased rate of
amplification with the site-specific primer versus a mismatch
primer is indicative of a subject having an allele for the genetic
disease, mutation, SNP, virus or microbe. In certain embodiments,
the microbe is a bacterium.
[0044] In certain embodiments, the method of diagnosing a disease
or pathogenic infection comprises the step of treating the patient
testing positive for the nucleotide of interest with an appropriate
therapeutic, e.g., antibiotic, drug, etc.
[0045] In any of the aspects or embodiments described herein, the
method further comprises a step of detecting the formation of an
amplicon. In certain embodiments, the amplification reaction
mixture comprises a fluorescently labeled dNTPs or a fluorescent
DNA intercalating dye. In certain embodiments, formation of an
amplicon is detected in real-time by measuring an increase in
fluorescence.
[0046] In any of the aspects or embodiments described herein, the
nucleic acid template comprises a plurality of primer binding
regions, wherein the primers serve as origins of synthesis and
define a polynucleotide region (i.e., "an amplicon") to be
amplified using a polymerase.
[0047] In any of the embodiments described herein, the method
further comprises the addition of at least one Displacement or
bumper primer in the amplification reaction.
[0048] In any of the embodiments described herein, the target
nucleic acid template comprises genomic DNA, cDNA or RNA or a
segment therefrom, from a virus, plant, microbe, or multicellular
organism, e.g., a mammal, such as a human. In certain embodiments,
the genomic DNA is from a pathogenic virus or microbe, e.g.,
bacteria or archae. In certain embodiments, the target nucleic acid
template is from tubercle bacillus (MTB or TB). In certain
additional embodimetns, the target nucleic acid template is from
the rpoB gene from MTB. In still further embodiments, the target
nucleic acid template is rpoB13.5 F6.
[0049] In any of the embodiments described herein, the method
further comprises the addition of at least one loop primer which is
complementary to a region in the first loop or the second loop of
the amplicon.
[0050] In any of the embodiments described herein, the
first-amplification reaction is preceeded by a heating step in
which the target nucleic acid template and primers are heated to
approximately 95.degree. C. for from about 1 minute to about 15
mintues. In certain embodiments, the target nucleic acid template
and primers are heated to approximately 95.degree. C. for from
about 5 minutes to about 10 minutes.
[0051] In any of the embodiments described herein, the
amplification reaction is performed at a temperature of from about
50.degree. C. to about 75.degree. C. In certain embodiments, the
amplification reaction is performed at a temperature of from about
55.degree. C. to about 65.degree. C.
[0052] In any of the embodiments described herein, the
site-specific primer (e.g., site-specific Stem primer) is in the
forward direction. In certain embodiments, the site-specific primer
is in the reverse direction. In still additional embodiments, both
forward and reverse site-specific primers are included in the
reaction.
[0053] In any of the embodiments described herein, 3' SNP specific
nucleotide is comprised within at least one of a loop-forming
primer, a displacement primer, or a loop primer.
[0054] In any of the embodiments described herein, the primers or
nucleotide reagents comprise a chemical modification.
[0055] In any of the embodiments described herein, the first-stage
and second-stage amplification reactions are performed sequentially
in the same reaction container or chamber. In certain embodiments,
the first-stage and second-stage amplification reactions (and any
subsequent amplification reactions) are performed sequentially but
in different reaction chambers.
[0056] In any of the embodiments described herein, the primers can
comprise an endonuclease restriction site, or recognition element
for a nicking enzyme.
[0057] In any of the embodimetns described herein, the
amplification reaction can comprise a hairpin primer comprising a
first and a second segment, wherein the first segment is
substantially complementary to a primer binding region on a
template and the second segment comprises a sequence that is
substantially complementary to another region in the primer;
[0058] In any of the embodiments described herein, the
amplification reaction can comprise a loop-providing primer,
comprising a hairpin primer in which the inverted repeats are
separated by a linker region.
[0059] In any of the embodiments described herein, the
amplification reaction can comprise a chimeric primer.
[0060] The preceding general areas of utility are given by way of
example only and are not intended to be limiting on the scope of
the present disclosure and appended claims. Additional objects and
advantages associated with the compositions, methods, and processes
of the present invention will be appreciated by one of ordinary
skill in the art in light of the instant claims, description, and
examples. For example, the various aspects and embodiments of the
invention may be utilized in numerous combinations, all of which
are expressly contemplated by the present description. These
additional advantages objects and embodiments are expressly
included within the scope of the present invention. The
publications and other materials used herein to illuminate the
background of the invention, and in particular cases, to provide
additional details respecting the practice, are incorporated by
reference.
BRIEF DESCRIPTION OF THE DRAWINGS
[0061] The accompanying drawings, which are incorporated into and
form a part of the specification, illustrate several embodiments of
the present invention and, together with the description, serve to
explain the principles of the invention. The drawings are only for
the purpose of illustrating an embodiment of the invention and are
not to be construed as limiting the invention. Further objects,
features and advantages of the invention will become apparent from
the following detailed description taken in conjunction with the
accompanying figures showing illustrative embodiments of the
invention, in which:
[0062] FIG. 1. Illustration of general principle for loop-mediated
isothermal amplification (LAMP). In an exemplary method as
described herein a first stage isothermal amplification reaction
based on the LAMP method is performed, which includes FIP and BIP
"loop-forming primers" (LFPs) (comprising F1c and F2, B1c and B2,
priming sites, respectively), and "displacement primers" (F3 and
B3). The LAMP reaction produces concatamers of the "dumbbell"
structure (c). As described herein, the initial LAMP reaction
proceeds at a relatively slow rate.
[0063] FIG. 2. Illustration of general principal for an exemplary
modified LAMP-STEM technique as described herein. As described
herein, a LAMP-STEM amplication reaction is performed as the
second-stage. The reaction includes at least one "site-specific
Stem primer," which is complementary to a location or sequence of
interest in the amplicon from the stage-one amplification reaction.
The site-speific Stem primer reaction is performed in parallel with
separate amplification reaction comprising a Stem primer having a
mismatch, e.g., a mismatch at its 3' end ("mismatch Stem primer");
and the two reactions are simultaneously monitored and compared,
wherein an incrase in the amplification rate of the site-specific
Stem primer reaction relative to the mismatch Stem primer reaction
is indicative of the presence of the site of interest in the
amplicon (or concatmers thereof), and wherein it is indicative of
the absence of the site of interest when the rate of the
site-specific Stem primer reaction is the same or slower than the
mismatch Stem primer reaction.
[0064] FIG. 3. Illustration of general principal for another
exemplary modified LAMP-STEM technique as described herein. The
technique is similar to that depicted in FIG. 2 but futher includes
"Loop primers" in addition to the SNP-Stem primers. See WO0028082,
incorporated herein by reference.
[0065] FIG. 4. Illustrates an exemplary system configured for
performing the two-stage amplification method as described herein.
In the example, the first-stage reaction is performed in a central
chamber, which is in communication, e.g., fluid communication, with
one or more additional chambers. In a preferred embodiment, the
first-stage reaction mixture is distributed evenly to the one or
more than one additional chambers where the second-stage
amplification reaction takes place.
[0066] FIG. 5. Real-time theoretical signal for 10.sup.2 and
10.sup.6 starting copies and 10.times. second-stage amplification
efficiency versus first-stage reaction efficiency. The upper panel
shows the two exponential reactions rates on a log scale, and the
lower panel shows them on a linear scale. The vertical axis
represents the number of copies of amplicon present; both input
material and amplified material. This axis also represents the
signal that can be generated and detected using an intercalating
dye. The dashed horizontal line represents the limit of detection
of an instrument that is measuring the fluorescence signal that can
be generated by said dye. The horizontal axisof both graphs
represent time in miniutes. The 8-minute time point is the point at
which the second-stage primers are added to the reaction. This is
where the accelerated reaction starts if the second-stage primer(s)
are matched to a site within the primary amplicon that was
generated by the first reaction, which is represented by the lines
with increased slopes in the log chart. The continuation of the
lower slope lines on the log chart indicates the signal that would
be present if the secondary primers do not match the site of
interest within the amplicon.
[0067] FIG. 6. Illlustrates the effect on rate of amplification due
to mismatched bases in Stem primers. (a) The left panel exemplifies
a Stem primer comprising a 3' end mismatch representing a primer
that is not specific for a SNP of interest. The 3' mismatch induces
a delay in the amplification reaction versus the matched or
SNP-specific Stem primer ("SNP-Stem primer"). The increase in rate
of amplification is exemplified in the right panel, wherein the
dotted line represents the earliest time (t) to the point of
maximum slope of fluorescence (t.sub.max1), and .DELTA.Ct1
represents the lag in time to t.sub.max between the SNP-Stem primer
and the 3' end mismatched Stem primer. (b) The right panel
exemplifies another embodiment as described herein, wherein the
Stem primers (SNP-Stem primer and 3' end mismatched primer) contain
another base pair mismatch in their sequence. The second mismatch
shifts to the right (i.e., reduces the rate) of amplification
(.DELTA.Ct2) and delays the time to t.sub.max2.
[0068] FIG. 7. Processed fluorescent traces showing matched Stem
primer (i.e., SNP-Stem primer) LAMP reactions (n=4), and mismatched
Stem primer LAMP reactions (n=4) using the Bio-Rad CFX realtime PCR
instrument.
[0069] FIG. 8. Illustrates the enhanced rate of amplification
observed according to an exemplary method as described herein. (a)
Provides raw traces showing matched Stem primer (i.e., SNP-STEM)
reactions (light traces) and mismatched Stem primer reactions (dark
traces). (b) Quantification cycle (Cq; See Hellemans et al., 2007)
is measured from the fitted raw traces as the point of maximum
slope. The Cq for matched primers is plotted (light dots) along
with mismatched Stem primers (dark dots) and no Stem primer LAMP
("dumbbell") reactions (open circles).
DETAILED DESCRIPTION
[0070] The following is a detailed description provided to aid
those skilled in the art in practicing the present invention. Those
of ordinary skill in the art may make modifications and variations
in the embodiments described herein without departing from the
spirit or scope of the present disclosure. All publications, patent
applications, patents, figures and other references mentioned
herein are expressly incorporated by reference in their
entirety.
[0071] The present description provides an improved nucleic acid
amplification technique (NAAT), and in particular iNAAT, which is
robust, cost-effective, provides for flexibility in primer
placement and design, and also demonstrates increased rate,
sensitivity, and reproducibility at low copy number, in particular,
as compared to, e.g., SDA or LAMP.
[0072] As described above, it is advantageous to have a platform
that separates amplification samples into multiple separate
reactions, so there is no interference of dyes or primers, so that
more tests can be reliably performed per sample. In order to do
this without diluting the sample and thus reducing sensitivity or
inducing non-uniformity between the multiple reaction chambers, the
nucleic acids in the sample should be amplified somewhat before
being distributed to the final reaction areas. This will ensure
that all the downstream reaction chambers have an adequate amount
of starting DNA (or RNA) to reliably deliver a meaningful
result.
[0073] A known way to do this is to use an initial PCR reaction
that amplifies a product that contains the regions of interest but
is somewhat larger, and then distributes that product to separate
downstream reactions that only amplify each small region of
interest (or SNP). This is known as nested PCR, since each target
sequence or SNP is "nested" within a larger amplified region. If
this method is used, a dilution step is typically required so that
the pre-amplification primers do not contaminate the final reaction
and detection step. A dilution step is highly undesirable in an
automated instrument because it requires an additional fluid source
and additional manipulations of the sample fluid. It is far simpler
and therefore more favorable to be able to use the fluid containing
the pre-amplified sample directly in the final amplification and
detection reaction.
[0074] Another way to do this is to use Irma instead of Thymine in
the pre-amplification primers, and then destroy the primers in a
subsequent step using an enzyme (that destroys the Uracil), and
then using the resulting pre-amp'd but primer-free solution for the
final amplification and detection step. This method has the
advantage of not requiring the introduction of a dilutent, but
requires an additional enzyme, which may be provided dry and
immobilized (lyophilized), which may be simpler than a dilution
step: it is further desirable to use a method that does not require
temperature cycling (isothermal). This is because isothermal
amplification reactions tend to be faster than temperature cycling
reactions (such as PCR), and because isothermal requirements result
in a lower cost and lower power instrument.
[0075] Another known method for pre-amplifying a sample is to use
whole genome amplification, whereby all of the genetic material in
the sample. is amplified equally. This is accomplished using a
library of short (6 or 7 base) primers that represent nearly all
possible sequences, and can thus cover all genomes. Nearly all
nucleic acid samples will be contaminated with nucleic acids from
organisms other than the ones of interest, and sometimes there is a
factor of over 10.sup.8 excess of this unwanted genetic material
than of the genetic material of interest.
[0076] Therefore, for this method, the vast majority of the
amplification resources required for this method of
pre-amplification will be consumed by the amplification of
unwanted, contaminating DNAs. Also, within the nucleic acids of
interest, only a tiny portion (0.01% or less typically) of the
genome is tested for in the final amplification reaction, so the
whole genome amplification method is further miss-directed at
non-informative genomic areas by a factor of over 10.sup.12. In
addition, whole genome amplification methods take a relatively long
time period (hours), and require special, highly processive
strand-displacing enzymes, at high concentrations, which add cost
to the assay. If too much material is pre-amplified using this
method, which could happen in a highly contaminated sample, then a
positive signal could result in the final detection area, even if
no DNA of interest was present. A dilution step would be required
to prevent this false positive signal, which adds cost and
complexity to the fluid handling system of an instrument employing
this technology.
[0077] A method that has neither of the above additional assay
requirements and their associated drawbacks is preferred.
[0078] The methods as described herein provide for a low-rate
isothermal pre-amplification followed by high rate site-specific
amplification and detection step. For instance, an exemplary method
as described herein includes a first-stage slow rate isothermal
reaction followed immediately by a separate or second-stage fast
rate exponential isothermal amplification reaction that proceeds at
an enhanced rate relative to the first reaction.
[0079] In another example, a regionspecific pre-amplification step
is done using the LAMP system without the presence of loop primers
or stem primers, thus resulting in a very slow exponential reaction
speed. Once an amplification of approximately 100-100,000.times. is
achieved (in a predetermined time frame), the reaction is split
into multiple reaction chambers, where in each chamber a different
set of loop or stem primers are introduced that are site-specific
sensitive by virtue of, e.g., a 3' end match/mismatch, or annealing
temperature difference, so that the much higher speed exponential
reaction only occurs if the loop or stem primers are correctly
matched to the sample sequence. The significant difference in
amplification rate can be detected by real-time fluorescent
measurement of, e.g., an intercalating dye, and thus multiple
site-specific reactions within the same region of interest can be
individually identified with a single assay.
[0080] Thus, in one aspect, the description provides two-stage
nucleic acid amplification reaction comprising: providing a target
nucleic acid template and at least one primer that anneals to the
target nucleic acid template near a region of interest to be
amplified; performing a first-stage nucleic acid amplification (or
"pre-amp") reaction to amplify the region of interest (amplicon).
In certain embodiments, a forward and reverse primer are provided
and used to synthesize and amplify the region of interest or
amplicon of interest.
[0081] Subsequently, the pre-amp reaction product ("primary
amplicon" or "amplified region of interest") is utilized in one or
more second-stage amplification reactions wherein at leaset one of
the reactions includes a site or sequence-specific secondary primer
("site-specific primer"), such that rapid amplification occurs only
if a complementary sequence for the site-specific primer (i.e., a
site-specific region of interest) exists in the primary amplicon or
amplified region of interest from stage-one. In other words, the
nucleic acid region of interest from stage-one is positive for the
site of interest. As described herein, the appearance of
amplification products in each second-stage reaction can be
detected and compared simultaneously and in real-time, wherein a
fast rate of amplification relative to the first-stage reaction, a
second-stage reaction in which no secondary primer is added, and a
second-stage mismatch primer reaction is indicative of the presence
of the site-specific region of interest.
[0082] Significantly, because in certain embodimetns, the region
being amplified is the same in both the first-stage and
second-stage reactions, it is advantageous to introduce the
second-stage amplification reaction primers well before there is a
measurable product from the first -stage amplification reaction,
otherwise the second-stage amplification product cannot be
detected.
[0083] The methods as described herein provide for a first-stage,
slow-rate isothermal pre-amplification followed by multiple,
discrete second-stage amplification and detection reactions
performed in parallel directly on the products from the first-stage
amplification. At least one of the second-stage reactions includes
a site-specific secondary primer, wherein if the primary amplicon
template comprises a complementary site for the site-specific
primer, the site-specific primer amplification reaction proceeds at
a faster rate relative to both the first-stage reaction and
second-stage reaction in which no secondary primer is added. In
certain embodiments, at least one of the second-stage reactions
includes a secondary primer having a mismatch nucleotide ("mismatch
primer"), e.g., a 3' mismatch ("3' mismatch primer"), wherein the
site-specific primer amplification reaction proceeds at a faster
rate relative to the first-stage reaction, second-stage reactions
in which no secondary primer is added, and the second-stage
mismatch primer reaction.
[0084] For example, the description provides a method wherein a
first-stage region-specific pre-amplification step is performed,
and then the reaction is split into multiple reaction chambers,
where in at least one chamber a secondary primer, e.g., loop or
stem primer, is introduced that is site-specific sensitive by
virtue of, e.g., a 3' end match/mismatch, or annealing temperature
difference, so that a much higher speed exponential reaction only
occurs if the secondary primer is correctly matched to the sample
sequence. The significant difference in amplification rate can be
detected by real-time fluorescent measurement of, e.g., an
intercalating dye, and thus multiple site-specific reactions within
the same region of interest can be individually identified with a
single assay.
[0085] Unless otherwise defined, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this invention belongs. The
terminology used in the description is for describing particular
embodiments only and is not intended to be limiting of the
invention.
[0086] Where a range of values is provided, it is understood that
each intervening value, to the tenth of the unit of the lower limit
unless the context clearly dictates otherwise (such as in the case
of a group containing a number of carbon atoms in which case each
carbon atom number falling within the range is provided), between
the upper and lower limit of that range and any other stated or
intervening value in that stated range is encompassed within the
invention. The upper and lower limits of these smaller ranges may
independently be included in the smaller ranges is also encompassed
within the invention, subject to any specifically excluded limit in
the stated range. Where the stated range includes one or both of
the limits, ranges excluding either both of those included limits
are also included in the invention.
[0087] The following terms are used to describe the present
invention. In instances where a term is not specifically defined
herein, that term is given an art-recognized meaning by those of
ordinary skill applying that term in context to its use in
describing the present invention.
[0088] The articles "a" and "an" as used herein and in the appended
claims are used herein to refer to one or to more than one (i.e.,
to at least one) of the grammatical object of the article unless
the context clearly indicates otherwise. By way of example, "an
element" means one element or more than one element.
[0089] The phrase "and/or," as used herein in the specification and
in the claims, should be understood to mean "either or both" of the
elements so conjoined, i.e., elements that are conjunctively
present in some cases and disjunctively present in other cases.
Multiple elements listed with "and/or" should be construed in the
same fashion, i.e., "one or more" of the elements so conjoined.
Other elements may optionally be present other than the elements
specifically identified by the "and/or" clause, whether related or
unrelated to those elements specifically identified. Thus, as a
non-limiting example, a reference to "A and/or B", when used in
conjunction with open-ended language such as "comprising" can
refer, in one embodiment, to A only (optionally including elements
other than B); in another embodiment, to B only (optionally
including elements other than A); in yet another embodiment, to
both A and B (optionally including other elements); etc.
[0090] As used herein in the specification and in the claims, "or"
should be understood to have the same meaning as "and/or" as
defined above. For example, when separating items in a list, "or"
or "and/or" shall be interpreted as being inclusive, i.e., the
inclusion of at least one, but also including more than one, of a
number or list of elements, and, optionally, additional unlisted
items. Only terms clearly indicated to the contrary, such as "only
one of" or "exactly one of," or, when used in the claims,
"consisting of," will refer to the inclusion of exactly one element
of a number or list of elements. In general, the term "or" as used
herein shall only be interpreted as indicating exclusive
alternatives (i.e., "one or the other but not both") when preceded
by terms of exclusivity, such as "either," "one of," "only one of,"
or "exactly one of."
[0091] In the claims, as well as in the specification above, all
transitional phrases such as "comprising," "including," "carrying,"
"having," "containing," "involving," "holding," "composed of," and
the like are to be understood to be open-ended, i.e., to mean
including but not limited to. Only the transitional phrases
"consisting of` and "consisting essentially of` shall be closed or
semi-closed transitional phrases, respectively, as set forth in the
United States Patent Office Manual of Patent Examining Procedures,
Section 2111.03.
[0092] As used herein in the specification and in the claims, the
phrase "at least one," in reference to a list of one or more
elements, should be understood to mean at least one element
selected from anyone or more of the elements in the list of
elements, but not necessarily including at least one of each and
every element specifically listed within the list of elements and
not excluding any combinations of elements in the list of elements.
This definition also allows that elements may optionally be present
other than the elements specifically identified within the list of
elements to which the phrase "at least one" refers, whether related
or unrelated to those elements specifically identified. Thus, as a
nonlimiting example, "at least one of A and B" (or, equivalently,
"at least one of A or B," or, equivalently "at least one of A
and/or B") can refer, in one embodiment, to at least one,
optionally including more than one, A, with no B present (and
optionally including elements other than B); in another embodiment,
to at least one, optionally including more than one, B, with no A
present (and optionally including elements other than A); in yet
another embodiment, to at least one, optionally including more than
one, A, and at least one, optionally including more than one, B
(and optionally including other elements); etc.
[0093] It should also be understood that, in certain methods
described herein that include more than one step or act, the order
of the steps or acts of the method is not necessarily limited to
the order in which the steps or acts of the method are recited
unless the context indicates otherwise.
[0094] The term "compound", as used herein, unless otherwise
indicated, refers to any specific chemical compound disclosed
herein and includes tautomers, regioisomers, geometric isomers, and
where applicable, stereoisomers, including optical isomers
(enantiomers) and other steroisomers (diastereomers) thereof, as
well as pharmaceutically acceptable salts and derivatives
(including prodrug forms) thereof where applicable, in context.
Within its use in context, the term compound generally refers to a
single compound, but also may include other compounds such as
stereoisomers, regioisomers and/or optical isomers (including
racemic mixtures) as well as specific enantiomers or
enantiomerically enriched mixtures of disclosed compounds. The term
also refers, in context to prodrug forms of compounds which have
been modified to facilitate the administration and delivery of
compounds to a site of activity. It is noted that in describing the
present compounds, numerous substituents and variables associated
with same, among others, are described. It is understood by those
of ordinary skill that molecules which are described herein are
stable compounds as generally described hereunder. When the bond is
shown, both a double bond and single bond are represented within
the context of the compound shown.
[0095] The term "patient" or "subject" is used throughout the
specification to describe an animal, preferably a human or a
domesticated animal, to whom treatment, including prophylactic
treatment, with the compositions according to the present invention
is provided. For treatment of those infections, conditions or
disease states which are specific for a specific animal such as a
human patient, the term patient refers to that specific animal,
including a domesticated animal such as a dog or cat or a farm
animal such as a horse, cow, sheep, etc. In general, in the present
invention, the term patient refers to a human patient unless
otherwise stated or implied from the context of the use of the
term.
[0096] The term "effective" is used to describe an amount of a
compound, composition or component which, when used within the
context of its intended use, effects an intended result. The term
effective subsumes all other effective amount or effective
concentration terms, which are otherwise described or used in the
present application.
[0097] The terms "nucleic acid," "polynucleotides," and
"oligonucleotides" refers to biopolymers of nucleotides and, unless
the context indicates otherwise, includes modified and unmodified
nucleotides, and both DNA and RNA. For example, in certain
embodiments, the nucleic acid is a peptide nucleic acid (PNA).
Typically, the methods as described herein are performed using DNA
as the nucleic acid template for amplification. However, nucleic
acid whose nucleotide is replaced by an artificial derivative or
modified nucleic acid from natural DNA or RNA is also included in
the nucleic acid of the present invention insofar as it functions
as a template for synthesis of complementary chain. The nucleic
acid of the present invention is generally contained in a
biological sample. The biological sample includes animal, plant or
microbial tissues, cells, cultures and excretions, or extracts
therefrom. In certain aspects, the biological sample includes
intracellular parasitic genomic DNA or RNA such as virus or
mycoplasma. The nucleic acid may be derived from nucleic acid
contained in said biological sample. For example, genomic DNA, or
cDNA synthesized from mRNA, or nucleic acid amplified on the basis
of nucleic acid derived from the biological sample, are preferably
used in the described methods.
[0098] The term "primer" or "oligonucleotide primer" can refer to a
short polynucleotide that satisfies the requirements that it must
be able to form complementary base pairing sufficient to anneal to
a desired nucleic acid template, and give an --OH group serving as
the origin of synthesis of complementary chain at the 3'-terminal.
Accordingly, its backbone is not necessarily limited to the one via
phosphodiester linkages. For example, it may be composed of a
phosphothioate derivative having S in place of O as a backbone or a
peptide nucleic acid based on peptide linkages. The bases may be
those capable of complementary base pairing. In the nature, there
are 5 bases, that is, A, C, T, G and U, but the base can be an
analogue such as bromodeoxyuridine. The oligonucleotides as used
herein can function not only as the origin of synthesis but also as
a template for synthesis of complementary chain. The term
polynucleotide includes oligonucleotides, which have a relatively
short chain length. Signficantly, a primer need not be fully
complementary in order to anneal to a binding site on a polynucleic
acid.
[0099] In certain embodiments, the primer is complementary to the
binding site sequence. In other embodiments, the primer comprises
one or more mismatched nucleotides (i.e., bases that are not
complementary to the binding site). In still other embodiments, the
primer can comprise a segment that does not anneal to the
polynucleic acid or that is complementary to the inverse strand of
the polynucleic acid to which the primer anneals. In certain
embodiments, a primer is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, 22, 23 ,24, 25, 26, 27, 28, 29, 30,
31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47
, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,
64, 65, 66, 67, 68, 69, 70 or more nucleotides in length. In a
preferred embodiment, the primer comprises from 2 to 100
nucleotides.
[0100] Oligonucleotides can be used to hybridize with genomic DNA
or cDNA sequences in the same or different organisms. Those of
skill in the art will appreciate that various degrees of stringency
of hybridization can be employed in the assay. The degree of
complementarity (sequence identity) required for detectable binding
will vary in accordance with the stringency of the hybridization
medium and/or wash medium. As the conditions for hybridization
become more stringent, there must be a greater degree of
complementarity between the probe and the target for duplex
formation to occur. The degree of stringency can be controlled by
one or more of temperature, ionic strength, pH and the presence of
a partially denaturing solvent, such as formamide. For example, the
stringency of hybridization is conveniently varied by changing the
polarity of the reactant solution through, for example,
manipulation of the concentration of formamide within the range of
0% to 50%. Minor sequence variations in the probes and primers can
be compensated for by reducing the stringency of the
hybridization.
[0101] "Complementarity" refers to the ability of a nucleic acid to
form hydrogen bond(s) or hybridize with another nucleic acid
sequence by either traditional Watson-Crick or other
non-traditional types. As used herein "hybridization," refers to
the binding, duplexing, or hybridizing of a molecule only to a
particular nucleotide sequence under low, medium, or highly
stringent conditions, including when that sequence is present in a
complex mixture (e.g., total cellular) DNA or RNA. See e.g.
Ausubel, et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley
& Sons, New York, N.Y., 1993
[0102] If a nucleotide at a certain position of a polynucleotide is
capable of forming a Watson-Crick pairing with a nucleotide at the
same position in an anti-parallel DNA or RNA strand, then the
polynucleotide and the DNA or RNA molecule are complementary to
each other at that position. The polynucleotide and the DNA or RNA
molecule are "substantially complementary" to each other when a
sufficient number of corresponding positions in each molecule are
occupied by nucleotides that can hybridize or anneal with each
other in order to effect the desired process. A complementary
sequence is a sequence capable of annealing under stringent
conditions to provide a 3'-terminal serving as the origin of
synthesis of complementary chain.
[0103] "Forward primer binding site" and "reverse primer binding
site" refers to the regions on the template DNA and/or the amplicon
to which the forward and reverse primers bind. The primers act to
delimit the region of the original template polynucleotide which is
exponentially amplified during amplification. In some embodiments,
additional primers may bind to the region 5' of the forward primer
and/or reverse primers. Where such additional primers are used, the
forward primer binding site and/or the reverse primer binding site
may encompass the binding regions of these additional primers as
well as the binding regions of the primers themselves. For example,
in some embodiments, the method may use one or more additional
primers which bind to a region that lies 5' of the forward and/or
reverse primer binding region. Such a method was disclosed, for
example, in WO0028082 which discloses the use of "displacement
primers" or "outer primers".
[0104] The term "template" used in the present invention means
nucleic acid serving as a template for synthesizing a complementary
chain in a nucleic acid amplification technique. A complementary
chain having a nucleotide sequence complementary to the template
has a meaning as a chain corresponding to the template, but the
relationship between the two is merely relative. That is, according
to the methods described herein a chain synthesized as the
complementary chain can function again as a template. That is, the
complementary chain can become a template. In certain embodiments,
the template is derived from a biological sample, e.g., plant,
animal, virus, micro-organism, bacteria, fungus, etc. In certain
embodiments, the animal is a mammal, e.g., a human patient.
[0105] "Patient sample" refers to any sample taken from a patient
and can include blood, stool, swabs, sputum, Broncho Alveolar
Lavage Fluid, tissue samples, urine or spinal fluids. Other
suitable patient samples and methods of extracting them are well
known to those of skill in the art. A "patient" or "subject" from
whom the sample is taken may be a human or a non-human animal. When
a sample is not specifically referred to as a patient sample, the
term also comprises samples taken from other sources. Examples
include swabs from surfaces, water samples (for example waste
water, marine water, lake water, drinking water), food samples,
cosmetic products, pharmaceutical products, fermentation products,
cell and micro-organism cultures and other samples in which the
detection of a micro-organism is desirable.
[0106] In the present invention, the terms "synthesis" and
"amplification" of nucleic acid are used. The synthesis of nucleic
acid in the present invention means the elongation or extension of
nucleic acid from an oligonucleotide serving as the origin of
synthesis. If not only this synthesis but also the formation of
other nucleic acid and the elongation or extension reaction of this
formed nucleic acid occur continuously, a series of these reactions
is comprehensively called amplification.
[0107] "Identity," as known in the art, is a relationship between
two or more polypeptide sequences or two or more polynucleotide
sequences, as determined by comparing the sequences. In the art,
"identity" also means the degree of sequence relatedness between
polypeptide or polynucleotide sequences, as determined by the match
between strings of such sequences. "Identity" and "similarity" can
be readily calculated by known methods, including, but not limited
to, those described in Computational Molecular Biology, Lesk, A.
M., ed., Oxford University Press, New York, 1988; Biocomputing:
Informatics and Genome Projects, Smith, D. W., ed., Academic Press,
New York, 1993; Computer Analysis of Sequence Data, Part I,
Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey,
1994; Sequence Analysis in Molecular Biology, von Heinje, G.,
Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M.
and Devereux, J., eds., M Stockton Press, New York, 1991; and
Carillo, H., and Lipman, D., Siam J. Applied Math., 48:1073 (1988).
In addition, values for percentage identity can be obtained from
amino acid and nucleotide sequence alignments generated using the
default settings for the AlignX component of Vector NTI Suite 8.0
(Informax, Frederick, Md.).
[0108] Preferred methods to determine identity are designed to give
the largest match between the sequences tested. Methods to
determine identity and similarity are codified in publicly
available computer programs. Preferred computer program methods to
determine identity and similarity between two sequences include,
but are not limited to, the GCG program package (Devereux, J., et
al., Nucleic Acids Research 12(1): 387 (1984)), BLASTP, BLASTN, and
FASTA (Atschul, S. F. et al., J. Molec. Biol. 215:403-410 (1990)).
The BLAST X program is publicly available from NCBI and other
sources (BLAST Manual, Altschul, S., et al., NCBINLM NIH Bethesda,
Md. 20894: Altschul, S., et al., J. Mol. Biol. 215:403-410 (1990).
The well-known Smith Waterman algorithm may also be used to
determine identity.
[0109] A "single-nucleotide polymorphism" (SNP) is a DNA sequence
variation occurring commonly within a population (e.g. 1%) in which
a single nucleotide--A, T, C or G--in the genome (or other shared
sequence) differs between members of a biological species or paired
chromosomes. For example, two sequenced DNA fragments from
different individuals, AAGCCTA to AAGCTTA, contain a difference in
a single nucleotide (i.e., there are two alleles). Almost all
common SNPs have only two alleles. SNPs can occur in coding,
non-coding or intergenic regions of DNA . The genomic distribution
of SNPs is not homogenous; SNPs occur in non-coding regions more
frequently than in coding regions or, in general, where natural
selection is acting and `fixing` the allele (eliminating other
variants) of the SNP that constitutes the most favorable genetic
adaptation. Other factors, like genetic recombination and mutation
rate, can also determine SNP densi. SNPs within a coding sequence
do not necessarily change the amino acid sequence of the protein
that is produced, due to degeneracy of the genetic code.
[0110] SNPs in the coding region are of two types, synonymous and
nonsynonymous SNPs. Synonymous SNPs do not affect the protein
sequence while nonsynonymous SNPs change the amino acid sequence of
protein. The nonsynonymous SNPs are of two types: missense and
nonsense. SNPs that are not in protein-coding regions may still
affect gene splicing, transcription factor binding, messenger RNA
degradation, or the sequence of non-coding RNA. Gene expression
affected by this type of SNP is referred to as an eSNP (expression
SNP) and may be upstream or downstream from the gene.
[0111] As there are for genes, bioinformatics databases exist for
SNPs. dbSNP is a SNP database from the National Center for
Biotechnology Information (NCBI). Kaviar is a compendium of SNPs
from multiple data sources including dbSNP. SNPedia is a wiki-style
database supporting personal genome annotation, interpretation and
analysis. The OMIM database describes the association between
polymorphisms and diseases (e.g., gives diseases in text form), the
Human Gene Mutation Database provides gene mutations causing or
associated with human inherited diseases and functional SNPs, and
GWAS Central allows users to visually interrogate the actual
summary-level association data in one or more genome-wide
association studies. The International SNP Map working group mapped
the sequence flanking each SNP by alignment to the genomic sequence
of large-insert clones in Genebank. Another database is the
International HapMap Project, where researchers are identifying Tag
SNP to be able to determine the collection of haplotypes present in
each subject.
[0112] The polynucleic acid produced by the amplification
technology employed is generically referred to as an "amplicon" or
"amplification product." The nature of amplicon produced varies
significantly depending on the NAAT being practised. For example,
NAATs such as PCR may produce amplicon which is substantially of
identical size and sequence. Other NAATs produce amplicon of very
varied size wherein the amplicon is composed of different numbers
of repeated sequences such that the amplicon is a collection of
concatamers of different length. The repeating sequence from such
concatamers will reflect the sequence of the polynucleic acid which
is the subject of the assay being performed.
[0113] In the present specification, the simple expression
"5'-side" or "3'-side" refers to that of a nucleic acid chain
serving as a template, wherein the 5' end generally includes a
phosphate group and a 3' end generally includes a free --OH
group.
[0114] The term "disease state or condition" is used to describe
any disease state or condition, in particular, those relating to
genetic abnormalities or due to the presence of a pathogenic
organism such as a virus, bacteria, archae, protozoa or
multicellular organism.
[0115] Methods
[0116] As described herein, it has been surprisingly and
unexpectedly discovered that performing a two-stage nucleic acid
amplification reaction using primers that provide for differential
reaction rates depending on the presence or absence of specific
sequences of interest allows for the rapid, real-time detection of
nucleic acid sequences of interest, which provides advantages for
point-of-care diagnosis.
[0117] In one aspect, the description provides two-stage nucleic
acid amplification reaction comprising: providing a target nucleic
acid template and at least one primer that anneals to the target
nucleic acid template near a region of interest to be amplified;
performing a first-stage nucleic acid amplification (or "pre-amp")
reaction to amplify the region of interest (amplicon). In certain
embodiments, a forward and reverse primer are provided and used to
synthesize and amplify the region of interest or amplicon of
interest.
[0118] Subsequently, the first-stage pre-amp reaction product
("primary amplicon" or "amplified region of interest") is utilized
in one or more discrete second-stage nucleic acid amplification
reactions, wherein in at least one second-stage reactiona
site-specific primer is included, such that rapid or accelerated
amplification occurs only if a complementary sequence for the
site-specific primer (i.e., site-specific region of interest)
exists in the primary amplicon. Stated differently, if the rate of
second-stage amplification reaction is accelerated relative to the
stage-one reaction, and any second-stage reactions lacking an
additional primer, and/or second-stage reactions having a mismatch
primer, the nucleic acid region of interest from stage-one is
positive for the site of interest.
[0119] Thus, according to certain methods described herein, the
rate of the second-stage reaction is selectively enhanced relative
to the first by the presence of specific primer binding sequences
that are fully complementary or at least complementary to the 3'
end of the second-stage primer (herein, the "site-specific
primer"). In a certain embodiments, the relative amplification
reaction rates are as follows: second-stage site-specific primer
amplification>>first-stage amplification reaction. In still
additional embodiments, the relative amplification reaction rates
are as follows: second-stage site-specific primer
amplification>>first-stage reaction second-stage mismatch
primer amplification. As used herein, the term "mismatch primer"
generally refers to a primer having a 3' end nucleotide that is not
complementary to the primer binding site on the template.
[0120] As indicated above, the differential relative amplification
reaction rates between the first-stage, and second-stage, as well
as between the second-stage site-specific primer versus
second-stage mismatch primer are important for being able to
selectively detect for the presence (i.e., amplification) of the
site of interest. For example, FIG. 5 demonstrates that the
first-stage pre-amplification reaction proceeds relatively slowly
to the threshold signal level (i.e., the Cq is longer). However, in
the presence of a complementary primer, the second-stage
amplification reaction proceeds exponentially (i.e., the Cq for the
complementary primer is faster than that of both the first-stage
reaction, and second-stage mismatch primer reaction).
[0121] In certain embodiments, the second-stage amplification rate
is exponential. In certain embodiments of the methods described
herein, the second-stage site-specific primer reaction rate is at
least about 5, 10, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,
80, 85, 90, 95, 100, 500, 1000, 10000, 100000 or more times faster
than the second-stage mismatch primer reaction. In certain
embodiments of the methods described herein, the second-stage
site-specific primer reaction rate is about 5, 10, 20, 25, 30, 35,
40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 500, 1000,
10000, 100000 or more times faster than the second-stage mismatch
primer reaction.
[0122] In certain embodiments of the methods described herein, the
resulting Cq (time to positive detection of the reaction) for the
second-stage site-specific primer reaction is at least about 10%,
15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%,
80%, 85%, 90%, 95%, 100%, 500%, 1000%, 10000% or more faster than
the second-stage mismatch primer reaction. In certain embodiments
of the methods described herein, the resulting Cq (time to positive
detection of the reaction) for the second-stage site-specific
primer reaction is about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%,
50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 500%,
1000%, 10000% or more faster than the second-stage mismatch primer
reaction. In certain embodiments of the methods described herein,
the resulting Cq (time to positive detection of the reaction) for
the second-stage site-specific primer reaction is at least about
25% faster than the second-stage mismatch primer reaction. In
certain embodiments of the methods described herein, the resulting
Cq (time to positive detection of the reaction) for the
second-stage site-specific primer reaction is from about 10% to
about 1000%, from about 20% to about 500%, or from about 25% to
about 100% faster than the second-stage mismatch primer reaction.
However, the important factor is that the differential in time be
far enough above the variability of the system to confidently
distinguish which second-stage reaction is matched (i.e., the
second-stage primer is complementary to the primer binding site on
the template, in particular at the 3' end).
[0123] As described below, in certain embodiments the first-stage
amplification reaction is a relatively slow LAMP-based
amplification. In additional embodiments, the second-stage
amplification reaction is a relatively rapid LAMP-STEM-based
amplification, wherein the reaction rate is enhanced by the binding
of site-specific Stem primers to the site of interest. As such, the
methods as described herein provide for robust, rapid, efficient,
and highly specific amplification of desired genetic sequences. The
amplification of the desired amplicons can be monitored or detected
by any known method, including, e.g., intercalating dyes, labeled
reagents, etc.
[0124] In certain embodiments, the site-specific primer is a
site-specific Stem primer. In certain embodiments, the mismatch
primer is a mismatch Stem primer. In any of the embodiments
described herein, the mismatch primer comprises at least one
mismatched nucleotide (i.e., a nucleotide that is not complementary
to the template). In certain embodiments, the mismatched nucleotide
is at the 3' end of the mismatch primer ("3' mismatch primer").
[0125] In certain embodiments, the site-specific primer and the
mismatch primer comprise at their 3' ends, respectively, a
nucleotide that is specific or complementary to one form of a
multi-allelic or polymorphic site such that, depending on which
allele or polymorphism the nucleic acid template comprises, the
site-specific primer could comprise a 3' end nucleotide mismatch,
and the mismatch primer could contain the 3' end complementary
nucleotide. In other words, in certain embodiments, the method
comprises performing a plurality of second-stage amplification
reactions, wherein each reaction comprises a primer that is
specific for a particular allele. However, as described herein,
only those amplification reactions comprising a secondary primer
that is complementary at its 3' end to the site of interest will
proceed at an increased rate relative to the first-stage reaction,
and relative to the second-stage reaction comprising a 3'
mismatch.
[0126] In certain embodiments, the method comprises performing a
plurality of second-stage amplification reactions, wherein each
respective reaction comprises a site-specific or allele-specific
primer. In certain embodiments, each site-specific primer in each
of the respective second-stage amplification reactions is specific
for a different allele, mutation or polymporphism. In such a
configuration, the methods provide for a multiplexing method for
determining the presence or absence of multiple polymorphisms
simultaneously. The methods as described are, therefore,
particularly advantageous for differentiating between multi-allelic
genes, genotypes, clades, forms, groups, subgroups, classes,
species or strains. For example, certain pathogenic bacteria are
closely related to non-pathogenic strains or species. As such, in
an exemplary aspect, the current description provides methods
comprisign multiple second-stage reactions, wherein each respective
reaction comprises a primer (or primer pair) that is specific for a
site or allele of interest that allows for the simultaneous
determination of, e.g., species and strain of a microbe.
[0127] For example, in one embodiment, the description provides a
two-stage nucleic acid amplification and real-time detection method
comprising [0128] a. providing a target nucleic acid template and
at least one primer that anneals to the target nucleic acid
template near a region of interest to be amplified; [0129] b.
performing a first-stage nucleic acid amplification reaction to
amplify the region of interest, thereby forming aprimary amplicon;
[0130] c. dividing (b) into at least tworeactions, including in at
least one of the reactions a secondary site-specific primer that is
complementary to a site-specific primer binding region (i.e., a
site-specific region of interest) in the primary amplicon and
defines a site of interest, and including at least onereaction in
which no secondary primer is included; [0131] d. performing a
second nucleic acid amplification reaction thereby amplifying the
region of interest; and [0132] e. detecting and comparing in
real-time the amplification rate of the site-specific primer
reaction and the mismatch primer reaction, wherein an enhanced rate
of amplification in the site-specific primer reaction relative to
the mismatch primer reaction is indicative of the presence of the
site of interest. In certain embodiments, a forward and reverse
primer are provided and used to synthesize and amplify the region
of interest or amplicon of interest.
[0133] In any of the aspects or embodiments described herein, the
mismatch primer comprises a 3' end terminal nucleotide mismatch. In
any of the aspects or embodiments described herein, a site-specific
primer can comprise on the 3' terminal end a nucleotide that is
complementary to a nucleotide of interest in the target nucleic
acid template. In certain embodiments, the site-specific primer
comprises a nucleotide mismatch at a site other than the 3'
terminus.
[0134] In certain embodiments, multiple second-stage nucleic acid
amplification reactions are performed in parallel. In a preferred
embodiment, the site-specific primer reaction is performed and
monitored in parallel with a separate reaction in which similar
site-specific primers are used but that comprise a mismatch in its
nucleic acid sequence. In other words, in one reaction the
site-specific primer is fully complementary to a site of interest
on the target nucleic acid, and in another reaction, the primer
anneals to the same site but comprises a mismatch, e.g., a 3' end
mismatch. The inventors have discovered that a mismatch in the
site-specific primer slows the amplification reaction rate enough
such that by direct, real-time detection or montoring and comparing
of both amplifications reactions in parallel it is possible to
identify the presence or absence of sequence variances that exist
in the nucleic acid sample. Stated differently, the rate of the
second amplification reaction is selectively enhanced or suppressed
based on the presence of a sequence that is complementary to the
site-specific primer. Without being bound by any particular theory,
it is believed that the rate of the second-stage amplification is
enhanced by the use of the site-specific primer because it serves
as another origin of extension.
[0135] In another aspect, a method is described comprising
performing multiple, separate or discrete second-stage
amplification reactions utilizing the first-stage amplification
product in which the rate of the second-stage amplification
reaction is compared as between at least one reaction having a
site-specific primer complementary to a region or sequence of
interest on the template, and a reaction having a primer that
anneals to the same site but comprises a base-pair mismatch
(herein, "a mismatch primer"), wherein a faster reaction rate
relative to the other is indicative of the presence or absence of
the specific site or region of interest.
[0136] In certain embodiments, the method includes performing at
least one additional second-stage amplification reaction in
parallel with the site-specific and mismatch amplification
reactions, wherein no additional primers are added, and monitoring
and comparing in real-time the rate of the second-stage
amplification reaction comprising the site-specific primer, the
reaction comprising the mismatch primer, and the reaction
comprising no primer, wherein an enhanced reaction rate relative to
the others is indicative of the presence of the specific site or
region of interest.
[0137] The target template used in the present invention may be any
polynucleic acid that comprises suitable primer binding regions
that allow for amplification of a polynucleic acid of interest. The
skilled person will understand that the forward and reverse primer
binding sites need to be positioned in such a manner on the target
template that the forward primer binding region and the reverse
primer binding region are positioned 5' of the sequence which is to
be amplified on the sense and antisense strand, respectively.
[0138] The target template may be single or double stranded. Where
the target template is a single stranded polynucleic acid, the
skilled person will understand that the target template will
initially comprise only one primer binding region. However, the
binding of the first primer will result in synthesis of a
complementary strand which will then contain the second primer
binding region.
[0139] The target template may be derived from an RNA molecule, in
which case the RNA needs to be transcribed into DNA before
practising the method of the invention. Suitable reagents for
transcribing the RNA are well known in the art and include, but are
not limited to, reverse transcriptase.
[0140] The methods as described herein can be practiced with any
NAAT. For example, known methods of DNA or RNA amplification
include, but are not limited to, polymerase chain reaction (PCR)
and related amplification processes (see, e.g., U.S. Pat. Nos.
4,683,195, 4,683,202, 4,800,159, 4,965,188, to Mullis, et at; U.S.
Pat. Nos. 4,795,699 and 4,921,794 to Tabor, et al; U.S. Pat. No.
5,142,033 to Innis; U.S. Pat. No. 5,122,464 to Wilson, et al.; U.S.
Pat. No. 5,091,310 to Innis; U.S. Pat. No. 5,066,584 to Gyllensten,
et al; U.S. Pat. No. 4,889,818 to Gelfand, et al; U.S. Pat. No.
4,994,370 to Silver, et al; U.S. Pat. No. 4,766,067 to Biswas; U.S.
Pat. No. 4,656,134 to Ringold) and RNA mediated amplification that
uses anti-sense RNA to the target sequence as a template for
double-stranded DNA synthesis (U.S. Pat. No. 5,130,238 to Malek, et
al, with the tradename NASBA), the entire contents of which
references are incorporated herein by reference. (See, e.g.,
Ausubel, supra; or Sambrook, supra.).
[0141] For instance, polymerase chain reaction (PCR) technology can
be used to amplify the sequences of polynucleotides of the present
invention and related genes directly from genomic DNA or cDNA
libraries. PCR and other in vitro amplification methods can also be
useful, for example, to clone nucleic acid sequences that code for
proteins to be expressed, to make nucleic acids to use as probes
for detecting the presence of the desired mRNA in samples, for
nucleic acid sequencing, or for other purposes. Examples of
techniques sufficient to direct persons of skill through in vitro
amplification methods are found in Berger, supra, Sambrook, supra,
and Ausubel, supra, as well as Mullis, et al., U.S. Pat. No.
4,683,202 (1987); and Innis, et al., PCR Protocols A Guide to
Methods and Applications, Eds., Academic Press Inc., San Diego,
Calif. (1990). Commercially available kits for genomic PCR
amplification are known in the art. See, e.g., Advantage-GC Genomic
PCR Kit (Clontech). Additionally, e.g., the T4 gene 32 protein
(Boehringer Mannheim) can be used to improve yield of long PCR
products.
[0142] In certain aspects, the NAAT that is utilized in the methods
described herein are isothermal nucleic acid amplification
techniques. Some isothermal amplification techniques are dependent
on transcription as part of the amplification process, for example
Nucleic Acid Sequence Based Amplification (NASBA; U.S. Pat. No.
5,409,818) and Transcription Mediated Amplification (TMA; U.S. Pat.
No. 5,399,491) while others are dependent on the action of a
Helicase or Recombinase for example Helicase Dependent
Amplification (HDA; WO2004027025) and Recombinase polymerase
amplification (RPA; WO03072805) respectively, others still are
dependent on the strand displacement activity of certain DNA
polymerases, for example Strand Displacement Amplification (SDA;
U.S. Pat. No. 5,455,166), Loop-mediated Isothermal Amplification
(LAMP; WO0028082, WO0134790, WO0224902), Chimera Displacement
Reaction (RDC; WO9794126), Rolling Circle Amplification (RCA;
Lizardi, P. M. et al. Nature Genetics, (1998) 19.225-231),
Isothermal Chimeric Amplification of Nucleic Acids (ICAN;
WO0216639), SMart Amplification Process (SMAP; WO2005063977),
Linear Isothermal Multimerization Amplification (LIMA; Isothermal
amplification and multimerization of DNA by Bst DNA polymerase,
Hafner G. J., Yang I. C., Wolter L. C., Stafford M. R., Giffard P.
M, BioTechniques, 2001, vol. 30, no4, pp. 852-867) also methods as
described in U.S. Pat. No. 6,743,605 (herein referred to as
`Template Re-priming Amplification` or TRA) and WO9601327 (herein
referred to as `Self Extending Amplification` or SEA).
[0143] A characteristic of these NAATs is that they provide for
both copying of a polynucleic acid via the action of a primer or
set of primers and for re-copying of said copy by a reverse primer
or set of primers. This enables the generation of copies of the
original polynucleic acid at an exponential rate. With reference to
NAATs in general it is helpful to differentiate between the
physical piece of nucleic acid being detected by the method, from
the first copy made of this original nucleic acid, from the first
copy of the copy made from this original nucleic acid, from further
copies of this copy of a copy. For the sake of clarity, the nucleic
acid whose provenance is from the sample being analysed itself will
be referred to as the "target nucleic acid template." With
referenct to the two-stage method described herein, the first-stage
primer-dependent amplification reaction is relatively slow as
compared to the second-stage reaction.
[0144] As would be understood by the skilled artisan, the
primer-generated amplicon gives rise to further generations of
amplicons through repeated amplification reactions of the target
nucleic acid template as well as priming of the amplicons
themselves. It is possible for amplicons to be comprised of
combinations with the target template.
[0145] The amplicon may be of very variable length as the target
template can be copied from the first priming site beyond the
region of nucleic acid delineated by the primers employed in a
particular NAAT. In general, a key feature of the NAAT will be to
provide a method by which the amplicon can be made available to
another primer employed by the methodology so as to generate (over
repeated amplification reactions) amplicons that will be of a
discrete length delineated by the primers used. Again, a key
feature of the NAAT is to provide a method by which the amplicons
are available for further priming by a reverse primer in order to
generate further copies. For some NAATs, the later generation
amplicons may be substantially different from the first generation
amplicon, in particular, the formed amplicon may be a concatamer of
the first generation amplicon.
[0146] Methods which produce amplicons in the form of concatamers
directly from linear target templates include LAMP (including,
LAMP-STEM), TRA, SEA and SMAP (the latter is a hybrid of LAMP and
SEA). In each case the concatamers arise from processes involving
the first generation amplicon. Thus, it is preferred that synthesis
of the polynucleic acid is performed using a NAAT selected from the
group consisting of LAMP, TRA, SEA and SMAP. In each case
therefore, the invention is associated with a NAAT which provides
one or more primers with the capability of producing a concatamer
directly from a linear target template.
[0147] The methods as described are preferably perfomed with a NAAT
that results in the formation of template concatamers. The term
"concatamer" as used herein refers to a polynucleic acid having
substantially similar nucleotide sequences linked alternately in a
single-stranded chain. These arrayed sequences may be simple
repeats of each other, inverted repeats or combinations thereof.
Further, the process is understood to be repeated by the next
generation amplicons such that longer and longer concatamers can be
formed.
[0148] NAATs which are suitable for the generation of concatamers
are well known in the art and generally include "isothermal"
amplification techniques. This means that the amplification of the
polynucleic acid does not require a change in the incubation
temperature, contrary to known thermocycling techniques, such as
polymerase chain reaction. For example, isothermal amplification
methods include, e.g., SDA, LAMP, LAMP-STEM as described above, can
be used in conjunction with the methods described herein.
[0149] A common feature of LAMP, TRA, SMAP and SEA is therefore
that of first generation amplicon dependent priming, i.e. where the
first generation amplicon acts as a primer itself, whether by an
intra-molecular event or inter-molecular event, leading to next
generation amplicon that is larger in size than the first
generation amplicon and which is concatameric in nature. In fact,
it is a characteristic of these NAATs that longer and longer
amplicon is generated from shorter amplicon such that the number of
binding sites for stem primers increases exponentially during the
amplification process and hence the ability for stem primers to
accelerate amplification. Appreciation of the mechanism of action
of the primers generating the concatamers in these NAATs is helpful
in understanding how stem primers have their effect. Furthermore,
the skilled person aware of the mechanisms which lead to generation
of a concatamer will readily be able to identify other suitable
NAATs which can be used in the methods of the present
invention.
[0150] In certain embodiments described herein, the first-stage
amplification reaction is an isothermal nucleic acid amplification
reaction. In certain embodiments, the second-stage amplification
reaction is an isothermal nucleic acid amplification reaction. In
additional embodiments, both the first-stage amplification
reaction, and the second-stage amplification reaction are
isothermal nucleic acid amplification reactions. In certain
embodiments, the first-stage and/or second-stage amplification
reaction is a LAMP-based isothermal amplification reaction. In a
preferred embodiment, the first-stage amplification is a LAMP-based
isothermal amplification reaction and the second-stage is a
LAMP-STEM-based isothermal amplification reaction, wherein the
site-specific primer accelerates the amplification rate (relative
to the first amplification reaction), and allows for earlier
detection of amplification products relative to the 3' mismatched
primer.
[0151] In certain embodiments, In addition to the forward and
reverse primer binding regions, the target template needs to
comprise a stem region that needs to have a sufficient length to
allow binding of the one or more stem primers (e.g., site-specific
Stem primer or mismatch Stem primer), as described herein. Thus it
is preferred that the stem region has a length of at least 5
nucleotides, at least 10 nucleotides, at least 15 nucleotides, at
least 20 nucleotides, at least 30 nucleotides, at least 50
nucleotides, at least 100 nucleotides at least 200 nucleotides, at
least 300 nucleotides or at least 500 nucleotides.
[0152] WO0028082 describes the use of loop-forming primers (LFPs),
where a LFP is understood to comprise a first and second segment,
wherein the first segment is substantially complementary to a
primer binding region on the template and the second segment
comprises a sequence that is substantially complementary to a
region in the amplicon generated from the first segment of the
first primer such that the second segment is able to form a loop,
and mentions that the NAAT uses two "outer primers" in addition to
the LFPs. These primers are characterised in that the "first outer
primer" binds 3' to the "F2" site in the template (i.e. the first
outer primer binds the "F3" site, FIG. 1) and the "second outer
primer" binds 3' to the binding region of the second LFP, the "R2c"
site (i.e. the second outer primer binds the "R3c" site, FIG. 1).
Thus, these primers do not bind in the stem-region of the amplicon,
which lies 5' of the primer binding sites of the LFPs.
[0153] A primer employed in LAMP generates single stranded loops in
the amplicon and is referred to herein as "loop forming primer."
Loop-forming primer, as used herein, refers to primers which
comprise a first and a second segment, wherein the first segment is
substantially complementary to the primer binding region on the
template and the second segment comprises a sequence that is
substantially complementary to a region in the amplicon generated
from the first segment of the first primer such that the second
segment is able to form a loop. The general structure of
loop-forming primers is shown in FIG. 1. The first (and next)
generation amplicon resulting from the priming of the target
template by a loop-forming primr contains a loop of single stranded
polynucleotide flanked by double-stranded polynucleotide formed
from Watson-Crick base-pairing of the inverted repeat sequence. The
single-stranded loop of polynucleotide is understood to be
available for binding by a further primer employed by the NAAT in
question but specifically not by a stem primer.
[0154] The primer oligonucleotides the present description can be
prepared by any method known in the art, including by direct
chemical synthesis (see, e.g., Ausubel, et al., supra). Chemical
synthesis generally produces a single-stranded oligonucleotide,
which can be converted into double-stranded DNA by hybridization
with a complementary sequence or by polymerization with a DNA
polymerase using the single strand as a template. One of skill in
the art will recognize that while chemical synthesis of DNA can be
limited to sequences of about 100 or more bases, longer sequences
can be obtained by the ligation of shorter sequences.
[0155] Nucleic acid extension is facilitated by a DNA polymerase,
for example, a thermostable strand-displacing (SD) DNA polymerase.
Because of the thermostable SD polymerase, there is no need for
thermocycling. Displacement or bumper primers (F3 and B3) can be
included to facilitate displacement of the FIP and BIP primers, and
allow more efficient extension of the complementary DNA strand.
[0156] The region between the forward and reverse primer binding
regions represents a region which is guaranteed to form part of the
amplicon but does not itself conventionally provide for any primer
binding sites. This region is referred to herein as the "stem
region" of the amplicon. Primers which bind to the stem region are
referred to herein as "stem primers." Stem primers can be defined
as primers which bind to the stem region (FIG. 2). They may further
be defined as primers that bind the region 3' of the forward primer
binding region on the forward strand and 3' of the reverse primer
binding site on the reverse strand. It is understood that the
primer binding sites and the binding sites of the stem primers do
not significantly overlap. It is preferred that the primer binding
sites and the binding sites of the stem primers do not overlap at
all.
[0157] "Significantly" in the context of overlapping primer binding
regions means that the primer binding sites overlap by less than 10
nucleotides, less than 9 nucleotides, less than 8 nucleotides, less
than 7 nucleotides, less than 6 nucleotides, less than 5
nucleotides, less than 4 nucleotides, less than 3 nucleotides, less
than 2 nucleotides or less than 1 nucleotide. It is preferred that
they do not overlap at all. Stem primers may further still be
defined as primers that bind the region 3' of the forward primer
binding region on the forward strand and 3' of the reverse primer
binding site on the reverse strand but where the primer binding
regions do not substantially overlap with any intra-molecular
secondary structure generated as a direct consequence of the
primers employed by a particular NAAT, especially a LFP.
[0158] The use of Stem primers significantly increases the rate of
amplification. This has the distinct advantage that diagnostic
tests, for example, can deliver test results in a shorter period of
time, something of common value amongst users of diagnostic tests.
An additional benefit of faster amplification is that it can
decrease the possibility of false positive results and hence
increase the specificity of a test. It has been observed that NAATs
employing strand displacing polymerases become increasingly prone
to non-specific amplification as the length of time required for
amplification increases. As such, faster amplification can also
lead to more accurate results. Therefore, the use of stem primers
increases the rate of amplification of NAATs such as Loop-mediated
Isothermal Amplification (LAMP), and provides greater flexibility
in primer selection for a given target template.
[0159] Thus, in another embodiment, the described methods include
the performance of an amplification technique based on the
isothermal approach used in LAMP and LAMP-STEM. The general
approach for loop-mediated isothermal amplification (LAMP) is
illustrated in FIG. 1. Briefly, forward and reverse loop-forming
primers (known as FIB and BIP primers) comprise, e.g., F1c and F2,
B1c and B2, priming sites, respectively, on a target
(single-stranded) nucleic acid template (FIG. 1a-b). The target
nucleic acid can be from genomic DNA, cDNA, RNA. It is sometimes
necessary to denature (via heat, ionic strength, or solvent
conditions) double-stranded nucleic acid template to allow the
primers to bind to the template.
[0160] In certain methods as described herein, a first-stage
amplification (i.e., "pre-amp") reaction, e.g., LAMP reaction, is
performed. The LAMP reaction, which includes, e.g., the
loop-forming primers and one or more displacement primers proceeds
at a relatively slow rate. The LAMP reaction results in the
formation of a single stranded amplicon referred to as a "dumbbell"
comprising a stem or middle region flanked by loops on the 3' end
and 5' end created by the loop-forming primers (Figure lc). Further
amplification cycles result in the production of concatamers of the
"dumbbell" amplicons having alternating complementarity such that
the loop-forming primers as well as the dumbbell structure drives
additional rounds of extension.
[0161] In an exemplary amplification method as described herein, a
first stage isothermal amplification reaction (i.e., "pre-amp
step") using a NAAT, for example, a LAMP method is performed (i.e.,
FIG. 1a-c), which includes forward and reverse primers, FIP and BIP
primers (comprising F1c and F2, B1c and B2, priming sites,
respectively), and displacement primers (F3 and B3) to amplify a
region on the target nucleic acid comprising one or more SNP
sequences. The reaction mixture, which includes, e.g., the
LAMP--generated amplicon, buffer and amplification reagents (e.g.,
dNTPs), and loop-forming primers can be utilized directly in the
second stage of an exemplary amplification method as described
herein.
[0162] In any of the embodiments described herein, the method
further comprises the addition of at least one displacement or
bumper primer in the first-stage and/or second-stage amplification
reaction.
[0163] The method of synthesizing or amplifying nucleic acid
according to the present invention is supported by the DNA
polymerase catalyzing the strand displacement-type reaction for
synthesis of complementary chain. During the reaction, a reaction
step not necessarily requiring the strand displacement-type
polymerase is also contained. However, for simplification of a
constitutional reagent and in an economical viewpoint, it is
advantageous to use one kind of DNA polymerase. As this kind of DNA
polymerase, the following enzymes are known. Further, various
mutants of these enzymes can be utilized in the present invention
insofar as they have both the sequence-dependent activity for
synthesis of complementary chain and the strand displacement
activity. The mutants referred to herein include those having only
a structure bringing about the catalytic activity required of the
enzyme or those with modifications to catalytic activity, stability
or thermostability by e.g. mutations in amino acids. Exemplary
polymerases for use in the described methods include, Bst DNA
polymerase, Bca (exo-)DNA polymerase, DNA polymerase I Klenow
fragment, Vent DNA polymerase, Vent (exo-)DNA polymerase (Vent DNA
polymerase deficient in exonuclease activity), Deep Vent DNA
polymerase, Deep Vent(exo-)DNA polymerase (Deep Vent DNA polymerase
deficient in exonuclease activity), .PHI.29 phage DNA polymerase,
MS-2 phage DNA polymerase, Z-Taq DNA polymerase (Takara Shuzo Co.,
Ltd.), KOD DNA polymerase (Toyobo Co., Ltd.).
[0164] Among these enzymes, Bst DNA polymerase and Bca (exo-) DNA
polymerase are particularly desired enzymes because they have a
certain degree of thermostability and high catalytic activity. The
reaction of this invention can be carried isothermally in a
preferred embodiment, but because of the adjustment of melting
temperature (Tm) etc., it is not always possible to utilize
temperature conditions desired for the stability of the enzyme.
Accordingly, it is one of the desired conditions that the enzyme is
thermostable. Although the isothermal reaction is feasible, heat
denaturation may be conducted to provide nucleic acid as a first
template, and in this respect too, utilization of a thermostable
enzyme broadens selection of assay protocol.
[0165] Vent (exo-) DNA polymerase is an enzyme having both strand
displacement activity and a high degree of thermostability. It is
known that the complementary chain synthetic reaction involving
strand displacement by DNA polymerase is promoted by adding a
single strand binding protein (Paul M. Lizardi et al., Nature
Genetics, 19, 225-232, July, 1998). This action is applied to the
present invention, and by adding the single strand binding protein,
the effect of promoting the synthesis of complementary chain can be
expected. For example, T4 gene 32 is effective as a single strand
binding protein for Vent (exo-) DNA polymerase.
[0166] FIG. 2 illustrates an exemplary embodiment of the
second-stage amplification reaction, a LAMP-STEM technique as
described herein. In this example, the second-stage amplication
reaction further comprises at least one site-specific primer (i.e.,
a site-specific Stem primer), which anneals or is complementary to
a site-specific Stem primer-binding region or sequence in the
amplicon from stage-one. In a preferred embodiment, the
site-specific Stem primer has at its 3' end a nucleotide that is
complementary to a nucleotide of interest (e.g., a SNP) in the
amplicon from stage-one.
[0167] In certain embodiments, the methods include monitoring and
comparing the rate of amplification in the second-stage reaction.
If the site-specific Stem primer binding region in the amplicon
from stage-one contains a nucleotide complementary to the 3' end of
the site-specific Stem primer, the template will be amplified at an
enhanced rate relative to a mismatch primer (i.e., a primer that
binds to the same location as the site-specific Stem primer but
that has a nucleotide at its 3' end that is not complementary to
the amplicon). Because of the differential amplification rate
between the SNP-Stem primer and a mismatch primer, it is possible
to run both reactions in parallel and compare the rates. The more
rapid appearance of amplification products in the site-specific
Stem primer relative to the mismatch primer is indicative of the
presence of the allele of interest.
[0168] The ability of loop-forming primers to generate stable,
single stranded regions of amplicon is important to rapidly
propagating further amplicon and represents a key aspect of
technologies employing these primers. It means that concatameric
amplicon can contain many new priming sites for the primers
employed by the NAAT in question. In, e.g., LAMP, the loop-forming
primers, which generate inverted repeats in the amplicon, also
provide for single stranded regions of amplicon which they can
themselves bind to and so initiate further re-copy of amplicon and
hence further propagate amplification. In LAMP further additional
primers may be used in addition to LFPs, which also bind to these
single-stranded regions of amplicon to help further propagate
amplification (known as loop primers). A facet of the present
invention is that the stem primers do not bind to said stable
single stranded loops generated by loop-forming primers and/or loop
primers but accelerate amplification via a distinct mechanism.
[0169] The LAMP-STEM component of the technique as described herein
can further include additional primers, for example, "Loop primers"
(FIG. 3) that anneal to regions within the loops generated by the
Loop-forming primers. Loop pimers can further enhance the rate of
the LAMP amplification reaction. In any of the embodiments
described herein, the method further comprises the addition of at
least one loop primer which is complementary to a region in the
first loop or the second loop of the amplicon.
[0170] In any of the embodiments described herein, first-stage
amplification reaction is preceeded by a heating step in which the
target nucleic acid template and primers are heated to
approximately 95.degree. C. for from about 1 minute to about 30
mintues, including 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 ,14, 15,
16, 17, 18, 19 , 20, 21, 22, 23, 24, 2,5 26, 27, 28, 29, 30,
including all times in between. In certain embodiments, the target
nucleic acid template and primers are heated to approximately
95.degree. C. for from about 5 minutes to about 10 minutes.
[0171] In any of the embodiments described herein, the
amplification reaction (i.e., first-stage and/or second stage) is
performed at a temperature of from about 50.degree. C. to about
80.degree. C. In certain embodiments, the amplification reaction is
performed at a temperature of about 55, 56, 57, 58, 59, 60, 61, 62,
63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79,
80.degree. C. In certain embodiments, the amplification reaction is
performed at a temperature of from about 55.degree. to about
65.degree. C.
[0172] In any of the embodiments described herein, the
site-specific primer is in the forward direction. In certain
embodiments, the site-specific primer is in the reverse direction.
In still additional embodiments, both forward and reverse
site-specific primers are included in the reaction.
[0173] In any of the embodiments described herein, a site-specific
nucleotide is comprised at the 3' end of at least one of a
loop-forming primer, a displacement primer, a site-specific primer,
a loop primer or combination thereof.
[0174] In any of the embodiments described herein, the primers or
nucleotide reagents comprise a chemical modification.
[0175] In accordance with the above, an exemplary two-stage
isothermal nucleic acid amplification method for the detection of a
site of interest comprises the steps of: [0176] A) performing a
first-stage nucleic acid amplification reaction comprising: [0177]
1) providing a target nucleic acid template which comprises at
least a first primer binding region, and a first and second
loop-forming primer, wherein the target nucleic acid template
defines a region of interest and comprises a site of interest;
[0178] 2) annealing a first loop-forming primer comprising a first
and a second segment to the target template, wherein the first
segment is substantially complementary to the first primer binding
region on the template and the second segment comprises a sequence
that is substantially complementary to another region in the first
primer or a region in the amplicon generated from the first segment
of the first loop-forming primer such that the second segment is
able, under suitable conditions, to form a first single-stranded
loop in the amplicon; [0179] 3) extending the first loop-forming
primer from its 3' end under suitable conditions with a polymerase
having strand displacement activity, to form a single-stranded
nucleic acid molecule, wherein the second segment of the first
loop-forming primer hybridizes to a region in the amplicon
generated from the first segment of the first loop-forming primer
to form a first single-stranded loop having the 5' end of the first
loop-forming primer; [0180] 4) annealing to the amplicon from (3) a
second loop-forming primer comprising a first and a second segment,
wherein the first segment is substantially complementary to a
second-loop forming primer binding region on the amplicon from (3),
and the second segment comprises a sequence that is substantially
complementary to another region in the second loop-forming primer
or a region in the amplicon generated from the first segment of the
second loop-forming primer such that the second region is able to
form a second single-stranded loop in the amplicon; [0181] 5)
extending the second loop-forming primer from its 3' end under
suitable conditions with a polymerase having strand displacement
activity, to form a single-stranded nucleic acid molecule, wherein
the second segment of the second loop-forming primer hybridizes to
a region in the amplicon to form a second single-stranded loop
having the 5' end of the second loop-forming primer; [0182] 6)
repeating steps A2-5, and thereby amplifying the nucleic acid
template region between the two loop-forming primers comprising the
site of interst, wherein a mixure is formed comprising the
amplified nucleic acid (primary amplicon), and first and second
loop-forming primers; and [0183] B) performing a second-stage
amplification reaction comprising: [0184] 1) providing the mixture
from step A6, and separating into a plurality ofreactions, wherein,
to at least one of thereactions, at least one site-specific Stem
primer is included, which is substantially complementary to a
site-specific primer binding region (site-specific region of
interest) in the primary amplicon, and wherein at least one other
reactionincludes no secondary primer; [0185] 2) annealing the Stem
primer, and the first and second loop-forming primers to theprimary
amplicon, and extending them from their 3' ends under suitable
conditions with a polymerase having strand displacement activity;
[0186] 3) repeating step B2, and thereby further amplifying the
primary amplicon; and [0187] 4) detecting and comparing in
real-time the rate of amplification by the site-specific Stem
primer and rate of amplification in the reaction with no secondary
primer, wherein an increased rate of amplification by the
site-specific Stem primer relative to other reaction is indicative
of the presence of the site of interest in the amplified nucleic
acid, and wherein a slower or similar rate is indicative of the
absence of the site of interest in the amplified nucleic acid.
[0188] In certain embodiments, the second-stage amplification
reaction proceeds at an increased rate relative to the first.
[0189] In certain embodiments, the plurality of reactions include
approximately equal volumes or amounts of the primary amplicon from
the first-stage amplification reaction.
[0190] In certain embodiments, step (B)(1) further comprises
including to at least one additional reaction a mismatch Stem
primer. In additional embodimetns, step (B)(4) comprises detecting
and comparing in real-time the amplification rate of the
site-specific primer reaction, the mismatch primer reaction, and
the reaction with no secondary primer, wherein an increase in the
amplification rate in the site-specific primer reaction relative to
the others (as well as the first-stage reaction) is indicative of
the presence of the site of interest.
[0191] As would be appreciated by those of skill in the art, in any
of the aspects or embodimens as described herein, the methods can
be modified so as to include any desired number of individual or
discrete second-stage reactions, any number of which can include,
respectively, no secondary primer, a site-specific primer or a
mismatch primer. Indeed, the methods include configurations where
the same or different site-specific primers and/or the same or
different mismatch primers are run in parallel in separate
reactions, and all are detected and compared simultaneously and in
real-time.
[0192] Where the primers further contain a second segment, the
second segment comprises a sequence that is substantially
complementary to another segment in the first primer or a region in
the amplicon generated from the first segment of the first primer
such that the second region is able to form a loop. "An amplicon
generated from the first segment of the first primer (or second
primer)" refers to the first copy of the template which is
generated when the first primer is extended by a polymerase. Said
amplicon includes the sequence of the first primer at its 5'
end.
[0193] In certain embodiments, the second segment is substantially
identical to a region on the target template and/or the amplicon to
which the primer binds. Such primers are referred to herein as
loop-forming primers. "Substantially identical" means that the
second segment has at least 70%, 80%, 90%, 95%, 99% or 100%
identity to the region on the target template and/or the amplicon.
It is also envisioned that only part of the second region shows
substantial identity with a region on the target template.
Regardless of whether the whole or only part of the second segment
of the primer shows substantial identity with a region on the
target template, the region of the second segment which is
substantially identical to a region on the target template and/or
amplicon is at least 5 nucleotides, at least 10 nucleotides, at
least 20 nucleotides, at least 30 nucleotides, at least 40
nucleotides, at least 50 nucleotides, at least 60 nucleotides, or
even at least 70 nucleotides in length. In this aspect of the
invention, once the first segment of the primer has been extended
to form a first amplicon, the second segment is able to bind to a
complementary region within the same strand and thereby form a
loop.
[0194] The methods of the invention may be practised using forward
and reverse primers of the same kind, e.g. loop-forming primers
(LFP), hairpin primers, etc. When referring to "the same kind of
primers", it is meant that the primers are all simple primers,
LFPs, LPPs or hairpin primers. The term "different kind of primers"
accordingly relates to a combination of two or more primers wherein
at least one of the primers is not of the same kind as the other
primer(s). For example, where a method uses four primers of which
three are LFPs and one is a LPP, the primers would be considered to
be of a different kind. Thus, it is also envisioned to use forward
and reverse primers which are not of the same kind. For example, a
forward primer may be used that is a LFP in combination with a
reverse primer that is a LPP or a hairpin primer. It is also
possible to combine LFPs or hairpin primers with simple primers
provided that the combination of primers results in the formation
of a concatamer. Where the NAAT used for amplification employs more
than one (i.e. two or more) forward and/or reverse primer, it is
also possible to combine the same or different kinds of primers on
the same primer binding site. In one aspect of the present
invention, the two or more forward and/or reverse primers are all
LFPs. Suitable combinations of primers will be evident to those of
skill in the art. For example, it will be evident to the skilled
person that the combination of forward and reverse primers that are
all simple primers may not provide a mechanism to provide for the
formation of a concatamer and therefore such a combination is not
suitable for use in the present invention.
[0195] It is to be understood that, in general, the forward and
reverse primers, or sets of primers, act on different strands of
the target template. Furthermore, the primers (or one of each set
of primers) will act to delimit the region of the original
polynucleotide copied and recopied. Thus exponential amplification
requires the coupling of activities between at least two primer
binding regions, a forward primer binding region and a reverse
primer binding region (FIG. 1). The forward and reverse primer
binding regions may each comprise a single binding site for a
primer whereby the sites are on opposite sense strands i.e. one
primer binding site is on the "forward strand", one on the "reverse
strand" (as shown in FIG. 1). The forward and reverse primer
regions may also comprise binding sites for two or more primers
each, where more than two primers are employed by a particular
NAAT. In this case, it is possible that the two or more primer
binding sites in the forward and/or reverse primer binding regions
are all situated on the same strand of the target template and/or
amplicon or on different strands of the target template and/or
amplicon.
[0196] Stem primers as used in certain methods described herein may
be positioned anywhere between the forward and reverse primer
binding regions provided that the binding site(s) of the stem
primer(s) do(es) not significantly overlap with the forward or
reverse binding site. It is to be understood that in the case where
a LFP is employed, where the LFP is a forward primer, the forward
primer binding region encompasses not only the F2 site (i.e. the
forward primer binding region) but also the F1 site (i.e. the
region on the forward strand which is substantially identical to
the second segment of the LFP), and where the LFP is a reverse
primer, the reverse primer binding region encompasses not only the
R2c site (i.e. the reverse primer binding region but also the Rlc
site (i.e. the region on the reverse strand which is substantially
identical to the second segment of the LFP; FIG. 1). In this way
the stem primers may be positioned anywhere between the R1(c) and
F1(c) sites where two LFPs are employed (as in LAMP and TRA); where
a single LFP is employed in a particular NAAT, the stem primers may
bind between either a R1(c) or F1(c) site and another primer
binding region occupied by a non-LFP.
[0197] It is possible to employ only one stem primer which binds
either the forward or reverse polynucleotide strand (as shown in
FIG. 2). Alternatively, two or more stem primers may be used which
can bind either to strand of the amplicon or to the same strand.
The methods of the present invention may be practised with one,
two, three, four or more stem primers which can be used in any
spatial combination and which may bind either the reverse or
forward strand provided that the binding sites for the stem primers
do not significantly overlap with the forward or reverse primer
binding regions or do not overlap at all. The stem primers may
further bind to any part within the stem region. Thus, the stem
primer(s) may have a binding site which is in close proximity to
the forward or reverse primer binding region. "Close proximity"
means that the binding region of the stem primer and the
forward/reverse primer binding region are no more than 10 bp, 50
bp, 100 bp, 200 bp, 300 bp, 400 bp, 500 bp, 600 bp, 700 bp, 800 bp,
900 bp or 1000 bp apart.
[0198] In certain embodiments, the stem primers may be at least 5
nucleotides, at least 10 nucleotides, at least 20 nucleotides, at
least 30 nucleotides, at least 40 nucleotides, at least 50
nucleotides, at least 60 nucleotides, at least 70 nucleotides, at
least 80 nucleotides or at least 90 nucleotides in length. The stem
primers may be simple primers. However, it is also envisioned to
use stem primers that are LFPs, hairpin primers, LPPs, chimeric
primers, or other derivatives. Where more than one stem primer is
used, the stem primers may be of the same kind or may be a
combination of different kinds of primers.
[0199] There is a great variety of possible combinations of "simple
primers", LFPs, hairpin primers, RNA containing primers, nickase
site containing primers and other novel primers which could be used
in novel combinations to generate derivatives of the methods
outlined in respective NAAT methods. Where said combinations result
in methods which generate concatameric amplicon capable of
self-copying to generate longer concatamers, stem primers are
anticipated to be applicable.
[0200] In certain embodiments, the site-specific Stem primer
comprises at its 3' end a nucleotide that is complementary to a
nucleotide of interest in the amplified nucleic acid template or
amplicon. In still additional embodiments, the mismatch Stem primer
comprises a 3' end nucleotide that is not complementary to a
nucleotide of interest in the amplified nucleic acid template or
amplicon.
[0201] In certain additional embodiments, the complementary or
site-specific Stem primers may decrease the time required to detect
a particular type and amount of target template by at least 1
minute, at least 2 minutes, at least 3 minutes, at least 5 minutes,
at least 10 minutes, at least 20 minutes, at least 30 minutes or at
least 60 minutes compared to a control reaction to which no stem
primer(s) or a mismatch stem primer has/have been added.
[0202] Stem primers act to increase the rate of amplification of
methods employing LFPs via the coupling of processes occurring at
the forward and reverse binding regions and since it has been
taught in the literature that the LAMP method has an upper limit to
the number of nucleotides separating the forward and reverse
binding sites for the LFPs employed (Notomi et al. Loop-mediated
isothermal amplification of DNA, Nucleic Acids Research, (2000) Vol
28., No. 12, e63), the use of stem primers can clearly allow the
forward and reverse binding sites to be located further apart in
the sequence than previously practicable (especially if several
stem primers are employed). This can have great benefit when it is
desirable to demonstrate that two regions of sequence occur
together on a polynucleotide but where the distance between the two
regions is too far to allow each respective region to be
effectively used as a forward and reverse binding region in the
NAATs described herein.
[0203] Since use of stem primers can allow for the forward and
reverse binding regions to be much further apart than in their
absence and still allow for effective amplification, the presence
of two distinct sites on a polynucleotide can be established. Thus
the invention provides a method for amplification of a polynucleic
acid wherein the forward and reverse primer binding regions are
located at a distance such that synthesis of a polynucleic acid can
occur only in the presence of the stem primer(s). This distance can
be defined experimentally by performing two separate NAATs in
parallel wherein the NAATs, the reagents and the amplification
conditions used are identical except that stem primer(s) are added
to one reaction but not the other. Where synthesis of the
polynucleic acid occurs only in the presence of the stem primer(s),
the primer binding sites are considered to be located at a distance
such that synthesis of a polynucleic acid can occur only in the
presence of the stem primer(s).
[0204] The stem primers may contain exclusively naturally occurring
nucleic acids. However, it is also envisioned to utilise primers
that contain modified bases. Examples of such modified bases
include, but are not limited to, N4-methylcytosine, inosine,
ribocleotides, fluorescent bases, photolysable bases or universal
bases. It is also envisioned to use nucleic acids that have been
labelled with a moiety that allows the stem primer and/or the
amplicon to which the labelled stem primer binds to be detected.
For example, the nucleic acid may be fluorescently labelled. The
stem primers may alternatively be labelled with capture moieties
(e.g. biotin).
[0205] Importantly, the stem primers are not directly responsible
for exponential amplification of the amplicon, which is mediated by
the primers binding to the forward and reverse primer binding
sites, but merely increase the rate of amplification. This is
because the stem primers are considered to function on the
amplification products of the other primers employed by a
particular NAAT. Hence, stem primers function by increasing the
amplification rate of the reaction mediated by the forward and
reverse primers. This is shown in FIG. 2, where it can be seen that
were the stem primer to prime and extend from the target template,
the partial copy of the target template would contain only either
the forward primer binding region or the reverse primer region, but
not both. Therefore, the principal amplicon generated from a stem
primer would not allow for reciprocal copying and hence would not
contribute to exponential amplification of the target template. The
same argument applies to stem primers copying a principal amplicon
generated by other primers employed by a particular NAAT and
similarly for first generation amplicons.
[0206] Also, stem primers are only anticipated to significantly
increase the rate of amplification of a target template if the next
generation amplicon (i.e. further copies of the first generation
amplicon (and copies of these copies)) is concatameric in nature.
The requirement for stem primers to work on concatamers follows
from the requirement that for a particular polynucleic acid to
contribute to exponential amplification it must contain regions
capable of acting as the forward and reverse primer binding
regions. Copying of a concatameric structure via a stem primer, can
produce a polynucleotide copy which has both forward and reverse
primer binding sites, whereas copying a non-concatameric structure
does not. Thus, the use of stem primers will be beneficial for
amplification methods that result in the formation of
concatamers.
[0207] The methods as described herein are well-suited for use with
isothermal nucleic acid amplification methods making them
relatively easy to perform, efficient, robust and reproducible. An
advantage of the described methods is that they allow for the rapid
identification of a desired target nucleic acid (e.g., genetic
mutation, SNP, pathogenic infection, etc.) in a sample, including a
complex mixture. The rapid amplification necessarily means that
less time is required to identify the presence or absence of a
targeted genetic element, and therefore, the present methods
provide a convenient means for point-of-care genetic detection and
diagnosis.
[0208] The term "substantially complementary" means that the first
segment has sufficient complementarity to bind to the primer
binding region on the template and/or amplicon under conditions
which are commonly used during NAATs. This requires that the first
segment of the primer has at least 70%, 80%, 90%, 95%, 99% or 100%
complementarity to the primer binding region on the template. The
first segment of the primer may be at least 5 nucleotides, at least
10 nucleotides, at least 20 nucleotides, at least 30 nucleotides,
at least 40 nucleotides, at least 50 nucleotides, at least 60
nucleotides, or even at least 70 nucleotides in length.
[0209] In any of the embodiments described herein, the first or
second-stage primers can comprise an endonuclease restriction site,
or recognition element for a nicking enzyme.
[0210] In any of the embodiments described herein, the
amplification reaction can comprise a hairpin primer comprising a
first and a second segment, wherein the first segment is
substantially complementary to a primer binding region on a
template and the second segment comprises a sequence that is
substantially complementary to another region in the primer;
[0211] In any of the embodiments described herein, the
amplification reaction can comprise a loop-providing primer,
comprising a hairpin primer in which the inverted repeats are
separated by a linker region.
[0212] In any of the embodiments described herein, the
amplification reaction can comprise a chimeric primer.
[0213] In any of the aspects or embodiments described herein, the
first-stage amplification reaction may be performed in a container
or chamber comprising a channel that is in fluid communication with
one or more additional containers or chambers comprising primers
for performing the second-stage amplification reaction (i.e.,
site-specific primer, site-specific Stem primer; mismatch primer,
mismatch Stem primer, etc). In still additional embodiments, the
first-stage reaction chamber comprises a channel that is in one-way
fluid communication with one or more additional containers or
chambers comprising primers for performing the second-stage
amplification reaction. For example, as illustrated in FIG. 4 the
first-stage reaction is performed in a central chamber that is in
fluid communication with a plurality of additional chambers for
performing the second-stage amplification reaction. In a preferred
embodiment, the reaction mixture from the first-stage amplification
reaction is automatically and simultaneously introduced into the
additional chambers, which comprise the primers for performing the
second-stage reaction.
[0214] In a preferred embodiment, an approximately equal amount or
volume of the first-stage reaction mixture is automatically
introduced from a central chamber to the axially arranged
additional chambers via, e.g., centrifugal force. In certain
embodiments, the method comprises performing a plurality of
separate or discrete second-stage amplification reactions
approximately simultaneously. In certain additional embodiments,
the discrete reactions comprise the same or different site-specific
primers. In still additional embodiments, the discrete reactions
comprise a plurality or combination of site-specific primers (i.e.,
"multiplexing reaction").
[0215] In any of the aspects or embodiments described herein, each
second-stage reaction volume can be about 1, 2, 3, 4, 5, 6, 7, 8,
9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,
43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59,
60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
77, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,
95, 96, 97, 98, 99, 1000 or more. In a preferred embodiment, each
respective second-stage reaction volume is 8 .mu.l.
[0216] In certain embodiments, the description provides a method
for detecting and comparing nucleic acid amplification comprising
providing a first-stage reaction chamber; performing a first-stage
pre-amplification reaction as described herein in the first-stage
reaction chamber; introducing an amount or volume of the
first-stage pre-amp reaction directly into a plurality of
second-stage reaction chambers, wherein at least one second-stage
reaction chamber comprises a site-specific primer, and at least one
other second-stage reaction chamber comprises a mismatched primer;
and performing in each second-stage reaction chamber a second-stage
amplification reaction as described herein; and detecting and
comparing in real-time the rate of amplification of each reaction
simultaneously, wherein a faster rate of amplification in the
site-specific primer reaction versus the mismatch primer reaction
is indicative of the presence of the site of interest.
[0217] In any of the aspects or embodiments described herein, the
first-stage amplification reaction can comprise site-specific
primers such that the first-stage pre-amplification reaction is
selective for a particular site of interest, and only if that site
or region exists in the sample will rapid amplification of the
template proceed at the second or later stage amplification
reaction.
[0218] In any of the aspects or embodiments described herein, the
second-stage (or later stage) amplification reaction can comprise
multiple site-specific primers (i.e., "multiplex reaction"). By
using differentially labeled site-specific oligonucleotides
different amplification products can be detected and compared
(i.e., multiplexed) within the same reaction.
[0219] Although several of the aspects and embodiments refer to a
two-staged amplification scheme, the invention is not so limited.
Indeed, the methods described herein are predicated upon the
surprising discovery that the presence of a specific site or
sequence of interest in a target nucleic acid region can be
detected by the enhanced rate of amplification with a site-specific
or sequence-specific (i.e., complementary) primer relative to the
slower rate of an amplification reaction with mismatch primer that,
but-for the mismatched base, anneals to the same target region. As
such, any number of additional amplification steps can be
performed, e.g., 3, 4, 5, 6, 7, 8, 9, etc., and therefore, any
number of sites, regions or sequences of interest can be detected.
Similarly, for each of the respective site-specific primer
reactions to be performed, a parallel mismatch primer reaction can
be performed and the rate of amplification of the two reactions
monitored.
[0220] The skilled person will be aware that, in addition to the
primers needed for amplification, the NAATs will require further
reagents in order to synthesize a polynucleic acid. The required
reagents will be evident to the person skilled in the art but will
generally include a suitable buffer, dNTPs, a polymerase, etc.
[0221] As the skilled person will appreciate, following addition of
all the necessary components for performing the NAAT in question,
it is necessary to provide suitable conditions for the synthesis of
the polynucleic acid. This can be achieved by providing a suitable
incubation temperature, for example. It is preferred that
amplification occurs under isothermal conditions. This means that
during amplification the temperature is kept constant. "Constant"
means that the temperature varies by no more than +/-10.degree. C.
However, methods that encompass a single temperature change of
greater than 10.degree. C., two temperature changes of greater than
10.degree. C., three temperature changes greater than 10.degree.
C., four temperature changes greater than 10.degree. C. or five
temperature changes greater than 10.degree. C. during the
amplification process are also within the scope of the present
invention.
[0222] In another aspect, the description provides a two-stage
isothermal nucleic acid amplification and detection method
comprising the steps of: [0223] a. providing a LAMP amplified
nucleic acid template comprising concatamerized amplicons, wherein
the amplicons are formed of (i) a 3' end portion comprising a first
region located 3' terminal that, under suitable conditions, anneals
to a first complementary region to form a first loop; and (ii) a 5'
end portion comprising a second region located 5' terminal that,
under suitable conditions, anneals to a second complementary region
to form a second loop; [0224] b. admixing a portion of the nucleic
acid template from (a) to: (i) a reaction mixture comprising at
least one site-specific Stem primer that is substantially
complementary to a site or region of interest between the first and
second primer binding regions, wherein the site-specific primer
includes at its 3' end a nucleotide that is complementary to a
nucleotide of interest in the template, and (ii) a reaction mixture
comprisingno secondary primer; [0225] c. annealing the primers from
(b) to the nucleic acid template; [0226] d. extending the primers
from the 3' end under suitable isothermal conditions with a
polymerase having strand displacement activity; and [0227] e.
repeating steps c-d, and thereby rapidly amplifying the nucleic
template, and detecting and comparing in real-time the
amplification rate of reaction (b)(i) with reaction (b)(ii),
wherein an increase in the amplification rate in reaction (b)(i)
relative to reaction (b)(ii) is indicative of the presence of the
site of interest.
[0228] In certain embodiments, each reaction mixture includes
approximately an equal volume or amount of the nucleic acid
template.
[0229] In certain embodiments, step (b) further comprises admixing
a portion of the nucleic acid template from (a) to (iii) a reaction
mixture comprising a mismatch Stem primer. In additional
embodimetns, step (e) comprises detecting and comparing in
real-time the amplification rate of reactions (b)(i), (b)(ii), and
(b)(iii), wherein an increase in the amplification rate in reaction
(b)(i) relative to reaction (b)(ii) and (b)(iii) is indicative of
the presence of the site of interest.
[0230] In any of the aspects or embodiments described herein, the
method further comprises a step of detecting the formation of an
amplicon in real-time. In certain embodiments, the amplification
reaction mixture comprises fluorescently labeled dNTPs, a
fluorescent DNA intercalating dye, chemiluminescent,
electrochemical or other reporter system as a means to follow the
extent of amplification in real-time. Thus, in certain embodiments,
the formation of an amplicon is detected in real-time by measuring
an increase in fluorescence. The amplification of the polynucleic
acid according to the invention may be detected by methods known to
those of skill in the art. Suitable methods include but are not
limited to the use of fluorescent intercalating dyes, fluorescent
primers or probes, measuring turbidity, electrochemical probes,
bioluminescent signals and chemiluminescent probes.
[0231] The amplification of the polynucleic acid may be detected
using real-time methods, i.e. methods that can detect the
polynucleic acid as it is amplified. Examples of such detection
systems include, but are not limited to, fluorescence (e.g.
fluorescent probes that are added during the amplification),
bioluminescent signals and electrochemical probes. In one aspect,
the primers themselves are labelled with a detectable moiety, e.g.
a fluorescent label, a chemiluminescent label or an electrochemical
label, that allows detection of the amplicon to which the primer(s)
bind(s). Thus, a further utility of stem primers in concatamer
forming NAATs could be as probe for use in a fluorescent,
chemiluminescent or electrochemical reporter system as a means to
follow the extent of amplification in real-time. Other suitable
reporter systems will be evident to those of skill in the art. Stem
primers could have benefit as probe containing primers over e.g.
LFP or hairpin primers since they are not required to generate
inverted repeats in amplicon which could affect certain types of
probes. Alternatively, the amplification product may be detected
using end-point measurements, i.e. measurements which take place
after the amplification of the polynucleic acid has been
completed.
[0232] The amplification of the polynucleic acid can also be
detected by other detection methods employed in NAAT detection.
Suitable examples include, but are not limited to, gene arrays,
lateral flow strips, electrophoresis, mass spectroscopy and
acoustic detection.
[0233] In one embodiment the Bioluminescent Assay in Real-Time
(BART) reporter system is used to detect the synthesis of the
polynucleic acid. This system has been explained in detail in
WO2004/062338 and WO2006/010948, which are hereby incorporated by
reference. BART is an example of a reporter system designed for
isothermal NAATs which gives a single type of signal from a sample:
a bioluminescent signal. BART utilizes the firefly
luciferase-dependent detection of inorganic pyrophosphate: this is
produced in large quantities when `target` sequences are amplified
using a NAAT. As such, molecular diagnostics can be achieved with
BART simply by measuring the light emitted from closed tubes, in a
homogeneous phase assay. BART is proven with several different
NAATs, operating between 50-63.degree. C. The BART reporter is a
particularly effective means to follow the rate of amplification of
a NAAT since the light output represents a measure of the
instantaneous rate of amplification (whereas, e.g. fluorescent
outputs show the accumulation of a signal and hence the
measurements have to be differentiated to obtain the amplification
rates).
[0234] BART being used in conjunction with LAMP to detect a
dilution series of a particular target DNA molecule. Note that as
the amount of target DNA in the sample decreases, the lag-phase to
reach the time of maximal light increase (which is proportional to
the lag-phase to reach maximal amplification) increases. Put
differently, the time to reach the characteristic light peak
associated with positive samples in BART increases in inverse
proportion to the amount of target polynucleic acid in the sample.
It is stressed that whilst the examples make use of the BART
reporter system, the present invention is not limited to the use of
BART and is equally applicable to methods such as fluorescence,
turbidity, other spectroscopic techniques or electrochemical
measurement methods irrespective of whether these are employed in
real-time measurement of amplification or as end-point
measurements.
[0235] Preferably, the method of the invention is performed in a
sealed vessel. This is of great utility since it reduces or even
prevents the possibility of the sample becoming contaminated.
Moreover, it reduces or even prevents the possibility of the
laboratory becoming contaminated. This is particularly important as
if even one copy of the template polynucleic acid or amplicon were
to escape into the laboratory, this could potentially contaminate
other samples to be tested and give false-positive results. Thus,
the ability to prevent contamination is of particular importance
where a method of the invention is used in a diagnostic
application.
[0236] In another aspect, the description provides methods for
determining whether a particular polynucleic acid sequence is
present in a nucleic acid sample or in organism's genetic code. For
example, the methods can be used for determining whether the
nucleic acid to which the template nucleic acid originates has been
genetically modified, for detection of DNA associated with a
particular non-genetically modified breed of plant or a genetically
modified plant, for detection of DNA associated with pedigree
breeds of animal or for medical or veterinary diagnostic
applications such as genetic testing or forensic.
[0237] In any of the embodiments described herein, the target
nucleic acid template can comprise genomic DNA, cDNA or RNA or a
segment therefrom, from a virus, plant, microbe, fungus,
mycoplasma, single cellular organism, or multicellular organism,
e.g., a mammal, such as a human. In certain embodiments, the
genomic DNA is from a pathogenic virus or microbe, e.g., bacteria
or mycoplasma.
[0238] Thus, in another aspect, the description provides methods
for diagnostic applications. In particular the methods allow
identification and quantification of organisms in a patient and
other samples. The methods of the present invention are also
suitable for the detection of mutations, genetic diseases, or
single-nucleotide polymorphisms (SNPs). The methods of the present
invention are also suitable for the detection of pathogenic and
non-pathogenic micro-organisms or viruses.
[0239] The organism may be any micro-organisms, such as viruses,
bacteria, mycoplasma and fungi. The micro-organism can be
pathogenic but it may also be a non-pathogenic micro-organism. The
microorganism may also be a genetically modified organism (GMO).
Furthermore, the methods of the present invention can be used to
identify genetically modified crops and animals, for the detection
of a disease state; for the prediction of an adverse reaction from
a therapy and also for the prediction of a disease state
susceptibility.
[0240] For example, in one embodiment, the description provides a
two-stage method of detecting the presence of a nucleic acid of
interest or diagnosing a disease. In certain embodiments, the
method as described herein can be used for the real-time, rapid
identification of a micro-organism, such as a virus, bacteria,
mycoplasma, fungus, or a genetic disease, mutation, SNP, wherein
said method comprises providing a nucleic acid sample from subject
to be tested, e.g., a patient sample, performing the two-stage
amplification reaction as described herein, and detecting and
comparing in real-time the amplification rate of a site-specific
primer amplification rate with a mismatch primer amplification
rate, wherein an increase in the site-specific primer amplification
rate relative to the mismatch primer amplification rate is
indicative of the presence of the specific site, region or
nucleotide(s) of interest, e.g., a site, region, or nucleotide(s)
associated with at least one of a genetic disease, mutation, SNP,
virus, or microbe, e.g., bacteria.
[0241] In certain embodiments, the microbe is a bacterium. In
certain embodiments, the bacteria is a member of a genus selected
from the group consisting of Bacillus, Bartonella, Bordetella,
Borrelia, Brucella, Campylobacter, Chlamydia, Chlamydophila,
Clostridium, Corynebacterium, Enterococcus, Escherichia,
Francisella, Haemophilus, Legionella, Leptospira, Listeria,
Mycobacterium, Mycoplasma, Neisseria, Pseudomonas, Rickettsia,
Salmonella, Shigella, Staphylococcus, Streptococcus, Treponema,
Ureaplasma, Vibrio, and Yershinia.
[0242] In certain embodiments, the bacteria is a member of the
group consisting of Bacillus anthracis, Bacillus cereus, Bartonella
henselae, Bartonella Quintana, Bordetella pertussis, Borrelia
burgdorferi, Borrelia garinii, Borrelia afzelii, Borrelia
recurrentis, Brucella abortus, Brucella canis, Brucella melitensis,
Brucella suis, Campylobacter jejuni, Chlamydia pneumonia, Chlamydia
trachomatis, Chlamydophila psittaci, Clostridium botulinum,
Clostridium difficile, Clostridium perfringens, Clostridium tetani,
Corynebacterium diphtheria, Enterococcus faecalis, Enterococcus
faecium, Escherichia coli, Francisella tularensis, Haemophilus
influenza, Helicobacter pylori, Legionella pneumophila, Leptospira
inlerrogans, Leptospira santarosai, Leptospira weilii, Leptospira
noguchii, Listeria monocytogenes, Mycobacterium leprae,
Mycobacterium tuberculosis, Mycobacterium ulcerans, Mycoplasma
pneumonia, Neisseria gonorrhoeae, Neisseria meningitides,
Pseudomonas aeruginosa, Rickettsia rickettsia, Salmonella typhi,
Salmonella typhimurium, Shigella sonnei, Staphylococcus aureus,
Staphylococcus epidermidis, Staphylococcus saprophyticus,
Streptococcus agalactiae, Streptococcus pneumonia, Streptococcus
pyogenes, Treponema pallidum, Ureaplasma urealyticum, Vibrio
cholera, Yersinia pestis, Yersinia enterocolitica, and Yersinia
pseudotuberculosis.
[0243] In certain embodiments, the target nucleic acid template is
from tubercle bacillus (MTB or TB). In certain additional
embodimetns, the target nucleic acid template is from the rpoB gene
from MTB. In still further embodiments, the target nucleic acid
template is rpoB13.5 F6.
[0244] In certain embodiments, the virus is a member of a family
selected from the group consisting of Adenoviridae, Herpesviridae,
Papillomaviridae, Polyomaviridae, Poxviridae, Hepadnaviridae,
Parvoviridae, Astroviridae, Caliciviridae, Picornaviridae,
Coronaviridae, Flaviviridae, Togaviridae, Hepeviridae,
Retroviridae, Orthomyxoviridae, Arenaviridae, Bunyaviridae,
Filoviridae, Paramyxoviridae, Rhabdoviridae, and Reoviridae.
[0245] In certain embodiments, the virus is a member selected from
the group consisting of Adenovirus, Herpes simplex type 1, Herpes
simplex type 2, Varicella-zoster virus, Epstein-Barr virus, Human
cytomegalovirus, Human herpesvirus type 8, Human papillomavirus, BK
virus, JC virus, Smallpox, Hepatitis B, Human bocavirus, Parvovirus
B19, Human astrovirus, Norwalk virus, coxsackievirus, hepatitis A
virus, poliovirus, rhinovirus, Severe acute respiratory syndrome
virus, Hepatitis C virus, yellow fever virus, dengue virus, West
Nile virus, Rubella virus, Hepatitis E virus, Human
immunodeficiency virus (HIV), Influenza virus, Guanarito virus,
Junin virus, Lassa virus, Machupo virus, Sabia virus, Crimean-Congo
hemorrhagic fever virus, Ebola virus, Marburg virus, Measles virus,
Mumps virus, Parainfluenza virus, Respiratory syncytial virus,
Human metapneumovirus, Hendra virus, Nipah virus, Rabies virus,
Hepatitis D, Rotavirus, Orbivirus, Coltivirus, and Banna virus.
[0246] In a further aspect, there is provided a kit for use in a
method according to the invention. Preferably such a kit comprises
all the components necessary to practice a method as described
herein, including paired site-specific and mismatch primers. In
certain aspects the kit comprises the target polynucleic acid which
is to be tested, and/or reagents for preparing the biological
sample for inclusion in the methods as described herein.
[0247] A kit for use in a method according to the invention
preferably comprises a polynucleic acid polymerase, the substrates
for the nucleic acid polymerase and primers suitable for isothermal
amplification of the target polynucleic acid, as described earlier.
More preferably, the kit further comprises buffer reagents, such as
a source of magnesium ions, or additives known in the art to
improve the performance of a NAAT such as Betaine or additives
known to improve the shelf-life of kit reagents such as trehelose
or additives known to help preserve reagents such as sodium azide.
Alternatively, a kit for use in a method according to the invention
may comprise only some of these components and/or additional
components. The sample and any other components that have been
omitted from the kit may then be added to the kit during use.
[0248] Preferably, at least one of the components of the kit is
lyophilized or is in another form which is suitable for storage in
the kit. More preferably, all of the components of the kit are
lyophilized or in one or more other forms suitable for storage.
Such other forms include components to which stabilizing factors
have been added and/or a refrigerated or frozen master mix that
contains the components of the kit.
[0249] In another aspect, the description provides a method of
treating or preventing a disease, comprising performing a two-stage
nucleic acid amplification as described herein on a patient sample,
and wherein if the patent tests positive for the presence of a site
of interest associated with a disease or infection, treating or
administering to the patient an effective amount of an appropriate
therapeutic or bioactive agent, e.g., antibiotic, anti-cancer
agent, anti-inflammatory, antimicrobial, antiviral, antifungal,
antipsychotic, etc. The term "bioactive agent" is used to describe
an agent with biological activity to assist in effecting an
intended therapy, inhibition and/or prevention/prophylaxis. The
terms "treat", "treating", and "treatment", etc., as used herein,
refer to any action providing a benefit to a patient including the
treatment of any disease state or condition.
[0250] Disease states of conditions which may be treated using
compounds according to the present invention include, for example,
asthma, autoimmune diseases such as multiple sclerosis, various
cancers, ciliopathies, cleft palate, diabetes, heart disease,
hypertension, inflammatory bowel disease, mental retardation, mood
disorder, obesity, refractive error, infertility, Angelman
syndrome, Canavan disease, Coeliac disease, Charcot-Marie-Tooth
disease, Cystic fibrosis, Duchenne muscular dystrophy,
Haemochromatosis, Hemophilia, Klinefelter's syndrome,
Neurofibromatosis, Phenylketonuria, Polycystic kidney disease,
(PKD1) or 4 (PKD2) Prader-Willi syndrome, Sickle-cell disease,
Tay-Sachs disease, Turner syndrome.
[0251] Further disease states or conditions which may be treated by
compounds according to the present invention include Alzheimer's
disease, Amyotrophic lateral sclerosis (Lou Gehrig's disease),
Anorexia nervosa, Anxiety disorder, Atherosclerosis, Attention
deficit hyperactivity disorder, Autism, Bipolar disorder, Chronic
fatigue syndrome, Chronic obstructive pulmonary disease, Crohn's
disease, Coronary heart disease, Dementia, Depression, Diabetes
mellitus type 1, Diabetes mellitus type 2, Epilepsy, Guillain-Barre
syndrome, Irritable bowel syndrome, Lupus, Metabolic syndrome,
Multiple sclerosis, Myocardial infarction, Obesity,
Obsessive-compulsive disorder, Panic disorder, Parkinson's disease,
Psoriasis, Rheumatoid arthritis, Sarcoidosis, Schizophrenia,
Stroke, Thromboangiitis obliterans, Tourette syndrome,
Vasculitis.
[0252] Still additional disease states or conditions which can be
treated by compounds according to the present invention include
aceruloplasminemia, Achondrogenesis type II, achondroplasia,
Acrocephaly, Gaucher disease type 2, acute intermittent porphyria,
Canavan disease, Adenomatous Polyposis Coli, ALA dehydratase
deficiency, adenylosuccinate lyase deficiency, Adrenogenital
syndrome, Adrenoleukodystrophy, ALA-D porphyria, ALA dehydratase
deficiency, Alkaptonuria, Alexander disease, Alkaptonuric
ochronosis, alpha 1-antitrypsin deficiency, alpha-1 proteinase
inhibitor, emphysema, amyotrophic lateral sclerosis Alstrom
syndrome, Alexander disease, Amelogenesis imperfecta, ALA
dehydratase deficiency, Anderson-Fabry disease, androgen
insensitivity syndrome, Anemia Angiokeratoma Corporis Diffusum,
Angiomatosis retinae (von Hippel-Lindau disease) Apert syndrome,
Arachnodactyly (Marfan syndrome), Stickler syndrome, Arthrochalasis
multiplex congenital (Ehlers-Danlos syndrome#arthrochalasia type)
ataxia telangiectasia, Rett syndrome, primary pulmonary
hypertension, Sandhoff disease, neurofibromatosis type II,
Beare-Stevenson cutis gyrata syndrome, Mediterranean fever,
familial, Benjamin syndrome, beta-thal assemi a, Bilateral Acoustic
Neurofibromatosis (neurofibromatosis type II), factor V Leiden
thrombophilia, Bloch-Sulzberger syndrome (incontinentia pigmenti),
Bloom syndrome, X-linked sideroblastic anemia, Bonnevie-Ullrich
syndrome (Turner syndrome), Bourneville disease (tuberous
sclerosis), prion disease, Birt-Hogg-Dube syndrome, Brittle bone
disease (osteogenesis imperfecta), Broad Thumb-Hallux syndrome
(Rubinstein-Taybi syndrome), Bronze Diabetes/Bronzed Cirrhosis
(hemochromatosis), Bulbospinal muscular atrophy (Kennedy's
disease), Burger-Grutz syndrome (lipoprotein lipase deficiency),
CGD Chronic granulomatous disorder, Campomelic dysplasia,
biotinidase deficiency, Cardiomyopathy (Noonan syndrome), Cri du
chat, CAVD (congenital absence of the vas deferens), Caylor
cardiofacial syndrome (CBAVD), CEP (congenital erythropoietic
porphyria), cystic fibrosis, congenital hypothyroidism,
Chondrodystrophy syndrome (achondroplasia),
otospondylomegaepiphyseal dysplasia, Lesch-Nyhan syndrome,
galactosemia, Ehlers-Danlos syndrome, Thanatophoric dysplasia,
Coffin-Lowry syndrome, Cockayne syndrome, (familial adenomatous
polyposis), Congenital erythropoietic porphyria, Congenital heart
disease, Methemoglobinemia/Congenital methaemoglobinaemia,
achondroplasia, X-linked sideroblastic anemia, Connective tissue
disease, Conotruncal anomaly face syndrome, Cooley's Anemia
(beta-thalassemia), Copper storage disease (Wilson's disease),
Copper transport disease (Menkes disease), hereditary
coproporphyria, Cowden syndrome, Craniofacial dysarthrosis (Crouzon
syndrome), Creutzfeldt-Jakob disease (prion disease), Cockayne
syndrome, Cowden syndrome, Curschmann-Batten-Steinert syndrome
(myotonic dystrophy), Beare-Stevenson cutis gyrata syndrome,
primary hyperoxaluria, spondyloepimetaphyseal dysplasia (Strudwick
type), muscular dystrophy, Duchenne and Becker types (DBMD), Usher
syndrome, Degenerative nerve diseases including de Grouchy syndrome
and Dejerine-Sottas syndrome, developmental disabilities, distal
spinal muscular atrophy, type V, androgen insensitivity syndrome,
Diffuse Globoid Body Sclerosis (Krabbe disease), Di George's
syndrome, Dihydrotestosterone receptor deficiency, androgen
insensitivity syndrome, Down syndrome, Dwarfism, erythropoietic
protoporphyria Erythroid 5-aminolevulinate synthetase deficiency,
Erythropoietic porphyria, erythropoietic protoporphyria,
erythropoietic uroporphyria, Friedreich's ataxia., familial
paroxysmal polyserositis, porphyria cutanea tarda, familial
pressure sensitive neuropathy, primary pulmonary hypertension
(PPH), Fibrocystic disease of the pancreas, fragile X syndrome,
galactosemia, genetic brain disorders, Giant cell hepatitis
(Neonatal hemochromatosis), Gronbl ad-Strandberg syndrome
(pseudoxanthoma elasticum), Gunther disease (congenital
erythropoietic porphyria), haemochromatosis, Hallgren syndrome,
sickle cell anemia, hemophilia, hepatoerythropoietic porphyria
(HEP), Hippel-Lindau disease (von Hippel-Lindau disease),
Huntington's disease, Hutchinson-Gilford progeria syndrome
(progeria), Hyperandrogenism, Hypochondroplasia, Hypochromic
anemia, Immune system disorders, including X-linked severe combined
immunodeficiency, Insley-Astley syndrome, Jackson-Weiss syndrome,
Joubert syndrome, Lesch-Nyhan syndrome, Jackson-Weiss syndrome,
Kidney diseases, including hyperoxaluria, Klinefelter's syndrome,
Kniest dysplasia, Lacunar dementia,Langer-Saldino achondrogenesis,
ataxia telangiectasia, Lynch syndrome, Lysyl-hydroxylase
deficiency, Machado-Joseph disease, Metabolic disorders, including
Kniest dysplasia, Marfan syndrome, Movement disorders, Mowat-Wilson
syndrome, cystic fibrosis, Muenke syndrome, Multiple
neurofibromatosis, Nance-Insley syndrome, Nance-Sweeney
chondrodysplasia, Niemann-Pick disease, Noack syndrome (Pfeiffer
syndrome), Osler-Weber-Rendu disease, Peutz-Jeghers syndrome,
Polycystic kidney disease, polyostotic fibrous dysplasia
(McCune-Albright syndrome), Peutz-Jeghers syndrome,
Prader-Labhart-Willi syndrome, hemochromatosis, primary
hyperuricemia syndrome (Lesch-Nyhan syndrome), primary pulmonary
hypertension, primary senile degenerative dementia, prion disease,
progeria (Hutchinson Gilford Progeria Syndrome), progressive
chorea, chronic hereditary (Huntington) (Huntington's disease),
progressive muscular atrophy, spinal muscular atrophy, propionic
acidemia, protoporphyria, proximal myotonic dystrophy, pulmonary
arterial hypertension, PXE (pseudoxanthoma elasticum), Rb
(retinoblastoma), Recklinghausen disease (neurofibromatosis type
I), Recurrent polyserositis, Retinal disorders, Retinoblastoma,
Rett syndrome, RFALS type 3, Ricker syndrome, Riley-Day syndrome,
Roussy-Levy syndrome, severe achondroplasia with developmental
delay and acanthosis nigricans (SADDAN), Li-Fraumeni syndrome,
sarcoma, breast, leukemia, and adrenal gland (SBLA) syndrome,
sclerosis tuberose (tuberous sclerosis), SDAT, SED congenital
(spondyloepiphyseal dysplasia congenita), SED Strudwick
(spondyloepimetaphyseal dysplasia, Strudwick type), SEDc
(spondyloepiphyseal dysplasia congenita) SEMD, Strudwick type
(spondyloepimetaphyseal dysplasia, Strudwick type), Shprintzen
syndrome, Skin pigmentation disorders, Smith-Lemli-Opitz syndrome,
South-African genetic porphyria (variegate porphyria),
infantile-onset ascending hereditary spastic paralysis, Speech and
communication disorders, sphingolipidosis, Tay-Sachs disease,
spinocerebellar ataxi a, Stickler syndrome, stroke, androgen
insensitivity syndrome, tetrahydrobi opterin deficiency,
beta-thalassemia, Thyroid disease, Tomaculous neuropathy
(hereditary neuropathy with liability to pressure palsies),
Treacher Collins syndrome, Triplo X syndrome (triple X syndrome),
Trisomy 21 (Down syndrome), Trisomy X, VHL syndrome (von
Hippel-Lindau disease), Vision impairment and blindness (Alstrom
syndrome), Vrolik disease, Waardenburg syndrome, Warburg Sjo
Fledelius Syndrome, Weissenbacher-Zweymuller syndrome,
Wolf-Hirschhorn syndrome, Wolff Periodic disease,
Weissenbacher-Zweymuller syndrome and Xeroderma pigmentosum, among
others.
[0253] The term "cancer" refers to the pathological process that
results in the formation and growth of a cancerous or malignant
neoplasm, i.e., abnormal tissue that grows by cellular
proliferation, often more rapidly than normal and continues to grow
after the stimuli that initiated the new growth cease. Malignant
neoplasms show partial or complete lack of structural organization
and functional coordination with the normal tissue and most invade
surrounding tissues, metastasize to several sites, and are likely
to recur after attempted removal and to cause the death of the
patient unless adequately treated. As used herein, the term
neoplasia is used to describe all cancerous disease states and
embraces or encompasses the pathological process associated with
malignant hematogenous, ascitic and solid tumors. Exemplary cancers
which may be treated by the present compounds either alone or in
combination with at least one additional anti-cancer agent include
squamous-cell carcinoma, basal cell carcinoma, adenocarcinoma,
hepatocellular carcinomas, and renal cell carcinomas, cancer of the
bladder, bowel, breast, cervix, colon, esophagus, head, kidney,
liver, lung, neck, ovary, pancreas, prostate, and stomach;
leukemias; benign and malignant lymphomas, particularly Burkitt's
lymphoma and Non-Hodgkin's lymphoma; benign and malignant
melanomas; myeloproliferative diseases; sarcomas, including Ewing's
sarcoma, hemangiosarcoma, Kaposi's sarcoma, liposarcoma,
myosarcomas, peripheral neuroepithelioma, synovial sarcoma,
gliomas, astrocytomas, oligodendrogliomas, ependymomas,
gliobastomas, neuroblastomas, ganglioneuromas, gangliogliomas,
medulloblastomas, pineal cell tumors, meningiomas, meningeal
sarcomas, neurofibromas, and Schwannomas; bowel cancer, breast
cancer, prostate cancer, cervical cancer, uterine cancer, lung
cancer, ovarian cancer, testicular cancer, thyroid cancer,
astrocytoma, esophageal cancer, pancreatic cancer, stomach cancer,
liver cancer, colon cancer, melanoma; carcinosarcoma, Hodgkin's
disease, Wilms' tumor and teratocarcinomas. Additional cancers
which may be treated using compounds according to the present
invention include, for example, T-lineage Acute lymphoblastic
Leukemia (T-ALL), T-lineage lymphoblastic Lymphoma (T-LL),
Peripheral T-cell lymphoma, Adult T-cell Leukemia, Pre-B ALL, Pre-B
Lymphomas, Large B-cell Lymphoma, Burkitts Lymphoma, B-cell ALL,
Philadelphia chromosome positive ALL and Philadelphia chromosome
positive CML.
[0254] The term "anti-cancer agent" is used to describe an
anti-cancer agent. These agents include, for example, everolimus,
trabectedin, abraxane, TLK 286, AV-299, DN-101, pazopanib,
GSK690693, RTA 744, ON 0910.Na, AZD 6244 (ARRY-142886), AMN-107,
TKI-258, GSK461364, AZD 1152, enzastaurin, vandetanib, ARQ-197,
MK-0457, MLN8054, PHA-739358, R-763, AT-9263, a FLT-3 inhibitor, a
VEGFR inhibitor, an EGFR TK inhibitor, an aurora kinase inhibitor,
a PIK-1 modulator, a Bcl-2 inhibitor, an HDAC inhbitor, a c-MET
inhibitor, a PARP inhibitor, a Cdk inhibitor, an EGFR TK inhibitor,
an IGFR-TK inhibitor, an anti-HGF antibody, a PI3 kinase inhibitor,
an AKT inhibitor, an mTORC1/2 inhibitor, a JAK/STAT inhibitor, a
checkpoint-1 or 2 inhibitor, a focal adhesion kinase inhibitor, a
Map kinase kinase (mek) inhibitor, a VEGF trap antibody,
pemetrexed, erlotinib, dasatanib, nilotinib, decatanib,
panitumumab, amrubicin, oregovomab, Lep-etu, nolatrexed, azd2171,
batabulin, ofatumumab, zanolimumab, edotecarin, tetrandrine,
rubitecan, tesmilifene, oblimersen, ticilimumab, ipilimumab,
gossypol, Bio 111, 131-I-TM-601, ALT-110, BIO 140, CC 8490,
cilengitide, gimatecan, IL13-PE38QQR, INO 1001, IPdR.sub.1
KRX-0402, lucanthone, LY317615, neuradiab, vitespan, Rta 744, Sdx
102, talampanel, atrasentan, Xr 311, romidepsin, ADS-100380,
sunitinib, 5-fluorouracil, vorinostat, etoposide, gemcitabine,
doxorubicin, liposomal doxorubicin, 5'-deoxy-5-fluorouridine,
vincristine, temozolomide, ZK-304709, seliciclib; PD0325901,
AZD-6244, capecitabine, L-Glutamic acid,
N-[4-[2-(2-amino-4,7-dihydro-4-oxo-1H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]-
benzoyl]-, disodium salt, heptahydrate, camptothecin, PEG-labeled
irinotecan, tamoxifen, toremifene citrate, anastrazole, exemestane,
letrozole, DES(diethylstilbestrol), estradiol, estrogen, conjugated
estrogen, bevacizumab, IMC-1C11, CHIR-258);
3-[5-(methylsulfonylpiperadinemethyl)-indolyl-quinolone, vatalanib,
AG-013736, AVE-0005, goserelin acetate, leuprolide acetate,
triptorelin pamoate, medroxyprogesterone acetate,
hydroxyprogesterone caproate, megestrol acetate, raloxifene,
bicalutamide, flutamide, nilutamide, megestrol acetate, CP-724714;
TAK-165, HKI-272, erlotinib, lapatanib, canertinib, ABX-EGF
antibody, erbitux, EKB-569, PKI-166, GW-572016, Ionafarnib,
BMS-214662, tipifarnib; amifostine, NVP-LAQ824, suberoyl analide
hydroxamic acid, valproic acid, trichostatin A, FK-228, SU11248,
sorafenib, KRN951, aminoglutethimide, arnsacrine, anagrelide,
L-asparaginase, Bacillus Calmette-Guerin (BCG) vaccine, adriamycin,
bleomycin, buserelin, busulfan, carboplatin, carmustine,
chlorambucil, cisplatin, cladribine, clodronate, cyproterone,
cytarabine, dacarbazine, dactinomycin, daunorubicin,
diethylstilbestrol, epirubicin, fludarabine, fludrocortisone,
fluoxymesterone, flutamide, gleevec, gemcitabine, hydroxyurea,
idarubicin, ifosfamide, imatinib, leuprolide, levamisole,
lomustine, mechlorethamine, melphalan, 6-mercaptopurine, mesna,
methotrexate, mitomycin, mitotane, mitoxantrone, nilutamide,
octreotide, oxaliplatin, pamidronate, pentostatin, plicamycin,
porfimer, procarbazine, raltitrexed, rituximab, streptozocin,
teniposide, testosterone, thalidomide, thioguanine, thiotepa,
tretinoin, vindesine, 13-cis-retinoic acid, phenylalanine mustard,
uracil mustard, estramustine, altretamine, floxuridine,
5-deooxyuridine, cytosine arabinoside, 6-mecaptopurine,
deoxycoformycin, calcitriol, vairubicin, mithramycin, vinblastine,
vinorelbine, topotecan, razoxin, marimastat, COL-3, neovastat,
BMS-275291 , squalamine, endostatin, SU5416, SU6668, EMD121974,
interleukin-12, IM862, angiostatin, vitaxin, droloxifene,
idoxyfene, spironolactone, finasteride, cimitidine, trastuzumab,
denileukin diftitox,gefitinib, bortezimib, paclitaxel,
cremophor-free paclitaxel, docetaxel, epithilone B, BMS- 247550,
BMS-310705, droloxifene, 4-hydroxytamoxifen, pipendoxifene,
ERA-923, arzoxifene, fulvestrant, acolbifene, lasofoxifene,
idoxifene, TSE-424, HMR- 3339, ZK186619, topotecan, PTK787/ZK
222584, VX-745, PD 184352, rapamycin,
40-0-(2-hydroxyethyl)-rapamycin, temsirolimus, AP-23573, RAD001,
ABT-578, BC-210, LY294002, LY292223, LY292696, LY293684, LY293646,
wortmannin, ZM336372, L-779,450, PEG-filgrastim, darbepoetin,
erythropoietin, granulocyte colony-stimulating factor,
zolendronate, prednisone, cetuximab, granulocyte macrophage
colony-stimulating factor, histrelin, pegylated interferon alfa-2a,
interferon alfa-2a, pegylated interferon alfa-2b, interferon
alfa-2b, azacitidine, PEG-L-asparaginase, lenalidomide, gemtuzumab,
hydrocortisone, interleukin-11, dexrazoxane, alemtuzumab,
all-transretinoic acid, ketoconazole, interleukin-2, megestrol,
immune globulin, nitrogen mustard, methylprednisolone, ibritgumomab
tiuxetan, androgens, decitabine, hexamethylmelamine, bexarotene,
tositumomab, arsenic trioxide, cortisone, editronate, mitotane,
cyclosporine, liposomal daunorubicin, Edwina-asparaginase,
strontium 89, casopitant, netupitant, an NK-1 receptor antagonist,
palonosetron, aprepitant, diphenhydramine, hydroxyzine,
metoclopramide, lorazepam, alprazolam, haloperidol, droperidol,
dronabinol, dexamethasone, methylprednisolone, prochlorperazine,
granisetron, ondansetron, dolasetron, tropisetron, pegfilgrastim,
erythropoietin, epoetin alfa, darbepoetin alfa and mixtures
thereof.
[0255] The term "antivirals" include, for example, nucleoside
reverse transcriptase inhibitors (NRTI), other non-nucleoside
reverse transcriptase inhibitors (i.e., those which are not
representative of the present invention), protease inhibitors,
fusion inhibitors, among others, exemplary compounds of which may
include, for example, 3TC (Lamivudine), AZT (Zidovudine), (-)-FTC,
ddl (Didanosine), ddC (zalcitabine), abacavir (ABC), tenofovir
(PMPA), D-D4FC (Reverset), D4T (Stavudine), Racivir, L-FddC,
L-FD4C, NVP (Nevirapine), DLV (Delavirdine), EFV (Efavirenz), SQVM
(Saquinavir mesylate), RTV (Ritonavir), IDV (Indinavir), SQV
(Saquinavir), NFV (Nelfinavir), APV (Amprenavir), LPV (Lopinavir),
fusion inhibitors such as T20, among others, fuseon and mixtures
thereof, including anti-HIV compounds presently in clinical trials
or in development.
[0256] Other anti-HIV agents which may be used include, for
example, other NNRTI's (i.e., other than the NNRTI's according to
the present invention) may be selected from the group consisting of
nevirapine (BI-R6-587), delavirdine (U-90152S/T), efavirenz
(DMP-266), UC-781
(N-[4-chloro-3-(3-methyl-2-butenyloxy)phenyl]-2methyl3-furancarbothiamide-
), etravirine (TMC125), Trovirdine (Ly300046.HCl), MKC-442
(emivirine, coactinon), HI-236, HI-240, HI-280, HI-281, rilpivirine
(TMC-278), MSC-127, HBY 097, DMP266, Baicalin (TJN-151) ADAM-II
(Methyl
3',3'-dichloro-4',4''-dimethoxy-5',5''-bis(methoxycarbonyl)-6,6-diphenylh-
exenoate), Methyl 3-Bromo -5-
(1-5-bromo-4-methoxy-3-(methoxycarbonyl)phenyl)hept-1-enyl)-2-methoxybenz-
oate (Alkenyldiarylmethane analog, Adam analog),
(5-chloro-3-(phenylsulfinyl)-2'-indolecarboxamide), AAP-BHAP
(U-104489 or PNU-104489), Capravirine (AG-1549, S-1153), atevirdine
(U-87201E), aurin tricarboxylic acid (SD-095345),
1-[(6-cyano-2-indolyl)carbonyl]-4-[3-(isopropylamino)-2-pyridinyl]piperaz-
ine,
1-[5-[[N-(methyl)methylsulfonylamino]-2-indolylcarbonyl-4-[3-(isoprop-
ylamino)-2-pyridinyl]piperazine,
1-[3-(Ethylamino)-2-[pyridinyl]-4-[(5-hydroxy-2-indolyl)carbonyl]piperazi-
ne,
1-[(6-Formyl-2-indolyl)carbonyl]-4-[3-(isopropylamino)-2-pyridinyl]pip-
erazine,
1-[[5-(Methylsulfonyloxy)-2-indoyly)carbonyl]-4-[3-(isopropylamin-
o)-2-pyridinyl]piperazine, U88204E, Bis(2-nitrophenyl)sulfone (NSC
633001), Calanolide A (NSC675451), Calanolide B,
6-Benzyl-5-methyl-2-(cyclohexyloxy)pyrimidin-4-one (DABO-546), DPC
961, E-EBU, E-EBU-dm, E-EPSeU, E-EPU, Foscarnet (Foscavir), HEPT
(1-[(2-Hydroxyethoxy)methyl]-6-(phenylthio)thymine), HEPT-M
(1-[(2-Hydroxyethoxy)methyl]-6-(3-methylphenyl)thio)thymine),
HEPT-S (1-[(2-Hydroxyethoxy)methyl]-6-(phenylthio)-2-thiothymine),
Inophyllum P, L-737,126, Michellamine A (NSC650898), Michellamine B
(NSC649324), Michellamine F,
6-(3,5-Dimethylbenzyl)-1-[(2-hydroxyethoxy)methyl]-5-isopropyluracil,
6-(3,5-Dimethylbenzyl)-1-(ethyoxymethyl)-5-isopropyluracil, NPPS,
E-BPTU (NSC 648400), Oltipraz
(4-Methyl-5-(pyrazinyl)-3H-1,2-dithiole-3-thione),
N-{2-(2-Chloro-6-fluorophenethyl]-N'-(2-thiazolyl)thiourea (PETT
Cl, F derivative),
N-{2-(2,6-Difluorophenethyl]-N'-[2-(5-bromopyridyl)]thiourea {PETT
derivative),
N-{2-(2,6-Difluorophenethyl]-N'-[2-(5-methylpyridyl)]thiourea {PETT
Pyridyl derivative),
N-[2-(3-Fluorofuranyl)ethyl]-N'-[2-(5-chloropyridyl)]thiourea,
N-[2-(2-Fluoro-6-ethoxyphenethyl)]-N'-[2-(5-bromopyridyl)]thiourea,
N-(2-Phenethyl)-N'-(2-thiazolyethiourea (LY-73497), L-697,639,
L-697,593, L-697,661, 3-
[2-(4,7-Difluorobenzoxazol-2-yl)ethyl}-5-ethyl-6-methyl(pypridin-2(1H)-th-
ione (2-Pyridinone Derivative),
3-[[(2-Methoxy-5,6-dimethyl-3-pyridyl)methyl]amine]-5-ethyl-6-methyl(pypr-
idin-2(1H)-thione, R82150, R82913, R87232, R88703, R89439
(Loviride), R90385, S-2720, Suramin Sodium, TBZ
(Thiazolobenzimidazole, NSC 625487), Thiazoloisoindol-5-one,
(+)(R)-9b-
(3,5-Dimethylphenyl-2,3-dihydrothiazolo[2,3-a]isoindol-5(9bH)-one,
Tivirapine (R86183), UC-38 and UC-84, among others.
[0257] Antimicrobial agents include, e.g., antibiotics. In certain
embodiments, the anti-microbial is an anti-tuberculosis drug, e.g.,
pyrazinamide or benzamide, pretomanid, and bedaquiline, among
others.
EXAMPLES
[0258] The contents of all references, patents, pending patent
applications and published patents, cited throughout this
application are hereby expressly incorporated by reference. The
above described compositions and methods are further exemplified by
reference to the Figures and accompanying description below.
[0259] FIG. 6 illustrates the effect on rate of amplification due
to mismatched bases in Stem primers. (a) The left panel exemplifies
a Stem primer comprising a 3' end mismatch representing a primer
that is not specific for a SNP of interest. The 3' mismatch induces
a delay in the amplification reaction versus the matched or
site-specific SNP Stem primer ("SNP-Stem primer"). The increase in
rate of amplification is exemplified in the right panel, wherein
the dotted line represents the earliest time (t) to the point of
maximum slope of fluorescence (t.sub.max1), and .DELTA.Ct1
represents the lag in time to t.sub.max between the SNP-Stem primer
and the 3' end mismatched Stem primer. (b) The right panel
exemplifies another embodiment as described herein, wherein the
Stem primers (SNP-Stem primer and 3' end mismatched primer) contain
another base pair mismatch in their sequence. The second mismatch
shifts to the right (i.e., reduces the rate) of amplification
(.DELTA.Ct2) and delays the time to t.sub.max2.
[0260] FIG. 7 processed fluorescent traces showing matched Stem
primer (i.e., SNP-Stem primer) LAMP reactions (n=4), and mismatched
Stem primer LAMP reactions (n=4) using the Bio-Rad CFX real-time PR
instrument. The reaction was held at 65.degree. C. and each cycle
consisted of a fluorescent measurement every 15 seconds. The
reaction was assembled on ice in a 48 well microplate. The solution
consisted of about 200 copies of MTB genomic DNA per reaction, 20
mM Tries pH 8.8, 10 mM ammonium sulfate, 50 mM KCl, and 2.0 mM
magnesium sulfate, 0.1% NP-40, 1.times. EVAgreen dye, Bst DNA
polymerase and 1.4 mM dNTPs.
[0261] FIG. 8 illustrates the enhanced rate of amplification
observed according to an exemplary method as described herein. (a)
Provides raw traces showing matched Stem primer reactions for
site-specific Stem primer reactions (light traces) and mismatched
Stem primer reactions (dark traces). (b) Quantification cycle (Cq;
See Hellemans et al., 2007) is measured from the fitted raw traces
as the point of maximum slope. The Cq for matched primers is
plotted (light dots) along with mismatched Stem primers (dark dots)
and no Stem primer LAMP ("dumbbell") reactions (open circles). The
cocktail for the first LAMP reaction (performed in a first chamber)
contained about 200 copies of MTB genomic DNA in a solution of AMP
buffer (20 mM Tris pH 8.8, 10 mM ammonium sulfate, 50 mM KCl, and
3.4 mM magnesium sulfate, 0.1% NP-40, 1.times. EVAgreen dye, Bst
DNA polymerase and 1.4 mM dNTPs). The solution was introduced into
a first chamber at 65.degree. C., and incubated for 5 minutes
before being distributed directly, automatically, and
simultaneously into to a number of second reaction chambers. LAMP
primers to the rpoB gene were dried in the first reaction chamber
and supported LAMP amplification.
[0262] Accelerating Stem primers were dried in the second reaction
chamber and were either perfectly matched (representing a SNP-Stem
primer) or mismatched at the 3' end to the D435 drug resistance
mutation of the MTB rpoB gene. As a negative control, several
second reaction chambers contained no Stem primers and demonstrated
no accelerated amplification. Amplification in the second reaction
chamber was detected by directly measuring the increase in
fluorescence caused by intercalation of EVAgreen dye into
double-stranded amplified DNA. The fluorescence reaction was
monitored continuously for 150 cycles of 15 seconds duration.
TABLE-US-00001 TABLE 1 rpoB STEM-LAMP Test. Matched Mismatched
Dumbbell .DELTA.(mismatched- .DELTA.(dumbbell- Stem Cq Stem Cq Cq
matched Stem) matched Stem) rpoB13.5 Unit 2 38.5 .+-. 13.5% 66.8
.+-. 9.6% 72.3 .+-. 16.6% 14 (24% acc.) 4 (8% acc.) F6 pre-amp
(33~45) (59~72) (49~96) Unit 3 57.5 .+-. 9.1% 76.5 .+-. 1.3% 79.7
.+-. 5.6% 13 (17% acc.) 6 (9% acc.) (50~62) (75~77) (68~86)
Exemplary Embodiments
[0263] In an embodiment, the description provides a two-stage
nucleic acid amplification and real-time detection method
comprising: a. providing a composition comprising a target nucleic
acid template and at least one primer that anneals to the target
nucleic acid template near a region of interest to be amplified; b.
performing a first nucleic acid amplification reaction to amplify
the region of interest, thereby forming aprimary amplicon; c.
dividing (b) into at least twosecondary reactions, and including in
at least one of the reactions a site-specific secondary primer that
is complementary to a site-specific primer binding site that may be
present within the primary amplicon and defines a site of interest
within the region of interest; d. performing a second nucleic acid
amplification reaction (second-stage reaction) thereby accelerating
the amplification of the region of interest only if the
site-specific primer binding site is complementary to the
site-specific primer; and e. detecting and comparing in real-time
the amplification rates of the at least two secondary reactions,
wherein an enhanced relative rate of amplification in the reaction
with the secondary primer indicates the presence of the sitee of
interest that is complementary to the secondary primer.
[0264] In any of the embodiments described herein, step (a)
includes a forward and reverse loop-forming primer. In any of the
embodiments described herein, step (a) includes a forward and
reverse displacement primer.
[0265] In any of the embodiments described herein, first nucleic
acid amplification is an isothermal nucleic acid amplification
reaction. In any of the embodiments described herein, the second
nucleic acid amplification is an isothermal nucleic acid
amplification reaction.
[0266] In any of the embodiments described herein, the first and/or
second isothermal nucleic acid amplification reactions is LAMP or
LAMP-STEM.
[0267] In any of the embodiments described herein, the primary
amplicon is a concatamer.
[0268] In any of the embodiments described herein, the
site-specific primer comprises a 3' end nucleotide complementary to
a mutation, single nucleotide polymorphism (SNP), allele or
biomarker on the amplicon.
[0269] In any of the embodiments described herein, the method
comprises dividing (b) into at least an additional secondary
reaction, wherein the additional secondary reaction includes a
mismatch secondary primer. In any of the embodiments described
herein, the mismatch primer comprises a 3' end nucleotide mismatch
or 3' end nucleotide complementary to an allele, mutation or
polymorphism different from the site-specific primer.
[0270] In any of the embodiments described herein, step (e)
comprises detecting and comparing in real-time the amplification
rates of all secondary rections, wherein an enhanced relative rate
of amplification as compared to the other two reactions indicates
the presence of the site of interest that is complementary to the
secondary primer.
[0271] In any of the embodiments described herein, the mutation,
SNP, or biomarker is specific for a genetic disease, a microbe or a
virus.
[0272] In any of the embodiments described herein, the step of
performing the second nucleic acid amplification reaction includes
amplification in the presence of a fluorescent label or dye,
thereby labeling the amplification products. In any of the
embodiments described herein, the step of detecting and comparing
in real-time the amplification rates includes detecting and
comparing a fluorescent signal from each of the reactions.
[0273] In any of the embodiments described herein, prior to the
first amplification reaction, the primer and template are heated to
a temperature of approximately 95.degree. C. for from about 1
minute to about 15 minutes. In any of the embodiments described
herein, the first and second amplification reactions are performed
at a temperature of from about 55.degree. C. to about 65.degree.
C.
[0274] In any of the methods described herein, the first
amplification reaction is performed in a first reaction chamber
including a channel that is in one-way fluid communication with a
plurality of second reaction chambers, and wherein step (c)
includes transporting approximately equal volumes of (b) through
the channels from the first reaction chamber to the second reaction
chambers.
[0275] In any of the embodiments described herein, the method of
claim 1, wherein the relative reaction rates of the amplification
reactions satisfy the following condition: Second-stage
amplification reaction+site-specific primer>>first-stage
amplification reaction+mismatch primer >/.apprxeq.first-stage
amplification reaction.
[0276] In any of the embodiments described herein, the method of
claim 1, wherein the Cq of the second-stage site-specific or
complementary primer amplification reaction is at least 25% faster
than the second-stage mismatch primer amplification reaction.
[0277] In another embodiment, the description also provides a
two-stage isothermal nucleic acid amplification method for
diagnosing or detecting a disease or infection method comprising:
a. providing a composition comprising a nucleic acid sample from a
patient, and at least one primer that anneals to a target nucleic
acid template near a region of interest to be amplified; b.
performing a first isothermal nucleic acid amplification reaction
to amplify the region of interest, thereby forming a primary
amplicon; c. dividing (b) into at least tworeactions, and including
to at least one of the reactions a site-specific secondary primer
that is complementary to a site-specific primer binding region that
may be present on the primary amplicon and defines a site of
interest that is indicative of a disease or infection; d.
performing a second isothermal nucleic acid amplification reaction
thereby amplifying the region of interest; e. detecting and
comparing in real-time the amplification rate of thesecondary
reactions, wherein an enhanced rate of amplification in the
site-specific secondary primer reaction relative to the other is
indicative of the presence of the site of interest; and f.
diagnosing the patient as having or not having a disease or
infection corresponding to the site of interest.
[0278] In any of the embodiments described herein, the target
nucleic acid template is from a microbe or virus. In any of the
embodiments described herein, the target nucleic acid template is
from tubercle bacillus (MTB or TB).
[0279] In any of the embodimetns described herein, the site of
interest is in the rpoB gene. In any of the embodiments described
herein, the site of interest is a SNP in the rpoB gene.
[0280] In any of the embodiments described herein, the method
comprises the step of treating the patient testing positive for the
site of interest by administering an effective amount of an
appropriate therapeutic to treat the disease or infection. In any
of the embodiments described herein, the therapeutic is an
anti-tuberculosis therapeutic.
[0281] In another embodiment, the description provides a two-stage
nucleic acid amplification and real-time detection method
comprising: a. providing a composition comprising a target nucleic
acid template and at least one primer that anneals to the target
nucleic acid template near a region of interest to be amplified; b.
performing a first nucleic acid amplification reaction to amplify
the region of interest, thereby forming a primary amplicon; c.
dividing (b) into at least three secondary reactions, and including
in at least one of the reactions a site-specific secondary primer
that is complementary to a site-specific primer binding site that
may be present within the primary amplicon and defines a site of
interest within the region of interest, and including in at least
another of the reactions a mismatch secondary primer that anneals
at or near the site of interest but is not complementary to the
site of interest; d. performing a second nucleic acid amplification
reaction (second-stage reaction) thereby accelerating the
amplification of the region of interest only if the secondary
primer binding site is complementary to the site-specific primer;
and e. detecting and comparing in real-time the amplification rates
of the secondary reactions, wherein an enhanced relative rate of
amplification in the reaction with the site-specific secondary
primer indicates the presence of the site of interest that is
complementary to the site-specific secondary primer.
[0282] In any of the embodiments described herein, the method
comprises dividing (b) into at least an additional secondary
reaction, wherein the additional secondary reaction includes a
mismatch secondary primer. In any of the embodiments described
herein, the mismatch primer comprises a 3' end nucleotide mismatch
or 3' end nucleotide complementary to an allele, mutation or
polymorphism different from the site-specific primer.
[0283] In any of the embodiments described herein, step (e)
comprises detecting and comparing in real-time the amplification
rates of all secondary rections, wherein an enhanced relative rate
of amplification as compared to the other two reactions indicates
the presence of the site of interest that is complementary to the
secondary primer.
[0284] In any of the embodiments described herein, the method
comprises dividing (b) into at least one additional secondary
reaction including a second site-specific secondary primer
complementary to a second site-of interest that may be present
within the primary amplicon and defines a second site of interest
within the region of interest.Those skilled in the art will
recognize, or be able to ascertain using no more than routine
experimentation, many equivalents to the specific embodiments of
the invention described herein. Such equivalents are intended to be
encompassed by the following claims. It is understood that the
detailed examples and embodiments described herein are given by way
of example for illustrative purposes only, and are in no way
considered to be limiting to the invention. Various modifications
or changes in light thereof will be suggested to persons skilled in
the art and are included within the spirit and purview of this
application and are considered within the scope of the appended
claims. For example, the relative quantities of the ingredients may
be varied to optimize the desired effects, additional ingredients
may be added, and/or similar ingredients may be substituted for one
or more of the ingredients described. Additional advantageous
features and functionalities associated with the systems, methods,
and processes of the present invention will be apparent from the
appended claims. Moreover, those skilled in the art will recognize,
or be able to ascertain using no more than routine experimentation,
many equivalents to the specific embodiments of the invention
described herein. Such equivalents are intended to be encompassed
by the following claims.
* * * * *