U.S. patent application number 15/843391 was filed with the patent office on 2018-08-02 for methods for quantitative amplification and detection over a wide dynamic range.
The applicant listed for this patent is GEN-PROBE INCORPORATED. Invention is credited to Kenneth A. Browne, Daniel L. Kacian.
Application Number | 20180216172 15/843391 |
Document ID | / |
Family ID | 43084221 |
Filed Date | 2018-08-02 |
United States Patent
Application |
20180216172 |
Kind Code |
A1 |
Kacian; Daniel L. ; et
al. |
August 2, 2018 |
METHODS FOR QUANTITATIVE AMPLIFICATION AND DETECTION OVER A WIDE
DYNAMIC RANGE
Abstract
Disclosed are compositions and methods for making differentiable
amplicon species at unequal ratios using a single amplification
system in a single vessel. The number of differentiable amplicons
and their ratios to one another are chosen to span the required
linear dynamic range for the amplification reaction and to
accommodate limitations of the measuring system used to determine
the amount of amplicon generated. Unequal amounts of
distinguishable amplicon species are generated by providing unequal
amounts of one or more amplification reaction components (e.g.,
distinguishable amplification oligomers, natural and unnatural NTP
in an NTP mix, or the like). The amount of target nucleic acid
present in a test sample is determined using the linear detection
range generated from detection of one or more amplicon species
having an amount within the dynamic range of detection.
Inventors: |
Kacian; Daniel L.; (San
Diego, CA) ; Browne; Kenneth A.; (Poway, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
GEN-PROBE INCORPORATED |
San Diego |
CA |
US |
|
|
Family ID: |
43084221 |
Appl. No.: |
15/843391 |
Filed: |
December 15, 2017 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14562922 |
Dec 8, 2014 |
9347098 |
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15843391 |
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14064427 |
Oct 28, 2013 |
8932817 |
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14562922 |
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12840971 |
Jul 21, 2010 |
8628924 |
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14064427 |
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61230938 |
Aug 3, 2009 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q 1/6865 20130101;
C12Q 1/6851 20130101; C12Q 1/6813 20130101; C12Q 1/6865 20130101;
C12Q 2545/101 20130101; C12Q 2537/143 20130101 |
International
Class: |
C12Q 1/6851 20060101
C12Q001/6851; C12Q 1/6813 20060101 C12Q001/6813; C12Q 1/6865
20060101 C12Q001/6865 |
Claims
1. A method for detecting a target nucleic acid sequence in a
sample comprising: (a) providing a sample suspected of containing a
target nucleic acid; (b) generating from the target nucleic acid a
defined ratio of at least two differentiable amplicon species,
wherein the at least two differentiable amplicon species are
generated using a single amplification oligomer that hybridizes to
one strand of the target nucleic acid and at least two
amplification oligomers that hybridize to the complementary strand
of the target nucleic acid, wherein the at least two amplification
oligomers hybridizing to the complementary strand of the target
nucleic acid are provided in different amounts and have distinct
nucleic acid sequences, such that the defined ratio of the at least
two differentiable amplicon species is generated and whereby the at
least two differentiable amplicon species differ in nucleic acid
composition; and (c) detecting the presence and amount of each
generated amplicon species, wherein a first amplicon species is
detectable in a first linear range representing a first
concentration of the target nucleic acid in the sample to a second
concentration of the target nucleic acid in the sample, and a
second amplicon species is detectable in a second linear range
representing a third concentration of the target nucleic acid in
the sample to a fourth concentration of the target nucleic acid in
the sample, and wherein the first concentration is less than the
third concentration, which is less than the second concentration,
which is less than the fourth concentration, such that said first
and second linear ranges overlap and provide an extended dynamic
range for determining the presence and amount of the target nucleic
acid in the sample; wherein the at least two amplification
oligomers hybridizing to the complementary strand of the target
nucleic acid hybridize to the same sequence on said strand, and one
of the at least two amplification oligomers contains one or more
nucleobase substitutions relative to the other; wherein the
generating and detecting steps are each performed in a single
vessel; and wherein the detecting step comprises hybridizing the at
least two differentiable amplicon species with distinguishable
probes that each hybridize to only one of the at least two
differentiable amplicons.
2. The method of claim 1, wherein the single amplification oligomer
that hybridizes to one strand of the target nucleic acid is a
promoter-based amplification oligomer.
3. The method of claim 1, wherein the single amplification oligomer
that hybridizes to one strand of the target nucleic acid is a
primer.
4. The method of claim 1, wherein the at least two amplification
oligomers that hybridize to the complementary strand of the target
nucleic acid are promoter-based amplification oligomers.
5. The method of claim 1, wherein the at least two amplification
oligomers that hybridize to the complementary strand of the target
nucleic acid are primers.
6. The method of claim 1, wherein the number of copies of each
amplicon species differs by at least three orders of magnitude.
7. The method of claim 1, wherein the number of copies of each
amplicon species differs by at least four orders of magnitude.
8. The method of claim 1, wherein the amounts of the at least two
amplification oligomers hybridizing to the complementary strand of
the target nucleic acid differ by at least two orders of
magnitude.
9. The method of claim 1, wherein the dynamic range is from about
10.sup.3 to 10.sup.7.
10. The method of claim 1, wherein the dynamic range is from about
10.sup.4 to 10.sup.6.
11. A method for detecting a target nucleic acid sequence in a
sample comprising: (a) providing a sample suspected of containing a
target nucleic acid; (b) generating from the target nucleic acid a
defined ratio of at least two differentiable amplicon species,
wherein the at least two differentiable amplicon species are
generated using a single amplification oligomer that hybridizes to
one strand of the target nucleic acid and at least two
amplification oligomers that hybridize to the complementary strand
of the target nucleic acid, wherein the at least two amplification
oligomers hybridizing to the complementary strand of the target
nucleic acid are provided in different amounts and have distinct
nucleic acid sequences, such that the defined ratio of the at least
two differentiable amplicon species is generated and whereby the at
least two differentiable amplicon species differ in nucleic acid
composition; and (c) detecting the presence and amount of each
generated amplicon species, wherein a first amplicon species is
detectable in a first linear range representing a first
concentration of the target nucleic acid in the sample to a second
concentration of the target nucleic acid in the sample, and a
second amplicon species is detectable in a second linear range
representing a third concentration of the target nucleic acid in
the sample to a fourth concentration of the target nucleic acid in
the sample, and wherein the first concentration is less than the
third concentration, which is less than the second concentration,
which is less than the fourth concentration, such that said first
and second linear ranges overlap and provide an extended dynamic
range for determining the presence and amount of the target nucleic
acid in the sample; wherein the at least two amplification
oligomers hybridizing to the complementary strand of the target
nucleic acid comprise identical nucleotide sequences except that
each of the at least two amplification oligomers comprises a unique
unhybridized nucleotide sequence that is at least one nucleobase in
length and that is joined to the 5' end of the target hybridizing
region of the amplification oligomer; wherein the generating and
detecting steps are each performed in a single vessel; and wherein
the detecting step comprises hybridizing the at least two
differentiable amplicon species with distinguishable probes that
each hybridize to only one of the at least two differentiable
amplicons.
12. The method of claim 11, wherein the single amplification
oligomer that hybridizes to one strand of the target nucleic acid
is a promoter-based amplification oligomer.
13. The method of claim 11, wherein the single amplification
oligomer that hybridizes to one strand of the target nucleic acid
is a primer.
14. The method of claim 11, wherein the at least two amplification
oligomers that hybridize to the complementary strand of the target
nucleic acid are promoter-based amplification oligomers.
15. The method of claim 11, wherein the at least two amplification
oligomers that hybridize to the complementary strand of the target
nucleic acid are primers.
16. The method of claim 11, wherein the number of copies of each
amplicon species differs by at least three orders of magnitude.
17. The method of claim 11, wherein the number of copies of each
amplicon species differs by at least four orders of magnitude.
18. The method of claim 11, wherein the amounts of the at least two
amplification oligomers hybridizing to the complementary strand of
the target nucleic acid differ by at least two orders of
magnitude.
19. The method of claim 11, wherein the dynamic range is from about
10.sup.3 to 10.sup.7.
20. The method of claim 11, wherein the dynamic range is from about
10.sup.4 to 10.sup.6.
Description
RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 15/162,263, filed May 23, 2016, which is a continuation of U.S.
application Ser. No. 14/562,922, filed Dec. 8, 2014, now U.S. Pat.
No. 9,347,098, which is a continuation of Ser. No. 14/064,427,
filed Oct. 28, 2013, now U.S. Pat. No. 8,932,817, which is a
continuation of U.S. application Ser. No. 12/840,971, filed Jul.
21, 2010, now U.S. Pat. No. 8,628,924, which claims the benefit of
U.S. Provisional Application Nos. 61/227,339, filed Jul. 21, 2009,
and 61/230,938, filed Aug. 3, 2009 each of which is hereby
incorporated by reference in its entirety.
SEQUENCE LISTING
[0002] The instant application contains a Sequence Listing which
has been submitted in ASCII format via EFS-Web and is hereby
incorporated by reference in its entirety.
FIELD
[0003] The present application relates to compositions and methods
for amplifying and detecting a nucleic acid sequence that may be
present in a test sample, more particularly, for amplifying and
quantitatively detecting a nucleic acid sequence over a wide
dynamic range for which the target nucleic acid sequence may be
present in the sample.
BACKGROUND
[0004] Methods that allow accurate detection and quantitation of
nucleic acid sequences are invaluable tools for diagnosis and
treatment of a wide range of diseases. For example, detection and
quantitation of an infectious agent's nucleic acid sequence can
provide diagnostic or prognostic information or allow a physician
to monitor a patient's response to therapy. Further, accurate
detection of low levels of viremia in infections such as human
immunodeficiency virus (HIV) or hepatitis C virus helps to prevent
spread of the virus, to estimate prognosis and response to therapy,
and to detect the emergence of drug-resistant viruses in treated
individuals. It is equally important to accurately measure high
levels of viremia in untreated patients to establish initial
infection levels.
[0005] Methods for amplifying a target nucleic acid sequence that
may be present in a test sample are known and include methods such
as the polymerase chain reaction (PCR; e.g., U.S. Pat. Nos.
4,683,195, 4,683,202, 4,965,188, 6,040,166, 6,197,563 and
6,514,736); reverse transcription polymerase chain reaction
(RT-PCR; e.g., U.S. Pat. Nos. 5,310,652 and 5,322,770);
transcription-mediated amplification (TMA; e.g., U.S. Pat. Nos.
5,399,491, 5,824,518 and 7,374,885); ligase chain reaction (LCR;
e.g., U.S. Pat. Nos. 5,427,930 and 5,516,663); strand displacement
amplification (SDA; e.g., U.S. Pat. Nos. 5,422,252, 5,547,861 and
5,648,211); rolling circle amplification (RCA; e.g., U.S. Pat. Nos.
5,648,245 and 5,854,033); helicase-dependent amplification (HDA;
e.g., U.S. Pat. Nos. 7,282,328 and 7,662,594); and nucleic acid
sequence based amplification (NASBA; e.g., U.S. Pat. No.
5,130,238).
[0006] Methods for detecting non-amplified or amplified target
nucleic acid sequences that may be present in a test sample are
also known. Some detection methods are "homogeneous" methods that
do not require separation of a detection agent associated with the
target nucleic acid from the detection agent that is not associated
with the target nucleic acid. Such methods include use of
intercalating dyes (e.g., U.S. Pat. Nos. 5,312,921, 5,814,447,
6,063,572, 6,541,205 and 6,569,627), a Hybridization Protection
Assay (HPA; e.g., U.S. Pat. No. 5,283,174), and use of molecular
beacon probes (e.g., U.S. Pat. No. 5,925,517) or molecular torch
probes (e.g., U.S. Pat. No. 6,361,945). Other methods are
"heterogeneous" and require physical separation of the detection
agent associated with the target nucleic acid from the detection
agent not associated with the target nucleic acid. One of the most
common heterogeneous methods involves the capture of target nucleic
acids onto a solid support, hybridization of a labeled detection
probe, and washing under appropriately stringent conditions to
remove non-specifically bound probe. The label (e.g, a
radioisotope) that remains bound to the support is then
measured.
[0007] While currently available amplification techniques may
provide sufficient sensitivity for some applications, other
diagnostic and therapeutic situations require more sensitivity than
is available from these available methods. Furthermore, under
certain circumstances, it is desirable to determine whether the
nucleic acid sequence is present at a high or low concentration
level. Thus, there is a need for methods through which target
nucleic acids in a test sample can be detected and quantified
accurately over a relatively large dynamic range in a single
experiment.
[0008] Nucleic acid analytes of interest from a specimen may be
present at concentrations that are less than can be detected by
routine methods. This problem is often circumvented by implementing
one of several nucleic acid amplification techniques (vide supra)
prior to detection. The nucleic acid analytes of interest from a
specimen may also be present in very small numbers (e.g., 1, 7, 29,
etc., or zero in the case of a non-infected specimen) or larger
numbers ranging into the millions, billions or more. Therefore, it
is critical for quantification that the nucleic acid analytes are
amplified proportionally to accurately reflect their initial
numbers. Attempts to achieve reproducible quantitation of nucleic
acids over a dynamic range by using nucleic acid amplification
methods has been a challenging endeavor and a number of problems
have been encountered including, for example, the need for
amplification internal standards and (even very slightly) different
amplification efficiencies of internal standards (Clin. Chem.
40(4): 630-636 (1994); Clin. Chem. 41(8): 1065-1067 (1995);
Biochim. Biophys. Acta 1219(2): 493-498 (1994); Biotechniques
15(1): 134-139 (1993); J. Infect. Dis. 165(6): 1119-1123 (1992);
Proc. Nat. Acad. Sci. USA 86(24): 9717-9721 (1989)). Two basic
approaches have been used to solve these problems, with mixed
success.
[0009] In the first basic approach, the concentration of a target
nucleic acid sequence present in a test sample is determined based
on the rate at which amplicons are produced over time. An example
of this approach is known as "real-time PCR;" increasing amplicon
levels are measured with probes that change their fluorescent
properties in response to increasing amplicon concentration. The
time it takes for the amplicon to reach a predefined level is
correlated with the concentration of the target nucleic acid
sequence present in the sample by comparing the results of the
experimentally detected amplicon to results from standards that
contain a range of known amounts of the target nucleic acid
sequences. Multiple standards may be used, often ranging from the
low to high ends of expected responses from the analyte of unknown
concentration. In amplification systems in which the reaction is
divided into cycles, such as the PCR or LCR, precision is limited
by the amount of amplification that occurs within each cycle; for
the PCR, the amount is theoretically a two-fold increase per cycle.
However, for amplification systems that lack discrete amplification
cycles, such as TMA or SDA, rate changes may be difficult to
measure accurately because amplicon concentration can change
rapidly over a very short period of time. The accuracy of time and
amplicon concentration measurements greatly affects the ability to
correlate measured results with an initial target nucleic acid
concentration with any degree of precision.
[0010] In the second basic approach, the amplification reaction is
run for a fixed time, and the amount of amplicon produced is
measured and correlated to the concentration of target nucleic acid
sequence present in the test sample. Such methods are sometimes
referred to as "endpoint" methods because the amplicons are
measured at a single point at the end of the reaction rather than
at multiple time points during the amplification reaction. These
methods typically require the use of an excess of nucleic acid
probe relative to the target nucleic acid so that the amount of
probe hybridized relates directly to the amount of target present
and avoids signal saturation due to excess target, referred to as
"target saturation" (e.g., U.S. Pat. No. 4,851,330). If target
saturation occurs, the probe signal reaches a plateau and the upper
end of the dynamic range is truncated. When large amounts of
amplicon are produced, even larger amounts of probe must be used to
extend the dynamic range, and the amplicon-probe hybridization
signal may exceed the detector's capacity for accurate detection.
Furthermore, the background signal is often elevated as probe
concentration increases, which limits sensitivity of detection at
the lower end of the dynamic range. Lowering the specific activity
of the probe can be used to reduce the background signal; however,
the sensitivity of detection at low target levels is also often
decreased. Thus, optimization of endpoint detection may reduce
accuracy on one or both ends of the dynamic range.
[0011] Generally, while known amplification systems have been
optimized to produce amplicons quantitatively over a large dynamic
range, detection systems have been unable to perform accurately
over that same broad range. This limitation requires additional
steps in the process, such as serial dilution of the amplicons or
physical separation steps, in order to reduce non-specific
background signal and to measure the amplicon concentration across
the full dynamic range. Physical separation or dilution steps
increase the complexity and length of the test procedure.
Manipulating amplicon products increases the danger of
cross-contaminating samples or amplification reaction mixtures,
which could lead to false positive results. In addition, amplicon
manipulation increases the possibility of errors in quantification,
including false negative results. Ideally, a nucleic acid detection
and quantitation system should include an amplification reaction
that generates measurable amounts of one or more amplicons
reproducibly and proportionately across a wide dynamic range, as
well as a detection system that can quantitate the amplicons across
the same dynamic range.
[0012] In certain known methods, a nucleic acid hybridization
reaction is used to determine the amount of amplicon by correlating
either the rate of hybridization or the extent of hybridization to
the amount of amplicon present. However, kinetic measurements of
hybridization pose many of the same disadvantages of kinetic
measurements of amplification reactions and are thus not
preferred.
[0013] In some variations of known in vitro nucleic acid
amplification procedures, researchers have sought to achieve an
extended dynamic range by individually adjusting the efficiencies
of amplification of one or more target sequences by optimizing the
reaction conditions for each target nucleic acid. However, such
optimization generally requires complex and extensive
experimentation and may not yield reproducible results because of
slight differences between samples, presence of inhibitors in
reaction mixtures, variations in test reagents and/or their
quantities in individual reaction mixtures, or conditions in which
the reactions are performed. Thus, there remains a need to extend
the dynamic range of quantitative endpoint assays that does not
require excess experimentation and provides a robust system with
wide dynamic range.
[0014] Compositions and methods that respond to this need would
allow quantitative measurement of a desired target nucleic acid in
a sample by using nucleic acid amplification and detection of the
amplified products over an extended dynamic range. The compositions
and methods described herein provide a simple solution to problems
associated with previous quantitative nucleic acid amplification
and detection methods.
SUMMARY
[0015] The present application provides compositions and methods
for making multiple differentiable amplicon species at unequal
ratios using a single amplification system in a single vessel. The
number of differentiable amplicon species and their ratios to one
another are chosen to span the required linear dynamic range for
the amplification reaction and to accommodate limitations of the
measuring system used to determine the amount of any one amplicon
generated. Unequal amounts of distinguishable amplicon species are
generated by providing unequal amounts of one or more amplification
reaction components (e.g., unequal amounts of distinguishable
amplification oligomers, unequal amounts of natural and unnatural
NTP in an NTP mix, or the like). If small amounts of target nucleic
acid are present in the sample, then the more abundant amplicons
species is detectable within the linear dynamic range, while the
lesser abundant amplicon species is/are below the detection
threshold. If greater amounts of target nucleic acid are present in
the sample, then less abundant amplicons species become detectable
within the linear dynamic range. Here, detection of target amounts
can be determined using the detection ranges generated from two or
more amplicon species. At higher amounts of target nucleic acid
present in the sample, the more abundant amplicon species can
saturate the detection system; however, lesser abundance amplicon
species are still detectable within their linear dynamic ranges.
Therefore, for two amplicons, when a large amount of target nucleic
acid is present in a test sample, large amounts of amplicon 1 are
generated but smaller amounts of amplicon 2 is also made. If the
amount of amplicon 1 is outside the dynamic range of the detection
system, then the amounts of amplicon 2 may lie within the dynamic
range and can be measured. The amount of original target nucleic
acid sequence may then be calculated from the amount of amplicon 2.
Additional amplicons can be made to further extend the dynamic
range (amplicon 3, etc.).
[0016] The present application provides a method for detecting a
target nucleic acid in a sample comprising the steps of: providing
a sample suspected of containing a target nucleic acid; generating
from the target nucleic acid, a defined ratio of at least two
differentiable amplicon species, wherein the generating step is
performed in a single vessel; and detecting the presence and amount
of each generated amplicon species, wherein a first amplicon
species is detectable in a first linear range representing a first
concentration of target nucleic acid in the sample to a second
concentration of target nucleic acid in the sample and a second
amplicon species is detectable in a second linear range
representing a third concentration of target nucleic acid in the
sample to a fourth concentration of target nucleic acid in the
sample, and wherein, the first concentration is less that the third
concentration, which is less than the second concentration, which
is less than the fourth concentration such that said first and
second linear ranges overlap and provide an extended dynamic range
for determining the presence and amount of the target nucleic acid
in the sample, and wherein the detecting step is performed in a
single vessel. Preferably, the single well used in the amplifying
step and the single vessel used in the vessel are the same vessel.
Thus, the amplification and detection reactions take place in the
same vessel.
[0017] In some aspects of the method, a third differentiable
amplicon species is generated. The third differentiable amplicon
species will provide a third linear range that is different than
the first and the second linear ranges, thereby further extending
the dynamic range for determining the presence and amount of the
target nucleic acid in the sample. In some aspects, the third
amplicon is detectable in a linear range representing a
representing a fifth concentration of target nucleic acid in the
sample to a sixth concentration of target nucleic acid in the
sample, wherein the first concentration is less than the third
concentration, which is less than the second concentration, which
is less than the fifth concentration, which is less than the fourth
concentration, which is less than the sixth concentrations such
that the first, second and third linear ranges overlap and provide
an extended dynamic range for determining the presence and amount
of said target nucleic acid in said sample. In some aspects n
differentiable amplicon species are generated to provide n
overlapping linear ranges to provide an extended dynamic range; n
being equal to a positive whole number.
[0018] In some aspects of the methods the at least two
differentiable amplicon species are generated using a single
amplification oligomer that hybridizes to one strand of the target
nucleic acid and at least two amplification oligomers that
hybridize to the complementary strand of the target nucleic acid,
wherein the at least two amplification oligomers hybridizing to a
complementary strand of the target nucleic acid are provided in
unequal amounts. In some aspects, the single amplification oligomer
is a promoter-based amplification oligomer. In some aspects, the
single amplification oligomer is a promoter-provider. In some
aspects, the single amplification oligomer is a promoter-primer. In
some aspects, the single amplification oligomer is a primer. In
some aspects, the at least two amplification oligomers that
hybridize to the complementary strand of the target nucleic acid
are promoter-based amplification oligomers. In some aspects, the at
least two amplification oligomers that hybridize to the
complementary strand of the target nucleic acid are
promoter-primers. In some aspects, the at least two amplification
oligomers that hybridize to the complementary strand of the target
nucleic acid are promoter-providers. In some aspects, the at least
two amplification oligomers that hybridize to the complementary
strand of the target nucleic acid are primers. In some aspects, the
at least two differentiable amplicon species are generated using a
single promoter based amplification oligomer that hybridizes to one
strand of the target nucleic acid and at least two primer that
hybridize to the complementary strand of the target nucleic acid.
The single promoter-based amplification oligomer is a
promoter-provider in some aspects of the methods. The single
promoter-based amplification oligomer-is a promoter primer in some
aspects of the methods. In some aspects, the at least two
differentiable amplicon species are generated using a single primer
that hybridizes to one strand of the target nucleic acid and at
least two promoter-based amplification oligomers that hybridize to
the complementary strand of the target nucleic acid. The at least
two promoter-based amplification oligomers are promoter-providers
in some aspects of the methods. The at least two promoter-based
amplification oligomers are promoter primers in some aspects of the
methods. In some aspects, the at least two differentiable amplicon
species are generated using a single primer that hybridizes to one
strand of the target nucleic acid and at least two primers that
hybridize to the complementary strand of the target nucleic
acid.
[0019] In some aspects of the methods wherein the at least two
differentiable amplicon species are generated using a single
amplification oligomer that hybridizes to one strand of the target
nucleic acid and unequal amounts of at least two amplification
oligomers that hybridize to the complementary strand of the target
nucleic acid, the at least two amplification oligomers hybridizing
to the complementary strand of the target nucleic acid hybridize to
distinct sequences of said target nucleic acid, thereby generating
from the target nucleic acid, a defined ratio of at least two
differentiable amplicon species that differ in length. In some
aspects, the distinct sequences of the target nucleic acid to which
the at least two amplification oligomers hybridize, are
non-overlapping sequences. In some aspects, the distinct sequences
of the target nucleic acid to which the at least two amplification
oligomers hybridize, are overlapping sequences.
[0020] In some aspects of the methods wherein the at least two
differentiable amplicon species are generated using a single
amplification oligomer that hybridizes to one strand of the target
nucleic acid and unequal amounts of at least two amplification
oligomers that hybridize to the complementary strand of the target
nucleic acid, the at least two amplification oligomers hybridizing
to the complementary strand of the target nucleic acid have
distinct nucleic acid sequences, thereby generating from the target
nucleic acid, a defined ratio of at least two differentiable
amplicon species that differ in nucleic acid composition. In some
aspects, the at least two amplification oligomers are substantially
identical in nucleotide sequence except that one amplification
oligomer has one or more of: at least one nucleotide mismatch, at
least one nucleotide insertion, at least one nucleotide deletion
and combinations thereof, thereby generating from said target
nucleic acid, a defined ratio of at least two differentiable
amplicon species that differ in nucleic acid composition. In some
aspects, the at least two amplification oligomers each contain at
least one insertion, wherein the at least one insertion in one of
the at least two amplification oligomers is different from the at
least one insertion of the other at least one amplification
oligomers. In some aspects, each of the at least one amplification
oligomers comprises a unique unhybridized nucleotide sequence that
is at least one nucleobase in length and that is joined to the 5'
end of the target hybridizing region of the amplification
oligomer.
[0021] In some aspects of the methods, the two differentiable
amplicon species are generated using an amplification method
wherein said amplification method generates RNA amplicon species
and DNA amplicon species to provide at least two differentiable
amplicons that differ in ribose sugar composition. In some aspects,
the amplification method is an isothermal amplification method that
uses at least one promoter-based amplification oligomer to generate
a greater amount of RNA amplicon species that of DNA amplicon
species.
[0022] In some aspects of the methods, the two differentiable
amplicon species are generated using a dNTP mixture wherein at
least one of said dNTP species in said mix is provided in both a
native form and in an analog form with one form in excess of the
other form to provide at least two differentiable amplicons that
differ in nucleic acid composition. In some aspects, the dNTP mix
contains native dATP and an analog of dATP. In some aspects, the
dNTP mix contains native dCTP and an analog of dCTP. In some
aspects, the dNTP mix contains native dTTP and an analog of dTTP.
In some aspects, the dNTP mix contains native dGTP and an analog of
dGTP. In some aspects, the dNTP mix contains native dUTP and an
analog of dUTP.
[0023] In some aspects, the amplification step is performed with an
isothermal amplification reaction. In some aspects, the
amplification step is performed with a cyclical amplification
reaction. In some aspects, the amplification step is performed with
a TMA amplification reaction. In some aspects, the amplification
step is performed with a NASBA amplification reaction. In some
aspects, the amplification step is performed with a PCR
amplification reaction. In some aspects, the amplification step is
performed with a Reverse Transcription (RT)-PCR amplification
reaction. In some aspects, the amplification step is performed with
a real time amplification reaction. In some aspects, the
amplification step is performed with a rolling circle amplification
reaction. In some aspects, the amplification step is performed with
a helicase dependent amplification reaction.
[0024] The present application provides a method for amplifying a
target nucleic acid sequence in a test sample comprising: (a)
contacting the test sample with a nucleic acid amplification
reaction mixture comprising at least two primers, wherein the at
least two primers hybridize to the same strand of the target
nucleic acid sequence but hybridize to distinct nucleotide
sequences on the strand, and each of the at least two primers is
present in the reaction mixture in a different amount; and (b)
subjecting the reaction mixture to amplification conditions under
which each of the at least two primers simultaneously and
independently produces one of each of two distinguishable amplicons
from the target nucleic acid sequence, wherein the number of copies
of each amplicon produced depends on the amount of each of the at
least two primers in the reaction mixture, and the number of copies
of each amplicon produced differs by at least two orders of
magnitude.
[0025] In some aspects, each of the at least two primers further
differ from one another by having one or more of (i) one of the
amplification oligomers has a modified target hybridizing sequence
and the other does not and/or (ii) each of the amplification
oligomers has a different unique unpaired 5' sequence.
[0026] The present application provides a method for quantitating a
target nucleic acid sequence in a test sample comprising: (a)
contacting the test sample with a nucleic acid amplification
reaction mixture comprising at least two primers, wherein the at
least two primers hybridize to the same strand of the target
nucleic acid sequence but hybridize to distinct nucleotide
sequences on the strand, and each of the at least two primers is
present in the reaction mixture in a different amount; (b)
subjecting the reaction mixture to amplification conditions under
which each of the at least two primers simultaneously and
independently produces one of at least two amplicons, wherein the
number of copies of each amplicon produced differs by at least two
orders of magnitude; (c) hybridizing the at least two amplicons
with at least two probes, wherein each of the at least two probes
is specific to one of the at least two amplicons, each probe is
detectable within a detection range, wherein the sum of the
detection ranges for each of the at least two probes is greater
than the detection range for each probe, such that the at least two
probes together are detectable across a wide dynamic range, and the
at least two probes produce distinguishable detection signals; (d)
detecting at least one of the at least two probes; and (e)
determining the initial amount of target nucleic acid sequence in
the test sample.
[0027] In some aspects, each of the at least two primers further
differ from one another by having one or more of (i) one of the
amplification oligomers has a modified target hybridizing sequence
and the other does not and/or (ii) each of the amplification
oligomers has a different unique unpaired 5' sequence.
[0028] The present application further provides a method for
quantitating a nucleic acid in a test sample comprising: (a)
providing a test sample suspected of containing a target nucleic
acid in an amount T.sub.1; (b) contacting the test sample with a
nucleic acid amplification reaction mixture comprising at least two
primers, wherein the at least two primers hybridize to the same
strand of the target nucleic acid sequence but each primer
hybridizes to a distinct nucleotide sequence on the strand, and
wherein each primer is present in the reaction mixture in a
different amount. In one aspect, each P.sub.x differs by at least
two orders of magnitude, and where x is an integer between 1 and
the number of primers in the mixture. (c) Subjecting the reaction
mixture to amplification conditions under which each of the at
least two primers simultaneously and independently produces one of
at least two amplicons, wherein for each amplicon, a number of
copies A.sub.x is produced, and wherein each A.sub.x differs by an
amount that is approximately the same as the amount of difference
in each P.sub.x for the primers present in the mix. In one aspect,
the A.sub.x for each amplicon differs by at least two orders of
magnitude. (d) Hybridizing the at least two amplicons with at least
two probes, wherein each of the at least two probes is specific to
one of the at least two amplicons, each probe is detectable within
a linear detection range C.sub.x(a) to C.sub.x(b), wherein
C.sub.x(a) is the minimum detectable number of copies of amplicon
and C.sub.x(b) is the maximum detectable number of copies of
amplicon for probe x, wherein for each probe, C.sub.x+1(a) is
greater than C.sub.x(a) and C.sub.x+1(b) is greater than C.sub.x(b)
such that the at least two probes together are detectable across a
wide dynamic range, wherein for each amplicon-probe combination,
A.sub.x is between C.sub.x(a) and C.sub.x(b), and wherein the at
least two probes produce distinguishable detection signals; (e)
detecting at least one of the at least two probes; and (f)
determining the initial amount of target nucleic acid sequence in
the test sample.
[0029] In some aspects, each of the at least two primers further
differ from one another by having one or more of (i) one of the
amplification oligomers has a modified target hybridizing sequence
and the other does not and/or (ii) each of the amplification
oligomers has a different unique unpaired 5' sequence.
[0030] The present application further provides a composition for
amplifying a target nucleic acid sequence in a test sample
comprising at least two primers, wherein (a) the at least two
primers hybridize to the same strand of the target nucleic acid
sequence but hybridize to distinct nucleotide sequences on the
strand, and each of the at least two primers is present in the
reaction mixture in a different amount; and (b) under amplification
conditions, each of the at least two primers simultaneously and
independently produces one of each of two detectable amplicons from
the target nucleic acid sequence, wherein the number of copies of
each amplicon produced depends on the amount of each of the at
least two primers in the reaction mixture, the number of copies of
each amplicon produced differs by at least two orders of magnitude,
and the amplicons are detectable across a wide dynamic range.
[0031] In some aspects, each of the at least two primers further
differ from one another by having one or more of (i) one of the
amplification oligomers has a modified target hybridizing sequence
and the other does not and/or (ii) each of the amplification
oligomers has a different unique unpaired 5' sequence.
[0032] The present application further provides a nucleic acid
amplification reaction mixture comprising at least two primers,
wherein: (a) the at least two primers hybridize to the same strand
of a target nucleic acid sequence but each primer hybridizes to a
distinct nucleotide sequence on the strand; wherein each primer is
present in the reaction mixture at a different amount P.sub.x,
where x is an integer between 1 and the number of primers in the
mixture; (b) under amplification conditions, each primer
simultaneously and independently produces one of at least two
amplicons from the target nucleic acid sequence, wherein for each
amplicon, a number of copies A.sub.x is produced, and wherein each
A.sub.x differs by an amount that is approximately same as the
amount of difference in each P.sub.x of the at least two primers.
In one aspect, the difference in the A.sub.x for each amplicon is
at least two orders of magnitude. (c) The at least two amplicons
are detectable by hybridization with at least two probes, wherein
each of the at least two probes is specific to one of the at least
two amplicons, and each probe is detectable within a linear
detection range C.sub.x(a) to C.sub.x(b), wherein C.sub.x(a) is the
minimum detectable number of copies of amplicon and C.sub.x(b) is
the maximum detectable number of copies of amplicon for probe x,
wherein for each probe, C.sub.x+1(a) is greater than C.sub.x(a) and
C.sub.x+1(b) is greater than C.sub.x(b) such that the at least two
probes together are detectable across a wide dynamic range, wherein
for each amplicon-probe combination, A.sub.x is between C.sub.x(a)
and C.sub.x(b), and wherein the at least two probes produce
distinguishable detection signals.
[0033] In some aspects, each of the at least two primers further
differ from one another by having one or more of (i) one of the
amplification oligomers has a modified target hybridizing sequence
and the other does not and/or (ii) each of the amplification
oligomers has a different unique unpaired 5' sequence.
[0034] The present application provides a method for amplifying a
target nucleic acid sequence in a test sample comprising: (a)
contacting the test sample with a nucleic acid amplification
reaction mixture comprising at least two amplification oligomers,
wherein the at least two amplification oligomers hybridize to the
same strand of the target nucleic acid sequence but hybridize to
distinct nucleotide sequences on the strand, and each of the at
least two amplification oligomers is present in the reaction
mixture in a different amount; and (b) subjecting the reaction
mixture to amplification conditions under which each of the at
least two amplification oligomers simultaneously and independently
produces one of each of two distinguishable amplicons from the
target nucleic acid sequence, wherein the number of copies of each
amplicon produced depends on the amount of each of the at least two
amplification oligomers in the reaction mixture, and the number of
copies of each amplicon produced differs by at least two orders of
magnitude.
[0035] In some aspects, the at least two amplification oligomers
are promoter-based amplification oligomers. In some aspects, each
of the at least two amplification oligomers further differ from one
another by having one or more of (i) one of the amplification
oligomers has a modified target hybridizing sequence and the other
does not and/or (ii) each of the amplification oligomers has a
different unique unpaired 5' sequence.
[0036] The present application provides a method for quantitating a
target nucleic acid sequence in a test sample comprising: (a)
contacting the test sample with a nucleic acid amplification
reaction mixture comprising at least two amplification oligomers,
wherein the at least two amplification oligomers hybridize to the
same strand of the target nucleic acid sequence but hybridize to
distinct nucleotide sequences on the strand, and each of the at
least two amplification oligomers is present in the reaction
mixture in a different amount; (b) subjecting the reaction mixture
to amplification conditions under which each of the at least two
amplification oligomers simultaneously and independently produces
one of at least two amplicons, wherein the number of copies of each
amplicon produced differs by at least two orders of magnitude; (c)
hybridizing the at least two amplicons with at least two probes,
wherein each of the at least two probes is specific to one of the
at least two amplicons, each probe is detectable within a detection
range, wherein the sum of the detection ranges for each of the at
least two probes is greater than the detection range for each
probe, such that the at least two probes together are detectable
across a wide dynamic range, and the at least two probes produce
distinguishable detection signals; (d) detecting at least one of
the at least two probes; and (e) determining the initial amount of
target nucleic acid sequence in the test sample.
[0037] In one aspect, the at least two amplification oligomers are
promoter-based amplification oligomers. In some aspects, each of
the at least two amplification oligomers further differ from one
another by having one or more of (i) one of the amplification
oligomers has a modified target hybridizing sequence and the other
does not and/or (ii) each of the amplification oligomers has a
different unique unpaired 5' sequence.
[0038] The present application further provides a method for
quantitating a nucleic acid in a test sample comprising: (a)
providing a test sample suspected of containing a target nucleic
acid in an amount T.sub.1; (b) contacting the test sample with a
nucleic acid amplification reaction mixture comprising at least two
amplification oligomers, wherein the at least two amplification
oligomers hybridize to the same strand of the target nucleic acid
sequence but each amplification oligomers hybridizes to a distinct
nucleotide sequence on the strand, and wherein each amplification
oligomers is present in the reaction mixture in a different amount.
In one aspect, each P.sub.x differs by at least two orders of
magnitude, and where x is an integer between 1 and the number of
amplification oligomers in the mixture. (c) Subjecting the reaction
mixture to amplification conditions under which each of the at
least two amplification oligomers simultaneously and independently
produces one of at least two amplicons, wherein for each amplicon,
a number of copies A.sub.x is produced, and wherein each A.sub.x
differs by an amount that is approximately the same as the amount
of difference in each P.sub.x for the at least two amplification
oligomers hybridizing to the same strand of the target nucleic acid
sequence present in the mix. In one aspect, the A.sub.x for each
amplicon differs by at least two orders of magnitude. (d)
Hybridizing the at least two amplicons with at least two probes,
wherein each of the at least two probes is specific to one of the
at least two amplicons, each probe is detectable within a linear
detection range C.sub.x(a) to C.sub.x(b), wherein C.sub.x(a) is the
minimum detectable number of copies of amplicon and C.sub.x(b) is
the maximum detectable number of copies of amplicon for probe x,
wherein for each probe, C.sub.x+1(a) is greater than C.sub.x(a) and
C.sub.x+1(b) is greater than C.sub.x(b) such that the at least two
probes together are detectable across a wide dynamic range, wherein
for each amplicon-probe combination, A.sub.x is between C.sub.x(a)
and C.sub.x(b), and wherein the at least two probes produce
distinguishable detection signals; (e) detecting at least one of
the at least two probes; and (f) determining the initial amount of
target nucleic acid sequence in the test sample.
[0039] In some aspects, the at least two amplification oligomers
are promoter-based amplification oligomers. In some aspects, each
of the at least two amplification oligomers further differ from one
another by having one or more of (i) one of the amplification
oligomers has a modified target hybridizing sequence and the other
does not and/or (ii) each of the amplification oligomers has a
different unique unpaired 5' sequence.
[0040] The present application further provides a composition for
amplifying a target nucleic acid sequence in a test sample
comprising at least two amplification oligomers, wherein: (a) the
at least two amplification oligomers hybridize to the same strand
of the target nucleic acid sequence but hybridize to distinct
nucleotide sequences on the strand, and each of the at least two
amplification oligomers is present in the reaction mixture in a
different amount; and (b) under amplification conditions, each of
the at least two amplification oligomers simultaneously and
independently produces one of each of two detectable amplicons from
the target nucleic acid sequence, wherein the number of copies of
each amplicon produced depends on the amount of each of the at
least two amplification oligomers in the reaction mixture, the
number of copies of each amplicon produced differs by at least two
orders of magnitude, and the amplicons are detectable across a wide
dynamic range.
[0041] In some aspects, the at least two amplification oligomers
are promoter-based amplification oligomers. In some aspects, each
of the at least two amplification oligomers further differ from one
another by having one or more of (i) one of the amplification
oligomers has a modified target hybridizing sequence and the other
does not and/or (ii) each of the amplification oligomers has a
different unique unpaired 5' sequence.
[0042] The present application further provides a nucleic acid
amplification reaction mixture comprising at least two
amplification oligomers, wherein: (a) the at least two
amplification oligomers hybridize to the same strand of a target
nucleic acid sequence but each amplification oligomer hybridizes to
a distinct nucleotide sequence on the strand; wherein each primer
is present in the reaction mixture at a different amount P.sub.x,
where x is an integer between 1 and the number of primers in the
mixture; (b) under amplification conditions, each primer
simultaneously and independently produces one of at least two
amplicons from the target nucleic acid sequence, wherein for each
amplicon, a number of copies A.sub.x is produced, and wherein each
A.sub.x differs by an amount that is approximately same as the
amount of difference in each P.sub.x of the at least two
amplification oligomers hybridizing to the same strand of the
target nucleic acid sequence. In one aspect, the difference in the
A.sub.x for each amplicon is at least two orders of magnitude; (c)
the at least two amplicons are detectable by hybridization with at
least two probes, wherein each of the at least two probes is
specific to one of the at least two amplicons, and each probe is
detectable within a linear detection range C.sub.x(a) to
C.sub.x(b), wherein C.sub.x(a) is the minimum detectable number of
copies of amplicon and C.sub.x(b) is the maximum detectable number
of copies of amplicon for probe x, wherein for each probe,
C.sub.x+1(a) is greater than C.sub.x(a) and C.sub.x+1(b) is greater
than C.sub.x(b) such that the at least two probes together are
detectable across a wide dynamic range, wherein for each
amplicon-probe combination, A.sub.x is between C.sub.x(a) and
C.sub.x(b), and wherein the at least two probes produce
distinguishable detection signals.
[0043] In some aspects, the at least two amplification oligomers
are promoter-based amplification oligomers. In some aspects, each
of the at least two amplification oligomers further differ from one
another by having one or more of (i) one of the amplification
oligomers has a modified target hybridizing sequence and the other
does not and/or (ii) each of the amplification oligomers has a
different unique unpaired 5' sequence.
[0044] The present application provides a method for amplifying a
target nucleic acid sequence in a test sample comprising: (a)
contacting the test sample with a nucleic acid amplification
reaction mixture comprising at least two amplification oligomers,
wherein the at least two amplification oligomers hybridize to the
same sequence on the same strand of the target nucleic acid
sequence but each of the at least two amplification oligomers
differ from one another by having one or more of (i) one of the
amplification oligomers has a modified target hybridizing sequence
and the other does not and/or (ii) each of the amplification
oligomers has a different unique unpaired 5' sequence, and each of
the at least two amplification oligomers is present in the reaction
mixture in a different amount; and (b) subjecting the reaction
mixture to amplification conditions under which each of the at
least two amplification oligomers simultaneously and independently
produces one of each of two distinguishable amplicons from the
target nucleic acid sequence, wherein the number of copies of each
amplicon produced depends on the amount of each of the at least two
amplification oligomers in the reaction mixture, and the number of
copies of each amplicon produced differs by at least two orders of
magnitude.
[0045] In some aspects, the at least two amplification oligomers
are promoter-based amplification oligomers. In some aspects, the at
least two amplification oligomers are primers.
[0046] The present application provides a method for quantitating a
target nucleic acid sequence in a test sample comprising: (a)
contacting the test sample with a nucleic acid amplification
reaction mixture comprising at least two amplification oligomers,
wherein the at least two amplification oligomers hybridize to the
same sequence on the same strand of the target nucleic acid
sequence but each of the at least two amplification oligomers
differ from one another by having one or more of (i) one of the
amplification oligomers has a modified target hybridizing sequence
and the other does not and/or (ii) each of the amplification
oligomers has a different unique unpaired 5' sequence, and each of
the at least two amplification oligomers is present in the reaction
mixture in a different amount; (b) subjecting the reaction mixture
to amplification conditions under which each of the at least two
amplification oligomers simultaneously and independently produces
one of at least two amplicons, wherein the number of copies of each
amplicon produced differs by at least two orders of magnitude; (c)
hybridizing the at least two amplicons with at least two probes,
wherein each of the at least two probes is specific to one of the
at least two amplicons, each probe is detectable within a detection
range, wherein the sum of the detection ranges for each of the at
least two probes is greater than the detection range for each
probe, such that the at least two probes together are detectable
across a wide dynamic range, and the at least two probes produce
distinguishable detection signals; (d) detecting at least one of
the at least two probes; and (e) determining the initial amount of
target nucleic acid sequence in the test sample.
[0047] In one aspect, the at least two amplification oligomers are
promoter-based amplification oligomers. In some aspects, the at
least two amplification oligomers are primers.
[0048] The present application further provides a method for
quantitating a nucleic acid in a test sample comprising: (a)
providing a test sample suspected of containing a target nucleic
acid in an amount T.sub.1; (b) contacting the test sample with a
nucleic acid amplification reaction mixture comprising at least two
amplification oligomers, wherein the at least two amplification
oligomers hybridize to the same sequence on the same strand of the
target nucleic acid sequence but each of the at least two
amplification oligomers differ from one another by having one or
more of (i) one of the amplification oligomers has a modified
target hybridizing sequence and the other does not and/or (ii) each
of the amplification oligomers has a different unique unpaired 5'
sequence, and wherein each amplification oligomers is present in
the reaction mixture in a different amount. In one aspect, each
P.sub.x differs by at least two orders of magnitude, and where x is
an integer between 1 and the number of amplification oligomers in
the mixture. (c) Subjecting the reaction mixture to amplification
conditions under which each of the at least two amplification
oligomers simultaneously and independently produces one of at least
two amplicons, wherein for each amplicon, a number of copies
A.sub.x is produced, and wherein each A.sub.x differs by an amount
that is approximately the same as the amount of difference in each
P.sub.x for the at least two amplification oligomers hybridizing to
the same strand of the target nucleic acid sequence present in the
mix. In one aspect, the A.sub.x for each amplicon differs by at
least two orders of magnitude. (d) Hybridizing the at least two
amplicons with at least two probes, wherein each of the at least
two probes is specific to one of the at least two amplicons, each
probe is detectable within a linear detection range C.sub.x(a) to
C.sub.x(b), wherein C.sub.x(a) is the minimum detectable number of
copies of amplicon and C.sub.x(b) is the maximum detectable number
of copies of amplicon for probe x, wherein for each probe,
C.sub.x+1(a) is greater than C.sub.x(a) and C.sub.x+1(b) is greater
than C.sub.x(b) such that the at least two probes together are
detectable across a wide dynamic range, wherein for each
amplicon-probe combination, A.sub.x is between C.sub.x(a) and
C.sub.x(b), and wherein the at least two probes produce
distinguishable detection signals; (e) detecting at least one of
the at least two probes; and (f) determining the initial amount of
target nucleic acid sequence in the test sample.
[0049] In some aspects, the at least two amplification oligomers
are promoter-based amplification oligomers. In some aspects, the at
least two amplification oligomers are primers.
[0050] The present application further provides a composition for
amplifying a target nucleic acid sequence in a test sample
comprising at least two amplification oligomers, wherein: (a) the
at least two amplification oligomers hybridize to the same sequence
of the same strand of the target nucleic acid sequence but each of
the at least two amplification oligomers differ from one another by
having one or more of (i) one of the amplification oligomers has a
modified target hybridizing sequence and the other does not and/or
(ii) each of the amplification oligomers has a different unique
unpaired 5' sequence, and each of the at least two amplification
oligomers is present in the reaction mixture in a different amount;
and (b) under amplification conditions, each of the at least two
amplification oligomers simultaneously and independently produces
one of each of two detectable amplicons from the target nucleic
acid sequence, wherein the number of copies of each amplicon
produced depends on the amount of each of the at least two
amplification oligomers in the reaction mixture, the number of
copies of each amplicon produced differs by at least two orders of
magnitude, and the amplicons are detectable across a wide dynamic
range.
[0051] In some aspect, the at least two amplification oligomers are
promoter-based amplification oligomers. In some aspects, the at
least two amplification oligomers are primers.
[0052] The present application further provides a nucleic acid
amplification reaction mixture comprising at least two
amplification oligomers, wherein: (a) the at least two
amplification oligomers hybridize to the same sequence of the same
strand of a target nucleic acid sequence but each of the at least
two amplification oligomers differ from one another by having one
or more of (i) one of the amplification oligomers has a modified
target hybridizing sequence and the other does not and/or (ii) each
of the amplification oligomers has a different unique unpaired 5'
sequence; wherein each primer is present in the reaction mixture at
a different amount P.sub.x, where x is an integer between 1 and the
number of primers in the mixture; (b) under amplification
conditions, each primer simultaneously and independently produces
one of at least two amplicons from the target nucleic acid
sequence, wherein for each amplicon, a number of copies A.sub.x is
produced, and wherein each A.sub.x differs by an amount that is
approximately same as the amount of difference in each P.sub.x of
the at least two amplification oligomers hybridizing to the same
strand of the target nucleic acid sequence. In one aspect, the
difference in the A.sub.x for each amplicon is at least two orders
of magnitude. (c) The at least two amplicons are detectable by
hybridization with at least two probes, wherein each of the at
least two probes is specific to one of the at least two amplicons,
and each probe is detectable within a linear detection range
C.sub.x(a) to C.sub.x(b), wherein C.sub.x(a) is the minimum
detectable number of copies of amplicon and C.sub.x(b) is the
maximum detectable number of copies of amplicon for probe x,
wherein for each probe, C.sub.x+1(a) is greater than C.sub.x(a) and
C.sub.x+1(b) is greater than C.sub.x(b) such that the at least two
probes together are detectable across a wide dynamic range, wherein
for each amplicon-probe combination, A.sub.x is between C.sub.x(a)
and C.sub.x(b), and wherein the at least two probes produce
distinguishable detection signals.
[0053] In some aspects, the at least two amplification oligomers
are promoter-based amplification oligomers. In some aspects, the at
least two amplification oligomers are primers.
[0054] The present application further provides reaction mixtures
comprising at least three amplification oligomers, wherein a one of
the amplification oligomers hybridizes to one strand of a target
nucleic acid and a second and a third of the amplification
oligomers hybridize to the other strand of a target nucleic acid in
order to produce two or more differentiable amplicons. Each species
of differentiable amplicon is defined at one end by the common
first amplification oligomer. The two amplification oligomers
hybridizing the same strand will define the opposite end of their
respective amplicon species. In some aspects, the at least three
amplification oligomers are at least three primers. In some
aspects, the at least three amplification oligomers are a primer
hybridizing to one strand of a target nucleic acid and two
promoter-based oligomers hybridizing to the other strand of a
target nucleic acid. In some aspects, the at least three
amplification oligomers are a promoter based amplification oligomer
hybridizing to one strand of a target nucleic acid and two primers
hybridizing to the other strand of a target nucleic acid. In some
aspects, the second and a third of the amplification oligomers
hybridizing to the same strand of a target nucleic acid, differ by
hybridizing to different sequences on the target nucleic acid. In
some aspects, the second and a third of the amplification oligomers
hybridizing to the same strand of a target nucleic acid, differ
from one another by having one or more of (i) one of the
amplification oligomers has a modified target hybridizing sequence
and the other does not and/or (ii) each of the amplification
oligomers has a different unique unpaired 5' sequence.
[0055] The present application further provides reaction mixtures
comprising at least two detection probe oligomers each of which
hybridize to one of two or more differentiable amplicons generated
using at least three amplification oligomers, wherein a one of the
amplification oligomers hybridizes to one strand of a target
nucleic acid and a second and a third of the amplification
oligomers hybridize to the other strand of a target nucleic acid.
In some aspects, the detectable probe oligomers are labeled
different chemiluminescent labels. In some aspects the detectable
probe oligomers are labeled different fluorescent labels. In some
aspects the detectable probe oligomers are labeled different
fluorescent labels and/or different chemiluminescent labels.
BRIEF DESCRIPTION OF THE FIGURES
[0056] FIG. 1 is a diagram that illustrates components of in vitro
amplification reactions described in Example 1. FIG. 1A depicts the
locations of the promoter-primer (Pr-primer; SEQ ID NO:1), Primer 1
(SEQ ID NO:2), and Primer 2 (SEQ ID NO:3) relative to a target RNA
transcript (SEQ ID NO:4) (described in the "Amplification
Compositions" section of the Examples). FIG. 1B shows a shorter
amplicon (SEQ ID NO:9) and a longer amplicon (SEQ ID NO:10) that
result from the reaction of (a) the Pr-primer and Primer 1 and (b)
the Pr-primer and Primer 2, respectively, and the locations of the
two amplicons relative to the sequences in FIG. 1A. FIG. 1C depicts
the positions of labeled detection probes of SEQ ID NOS:5 and 6
(described in the "Detection Compositions" section of the Examples)
relative to the amplicons of FIG. 1B.
[0057] FIG. 2 is a graph that shows the mean,
background-subtracted, specific activity-adjusted signal output
(y-axis, reported across a range of about 10.sup.4 to about
10.sup.9 RLU for "relative light units") detected by using linear
AE-labeled probes hybridized to amplicons of target RNA across a
range of 10.sup.2 to 10.sup.9 input target RNA copies (x-axis) as
described in Example 1. Results are shown for (a) labeled probes (1
nM; SEQ ID NO:5) mixed with unlabeled oligonucleotides (50 nM; SEQ
ID NO:5) (black circles); (b) labeled probes (1 nM; SEQ ID NO:6)
mixed with unlabeled oligonucleotides (200 nM; SEQ ID NO:6) (black
squares); and (c) the sum of detection signals from (a) and (b)
(white triangles).
[0058] FIG. 3 is a graph that shows the mean,
background-subtracted, specific activity-adjusted signal output
(y-axis, reported across a range of about 10.sup.4 to about
10.sup.11 RLU) detected by using linear AE-labeled probes
hybridized to amplicons of target RNA across a range of 10.sup.2 to
10.sup.9 input target RNA copies (x-axis). In this Figure, values
obtained in Example 1 for the reactions of labeled and unlabeled
probes of SEQ ID NO:6 have been multiplied by a factor "k" of 46.6
(results shown as black squares) to allow direct visual comparison
of these results to those obtained from the reaction of labeled and
unlabeled probes of SEQ ID NO:5 (black circles). The sum of the two
sets of detection signals (white triangles) demonstrate that the
reaction system creates a continuous linear dynamic range of at
least 10.sup.3 to 10.sup.9 input copies.
[0059] FIG. 4 is a diagram that illustrates the relative alignment
of the primers to the RNA transcript, the resulting amplicons, and
the relative alignment of the probes to the amplicons used in
Examples 2, 3 and 5. As in FIG. 1, FIG. 4A depicts the locations of
the promoter primer (Pr-primer; SEQ ID NO:1), Primer 1 (SEQ ID
NO:2), and Primer 2 (SEQ ID NO:3) relative to a target RNA
transcript (SEQ ID NO:4), and FIG. 4B shows the two amplicons (SEQ
ID NOS:9 and 10) which result from the reaction of (a) the
Pr-primer and Primer 1 and (b) the Pr-primer and Primer 2, and the
locations of the two amplicons relative to the sequences in FIG.
4A. FIG. 4C depicts the positions of labeled and unlabeled
detection probes SEQ ID NO:7 and SEQ ID NO:8 (described in the
"Detection Compositions" section of the Examples) relative to the
amplicons of FIG. 4B.
[0060] FIG. 5 is a graph showing the mean, background-subtracted
PMT 1 (low wavelength) RLU output from reactions of self-quenching
AE probes with amplicons of RNA transcripts at the indicated range
of copy inputs as obtained in Example 2 for (a) 10 nM labeled probe
of SEQ ID NO:7 (black circles) and (b) 10 nM labeled probe of SEQ
ID NO:7 plus 100 nM labeled probe of SEQ ID NO:8 (white
circles).
[0061] FIG. 6 is a graph showing the mean background-subtracted PMT
2 (high wavelength) RLU output from reactions of self-quenching AE
probes with amplicons of RNA transcripts at the indicated range of
copy inputs as obtained in Example 2. Results are shown for (a) 100
nM labeled probe of SEQ ID NO:8 (black triangles) and (b) 100 nM
labeled probe of SEQ ID NO:8 plus 10 nM labeled probe of SEQ ID
NO:7 (white triangles).
[0062] FIG. 7 is a graph depicting the mean, background-subtracted
RLU output from the reactions of self-quenching AE probes with
amplicons of RNA transcripts at the indicated range of copy inputs
as obtained in Example 2. Results shown are (a) PMT 1 RLU for 10 nM
labeled probe of SEQ ID NO:7 plus 100 nM labeled probe of SEQ ID
NO:8 (white circles) and (b) PMT 2 RLU for 10 nM labeled probe of
SEQ ID NO:7 plus 100 nM labeled probe of SEQ ID NO:8 (white
triangles).
[0063] FIG. 8 is a graph showing the mean, background-subtracted
PMT 1 RLU output from the reactions of self-quenching AE probes
with amplicons of RNA transcripts at the indicated range of copy
inputs as obtained in Example 3. Results shown are for (a) 10 nM
labeled probe of SEQ ID NO:7 (black circles) and (b) 10 nM labeled
probe of SEQ ID NO:7 plus 100 nM labeled probe of SEQ ID NO:8
(white circles).
[0064] FIG. 9 is a graph showing the mean, background-subtracted
PMT 2 RLU output from the reactions of self-quenching AE probes
with amplicons of RNA transcripts at the indicated range of copy
inputs as obtained in Example 3. Results shown are from (a) 100 nM
labeled probe of SEQ ID NO:8 (black triangles) and (b) 100 nM
labeled probe of SEQ ID NO:8 plus 10 nM labeled probe of SEQ ID
NO:7 (white triangles).
[0065] FIG. 10 is a graph showing the mean, background-subtracted
RLU output from the reactions of self-quenching AE probes with
amplicons of RNA transcripts at the indicated range of copy inputs
as obtained in Example 3. Results shown are (a) PMT1 RLU for 10 nM
labeled probe of SEQ ID NO:7 plus 100 nM labeled probe of SEQ ID
NO:8 (white circles), and (b) PMT 2 RLU for 100 nM labeled probe of
SEQ ID NO:8 plus 10 nM labeled probe of SEQ ID NO:7 (white
triangles).
[0066] FIG. 11 is a graph showing the mean, background-subtracted
PMT 1 RLU output from the reactions of self-quenching AE probes
with amplicons of RNA transcripts at the indicated range of copy
inputs as obtained in Example 5. Results shown are (a) 10 nM
labeled probe of SEQ ID NO:7 (black circles) and (b) 10 nM labeled
probe of SEQ ID NO:7 plus 100 nM labeled probe of SEQ ID NO:8
(white circles).
[0067] FIG. 12 is a graph showing the mean, background-subtracted
PMT 2 RLU output from the reactions of self-quenching AE probes
with amplicons of RNA transcripts at the indicated range of copy
inputs as obtained in Example 5. Results shown are (a) 100 nM
labeled probe of SEQ ID NO:8 (black triangles) and (b) 100 nM
labeled probe of SEQ ID NO:8 plus 10 nM labeled probe of SEQ ID
NO:7 (white triangles).
[0068] FIG. 13 is a graph depicting the mean, background-subtracted
RLU output from the reactions of self-quenching AE probes with
amplicons of RNA transcripts at the indicated range of copy inputs
as obtained in Example 5. Results shown are (a) PMT1 RLU for 10 nM
labeled probe of SEQ ID NO:7 plus 100 nM labeled probe of SEQ ID
NO:8 (white circles), and (b) PMT 2 RLU for 100 nM labeled probe of
SEQ ID NO:8 plus 10 nM labeled probe of SEQ ID NO:7 (white
triangles).
DETAILED DESCRIPTION
[0069] As used herein, the terms "including," "containing," and
"comprising" are used in their open, non-limiting sense.
[0070] As used herein, "a" or "an" means "at least one" or "one or
more."
[0071] For any quantitative expression used herein, it is
understood the quantity is meant to refer to the actual value and
is also meant to refer to the approximation of the value that would
be inferred by one of skill in the art, including approximations
due to the experimental and/or measurement conditions for the given
value. This inference is intended regardless of whether the term
"about" is used explicitly with the quantity or not.
[0072] Target nucleic acids for the present methods and
compositions include double-stranded and single-stranded targets.
Target nucleic acids may be full-length sequences or fragments
thereof and may be RNA or DNA. In its broadest use, the term target
nucleic acids refers to the nucleic acids present in the biological
sample and the amplified copy thereof. The amplified copy, may be
referred to herein as "amplified copy," "amplified strand," "cDNA,"
"synthesized complementary sequence," "RNA transcript" or other
similar term indicating that the referenced strand is not from the
biological sample. Under the present method, target nucleic acid in
a test sample may be detected and quantified in amounts ranging
from 0 to about 10.sup.12 copies.
[0073] The term "dynamic range," as used herein, refers to the
ratio between the largest and smallest concentrations or number of
copies of a target nucleic acid that can be detected. In such
cases, the dynamic range is used without any designated units. In
some circumstances, "dynamic range" is used to refer to limiting
values of detection (e.g., the high and low limits of detection),
in which case the appropriate unit measure, such as .mu.M or
copies, is designated. A "wide" or "broad" dynamic range for the
present invention is about 10.sup.2 to 10.sup.10 in terms of the
detectable number of copies, or may be range of 10.sup.3 to
10.sup.7 in terms of ratio. For example, a detection method
according to the invention may accurately detect amounts ranging
from about 10.sup.3 to 10.sup.10 input target nucleic acid copies
(a dynamic range of about 10.sup.7), from about 10.sup.4 to
10.sup.10 input sequence copies (a dynamic range of 10.sup.6),
amounts ranging from 10.sup.3 to 10.sup.9 input sequence copies (a
dynamic range of 10.sup.6), or amounts ranging from 10.sup.6 to
10.sup.10 input sequence copies (a dynamic range of 10.sup.4).
Thus, in some embodiments, the methods and compositions provided
herein allow for a detection range from about 10.sup.3 to 10.sup.7
or from about 10.sup.4 to 10.sup.6. Ranges are understood to be the
recited values and the whole and partial values in between (e.g.
10.sup.2 to 10.sup.10 includes the recited values and values in
between such as 10.sup.5, 2.5.times.10.sup.6, 10.sup.4.5,
10.sup.8.3, etc.).
[0074] The term "distinguishable," as used herein, refers to the
characteristic of a nucleic acid sequence that allows it to be
detected in a manner that distinguishes it from another nucleic
acid sequence. For example, two amplicons are distinguishable when
they are capable of being independently detected by two selective
probes. The two probes will generate signals that may be detected
individually and without significant interference between them,
e.g., through different wavelengths, different radioligands, or
different chemically-detectable devices (such as a fluorophore and
a chemiluminescent probe), or a mixture of such signaling
mechanisms.
[0075] In particular, the term "distinguishable detection signal"
refers to the signals produced by two or more probes. To be
"distinguishable," the signals produced by the individual probes
are differentiable by standard detection devices. The signals are
readily quantifiable by a detection instrument without unwarranted
interference or overlap between the signals. For example, probes
that produce distinguishable detection signals are those that
produce signals at wavelengths sufficiently separated to be
accurately detected and quantified by a detection instrument.
[0076] The term "amplification oligomer" refers to oligonucleotide
sequences useful for amplification of a target nucleic acid.
Amplification oligomers include primers, promoter-based
amplification oligomers, promoter primers, promoter providers and
the like.
[0077] The term "promoter-based amplification oligomer" includes
promoter-primers and promoter-providers. A "promoter-provider" or
"provider" refers to an oligonucleotide comprising first and second
regions, and which is modified to prevent the initiation of DNA
synthesis from its 3'-terminus. The "first region" or "target
hybridizing region" of a promoter-provider oligonucleotide
comprises a base sequence which hybridizes to a DNA template, where
the hybridizing sequence is situated 3', but not necessarily
adjacent to, a promoter region. The target hybridizing region of a
promoter-based oligonucleotide is typically at least 10 nucleotides
in length, and may extend up to 50 or more nucleotides in length.
The "second region" or "promoter region" comprises a promoter
sequence for an RNA polymerase. A promoter provider is engineered
so that it is incapable of being extended by an RNA- or
DNA-dependent DNA polymerase, e.g., reverse transcriptase,
preferably comprising a blocking moiety at its 3'-terminus as
described above. As referred to herein, a "T7 Provider" or T7
Promoter Provider is a blocked promoter-provider oligonucleotide
that provides an oligonucleotide sequence that is recognized by T7
RNA polymerase. A similar oligomer that lacks modification to the
3'-terminus is called a "promoter primer." T7 or other promoter
sequences are useful for promoter-based amplification oligomers. As
used herein, a "promoter" is a specific nucleic acid sequence that
is recognized by a DNA-dependent RNA polymerase ("transcriptase")
as a signal to bind to the nucleic acid and begin the transcription
of RNA at a specific site.
[0078] As used herein, the term "primer" refers to an
oligonucleotide that hybridizes a target nucleic acid and produces
an amplicon therefrom.
[0079] For some embodiments of the presently disclosed methods and
compositions, at least three amplification oligomers are used
together, one amplification oligomer hybridizing one strand and two
amplification oligomers hybridizing the other strand. In any given
method or composition, at least two amplification oligomers read
the target nucleic acid in the same direction, i.e., either all
forward amplification oligomers or all reverse amplification
oligomers. The at least three amplification oligomers include,
then, a forward or reverse amplification oligomer and at least two
reverse or forward amplification oligomers, respectively. The at
least two amplification oligomers hybridizing the same strand of
the target nucleic acid (i.e. same direction) generate
differentiable amplicons by hybridizing two distinct sequences
within the target nucleic acid sequence, by hybridizing the same
sequences within the target nucleic acid sequence but by also
providing differentiable sequences (modified and unmodified
sequences, unique non-hybridizing 5' sequences or the like). For
the same direction amplification oligomers, their target sequences
on the target nucleic acid, when distinct, may overlap. The at
least two amplification oligomers are provided in unequal amounts,
thereby generating their respective differentiable amplicons in
approximately the same unequal amounts.
[0080] For some embodiments of the presently disclosed methods and
compositions, at least two amplification oligomers are used
together, one amplification oligomer hybridizing one strand and one
amplification oligomer hybridizing the other strand. Using this
embodiment, the differentiable amplicons generated with these
amplification oligomers differ in their nucleotide composition. For
example, using a dNTP mix that provides one of the dNTPs in an
unequal ratio of native dNTP to analog dNTP will generate unequal
amplicons species having the native or analogue residues. As a
further example, using an amplification reaction that generates RNA
amplicon species and DNA amplicon species will also generate
unequal amplicons species comprising RNA or DNA.
[0081] As used herein, the term "amplicon" refers to the product
generated from the hybridization of an amplification oligomer with
its target sequence under amplification conditions. Amplicons can
include double stranded DNA, as is generated in PCR amplification
reactions and some steps of isothermal amplification reactions,
DNA:RNA hybrids as are generated in some steps of RT-PCR and some
steps of isothermal amplification reactions, or single stranded RNA
as are generated in some steps of isothermal amplification.
[0082] As used herein, the term "amplification oligomer-amplicon
combination" or "amplification oligomer-amplicon system" refers to
an amplification oligomer and the specific amplicon produced
therefrom. The amplification oligomer referred to in some
embodiments is one of the differentiable same direction
amplification oligomers that are described herein for generating
differentiable amplicons.
[0083] As used herein, the term "probe" refers to a DNA or RNA
fragment, oligonucleotide or transcript capable of detecting the
presence of a particular nucleotide sequence that is complementary
to the sequence in the probe. Probes are suitably tagged or labeled
with a molecular marker that can be detected by a detection
instrument. Suitable probes and instruments are known in the art.
Probes useful in the methods and compositions described herein may
be any probe which allows for quantitative detection of a nucleic
acid product. Suitable probes include chemiluminescent probes
(including self-quenching varieties), fluorophore-based probes,
wavelength-detectable probes, radiolabelled probes, and the like.
Particularly useful probes include those labeled with
chemiluminescent labels, such as acridinium esters (AE),
hybridization-induced chemiluminescent signal (HICS) labels,
fluorophore-AE hybrid labels, and the like. In particular, HICS
probes are described in, e.g., U.S. Pat. No. 7,169,554. HICS probes
may include wavelength-shifted HICS (wsHICS) probes in which the
emission wavelength is shifted from AE to that of a proximal
fluorophore in a self-quenching probe format (e.g., U.S. Pat. No.
6,165,800). Thus, self-quenching energy transfer probes are
examples of suitable probes for use in the present methods.
Particularly suitable probes include acridinium ester probes or
HICS probes.
[0084] Suitable amplification conditions include the amplification
methods described herein. For example, the isothermal amplification
or cyclical amplification methods are appropriate for use in the
methods and with the compositions described herein.
[0085] The methods and compositions described herein provide
quantitative amplification of target nucleic acid sequences that
may be present in a test sample by using various means to produce
different quantities of distinguishable detectable amplicon
products in known proportions. The described methods and
compositions generate multiple differentiable amplicons at ratios
relative to each other and relative to the amount of target nucleic
acid sequence. Amplification of a target nucleic acid sequence with
a single pair of amplification oligomer could generate an amplicon
with a concentration outside the accurate detection range of a
probe or the detection instrument. According to the present
invention, in contrast, multiple amplification oligomer-amplicon
systems are used to simultaneously generate multiple differentiable
amplicons at differing amplicon concentrations. Thus, rather than
one narrow window of accurate detection, the present method creates
multiple overlapping detection ranges, each of which is accurate
for a particular species of amplicon product. The present method
produces multiple differentiable amplicons in a single
amplification system, which is preferably performed in a single
vessel. The differentiable amplicons may differ in length, wherein
the amplicon species share a common sequence, but wherein each
longer amplicon species adds additional sequence that is unique to
the longer species compared to the shorter. The differentiable
amplicons may differ in composition, wherein one or more modified
nucleobases in incorporated into a species of amplicon, but not
into other(s). Similarly, the differentiable amplicons may differ
in composition, wherein separately unique 5' sequences are
incorporated into each species of amplicon by using amplification
oligomers with 5' non-hybridizing sequences. The differentiable
amplicons may differ in composition, wherein a modified nucleobase
is combined with an unmodified nucleobase for incorporation into a
subset of amplicons (e.g., a dNTP mix having a ratio of dATP and
modified dATP or a substitute for dATP).
[0086] In these methods, the number of differentiable amplicons and
their fixed ratios relative to one another are chosen to span the
required dynamic range for the amplification reaction and to
accommodate limitations of the measuring system that detects the
amount of the amplicons generated in the amplification reaction. In
essence, the amplicons are surrogate markers for the target nucleic
acid sequence and appear (and are thus detectable) at a wide range
of amounts rather than the single amount of the target sequence.
For example, the compositions and conditions are selected to
generate a large amount of amplicon 1 and a relatively smaller
amount of amplicon 2 (and, optionally, a still smaller amount of
amplicon 3, and etc for each amplicon species made to extend the
dynamic range of detection) in a single reaction mixture. If the
amount of amplicon 1 produced in the amplification reaction exceeds
the dynamic range of the detection system, the amounts of amplicon
2 (and/or amplicon 3) produced may be detected instead, as their
concentrations fall within the dynamic range of the system. In some
embodiments, the number of copies of each amplicon species differs
by two, three, four or more orders of magnitude.
[0087] The amplicons and amounts thereof are selected to ensure
that one or more of the amplicons made in the amplification
reaction mixture may be precisely measured in the detection system.
From the precise amplicon measurements, the amount of original
target nucleic acid sequence present in the test sample is
calculated. Overall, then, the system is capable of accurately
detecting and quantifying the target nucleic acid sequence over an
extended dynamic range. In a preferred embodiment, different
amounts of amplification oligomers that target the same strand of
the target nucleic acid are used to produce the different amounts
of distinguishable amplicons. In some embodiments, the amount of
each amplification oligomer differs by at least two orders of
magnitude. In some embodiments, the distinguishable amplicons are
made from the same target region of the target nucleic acid
sequence. In other embodiments, the distinguishable amplicons are
made from overlapping target regions. In yet other embodiments, the
distinguishable amplicons are made from distinct target
regions.
[0088] In some embodiments, the starting target amount is
determined using one or more equations that include terms
containing the concentration of each primer or terms that express
the relative relationship among the concentrations of the primers,
such as a ratio, that lead to the formation of a distinguishable
product. Relevant variables for the calculation include the
concentrations of the various amplification oligomers and their
amplification efficiencies.
[0089] In other embodiments, the methods use primers selected to
produce distinguishable amplicons in which the amounts of those
primers are chosen to stop amplification of each distinguishable
amplicon at a preselected level that cannot exceed the amounts of
the relevant primers for that amplicon.
[0090] The actual ratios at which the distinguishable amplification
oligomer targeting the same strand of a target nucleic acid are
present in the reaction will depend upon the inherent dynamic range
of the detection system. The ranges of the amounts of amplicon
produced by each primer may ideally overlap somewhat to produce an
unbroken extended dynamic range unless there are reasons that
separate dynamic ranges with a gap between them is desired. For
example, if acridinium ester-labeled probes and a luminometer
capable of detecting amplicon over a span of 4 logs are used in a
system in which two distinguishable products are made, then the
ratio of the primers used to make the two distinguishable products
should be between 1,000 and 10,000 and, more preferably, about
3000, the midpoint of the logarithmic range between those two
extremes.
[0091] The methods of the invention may be described according to
the following exemplary scheme. Although the scheme is depicted
with just two amplification oligomer-amplicon systems, one of skill
in the art will recognize that additional amplification
oligomer-amplicon-probe systems may be added to create an even
broader dynamic range. It is also notable that the schematic below
showing the two amplification oligomer-amplicon system is not
showing the opposite strand amplification oligomer that works with
P1 and P2 to generate A1 and A2. The variables P.sub.x, A.sub.x,
and C.sub.x are defined above.
##STR00001##
[0092] As discussed above, the detection ranges for the individual
probes may be discreet (i.e., a gap between the ranges) or
overlapping. The scheme above depicts the overlapping variant.
Thus, in particular embodiments, each C.sub.x(b) is greater than
C.sub.x+1(a) such that the ranges of detection for the probes
overlap, creating a continuous dynamic range.
[0093] As used herein, the variable T.sub.1 refers to the number of
copies of target nucleic acid sequence in a test sample. T.sub.1
falls within a range from about T.sub.a to T.sub.b, wherein the
range represents the amount of target nucleic acid sequence that
will produce an amount of amplicon that falls within the dynamic
detection range of the system. For example, according to the Scheme
above, for a given T.sub.1, the amounts of Amplification Oligomer 1
(P.sub.1) and Amplification Oligomer 2 (P.sub.2) are selected such
that the resulting amounts Amplicon 1 (A.sub.1) and Amplicon 2
(A.sub.2) fall within the C.sub.1(a) to C.sub.2(b) range of
detection for the system.
Distinguishable Products Made Using Modified and Unmodified
Primers
[0094] In one embodiment of the method, the amplification oligomers
generate amplicon species that differ one from the other by the
presence or absence of a modified nucleobase. In one aspect, the
amplification oligomers targeting the same strand of a target
nucleic acid differ from one another by having one or more modified
nucleobases in the target hybridizing sequence of one amplification
oligomer, compared to another. The modified and unmodified
amplification oligomers can hybridize to the same sequence on the
same strand of a target nucleic acid, yet produce differentiable
amplicons based on the incorporation of the modified nucleobase in
some of the amplification products. For example, a TMA reaction is
run using a single promoter-based amplification oligomer and two
primer oligomers, wherein the one of the two primers is an
unmodified primer and the other is a modified primer. A modified
primer is derived from the sequence of the unmodified primer to
contain a distinguishable modification that is incorporated into
its amplicon. In a preferred embodiment of the modified primer, one
or more of the nucleotides in the unmodified primer are replaced by
other nucleotides. In an especially preferred embodiment, the
substitution does not substantially alter the ability of the
modified primer to anneal to its intended target nucleic acid
sequences and promote amplification relative to the unmodified
primer. The amplification reaction is then run using the unmodified
primer and a small fraction, for example 1/1000, of the modified
primer. Thus, the amplification reaction will generate a first
amplicon corresponding to the modified primer and a second amplicon
corresponding to the unmodified primer. Assuming the modified and
unmodified primers are equally efficient, the number of first
amplicon molecules with the modified sequence will be about 1/1000
of the number of second amplicon molecules with the unmodified
sequence. The amplicon populations are then detected and quantified
using two distinguishable probes. One probe detects the second
amplicon molecules that contain the unmodified sequence; the other
probe detects the first amplicon molecules that contain the
modified sequence. If little amplicon is produced due to low
initial target levels, only the probe complementary to the
unmodified sequence will show significant hybridization because
this amplicon is produced in excess over the modified amplicon
species. This hybridization should be quantitative over about 3-4
logs. If, however, the amount of amplicon produced in the
amplification reaction is much greater, then the probe that is
complementary to the unmodified sequence will reach hybridization
saturation and signal will be detected with the probe complementary
to the modified sequence. The latter signal will also be
quantifiable over about 3-4 logs; however, to determine the amount
of amplicon generated that signal needs to be multiplied by 1000
(the "ratio factor") since it represents only 1/1000 of the number
of amplicon molecules that have been produced in the amplification
reaction.
[0095] Ideally, the distinguishable products will be produced in
amounts equivalent to the ratios of the primers used in their
synthesis, those skilled in the art however will recognize that
exactly matching amplification efficiencies of different primers
may be difficult and expensive. In other preferred embodiments of
the invention, the efficiencies of amplification of the
distinguishable products are matched to the degree desired and any
difference in efficiencies is taken into account when the total
amount of amplicon produced is calculated from the amounts of each
distinguishable product. In the previous example in which the
modified primer was present in 1000-fold smaller amount than the
unmodified primer but amplification efficiencies were the same, the
amount of modified amplicon was multiplied by 1000. If, however,
the efficiency of amplification with the modified primer were to be
only 80% of the efficiency of the unmodified primer, then only 0.8
molecules of modified product would be synthesized for each 1000
molecules of unmodified product. In that case, the amount of total
amplified product would be calculated by multiplying the signal
from the modified product by the ratio factor (1000) and by an
"efficiency factor" (expected/actual=1.0/0.8=1.25) to take into
account the lower efficiency.
[0096] For reactions in which hybridization is measured by the
number of relative light units (RLU) produced from a
chemiluminescent label, the amount of total amplicon would be
calculated as a function of the signal from each probe as
follows:
Total amplicon (probe U signal)=Net RLU.sub.probe U.times.(pmoles
probe U/RLU.sub.probe U); (1)
Total amplicon (probe M signal)=Net RLU.sub.probe M.times.(pmoles
probe U/RLU.sub.probe M).times.ratio factor.times.efficiency factor
(2)
[0097] where "probe U" and "probe M" target the unmodified and
modified amplicons, respectively.
[0098] If both calculated values lie within the overlap region of
the dynamic range, then in a preferred embodiment they are compared
to determine if they are acceptably close to one another. If they
do not differ by more than a predetermined acceptable amount, then
they are combined to produce the best estimate of the total
amplicon amount. In general, the mean value will be determined by
summing the two values and dividing by 2.
[0099] In general, where the amount of amplicon produced is above
the overlap range, the signal from probe M will be used to
calculate the total amount of amplicon. In this case, the signal
from probe U is expected to be saturated. In the case where the
amount of amplicon produced is below the overlap range, the signal
from probe U will be used to calculate the total amount of
amplicon. In this case, the signal from probe M is expected to be
less than the signal from probe U. How much less will depend upon
the ratio factor, the efficiency factor, and the specific
activities of the two probes as well as the amount of target.
[0100] The amount of target nucleic acid sequence in the test
sample is then determined in comparison to values of total amplicon
produced under the same reaction conditions from a set of standards
of known target nucleic acid sequence concentration.
[0101] In the example discussed above, two distinguishable products
were produced and the amount of target nucleic acid sequence in the
test sample was calculated based upon the amounts of each of the
two amplicons generated in the amplification reaction. Those
skilled in the art will appreciate that further increases in the
dynamic range of an assay can be achieved by making additional
numbers of distinguishable amplicons in the amplification reaction
through the use of additional primers as needed to achieve the
desired dynamic range (e.g., P.sub.3, P.sub.4, etc.). Each new
amplicon should be distinguishable from the others and be made in
an amount that generates a signal within the range of the detection
instrument when it is hybridized to a probe with an appropriate
specific activity. The amount of primer used to generate each
specific amplicon must result in an amount of product that
contributes to the extension of the dynamic range. In particular
embodiments, as discussed earlier for the case in which two
distinguishable amplicons are used, the amount of product produced
from each added primer will fall within a detection range that
partially, but not completely, overlaps the detection range for
product produced by any of the other primers in order to extend the
dynamic range beyond the limits it had without the new primer.
[0102] In a preferred embodiment, the specific activities of the
probes are similar or identical and the dynamic range is spanned by
differences in the amounts of each distinguishable product that is
made. However, in other embodiments both the amounts of
distinguishable products made and the specific activities of the
probes used to detect them may be varied to further expand the
dynamic range or simply for convenience. The specific activity of
each probe (that is, the amount of signal per molar amount of
probe) is a term of the equations given above to calculate the
amount of each distinguishable amplicon that is produced. In
practice, it may be difficult to achieve similar or identical
specific activities when labeling probes; therefore, the ability of
the invention to accommodate some variability in specific activity
is often of value.
[0103] As noted above, the modified primer may contain one or more
base substitutions. These may be located at different positions
within the primer with intervening unsubstituted bases or they may
be clustered together in a single region. A sufficient number of
nucleotides may be substituted to form a region that loops out when
the primer hybridizes to the target nucleic acid sequence. Any of a
large number of modifications is possible so long as they do not
substantially alter the efficiency of priming and amplification. By
"not substantially alter" is meant that the base substitutions do
not change the efficiency of amplification so that the amounts of
product produced from them are below the levels needed to span the
intended dynamic range in accordance with the teachings herein of
the invention or cause the amount of product synthesized from them
to be excessively variable under the reaction conditions and with
the target nucleic acid sequences and test sample types used. By
"excessively variable" is meant that the amount of amplicon
produced cannot be held within the desired range of performance
needed when the assay is applied for its intended use. In the case
of an assay intended for measurement of viral loads in patient
blood samples, the coefficient of variation of the assay should
generally be no more than about 25% and preferably less than about
10%.
[0104] The modified and unmodified amplicons could either be
detected using probes that can distinguish between the two forms,
or an enzyme that distinguishes the two could be used to help
effect discrimination. For example, if the modified base is a
methylated base, then a restriction enzyme that does not recognize
the methylated sequence might be employed. Alternately, for
example, if the modified base is a methylated base, then a
restriction enzyme that does recognize the methylated sequence
might be employed. Alternatively, the presence of the modified base
may cause a different base to be inserted in the amplicon on the
next round of replication. In this case, the base could be a
deoxyribonucleotide or a ribonucleotide. The modified sequence that
is produced could be differentiated from the unmodified sequence
using two distinguishable probes that each hybridize to only one of
the two forms.
Distinguishable Products Made Using Primers with 5' Unpaired
Bases
[0105] Another method for providing distinguishable amplicons
involves using same direction amplification oligomers with 5'
unpaired bases. For example, two primers might each contain one or
more originally unpaired bases at or near their 5' termini, wherein
the unpaired bases of one amplification oligomer is different from
the unpaired bases of the other amplification oligomer. By
"originally unpaired" is meant that these bases are not hybridized
when the primer anneals to the target nucleic acid sequence in the
test sample. Once the primer and its 5' unpaired base is
incorporated into an amplicon as the amplification reaction
proceeds, then each primer will be completely complementary to
those amplicon molecules that are derived from the same primer
sequence but will not be completely complementary to those amplicon
molecules that were derived from the other primer sequence. These
two forms of primer are likely to have similar kinetics with
respect to amplification.
Distinguishable Products Made Using Substituted Nucleotides
[0106] In another embodiment of the method, one of the nucleotide
triphosphates (NTPs) present in the amplification reaction is
replaced in part with a modified NTP analog with different
hybridization or other recognition characteristics once
incorporated into the amplicons. The modified NTPs are present at,
for example, about 1/1000 of the numbers of the unmodified NTPs. As
amplicon is produced, the sequence complementary to the detection
probe will contain, on average, 1 molecule with the modified base
in a particular position instead of the unmodified base per 1000
nucleotides incorporated. The modified base could either be
detected using probes that can distinguish between the two forms,
or an enzyme that distinguishes the two could be used to help
effect discrimination. For example, if the modified base is a
methylated base, then a restriction enzyme that does not recognize
the methylated sequence might be employed. Alternately, a probe
could have a modified nucleotide at a position that is
complementary to the modified nucleotide incorporated into a
fraction of the amplicons but not complementary to other
nucleotides incorporated in that position. Modified nucleotides, as
well as enzymatic incorporation of modified nucleotide
triphosphates, are known in the art (e.g., Nucleic Acids Res.
26(21): 4975-4982 (1998); J. Am. Chem. Soc. 122(32): 7621-7632
(2000); Proc. Natl. Acad. Sci. U.S.A. 100(8): 4469-4473 (2003); J.
Am. Chem. Soc. 125(33): 9970-9982 (2003); J. Am. Chem. Soc. 126(4):
1102-1109 (2004); J. Am. Chem. Soc. 127(43): 15071-15082 (2005)).
Alternatively, the presence of the modified base may cause a
different base to be inserted in the amplicon on the next round of
replication. In this case, the base could be a deoxyribonucleotide
or a ribonucleotide. The modified sequence that is produced could
be differentiated from the unmodified sequence using two
distinguishable probes that each hybridize to only one of the two
forms.
Distinguishable DNA and RNA Targets
[0107] Certain amplification systems inherently produce different
amounts of distinguishable amplicons as part of the amplification
process. In one embodiment of the method, differential detection of
the final and intermediate products of these amplification
reactions is used to extend the dynamic range. For example, in a
commonly practiced variant of TMA, the most abundant amplicon is
RNA that is complementary to the target nucleic acid.
Double-stranded DNA is also produced in much smaller amounts,
generally at levels that are about 100- to 1000-fold less. Probes
can be made to detect the negative strand RNA amplicon species and
either, or both, strands of the DNA amplicon species. Thus, the
general principle of the invention, namely the detection of
multiple forms of amplicon that are present in substantially
different numbers to widen the dynamic range, can be applied
provided that the ratio of negative strand RNA amplicon to positive
strand DNA amplicon is constant under the conditions used to
conduct the TMA reaction. The relative amounts of RNA and
double-stranded DNA products that are produced in a TMA reaction
can be varied by changing the sequence of the promoter used as
described, for example, in Nucleic Acids Res. 15(13): 5413-5432
(1987), Nucleic Acids Res. 15(21): 8783-8798 (1987), Nucleic Acids
Res. 20(10): 2517-2524 (1992), Nucleic Acids Res. 24(18): 3659-3660
(1996), Pac. Symp. Biocomput. 15: 433-443 (2010), Biochemistry
41(11): 3586-3595 (2002) and J. Biol. Chem. 280(49): 40707-40713
(2005). Since transcription efficiency is also dependent upon the
concentration of ribonucleotides, it can be varied by changing both
the total concentration of these reaction components as well as the
relative amounts of each of the four ribonucleotides (Science
278(5346): 2092-2097 (1997); J. Mol. Biol. 281(5): 777-792 (1998)).
The activity of reverse transcriptase in copying both the RNA and
DNA templates in the reaction can be varied similarly by altering
the concentrations of deoxyribonucleotides as well as the relative
amounts of each of the four deoxyribonucleotides. Reducing the
concentrations of all four deoxyribonucleotides will slow the
reverse transcriptase DNA polymerase reaction relative to the RNA
polymerase reaction. For specific target regions, analysis of the
percentages of each base in the DNA and RNA components of the
reaction may be used to select concentrations of each base that
will increase or decrease the rate of synthesis of either the
transcribed RNA or the double-stranded DNA. For example, if an
amplicon contains a high percentage of cytosine nucleotides
relative to another amplicon, lowering the concentration of
cytosine in the reaction mixture can be used to slow synthesis of
that particular amplicon. Alterations in other reaction parameters
such as those described, for example, in U.S. Pat. Nos. 5,705,365
and 5,710,029 can also be used to differentially affect the ratio
of synthesis of transcribed RNA and double-stranded DNA products.
Detection of the positive strand DNA is complicated by the possible
presence of competing negative strand RNA amplicon in substantially
larger amounts; therefore, the negative strand DNA may be a
preferable target. Since the DNA amplicons in TMA contain the
promoter sequence, modifications of the promoter-primer that are
readily detectable may be preferred. A probe may be used to confirm
the presence of the promoter region, the adjacent primer region,
and a portion of the desired target sequence in the amplicon. These
three sequences will only be present in tandem in DNA intermediates
in the reaction.
[0108] Likewise, in another commonly practiced variant of TMA,
single-primer TMA described in U.S. Pat. No. 7,374,885, the most
abundant amplicon is RNA that is the same sense as the target
nucleic acid. Negative strand DNA is also produced in much smaller
amounts. Probes can be made to detect the positive strand RNA and
the negative strand DNA to widen the dynamic range.
Distinguishable Products Based Upon Differential Target Capture
[0109] In another embodiment of the method, suitable target capture
oligonucleotides are made that are complementary or partially
complementary to one of the primer sites and extend into a part of
the desired probe-binding site. These target capture oligomers are
able to serve as both target capture oligonucleotides and same
direction amplification oligomers. In a small percentage of these
target capture oligonucleotides, the sequence is altered so that a
distinguishable amplicon is produced in the probe-binding region in
the same way as described above for a primer that does not also
function in target capture. After target capture and washing to
remove unwanted materials, including unbound capture probe, the
remaining components of the amplification reaction are added and
the amplification process permitted to occur. The initial DNA:RNA
(original target RNA) or DNA:DNA (original target DNA) duplexes
that are generated by extension of the target capture
oligonucleotides will contain the modified sequence in a known
proportion of the molecules. Assuming that the two target sequences
amplify at a consistent ratio thereafter, probes that distinguish
between the two species can be used to quantitate the original
target over a wider range as discussed above.
Distinguishable Products Made Using Semi-Nested Primers
[0110] In yet another embodiment of the method, semi-nested primers
are provided in an amplification reaction at different
concentrations. For example, the at least two primers comprise a
first inner primer and a second outer primer. The first inner and
second outer primers are both forward primers or are both reverse
primers. The reaction mixture may further comprise a single
promoter-based amplification oligomer that operates in a direction
opposite that of the first inner and second outer primers. Thus,
the at least two amplicons produced from these primers comprise a
first amplicon produced from the first inner primer and a second
amplicon produced from the second outer primer. The first inner
primer is provided at a low concentration while the second outer,
reverse primer is provided at a higher concentration. When target
nucleic acid sequences are included in the reactions, shorter
amplicons are synthesized from the promoter-based amplification
oligomer and first inner primer while longer amplicons are
synthesized from the promoter-based amplification oligomer and the
second outer primer. The longer amplicons can serve as templates
for further synthesis of longer or shorter amplicons. By choosing
different reverse primer concentrations, differential amounts of
the longer and shorter amplicons are synthesized in a single
reaction. The shorter amplicons include sequences that are in
common with the longer amplicons. The longer amplicons include
sequences that are in common with the shorter amplicons and others
that are different than those in the shorter amplicons. Because
differential amounts of longer and shorter amplicons are
synthesized in a single reaction, quantifying the amounts of longer
and shorter amplicons can provide two overlapping ranges,
effectively extending the dynamic range of detection.
Quantification of different amounts of amplicons can be further
brought into dynamic range of a detection system by adjustment of
probe specific activity.
[0111] Alternate configurations of semi-nested amplification
oligomers at different concentrations are possible in an
amplification reaction at different concentrations. For example,
opposite a single reverse primer, an inner forward primer is
provided at a low concentration while an outer forward primer is
provided at a higher concentration. When target nucleic acid
sequences are included in the reactions, shorter amplicons are
synthesized from the reverse primer and inner forward primer while
longer amplicons are synthesized from the reverse primer and the
outer forward primer. The longer amplicons can serve as templates
for further synthesis of longer or shorter amplicons. From this
process, differential amounts of longer and shorter amplicons are
synthesized in a single reaction. Choosing different forward primer
concentrations can vary these differential amounts of amplicons.
The shorter amplicons include sequences that are in common with the
longer amplicons. The longer amplicons include sequences that are
in common with the shorter amplicons and others that are different
than those in the shorter amplicons. Since differential amounts of
longer and shorter amplicons are synthesized in a single reaction,
quantifying the amounts of longer and shorter amplicons can provide
two overlapping ranges, effectively extending the dynamic range of
detection. Quantification of different amounts of amplicons can be
further brought into dynamic range of a detection system by
adjustment of probe specific activity.
[0112] The following examples are provided to further illustrate
the present method and are not intended to limit to it.
EXAMPLES
Amplification Compositions for Examples 1-3 and 5
[0113] 0.2 .mu.m filtered water (H.sub.2O) [0114] 4.times.
Amplification Reagent: 160 mM tris(hydroxymethyl)aminomethane (Tris
base), 100 mM MgCl.sub.2, 70 mM KCl, 16 mM each of rATP, rCTP, rGTP
and rUTP, 4 mM each of dATP, dCTP, dGTP and dTTP, 20%
polyvinylpyrrolidone, 0.3% ethyl alcohol, 0.02% methyl paraben,
0.01% propyl paraben, pH 7.5 [0115] 4.times. Enzyme Reagent: 8 mM
N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) (HEPES free
acid), 140 mM Tris base, 70 mM KCl, 50 mM N-acetyl-L-cysteine, 1.04
mM ethylenediaminetetraacetic acid (EDTA), 0.04 mM zinc acetate,
10% TRITON X.RTM.-102, 80 mM trehalose, 20% glycerol, 80
units/.mu.L Moloney murine leukemia virus (MMLV) reverse
transcriptase (RT), 80 units/.mu.L T7 RNA polymerase (T7RNAP), pH
8.0 [0116] Silicone Oil Reagent: polydimethylsiloxane,
trimethylsiloxy terminated [0117] Primers: [0118] 4.times.
(Promoter primer or Pr-primer (300 nM in water)
TABLE-US-00001 [0118] (SEQ ID NO: 1)
5'-AATTTAATACGACTCACTATAGGGAGAGTTTGTATGTCTGTTGCTAT TAT-3'
[0119] 4.times. Primer 1 (15 nM in water)
TABLE-US-00002 [0119] 5'-ACAGCAGTACAAATGGCAG-3' (SEQ ID NO: 2)
[0120] 4.times. Primer 2 (285 nM in water)
TABLE-US-00003 [0120] 5'-ATTCCCTACAATCCCCAAAGTCAA-3' (SEQ ID NO:
3)
[0121] Target sequence--RNA, 1,016 nt, in vitro transcript (IVT);
the 51 nt from the 5' part of the IVT are from the T7 promoter and
cloning vector; the remaining 965 nt include the 3' part of the
HIV-1 subtype B pol gene, possibly a little of the 5' part of the
subsequent gene depending on who assigned the division of genes in
water
TABLE-US-00004 [0121] (SEQ ID NO: 4)
5'-GGGAGACAAGCUUGCAUGCCUGCAGGUCGACUCUAGAGGAU
CCCCGGGUACCAGCACACAAAGGAAUUGGAGGAAAUGAACAAGUAGAUAA
AUUAGUCAGUGCUGGAAUCAGGAAAAUACUAUUUUUAGAUGGAAUAGAUA
AGGCCCAAGAUGAACAUGAGAAAUAUCACAGUAAUUGGAGAGCAAUGGCU
AGUGAUUUUAACCUGCCACCUGUAGUAGCAAAAGAAAUAGUAGCCAGCUG
UGAUAAAUGUCAGCUAAAAGGAGAAGCCAUGCAUGGACAAGUAGACUGUA
GUCCAGGAAUAUGGCAACUAGAUUGUACACAUUUAGAAGGAAAAGUUAUC
CUGGUAGCAGUUCAUGUAGCCAGUGGAUAUAUAGAAGCAGAAGUUAUUCC
AGCAGAAACAGGGCAGGAAACAGCAUAUUUUCUUUUAAAAUUAGCAGGAA
GAUGGCCAGUAAAAACAAUACAUACAGACAAUGGCAGCAAUUUCACCAGU
GCUACGGUUAAGGCCGCCUGUUGGUGGGCGGGAAUCAAGCAGGAAUUUGG
AAUUCCCUACAAUCCCCAAAGUCAAGGAGUAGUAGAAUCUAUGAAUAAAG
AAUUAAAGAAAAUUAUAGGACAGGUAAGAGAUCAGGCUGAACAUCUUAAG
ACAGCAGUACAAAUGGCAGUAUUCAUCCACAAUUUUAAAAGAAAAGGGGG
GAUUGGGGGGUACAGUGCAGGGGAAAGAAUAGUAGACAUAAUAGCAACAG
ACAUACAAACUAAAGAAUUACAAAAACAAAUUACAAAAAUUCAAAAUUUU
CGGGUUUAUUACAGGGACAGCAGAAAUCCACUUUGGAAAGGACCAGCAAA
GCUCCUCUGGAAAGGUGAAGGGGCAGUAGUAAUACAAGAUAAUAGUGACA
UAAAAGUAGUGCCAAGAAGAAAAGCAAAGAUCAUUAGGGAUUAUGGAAAA
CAGAUGGCAGGUGAUGAUUGUGUGGCAAGUAGACAGGAUGAGGAUUAGAA
CAUGGAAAAGUUUAGUAAAACACCA-3'
Detection Compositions for Examples 1-3 and 5
[0122] Hybridization Reagent: 100 mM succinic acid, 2% (w/v)
lithium lauryl sulfate (LLS), 230 mM LiOH, 15 mM Aldrithiol-2, 1.2
M LiCl, 20 mM ethylene
glycol-bis(2-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA), 20
mM EDTA, 3% (v/v) ethyl alcohol, pH 4.7 [0123] Hybridization
Diluent: 0.1% (w/v) LLS, 10 mM succinic acid, pH 5 [0124] Alkaline
Reagent: 600 mM boric acid, 182 mM NaOH, 1% TRITON X.RTM.-100, pH
8.5 [0125] TMA Separation Suspension Reagent: 0.25 .mu.g/.mu.L
magnetic particles (BioMag M4100), 0.2 mM EDTA, 0.08% (w/v) LLS, 8
mM succinic acid, pH 5 [0126] Separation Reagent: 1.25 .mu.g/.mu.L
magnetic particles (BioMag M4100), 1 mM EDTA [0127] Read Reagent:
125 mM LiOH, 1.5 mM EGTA, 1.5 mM EDTA, 95 mM succinic acid, 8.5%
(w/v) LLS, pH 5.2 [0128] Detection Reagents [0129] Detection
Reagent 1: 32 mM H.sub.2O.sub.2, 1 mM HNO.sub.3 [0130] Detection
Reagent 2: 1.5 M NaOH [0131] Detection Reagent 3: 240 mM
H.sub.2O.sub.2, 1 mM HNO.sub.3 [0132] Detection Reagent 4: 2 M Tris
base, pH 9.0 with HCl [0133] Detection Reagent 5: 1 mM HNO.sub.3
[0134] Probes: [0135] acridinium ester (AE)-labeled linear
oligonucleotide probe 1
TABLE-US-00005 [0135] 5'-CCACAAUUUUAAAAGAAAAGGG-3' (SEQ ID NO:
5)
[0136] AE-labeled linear oligonucleotide probe 2
TABLE-US-00006 [0136] 5'-AGAAAAUUAUAGGACAGGUAAG-3' (SEQ ID NO:
6)
[0137] unlabeled oligonucleotide probe 3
TABLE-US-00007 [0137] 5'-CCACAAUUUUAAAAGAAAAGGG-3' (SEQ ID NO:
5)
[0138] unlabeled oligonucleotide probe 4
TABLE-US-00008 [0138] 5'-AGAAAAUUAUAGGACAGGUAAG-3' (SEQ ID NO:
6)
[0139] AE-labeled, Hybridization Induced Chemiluminescent Signal
(HICS) probe 5 with a 5'-AE and a
3'-[4-(dimethylamino)azobenzene-4'-carboxylic acid] (dabcyl)
moiety
TABLE-US-00009 [0139] (SEQ ID NO: 7) 5'-C6amine(LiAE)-
CUCGUCCACAAUUUUAAAAGAAAAGGGACGAG-D-3'
[0140] AE-labeled, wavelength-shifted Hybridization Induced
Chemiluminescent Signal (wsHICS) probe 6 with a
5'-tetramethylrhodamine (TAMRA), 5'-penultimate AE and a 3'-dabcyl
moiety
TABLE-US-00010 [0140] (SEQ ID NO: 8) 5'-TAMRA-rxl(LiAE)-
CCUCUAGAAAAUUAUAGGACAGGUAAGAGAGG-D-3'
Amplification Methods for Examples
[0141] Replicate TMA reactions were performed in Examples 1-3 and 5
as follows: 25 .mu.L volumes each of 4.times. Amplification
Reagent, primers in water, and RNA transcripts in water plus 100
.mu.L volumes of Silicone Oil Reagent were mixed and incubated at
60.degree. C. for 10 minutes then at 42.degree. C. for 5 minutes;
25 .mu.L, volumes of 4.times. Enzyme Reagent were added to the
solutions, the solutions were mixed and then incubated at
42.degree. C. for 90 minutes. The relative placement of the
Pr-primer and Primers 1 and 2 on the RNA transcript and the
resulting amplicons are shown diagrammatically in FIGS. 1 and 4.
Because different concentrations of Primers 1 and 2 were used,
different amounts of the respective amplicons and probe binding
regions were synthesized in a single reaction.
Example 1: Quantitative Detection of Amplicons with AE Probes Over
a Dynamic Range in Separate Reaction Chambers
[0142] This example demonstrates quantitative detection of
amplicons over a range of 10.sup.3 to 10.sup.9 copies of target
nucleic acid in separate reaction tubes.
[0143] At the completion of the TMA amplification reactions, 100
.mu.L, volumes of probes in Hybridization Reagent were added to the
amplification reaction mixtures, which were mixed and incubated at
60.degree. C. for 15 minutes to allow hybridization of probes
specific for complementary sequences in the synthesized amplicons.
The probes used were: (a) AE-labeled probe of SEQ ID NO:5 (1 nM)
plus unlabeled probe of SEQ ID NO:5 (50 nM), which was used to
attenuate the specific activity of the labeled probe; or (b)
AE-labeled probe of SEQ ID NO:6 (1 nM) plus unlabeled probe of SEQ
ID NO:6 (200 nM), which was used to attenuate the specific activity
of the labeled probe. The relative placement of the probes on the
distinguishable amplicons is shown diagrammatically in FIG. 1. In
this example, the AE-labeled probe of SEQ ID NO:5 is able to detect
both amplicons, whereas the AE-labeled probe of SEQ ID NO:6 is only
able to detect the longer amplicon.
[0144] The initial specific activities for the AE-labeled probes of
SEQ ID NO:5 and SEQ ID NO:6 were about 1.1.times.10.sup.8 and
1.6.times.10.sup.8 RLU/pmol, respectively. The specific activities
were adjusted by adding various amounts of unlabeled
oligonucleotides of the same sequence as the labeled probe to
balance the dynamic range of the probes and the amplicon output.
The amount of amplicon produced by the end of the amplification
reaction was empirically determined by titrating each detection
region with its respective probe plus increasing amounts of
unlabeled probe until the highest amount of amplicon output was
slightly less than the amount of total probe. For the probe of SEQ
ID NO:6, 20 pmol total probe/100 .mu.L, Hybridization Reagent (200
nM with specific activity=8.times.10.sup.5 RLU/pmol) was needed to
exceed amplicon from 10.sup.9 copies input. For probe of SEQ ID
NO:5, 5 pmol total probe/100 .mu.L, Hybridization Reagent (50 nM
with specific activity=2.2.times.10.sup.6 RLU/pmol) was needed to
exceed amplicon from 10.sup.5 copies input.
[0145] At the completion of the hybridization reactions, 300 .mu.L,
volumes of Alkaline Reagent were added to the hybridization
reactions, and the resulting mixtures were incubated at 60.degree.
C. for 20 minutes to selectively hydrolyze AE-labeled probes that
were not hybridized to complementary amplicons.
[0146] Chemiluminescence from these reactions was initiated in a
GEN-PROBE.RTM. LEADER.RTM. HC+ Luminometer with addition of 200
.mu.L, Detection Reagent 1, a two second pause prior to addition of
200 .mu.L, Detection Reagent 2, a 0.04 second pause, then
acquisition of 50.times.0.04 second intervals with no delays
between intervals. The chemiluminescent output in relative light
units (RLUs) from these intervals was summed and the mean values
from replicates was calculated (Tables 1 and 2).
TABLE-US-00011 TABLE 1 1 nM AE-labeled probe of SEQ ID NO: 5 + 50
nM unlabeled probe of SEQ ID NO: 5 specific activity- copies mean
mean RLU - adjusted, mean input RLU bkgd RLU - bkgd .sup. 0 4,677
10.sup.2 5,625 948 47,388 10.sup.3 13,639 8,962 448,100 10.sup.4
64,087 59,410 2,970,500 10.sup.5 679,369 674,691 33,734,563
10.sup.6 1,508,029 1,503,351 75,167,563 10.sup.7 1,606,846
1,602,169 80,108,438 10.sup.8 1,645,605 1,640,928 82,046,375
10.sup.9 1,715,148 1,710,471 85,523,538
TABLE-US-00012 TABLE 2 1 nM AE-labeled probe of SEQ ID NO: 6 + 200
nM unlabeled probe of SEQ ID NO: 6 specific specific activity- mean
activity- adjusted, copies mean RLU - adjusted, mean mean RLU -
input RLU bkgd RLU - bkgd bkgd, x k = 46.6 .sup. 0 6,963 10.sup.2
6,667 10.sup.3 6,859 10.sup.4 7,912 949 189,750 8,842,350 10.sup.5
10,583 3,621 724,100 33,743,060 10.sup.6 34,004 27,041 5,408,150
252,019,790 10.sup.7 180,227 173,264 34,652,800 1,614,820,480
10.sup.8 956,357 1,496,352 299,270,400 13,946,000,640 10.sup.9
7,175,753 7,168,790 1,433,757,950 66,813,120,470
[0147] The mean RLU from the zero RNA transcript input (first entry
in each table) was used as the background ("bkgd") measurement and
was subtracted from the results of experiments containing 10.sup.2,
10.sup.3, 10.sup.4, 10.sup.5, 10.sup.6, 10.sup.7, 10.sup.8 and
10.sup.9 copies RNA transcripts input (mean RLU minus bkgd). The
mean background-subtracted values (mean RLU-bkgd) were adjusted to
account for the specific activity of the linear AE-labeled probes
by multiplying by the fold excess of the linear probes without AE,
resulting in specific activity-adjusted, mean background-subtracted
values (specific activity-adjusted, mean RLU-bkgd). The specific
activity-adjusted, mean background-subtracted values for the two
probes measured from separate tubes were added, leading to summed
specific activity-adjusted, mean background-subtracted values
(Table 3, specific activity-adjusted, mean RLU-bkgd).
TABLE-US-00013 TABLE 3 Sum of Tables 1 & 2 specific activity-
specific activity- copies adjusted, mean adjusted, mean RLU - input
RLU - bkgd bkgd, x k = 46.6 .sup. 0 10.sup.2 47,388 47,388 10.sup.3
448,100 448,100 10.sup.4 3,160,250 11,812,850 10.sup.5 34,458,663
67,477,623 10.sup.6 80,575,713 327,187,353 10.sup.7 114,761,238
1,694,928,918 10.sup.8 381,316,755 14,028,047,015 10.sup.9
1,519,281,488 66,898,644,008
[0148] Each of the replicates for the specific activity-adjusted,
mean background-subtracted values for each probe and for the summed
probe values is shown in FIG. 2. Chemiluminescence from AE-labeled
probe of SEQ ID NO:5 plus unlabeled probe of SEQ ID NO:5
demonstrated a linear increase in RLU from about 10.sup.3 to
10.sup.5 copies per reaction of RNA transcript input.
Chemiluminescence from AE-labeled probe of SEQ ID NO:6 plus
unlabeled probe of SEQ ID NO:6 demonstrated a linear increase in
RLU from about 10.sup.5 to 10.sup.9 copies per reaction of RNA
transcript input. The slopes of responses from the two sets of
probes were about collinear. Their summed RLU values demonstrate
two discontinuous linear increases in RLU from about 10.sup.3 to
10.sup.5 copies per reaction and from about 10.sup.4 to 10.sup.9
copies per reaction. However, transforming the RLU values from
AE-labeled probe of SEQ ID NO:6 plus unlabeled probe of SEQ ID NO:6
by a multiplying by a constant (k), in this case 46.6, demonstrated
the continuous linear dynamic range of detection from these two
sets of probes from about 10.sup.3 to 10.sup.9 copies per reaction
(Tables 2 and 3, FIG. 3). The constant (k) is a visualization tool
used to adjust the slopes of both linear regression to a common
x-intercept, but is not necessary for the quantification of the two
regions of amplicons. The constant (k) was calculated by dividing
the mean RLU value from a first probe by the mean RLU value from a
second probe taken at a target input concentration in which RLU
values from both probes are part of the same linear regression. The
value varies depending on at least the primer concentrations, probe
specific activities, and amplification efficiencies.
Example 2: Quantitative Detection of Amplicons with AE-HICS Probes
Over a Dynamic Range in the Same Reaction Chamber
[0149] This example demonstrates an embodiment that provides
quantitative detection of amplicons over a dynamic range from
10.sup.6 to 10.sup.10 copies of target input in the same reaction
chamber.
[0150] At the completion of TMA reactions, 100 .mu.L, volumes of
Hybridization Reagent were added, mixed and incubated at room
temperature for 20 minutes. TMA Separation Suspension Reagent (250
.mu.L) was added, mixed and incubated at 60.degree. C. for 10
minutes. The tubes containing the above solutions were placed on a
magnetic separation rack at room temperature for 5 minutes, the
liquid phase was removed, 100 .mu.L, of probes in half-strength
Hybridization Reagent were added, and the resulting mixtures were
incubated at 60.degree. C. for 30 minutes and at room temperature
for 5 minutes. The probes used were (a) 10 nM self-quenching
AE-labeled HICS probe of SEQ ID NO:7, (b) 100 nM self-quenching,
wavelength-shifted AE-labeled wsHICS probe of SEQ ID NO:8), or (c)
both probes at the concentrations indicated in (a) and (b). The
relative placement of the probes on the distinguishable amplicons
is shown diagrammatically in FIG. 4. Labeled probe of SEQ ID NO:7
detects both amplicons, whereas the labeled probe of SEQ ID NO:8
detects only the longer amplicons.
[0151] At the completion of the hybridization reactions, 100 .mu.L,
volumes of Hybridization Diluent were added to the hybridization
reactions, and the resulting mixtures were incubated at 60.degree.
C. for 10 minutes. The tubes containing the above solutions were
placed on a magnetic separation rack at room temperature for 5
minutes, the liquid phase was removed, and 100 .mu.L, volumes of
Read Reagent were added and mixed.
[0152] Chemiluminescence from these reactions was initiated in a
modified luminometer equipped with two high-count photomultiplier
tube modules (PMT; 28 mm diameter, head-on, bialkali cathode;
Hamamatsu Photonics, Hamamatsu City, Japan) on opposite sides of
and directed towards a light-tight detection chamber fitted with
injector tubing from two reagent pumps. Filters (25.4 mm diameter;
430AF60 from Omega Optical (Brattleboro, Vt.) and OG550 from
Newport Corp. (Franklin, Mass.)) were fitted between the PMTs and
the detection chamber to allow discrimination of emissions from the
two probes. Similar multiple wavelength luminometers are known in
the art (e.g., U.S. Pat. No. 5,447,687 and Clin. Chem. 29(9),
1604-1608 (1983)). Chemiluminescence from these reactions was
initiated by addition of 200 .mu.L, Detection Reagent 3, a two
second pause prior to addition of 200 .mu.L, Detection Reagent 4,
then simultaneous acquisition of 100.times.0.4 second intervals of
time-resolved chemiluminescent data from both channels with no
delays between intervals.
[0153] The chemiluminescent output in RLUs from these intervals is
reported in Tables 4 and 5. The last column in each table reflects
the sum of the individual results.
TABLE-US-00014 TABLE 4 10 nM AE-labeled probe of SEQ ID NO: 7 10 nM
AE-labeled probe 100 nM AE-labeled probe 100 nM AE-labeled probe
PMT1 of SEQ ID NO: 7 of SEQ ID NO: 8 of SEQ ID NO: 8 copies input
rep RLU RLU - bkgd RLU RLU - bkgd RLU RLU - bkgd 0 1 377 1,176
1,487 0 2 390 1,117 1,498 10.sup.2 1 465 82 1,544 52 10.sup.2 2 622
239 2,161 669 10.sup.3 1 526 143 1,868 376 10.sup.3 2 669 286 1,632
140 10.sup.4 1 641 258 1,529 37 10.sup.4 2 705 322 1,823 331
10.sup.5 1 660 277 1,405 259 1,631 139 10.sup.5 2 836 453 1,165 19
1,783 291 10.sup.6 1 1,128 745 1,072 -75 1,974 482 10.sup.6 2 1,389
1,006 1,154 8 2,160 668 10.sup.7 1 2,973 2,590 1,448 302 3,376
1,884 10.sup.7 2 2,667 2,284 1,312 166 3,741 2,249 10.sup.8 1 1,376
230 7,624 6,132 10.sup.8 2 1,423 277 8,208 6,716 10.sup.9 1 2,027
881 11,281 9,789 10.sup.9 2 2,343 1,197 13,897 12,405 10.sup.10 1
5,496 4,350 19,736 18,244 10.sup.10 2 5,726 4,580 20,159 18,667
TABLE-US-00015 TABLE 5 10 nM AE-labeled probe of SEQ ID NO: 7 10 nM
AE-labeled probe 100 nM AE-labeled probe 100 nM AE-labeled probe
PMT2 of SEQ ID NO: 7 of SEQ ID NO: 8 of SEQ ID NO: 8 copies input
rep RLU RLU - bkgd RLU RLU - bkgd RLU RLU - bkgd 0 1 314 16,147
16,464 0 2 767 15,321 16,006 10.sup.2 1 633 93 18,291 2,056
10.sup.2 2 642 102 26,609 10,374 10.sup.3 1 614 74 19,620 3,385
10.sup.3 2 630 90 18,419 2,184 10.sup.4 1 613 73 17,711 1,476
10.sup.4 2 629 89 21,987 5,752 10.sup.5 1 642 102 21,097 5,363
17,883 1,648 10.sup.5 2 629 89 16,355 621 19,147 2,912 10.sup.6 1
689 149 15,224 -510 14,504 -731 10.sup.6 2 642 102 17,258 1,524
16,087 -148 10.sup.7 1 702 162 24,409 8,675 20,506 4,271 10.sup.7 2
719 179 20,781 5,047 24,571 8,336 10.sup.8 1 28,655 12,921 39,411
23,176 10.sup.8 2 26,900 11,166 49,451 33,216 10.sup.9 1 70,691
54,957 92,458 76,223 10.sup.9 2 80,236 64,502 118,738 102,503
10.sup.10 1 283,009 267,275 273,576 257,341 10.sup.10 2 308,126
292,392 309,765 293,530
[0154] The mean RLU from the zero RNA transcript input (first entry
in each table) was used as the background ("bkgd") measurement and
was subtracted from the results of experiments containing (a)
10.sup.2, 10.sup.3, 10.sup.4, 10.sup.5, 10.sup.6 and 10.sup.7
copies RNA transcripts input for AE-labeled probe of SEQ ID NO:7,
(b) 10.sup.5, 10.sup.6, 10.sup.7, 10.sup.8, 10.sup.9 and 10.sup.10
copies RNA transcripts input for AE-labeled probe of SEQ ID NO:8,
or (c) 10.sup.2, 10.sup.3, 10.sup.4, 10.sup.5, 10.sup.6, 10.sup.7,
10.sup.8, 10.sup.9 and 10.sup.10 copies RNA transcripts input for
both probes (Tables 4 and 5, FIGS. 5 and 6).
[0155] FIG. 5 demonstrates that low wavelength RLU (captured by
filtered PMT1) response from AE-labeled probe of SEQ ID NO:7
corresponds linearly from at least about 10.sup.6 to 10.sup.7
copies per reaction of RNA transcript input and that this response
is very similar when the probe was used alone or in concert with
AE-labeled probe of SEQ ID NO:8.
[0156] FIG. 6 demonstrates that high wavelength RLU (captured by
filtered PMT2) response from AE-labeled probe of SEQ ID NO:8
corresponds linearly from at least about 10.sup.7 to 10.sup.9
copies per reaction of RNA transcript input and that this response
is very similar whether the probe was used alone or in concert with
AE-labeled probe of SEQ ID NO:7.
[0157] FIG. 7 demonstrates that when each reaction is
simultaneously treated with both probes, chemiluminescent data
acquired from single tubes was separated into low and high
wavelength emissions by filtered PMT1 and filtered PMT2. FIG. 7
clearly demonstrates that RLU from these two sets of emissions in
single tubes allows linear quantitative detection of amplicons from
about 10.sup.6 to 10.sup.10 copies per reaction of RNA transcript
input.
Example 3: Quantitative Detection of Amplicons with AE-HICS Probes
Over a Dynamic Range in the Same Reaction Chamber
[0158] This example demonstrates an embodiment that provides
quantitative detection of amplicons over a dynamic range from
10.sup.4 to 10.sup.10 copies of target input in the same reaction
chamber.
[0159] At the completion of TMA reactions, 100 .mu.L, volumes of
Hybridization Reagent were added and mixed. Separation Reagent (50
.mu.L) was added, and the resulting mixtures were incubated at
60.degree. C. for 10 minutes and at room temperature for 10
minutes. The tubes containing the above solutions were placed on a
magnetic separation rack at room temperature for 5 minutes, the
liquid phase was removed, 100 .mu.L, of probes in Hybridization
Reagent were added, mixed and incubated at 60.degree. C. for 15
minutes and at room temperature for 5 minutes. The same probes,
combinations of probes, and concentrations were used as in Example
2.
[0160] At the completion of the hybridization reactions, the tubes
containing the above solutions were placed on a magnetic separation
rack at room temperature for 5 minutes and the liquid phase was
removed. Next, 100 .mu.L, of Hybridization Reagent was added,
mixed, placed on a magnetic separation rack at room temperature for
5 minutes and the liquid phase was removed. Finally, 100 .mu.L,
volumes of Read Reagent were added and mixed.
[0161] Chemiluminescence from these reactions was acquired as in
Example 2. The chemiluminescent output in RLUs from these intervals
is reported in Tables 6 and 7. The last column in each table
reflects the sum of the individual results.
TABLE-US-00016 TABLE 6 10 nM AE-labeled probe of SEQ ID NO: 7 10 nM
AE-labeled probe 100 nM AE-labeled probe 100 nM AE-labeled probe
PMT1 of SEQ ID NO: 7 of SEQ ID NO: 8 of SEQ ID NO: 8 copies input
rep RLU RLU - bkgd RLU RLU - bkgd RLU RLU - bkgd 0 1 241 2,186
2,083 0 2 274 2,205 2,044 10.sup.2 1 265 8 2,005 -59 10.sup.2 2 285
28 2,108 45 10.sup.3 1 282 25 2,091 28 10.sup.3 2 308 51 2,075 12
10.sup.4 1 345 88 2,289 226 10.sup.4 2 350 93 2,042 -22 10.sup.5 1
949 692 2,103 -93 2,600 537 10.sup.5 2 877 620 2,027 -169 2,594 531
10.sup.6 1 2,481 2,224 2,138 -58 4,386 2,323 10.sup.6 2 2,685 2,428
2,066 -130 4,514 2,451 10.sup.7 1 6,093 5,836 2,458 263 8,162 6,099
10.sup.7 2 6,044 5,787 2,347 152 7,431 5,368 10.sup.8 1 3,570 1,375
12,833 10,770 10.sup.8 2 3,188 993 13,244 11,181 10.sup.9 1 7,238
5,043 22,468 20,405 10.sup.9 2 6,904 4,709 21,679 19,616 10.sup.10
1 18,439 16,244 35,697 33,634 10.sup.10 2 18,364 16,169 37,785
35,722
TABLE-US-00017 TABLE 7 10 nM AE-labeled probe of SEQ ID NO: 7 10 nM
AE-labeled probe 100 nM AE-labeled probe 100 nM AE-labeled probe
PMT2 of SEQ ID NO: 7 of SEQ ID NO: 8 of SEQ ID NO: 8 copies input
rep RLU RLU - bkgd RLU RLU - bkgd RLU RLU - bkgd 0 1 408 49,859
47,502 0 2 443 49,554 44,108 10.sup.2 1 465 40 44,440 -1365
10.sup.2 2 456 31 45,037 -768 10.sup.3 1 471 46 44,644 -1161
10.sup.3 2 458 33 45,240 -565 10.sup.4 1 492 67 48,723 2,918
10.sup.4 2 509 84 41,912 -3893 10.sup.5 1 479 54 50,653 947 49,501
3,696 10.sup.5 2 527 102 48,818 -889 44,034 -1771 10.sup.6 1 551
126 50,255 549 51,810 6,005 10.sup.6 2 566 141 48,679 -1028 51,876
6,071 10.sup.7 1 645 220 64,907 15,201 67,800 21,995 10.sup.7 2 673
248 59,778 10,072 61,545 15,740 10.sup.8 1 143,945 94,239 114,205
68,400 10.sup.8 2 113,554 63,848 127,507 81,702 10.sup.9 1 393,948
344,242 383,192 337,387 10.sup.9 2 351,286 301,580 376,625 330,820
10.sup.10 1 1,029,786 980,080 997,605 951,800 10.sup.10 2 1,034,798
985,092 1,011,646 965,841
[0162] The mean RLU from the zero RNA transcript input (first entry
in each table) was used as the background ("bkgd") measurement and
was subtracted from the results of experiments containing (a)
10.sup.2, 10.sup.3, 10.sup.4, 10.sup.5, 10.sup.6, and 10.sup.7
copies RNA transcripts input for AE-labeled probe of SEQ ID NO:7,
(b) 10.sup.5, 10.sup.6, 10.sup.7, 10.sup.8, 10.sup.9 and 10.sup.10
copies RNA transcripts for AE-labeled probe of SEQ ID NO:8, or (c)
10.sup.2, 10.sup.3, 10.sup.4, 10.sup.5, 10.sup.6, 10.sup.7,
10.sup.8, 10.sup.9 and 10.sup.10 copies RNA transcripts for both
probes (Tables 6 and 7, FIGS. 8 and 9).
[0163] FIG. 8 demonstrates that low wavelength RLU (captured by
filtered PMT1) response from AE-labeled probe of SEQ ID NO:7
corresponds linearly from at least about 10.sup.4 to 10.sup.6
copies per reaction of RNA transcript input and that this response
is similar whether the probe is used alone or in concert with
AE-labeled probe of SEQ ID NO:8.
[0164] FIG. 9 demonstrates that high wavelength RLU (captured by
filtered PMT2) response from AE-labeled probe of SEQ ID NO:8)
corresponds linearly from at least about 10.sup.7 to 10.sup.10
copies per reaction of RNA transcript input and that this response
is very similar whether the probe is used alone or in concert with
AE-labeled probe of SEQ ID NO:7.
[0165] FIG. 10 demonstrates that when each reaction is
simultaneously treated with both probes, chemiluminescent data
acquired from single tubes was separated into low and high
wavelength emissions by filtered PMT1 and filtered PMT2. FIG. 10
clearly demonstrates that RLU from these two sets of emissions in
single tubes allows linear quantitative detection of amplicons from
at least about 10.sup.4 to 10.sup.10 copies per reaction of RNA
transcript input.
Example 4: Quantitative Detection of Amplicons with AE-Fluorophore
Probes Over a Dynamic Range in the Same Reaction Chamber
[0166] This example describes steps for detection of amplified
products over a broad dynamic range of input target nucleic acids
in the same reaction chamber.
[0167] TMA reactions are performed as described in the
"Amplification Methods" section above. Hybridization workup and
probe selection is performed as in Examples 2 or 3. The probes are
present in total concentrations similar to those in the previous
examples, i.e., sufficient to span the ranges of the amplicons
synthesized and the detection apparatus. One of the probes has a
standard type of AE attached to an oligonucleotide, as in Example
1. The other probe has a conjugate of an AE linked to a
fluorophore, similar to AE conjugates with rhodamine and Texas Red
described in U.S. Pat. No. 6,165,800 (emission spectra in FIGS. 1B
and 1C), with the AE-fluorophore moiety attached to an
oligonucleotide.
[0168] The luminescent probes are distinguishable from one another
by different wavelength ranges of electromagnetic radiation emitted
by each probe after initiation by addition and mixing of
appropriate chemicals similar to those described in the previous
examples, especially Example 1. Output emissions from a single
detection vessel containing both the longer and shorter amplicons
are simultaneously collected and separated into their respective
wavelength ranges with, for example, a multiple wavelength
luminometer like the one described in Example 2. The output from
the first wavelength range corresponds to the first probe
hybridized to both amplicons; the output from the second wavelength
range corresponds to the second probe hybridized only to one of the
amplicons. Alternately, the output from the second wavelength range
corresponds to the first probe hybridized to both amplicons; the
output from the first wavelength range corresponds to the second
probe hybridized only to one of the amplicons. Unhybridized probes
yield low emissions due to designs in the previous examples,
especially due to treatment with Alkaline Reagent as in Example
1.
[0169] The mean RLU from the zero RNA transcript input (background
or bkgd) is subtracted from the results of experiments containing
10.sup.2, 10.sup.3, 10.sup.4, 10.sup.5, 10.sup.6, 10.sup.7,
10.sup.8 and 10.sup.9 copies RNA transcripts input.
Background-subtracted chemiluminescence from the first probe
demonstrates a linear increase in RLU from about 10.sup.2 to about
10.sup.6 copies per reaction of RNA transcript input;
background-subtracted chemiluminescence from the second probe
demonstrates a linear increase in RLU from about 10.sup.5 to about
10.sup.9 copies per reaction of RNA transcript input. Alternately,
background-subtracted chemiluminescence from the second probe
demonstrates a linear increase in RLU from about 10.sup.2 to about
10.sup.6 copies per reaction of RNA transcript input;
background-subtracted chemiluminescence from the first probe
demonstrates a linear increase in RLU from about 10.sup.5 to about
10.sup.9 copies per reaction of RNA transcript input. The slopes of
responses from the two sets of probes are co-linear. Linear output
responses from these two probes overlap. However, taken together,
the output from these two probes demonstrates quantitative
detection of amplicons from about 10.sup.2 to about 10.sup.9 copies
per reaction of RNA transcript input.
Example 5: Quantitative Detection of Amplicons with AE-HICS Probes
Over a Dynamic Range in the Same Reaction Chamber
[0170] This example demonstrates methods that show quantitative
detection of amplified nucleic acid sequences resulting from target
nucleic acids over a dynamic range from about 10.sup.7 to 10.sup.9
copies of input target nucleic acid in the same reaction
chamber.
[0171] At the completion of TMA reactions, samples were processed
using methods substantially similar to those described in Examples
2 and 3. The probes used were (a) 10 nM self-quenching AE-labeled
probe of SEQ ID NO:7, (b) 100 nM self-quenching, wavelength-shifted
AE-labeled probe of SEQ ID NO:8, or (c) both probes at the
concentrations indicated for individual probes in (a) and (b). The
relative placement of the probes on the distinguishable amplicons
is shown diagrammatically in FIG. 4. The AE-labeled probe of SEQ ID
NO:7 is able to detect both amplicons, whereas the AE-labeled probe
of SEQ ID NO:8 is only able to detect one of the amplicons.
[0172] Chemiluminescence from these reactions was acquired as in
Examples 2 and 3 except the probes were pretreated and then the
detection reactions were initiated by addition of 200 .mu.L of
Detection Reagent 5 instead of Detection Reagent 3 followed by
addition of 200 .mu.L Detection Reagent 4. The chemiluminescent
output in RLUs from these intervals is reported in Tables 8 and 9.
The last column in each table reflects the sum of the individual
probe outputs.
TABLE-US-00018 TABLE 8 10 nM AE-labeled probe of SEQ ID NO: 7 10 nM
AE-labeled probe 100 nM AE-labeled probe 100 nM AE-labeled probe
PMT1 of SEQ ID NO: 7 of SEQ ID NO: 8 of SEQ ID NO: 8 copies input
rep RLU RLU - bkgd RLU RLU - bkgd RLU RLU - bkgd 0 1 14,562 26,106
36,423 0 2 14,438 24,472 36,827 0 3 14,082 26,331 36,803 10.sup.2 1
14,794 433 25,179 -457 35,358 -1326 10.sup.2 2 14,929 568 27,807
2,171 37,238 554 10.sup.2 3 14,862 501 27,130 1,494 37,488 804
10.sup.3 1 15,678 1,317 25,340 -296 39,793 3,109 10.sup.3 2 21,002
6,641 27,005 1,369 38,311 1,627 10.sup.3 3 16,434 2,073 26,027 391
38,101 1,417 10.sup.4 1 24,766 10,405 25,362 -274 51,125 14,441
10.sup.4 2 23,483 9,122 25,919 283 47,760 11,076 10.sup.4 3 26,572
12,211 25,078 -558 54,378 17,694 10.sup.5 1 72,559 58,198 26,854
1,218 121,786 85,102 10.sup.5 2 78,041 63,680 25,406 -230 106,645
69,961 10.sup.5 3 95,444 81,083 23,635 -2001 115,123 78,439
10.sup.6 1 186,102 171,741 25,108 -528 203,978 167,294 10.sup.6 2
191,297 176,936 26,075 439 271,260 234,576 10.sup.6 3 199,336
184,975 24,664 -972 255,668 218,984 10.sup.7 1 588,202 573,841
27,084 1,448 586,704 550,020 10.sup.7 2 413,767 399,406 26,679
1,043 602,568 565,884 10.sup.7 3 450,198 435,837 28,763 3,127
526,836 490,152 10.sup.8 1 723,259 708,898 37,317 11,681 961,790
925,106 10.sup.8 2 723,269 708,908 39,453 13,817 944,710 908,026
10.sup.8 3 763,899 749,538 37,161 11,525 984,831 948,147 10.sup.9 1
1,034,534 1,020,173 55,336 29,700 1,100,567 1,063,883 10.sup.9 2
994,327 979,966 54,090 28,454 1,136,950 1,100,266 10.sup.9 3
1,076,328 1,061,967 52,833 27,197 1,130,972 1,094,288 10.sup.10 1
1,110,316 1,095,955 60,085 34,449 1,106,720 1,070,036 10.sup.10 2
1,080,085 1,065,724 59,140 33,504 1,149,267 1,112,583 10.sup.10 3
1,136,136 1,121,775 56,674 31,038 1,112,549 1,075,865
TABLE-US-00019 TABLE 9 10 nM AE-labeled probe of SEQ ID NO: 7 10 nM
AE-labeled probe 100 nM AE-labeled probe 100 nM AE-labeled probe
PMT2 of SEQ ID NO: 7 of SEQ ID NO: 8 of SEQ ID NO: 8 copies input
rep RLU RLU - bkgd RLU RLU - bkgd RLU RLU - bkgd 0 1 2,952 236,010
208,897 0 2 2,913 232,904 221,790 0 3 3,112 227,080 233,341
10.sup.2 1 3,013 21 196,451 -35547 206,041 -15302 10.sup.2 2 3,063
71 315,433 83,435 203,440 -17903 10.sup.2 3 3,159 167 223,865 -8133
194,955 -26388 10.sup.3 1 3,126 134 200,219 -31779 238,950 17,607
10.sup.3 2 3,231 239 218,126 -13872 201,506 -19837 10.sup.3 3 3,165
173 216,653 -15345 210,847 -10496 10.sup.4 1 3,335 343 242,834
10,836 254,037 32,694 10.sup.4 2 3,388 396 230,274 -1724 189,268
-32075 10.sup.4 3 3,507 515 231,765 -233 299,412 78,069 10.sup.5 1
4,250 1,258 262,302 30,304 199,632 -21711 10.sup.5 2 4,139 1,147
262,013 30,015 211,301 -10042 10.sup.5 3 4,527 1,535 203,150 -28848
220,057 -1286 10.sup.6 1 5,777 2,785 250,081 18,083 224,196 2,853
10.sup.6 2 5,973 2,981 257,312 25,314 229,233 7,890 10.sup.6 3
6,076 3,084 246,642 14,644 227,106 5,763 10.sup.7 1 12,273 9,281
453,599 221,601 461,451 240,108 10.sup.7 2 9,704 6,712 373,223
141,225 646,791 425,448 10.sup.7 3 10,029 7,037 521,274 289,276
332,741 111,398 10.sup.8 1 14,422 11,430 1,326,590 1,094,592
1,280,870 1,059,527 10.sup.8 2 14,559 11,567 1,466,518 1,234,520
1,238,109 1,016,766 10.sup.8 3 15,583 12,591 1,368,674 1,136,676
1,283,745 1,062,402 10.sup.9 1 19,047 16,055 4,248,797 4,016,799
4,424,877 4,203,534 10.sup.9 2 19,191 16,199 4,357,020 4,125,022
4,280,862 4,059,519 10.sup.9 3 20,178 17,186 4,228,440 3,996,442
3,605,149 3,383,806 10.sup.10 1 20,793 17,801 6,357,492 6,125,494
6,096,242 5,874,899 10.sup.10 2 21,125 18,133 6,265,950 6,033,952
6,208,776 5,987,433 10.sup.10 3 20,856 17,864 6,316,084 6,084,086
5,881,110 5,659,767
[0173] The mean RLU from the zero RNA transcript input (first entry
in each table) was used as the background ("bkgd") measurement and
was subtracted from the results of experiments containing 10.sup.2,
10.sup.3, 10.sup.4, 10.sup.5, 10.sup.6, 10.sup.7, 10.sup.8,
10.sup.9 and 10.sup.10 copies RNA transcripts input for AE-labeled
probes of SEQ ID NO:7, SEQ ID NO:8, or both probes (Tables 8 and 9,
FIGS. 11 and 12).
[0174] FIG. 11 demonstrates that low wavelength RLU (captured by
filtered PMT1) response from AE-labeled probe of SEQ ID NO:7
corresponds linearly from at least about 10.sup.2 to 10.sup.7
copies per reaction of RNA transcript input and that this response
is similar whether the probe is used alone or in concert with
AE-labeled probe of SEQ ID NO:8.
[0175] FIG. 12 demonstrates that high wavelength RLU (captured by
filtered PMT2) response from AE-labeled probe of SEQ ID NO:8
corresponds linearly from at least about 10.sup.7 to 10.sup.9
copies per reaction of RNA transcript input and that this response
is very similar whether the probe is used alone or in concert with
AE-labeled probe of SEQ ID NO:7.
[0176] FIG. 13 demonstrates that when each reaction is
simultaneously treated with both probes, chemiluminescent data
acquired from single tubes was separated into low and high
wavelength emissions by filtered PMT1 and filtered PMT2. FIG. 13
clearly demonstrates that RLU from these two sets of emissions in
single tubes allows linear quantitative detection of amplicons from
about 10.sup.2 to 10.sup.9 copies per reaction of RNA transcript
input.
Example 6: Detection of Distinguishable Amplicons Made Using
Modified and Unmodified Primers
[0177] This example demonstrates quantitative detection of
amplicons from over a range of 10.sup.3 to 10.sup.9 copies of
target nucleic acid in the same reaction tubes. The amplification
oligonucleotides are a first promoter provider and a second
promoter provider wherein the two promoter providers comprise
substantially identical nucleotide sequences except that at least
one of the two promoter providers is modified so to produce a
distinguishable amplicon relative to that produced by the other
promoter provider. The first and the second promoter providers are
also present in the TMA reaction in different concentrations so as
to generate a differentiable ratio of their respective
amplicons.
[0178] Using the illustrative amplification system described above,
the first promoter provider is SEQ ID NO:1 and the second promoter
provider is substantially identical to SEQ ID NO:1 except that the
target hybridizing sequence contains a modified nucleobase. The
first promoter provider is present in the amplification reaction at
a concentration that is 1000 times in excess as the concentration
for the second promoter provider. In addition, SEQ ID NO:2 is used
as the amplification oligonucleotide member in conjunction with
both the first and the second promoter providers. Isothermal
amplification is performed.
[0179] At the completion of the TMA amplification reactions, 100
.mu.L, volumes of probes in Hybridization Reagent is added to the
amplification reaction mixtures, which are mixed and incubated at
60.degree. C. for 15 minutes, which will allow hybridization of
probes specific for complementary sequences in the synthesized
amplicons. The probes are: (a) an AE-labeled probe that hybridizes
to the amplicon produced using the first promoter provider but not
the amplicon produced using the second promoter provider; and (b)
AE-labeled probe that hybridizes to the amplicon produced using the
second promoter provider but not the amplicon produced using the
first promoter provider. These AE-labeled probes hybridize their
respective amplicons at a position that includes the
distinguishable position represented by the modification present in
the second promoter provider but not the first promoter
provider.
[0180] Chemiluminescence from these reactions is acquired
essentially as in Example 5. Reactions can be initiated by addition
of 200 .mu.L, Detection Reagent 5 instead of Detection Reagent
3.
Example 7: Detection of Distinguishable Products Made Using
Promoter-Based Amplification Oligomers with 5' Unpaired Base(s)
Provided Between the 3' End of their Promoter Sequences Ans the 5'
End of their Target Hybridizing Sequences
[0181] This example demonstrates quantitative detection of
amplicons over a range of 10.sup.3 to 10.sup.9 copies of target
nucleic acid in the same reaction tubes. The amplification
oligonucleotides are a first promoter amplification oligonucleotide
and a second promoter oligonucleotide, wherein the two promoter
amplification oligonucleotides comprise substantially identical
nucleotide sequences except that each of the two promoter
amplification oligonucleotides comprise between the 5' end of their
target hybridizing sequences and the 3' end of their promoter
sequences, at least one separately unique unpaired base so to
produce a distinguishable amplicon relative to that produced by the
other promoter amplification oligonucleotide. The first and the
second promoter oligonucleotides are also present in the TMA
reaction in different concentrations so as to generate a
differentiable ratio of their respective amplicons.
[0182] Using the illustrative amplification system described above,
the first promoter oligonucleotide is SEQ ID NO:1 further
comprising a 5' unpaired base (5'-AATTTAATACGACTCACTATAGGGAGA(X)
GTTTGTATGTCTGTTGCTATTAT-3' (5' unpaired base X version of SEQ ID
NO:1, wherein X represents one or more unpaired bases)) and the
second promoter oligonucleotide is also SEQ ID NO:1 further
comprising a 5' unpaired base that is distinguishable from that
present on the first promoter oligonucleotide
(5'-AATTTAATACGACTCACTATAGGGAGA(Y)GTTTGTATGTCTGTTGCTATTAT-3' (5'
unpaired base Y version of SEQ ID NO:1, wherein Y represents one or
more unpaired bases and wherein the contiguous nucleotide sequence
Y is not the same as the contiguous nucleotide sequence X)). The
first promoter oligonucleotide is present in the amplification
reaction at a concentration that is 1000 times in excess as the
concentration for the second promoter oligonucleotide. In addition,
SEQ ID NO:2 is used as the amplification oligonucleotide member in
conjunction with both the first and the second promoter
oligonucleotides. Isothermal amplification is performed.
[0183] At the completion of the TMA amplification reactions, 100
.mu.L volumes of probes in Hybridization Reagent are added to the
amplification reaction mixtures, which are mixed and incubated at
60.degree. C. for 15 minutes to allow hybridization of probes
specific for complementary sequences in the synthesized amplicons.
The probes are: (a) an AE-labeled probe that hybridizes to the
amplicon produced using the first promoter oligonucleotide but not
the amplicon produced using the second promoter oligonucleotide;
and (b) AE-labeled probe that hybridizes to the amplicon produced
using the second promoter oligonucleotide but not the amplicon
produced using the first promoter oligonucleotide. These AE-labeled
probes hybridize their respective amplicons at a position that
includes the distinguishable position represented by the
modification present in the second promoter oligonucleotide but not
the first promoter oligonucleotide.
[0184] Chemiluminescence from these reactions is acquired
essentially as in Example 5.
Example 8: Detection of Distinguishable Products Made Using
Amplification Oligonucleotides with 5' Unpaired Bases
[0185] This example demonstrates quantitative detection of
amplicons over a range of 10.sup.3 to 10.sup.9 copies of target
nucleic acid in the same reaction tubes. The amplification
oligonucleotides are a first amplification oligonucleotide and a
second oligonucleotide wherein the two amplification
oligonucleotides comprise substantially identical nucleotide
sequences except that each of the two amplification
oligonucleotides comprise a separately unique 5' unpaired base so
to produce a distinguishable amplicon relative to that produced by
the other amplification oligonucleotide. The first and the second
amplification oligonucleotides are also present in the TMA reaction
in different concentrations so as to generate a differentiable
ratio of their respective amplicons.
[0186] Using the illustrative amplification system described above,
the first amplification oligonucleotide is SEQ ID NO:2 further
comprising a 5' unpaired base (5'-(X)ACAGCAGTACAAATGGCAG-3' (5'
unpaired base X version of SEQ ID NO:2, wherein X represents one or
more unpaired bases)) and the second amplification oligonucleotide
is also SEQ ID NO:2 further comprising a 5' unpaired base that is
distinguishable from that present on the first promoter
oligonucleotide (5'-(Y)ACAGCAGTACAAATGGCAG-3' (5' unpaired base Y
version of SEQ ID NO:2, wherein Y represents one or more unpaired
bases and wherein the contiguous nucleotide sequence Y is not the
same as the contiguous nucleotide sequence X)). In this example, X
is a contiguous nucleic acid sequence that is 5 nucleobases in
length and Y is a contiguous nucleic acid sequence that is 5
nucleobases in length, wherein the contiguous nucleic acid
sequences of X and Y are dissimilar thus allowing for separately
detecting and distinguishing each subsequent amplicon species. The
first amplification oligonucleotide is present in the amplification
reaction at a concentration that is 1000 times in excess as the
concentration for the second amplification oligonucleotide. In
addition, SEQ ID NO:1 is used as the promoter amplification
oligonucleotide member in conjunction with both the first and the
second amplification oligonucleotides. Isothermal amplification is
performed.
[0187] At the completion of the TMA amplification reactions, 100
.mu.L volumes of probes in Hybridization Reagent are added to the
amplification reaction mixtures, which are mixed and incubated at
60.degree. C. for 15 minutes, which allows hybridization of probes
specific for complementary sequences in the synthesized amplicons.
The probes are: (a) an AE-labeled probe that hybridizes to the
amplicon produced using the first amplification oligonucleotide but
not the amplicon produced using the second amplification
oligonucleotide; and (b) AE-labeled probe that hybridizes to the
amplicon produced using the second amplification oligonucleotide
but not the amplicon produced using the first amplification
oligonucleotide. These AE-labeled probes hybridize their respective
amplicons at a position that includes the distinguishable position
represented by the modification present in the second promoter
amplification oligonucleotide but not the first promoter
amplification oligonucleotide.
[0188] Chemiluminescence from these reactions is acquired
essentially as in Example 5.
Example 9: Detection of Distinguishable Products Made Using
Promoter Amplification Oligonucleotides with Different Promoter
Sequences
[0189] This example demonstrates quantitative detection of
amplicons over a range of 10.sup.3 to 10.sup.9 copies of target
nucleic acid in the same reaction tubes. The amplification
oligonucleotides are a first promoter-based amplification
oligonucleotide and a second promoter-based amplification
oligonucleotide wherein the two promoter-based amplification
oligonucleotides comprise substantially identical nucleotide
sequences except that at least one of the two promoter-based
amplification oligonucleotides is modified so to produce a
distinguishable amplicon relative to that produced by the other
promoter-based amplification oligonucleotide (for example, as in
Example 6). The first and the second promoter-based amplification
oligonucleotides are present in the TMA reaction in similar
concentrations. The promoter sequence of the second promoter-based
amplification oligonucleotide is modified relative to the promoter
sequence of the first promoter-based amplification oligonucleotide
so as to generate a differentiable ratio of their respective
amplicons.
[0190] Using the illustrative amplification system described above,
the first promoter-based amplification oligonucleotide is SEQ ID
NO:1 and the second promoter-based amplification oligonucleotide is
substantially identical to SEQ ID NO:1 except that the target
hybridizing sequence contains a modified nucleobase. In addition,
the second promoter-based amplification oligonucleotide contains a
change to its promoter sequence (e.g., a modified nucleobase,
missing nucleobase, extra nucleobase or non-deoxyribonucleotide
nucleobase, e.g., a ribonucleotide nucleobase). The promoter
sequence of the second promoter-based amplification oligonucleotide
is about 1000 times less efficient in synthesizing RNA transcripts
than the unmodified promoter sequence of the first promoter-based
amplification oligonucleotide. In addition, SEQ ID NO:2 is used as
the amplification oligonucleotide member in conjunction with both
the first and the second promoter-based amplification
oligonucleotides. Isothermal amplification is performed.
[0191] At the completion of the TMA amplification reactions, 100
.mu.L volumes of probes in Hybridization Reagent are added to the
amplification reaction mixtures, which are mixed and incubated at
60.degree. C. for 15 minutes, which allows hybridization of probes
specific for complementary sequences in the synthesized amplicons.
The probes are: (a) an AE-labeled probe that hybridizes to the
amplicon produced using the first promoter-based amplification
oligonucleotide but not the amplicon produced using the second
promoter-based amplification oligonucleotide; and (b) AE-labeled
probe that hybridizes to the amplicon produced using the second
promoter-based amplification oligonucleotide but not the amplicon
produced using the first promoter-based amplification
oligonucleotide. These AE-labeled probes hybridize their respective
amplicons at a position that includes the distinguishable position
represented by the modification present in the second
promoter-based amplification oligonucleotide but not the first
promoter-based amplification oligonucleotide.
[0192] Chemiluminescence from these reactions is acquired
essentially as in Example 5.
Example 10: Distinguishable DNA and RNA Products
[0193] This example demonstrates quantitative detection of
amplicons over a range of 10.sup.3 to 10.sup.9 copies of target
nucleic acid in the same reaction tubes. The amplification
oligonucleotides used herein are a single primer and a single
promoter provider. The distinguishable amplification products are
(i) the DNA amplicons made during some of the steps of the TMA
reaction, and (ii) the RNA transcripts made during some of the
steps of the TMA reaction. DNA and RNA are generated in TMA such
that the RNA amplification products are in excess compared to the
DNA amplification products so as to generate a differentiable ratio
of these respective amplicons.
[0194] Using the illustrative amplification system described above,
the amplification oligonucleotide is SEQ ID NO:2, and SEQ ID NO:1
is used as the promoter amplification oligonucleotide member.
Isothermal amplification is performed.
[0195] At the completion of the TMA amplification reactions, 100
.mu.L volumes of probes in Hybridization Reagent are added to the
amplification reaction mixtures, which are mixed and incubated at
60.degree. C. for 15 minutes, which allows hybridization of probes
specific for complementary sequences in the synthesized amplicons.
The probes are: (a) an AE-labeled probe that hybridizes to the DNA
amplicon; and (b) an AE-labeled probe that hybridizes to the RNA
amplicon. The probe hybridizing to the DNA amplicon preferably
hybridizes to the strand that is antisense to the RNA amplicon.
These AE-labeled probes hybridize their respective amplicons at
positions that are distinguishable.
[0196] Chemiluminescence from these reactions is acquired
essentially as in Example 5.
Example 11: Detection of Distinguishable Products Made Using
Distinguishable Nucleotide Triphosphates (NTPs)
[0197] This example demonstrates quantitative detection of
amplicons over a range of 10.sup.3 to 10.sup.9 copies of target
nucleic acid in the same reaction tubes. The amplification
oligonucleotides used herein are a single amplification
oligonucleotide and a single promoter amplification
oligonucleotide. A fifth NTP is included in the amplification
composition. The NTP mix, then, is A, T, G and a ratio of C and
IsoC, wherein the amount of C is greater than the amount of IsoC.
Amplicons species incorporate the C of the IsoC at an unequal ratio
that approximately equals the unequal ratio of C:IsoC provided into
the amplification reaction. Therefore, the probe binding site on
each amplicon species has either a C or an IsoC, which provides
differentiable amplicons species at unequal amounts (e.g., (i) the
RNA amplicon species having A, C, T and G incorporated into the
probe binding site, and (ii) the RNA amplicon species having A,
IsoC, T and G incorporated into the probe binding site).
[0198] Using the illustrative amplification system described above,
the amplification oligonucleotide is SEQ ID NO:2, and SEQ ID NO:1
is used as the promoter amplification oligonucleotide member. The
NTP mix is A, T, G, and C:IsoC in an 1000:1 ratio. Isothermal
amplification is performed.
[0199] At the completion of the TMA amplification reactions, 100
.mu.L volumes of probes in Hybridization Reagent are added to the
amplification reaction mixtures, which are mixed and incubated at
60.degree. C. for 15 minutes, which allows hybridization of probes
specific for complementary sequences in the synthesized amplicons.
The probes are: (a) an AE-labeled probe that is 12-nt in length and
comprises a contiguous nucleotide sequence that is made of the
natural NTPs so that the probe hybridizes and detects the more
abundant amplicon species that incorporate the native C residue
into their primer binding site; and (b) an AE-labeled probe that is
12-nt in length and comprises a contiguous nucleotide sequence that
is made of the natural A, T and C residues and IsoG residues so
that the probe hybridizes and detects the less abundant amplicon
species that incorporate the IsoC residue into their primer binding
site. These AE-labeled probes hybridize their respective amplicons
at positions that are distinguishable.
[0200] Chemiluminescence from these reactions is acquired
essentially as in Example 5.
Example 12: Detection of Distinguishable Products Made Using Two
Pairs of Amplification Oligonucleotides that Synthesize Amplicons
that do not Overlap
[0201] This example demonstrates quantitative detection of
amplicons over a range of 10.sup.3 to 10.sup.9 copies of target
nucleic acid in the same reaction tubes. The amplification
oligonucleotides are a first set comprising a first amplification
oligonucleotide and a first promoter amplification oligonucleotide,
and a second set comprising a second amplification oligonucleotide
and a second promoter amplification oligonucleotide, wherein the
two sets of amplification oligonucleotides comprise substantially
non-overlapping target binding sites such that each of the two sets
of amplification oligonucleotides produce a distinguishable
amplicon relative to that produced by the other amplification
oligonucleotide. The first and the second sets of amplification
oligonucleotides are also present in the TMA reaction in different
concentrations so as to generate a differentiable ratio of their
respective amplicons.
[0202] Using the illustrative amplification system described above,
the first amplification oligonucleotide is SEQ ID NO:2 and the
first promoter amplification oligonucleotide is SEQ ID NO:1, and
the second amplification oligonucleotide is SEQ ID NO:3 and the
second promoter amplification oligomer has a target binding
sequence that is complementary to the target sequence between SEQ
ID NO:2 and SEQ ID NO:3 and that is near the target sequence
complementary to SEQ ID NO:2. The first amplification
oligonucleotide is present in the amplification reaction at a
concentration that is 1000 times in excess as the concentration for
the second amplification oligonucleotide. Isothermal amplification
is performed.
[0203] At the completion of the TMA amplification reactions, 100
.mu.L, volumes of probes in Hybridization Reagent are added to the
amplification reaction mixtures, which are mixed and incubated at
60.degree. C. for 15 minutes, which allows hybridization of probes
specific for complementary sequences in the synthesized amplicons.
The probes are: (a) an AE-labeled probe that hybridizes to the
amplicon produced using the first set of amplification
oligonucleotides but not the amplicon produced using the second set
of amplification oligonucleotides; and (b) AE-labeled probe that
hybridizes to the amplicon produced using the second set of
amplification oligonucleotides but not the amplicon produced using
the first set of amplification oligonucleotides. These AE-labeled
probes hybridize to their respective amplicons at a position that
includes the distinguishable position represented by the unique
sequences synthesized between the first set of amplification
oligonucleotides or between the second set of amplification
oligonucleotides.
[0204] Chemiluminescence from these reactions is acquired
essentially as in Example 5.
TABLE-US-00020 TABLE 10 SEQ ID NO: Sequence (5' to 3') Comment 1
AATTTAATACGACTCACTATAGGGAGAGTTTGTATGTCTGTTGCTATTAT Promoter- primer
2 ACAGCAGTACAAATGGCAG Primer 3 ATTCCCTACAATCCCCAAAGTCAA Primer 4
GGGAGACAAGCUUGCAUGCCUGCAGGUCGACUCUAGAGGAUCCCCGGGUACCAGC in vitro
ACACAAAGGAAUUGGAGGAAAUGAACAAGUAGAUAAAUUAGUCAGUGCUGGAAUC transcript
AGGAAAAUACUAUUUUUAGAUGGAAUAGAUAAGGCCCAAGAUGAACAUGAGAAAU
AUCACAGUAAUUGGAGAGCAAUGGCUAGUGAUUUUAACCUGCCACCUGUAGUAGC
AAAAGAAAUAGUAGCCAGCUGUGAUAAAUGUCAGCUAAAAGGAGAAGCCAUGCAU
GGACAAGUAGACUGUAGUCCAGGAAUAUGGCAACUAGAUUGUACACAUUUAGAAG
GAAAAGUUAUCCUGGUAGCAGUUCAUGUAGCCAGUGGAUAUAUAGAAGCAGAAGU
UAUUCCAGCAGAAACAGGGCAGGAAACAGCAUAUUUUCUUUUAAAAUUAGCAGGA
AGAUGGCCAGUAAAAACAAUACAUACAGACAAUGGCAGCAAUUUCACCAGUGCUA
CGGUUAAGGCCGCCUGUUGGUGGGCGGGAAUCAAGCAGGAAUUUGGAAUUCCCUA
CAAUCCCCAAAGUCAAGGAGUAGUAGAAUCUAUGAAUAAAGAAUUAAAGAAAAUU
AUAGGACAGGUAAGAGAUCAGGCUGAACAUCUUAAGACAGCAGUACAAAUGGCAG
UAUUCAUCCACAAUUUUAAAAGAAAAGGGGGGAUUGGGGGGUACAGUGCAGGGGA
AAGAAUAGUAGACAUAAUAGCAACAGACAUACAAACUAAAGAAUUACAAAAACAA
AUUACAAAAAUUCAAAAUUUUCGGGUUUAUUACAGGGACAGCAGAAAUCCACUUU
GGAAAGGACCAGCAAAGCUCCUCUGGAAAGGUGAAGGGGCAGUAGUAAUACAAGA
UAAUAGUGACAUAAAAGUAGUGCCAAGAAGAAAAGCAAAGAUCAUUAGGGAUUAU
GGAAAACAGAUGGCAGGUGAUGAUUGUGUGGCAAGUAGACAGGAUGAGGAUUAGA
ACAUGGAAAAGUUUAGUAAAACACCA 5 CCACAAUUUUAAAAGAAAAGGG Probe 6
AGAAAAUUAUAGGACAGGUAAG Probe 7 CUCGUCCACAAUUUUAAAAGAAAAGGGACGAG
Probe 8 CCUCUAGAAAAUUAUAGGACAGGUAAGAGAGG Probe 9
GGGAGAGUUUGUAUGUCUGUUGCUAUUAUGUCUACUAUUCUUUCCCCUGCACUGU Amplicon
ACCCCCCAAUCCCCCCUUUUCUUUUAAAAUUGUGGAUGAAUACUGCCAUUUGUAC UGCUGU 10
GGGAGAGUUUGUAUGUCUGUUGCUAUUAUGUCUACUAUUCUUUCCCCUGCACUGU Amplicon
ACCCCCCAAUCCCCCCUUUUCUUUUAAAAUUGUGGAUGAAUACUGCCAUUUGUAC
UGCUGUCUUAAGAUGUUCAGCCUGAUCUCUUACCUGUCCUAUAAUUUUCUUUAAU
UCUUUAUUCAUAGAUUCUACUACUCCUUGACUUUGGGGAUUGUAGGGAAU
[0205] SEQ ID NO:1 is a sequence of a 50-nucleotide
Promoter-primer. It may be comprised of one or more
deoxyribonucleotides. Nucleotides 1-27 are one strand of a T7 RNA
polymerase promoter sequence, and nucleotides 27-50 are
complementary to a region of SEQ ID NO:4. SEQ ID NO:2 is a sequence
of a 19-nucleotide Primer. It may be comprised of one or more
deoxyribonucleotides. Nucleotides 1-19 are complementary to a
complementary sequence of a region of SEQ ID NO:4. SEQ ID NO:3 is a
sequence of a 24-nucleotide Primer. It may be comprised of one or
more deoxyribonucleotides. Nucleotides 1-24 are complementary to a
complementary sequence of a region of SEQ ID NO:4. SEQ ID NO:4 is a
sequence of a 1,016 nucleotide RNA in vitro transcript (IVT).
Nucleotides 1-51 are from an RNA polymerase promoter sequence and a
cloning vector, and nucleotides 52-1,016 are from an HIV-1 genome
that includes a 3' region of the HIV-1 subtype B pol gene.
[0206] SEQ ID NO:5 is a sequence of a 22-nucleotide Probe. It may
be comprised of one or more 2'-O-methyl ribonucleotides.
Nucleotides 1-22 are complementary to regions of SEQ ID NOS:9 and
10. It may have an attached, detectable label. The attached
detectable label may be an acridinium ester. The acridinium ester
may be of a composition to include a fluoro moiety at the ortho
position of the phenyl ring as disclosed in U.S. Pat. No.
5,840,873. The acridinium ester may be attached to a linker such as
those derived from internucleotidyl linker intermediates such as
those described in U.S. Pat. No. 5,585,481. The acridinium ester
may be attached to the linker from the direction of the C9 position
of the acridinium ester substantially as described in U.S. Pat. No.
5,185,439. The linker may be inserted between two nucleotides of
SEQ ID NO:5. The linker may be inserted between nucleotides 10 and
11 of SEQ ID NO:5. SEQ ID NO:6 is a sequence of a 22-nucleotide
Probe. It may be comprised of one or more 2'-O-methyl
ribonucleotides. Nucleotides 1-22 are complementary to a region of
SEQ ID NO:10. It may have an attached, detectable label. The
attached detectable label may be an acridinium ester. The
acridinium ester may be of a composition to include a methyl moiety
at the 2 position of the acridinium ring system as disclosed in
U.S. Pat. No. 5,840,873. The acridinium ester may be attached to a
linker such as those derived from internucleotidyl linker
intermediates such as those described in U.S. Pat. No. 5,585,481.
The acridinium ester may be attached to the linker from the
direction of the C9 position of the acridinium ester substantially
as described in U.S. Pat. No. 5,185,439. The linker may be inserted
between two nucleotides of SEQ ID NO:6. The linker may be inserted
between nucleotides 8 and 9 of SEQ ID NO:6. SEQ ID NO:7 is a
sequence of a 32-nucleotide Probe. It may be comprised of one or
more 2'-O-methyl ribonucleotides. Nucleotides 5-27 are
complementary to regions of SEQ ID NOS:9 and 10, and nucleotides
1-7 and 26-32 are complementary to each other. It may have an
attached, detectable label. The attached detectable label may be an
acridinium ester. The acridinium ester may be of a composition as
disclosed in US Published Patent Appl. No. US 2007-0166759 A1. The
acridinium ester may be attached to a linker such as those derived
from internucleotidyl linker intermediates such as those described
in U.S. Pat. No. 5,585,481 or from terminal linker intermediates
such as 5'-Amino-Modifier C6 (part number 10-1906-90) or
3'-Amino-Modifier C7 CPG (part number 20-2958-01) from Glen
Research Corporation, Sterling, Va. The acridinium ester may be
attached to the linker from the direction of the N10 position of
the acridinium ester substantially as described in US Published
Patent Appl. No. US 2007-0166759 A1. The linker may be inserted
between two nucleotides or at one of the termini of SEQ ID NO:7.
The linker may be at the 5' terminus of SEQ ID NO:7. The probe may
also have an attached quencher moiety that accepts the energy from
the acridinium ester but does not reemit the energy as light. The
quencher may attached through an internucleotidyl or terminal
linker alternate to that used for the acridinium ester, through a
linker on a nucleotide base or as a dedicated phosphoramidite. The
quencher may be from the precursor 3'-BHQ-2 CPG (part number
20-5932-01) or 3'-Dabcyl CPG (part number 20-5912-01) from Glen
Research Corporation, Sterling, Va. The quencher may be at the 3'
terminus of SEQ ID NO:7. SEQ ID NO:8 is a sequence of a 32
nucleotide Probe. It may be comprised of one or more 2'-O-methyl
ribonucleotides. Nucleotides 6-30 are complementary to a region of
SEQ ID NO:10, and nucleotides 1-5 and 28-32 are complementary to
each other. It may have an attached, detectable label. The attached
detectable label may be an acridinium ester. The acridinium ester
may be of a composition as disclosed in US Published Patent Appl.
No. US 2007-0166759 A1. The acridinium ester may be attached to a
linker such as those derived from internucleotidyl linker
intermediates such as those described in U.S. Pat. No. 5,585,481 or
from terminal linker intermediates such as 5'-Amino-Modifier C6
(part number 10-1906-90) or 3'-Amino-Modifier C7 CPG (part number
20-2958-01) from Glen Research Corporation, Sterling, Va. The
acridinium ester may be attached to the linker from the direction
of the N10 position of the acridinium ester substantially as
described in US Published Patent Appl. No. US 2007-0166759 A1. The
linker may be inserted between two nucleotides or at one of the
termini of SEQ ID NO:8. The linker may be at the penultimate
position to the 5' terminus of SEQ ID NO:8. An energy acceptor
moiety capable of accepting energy from the acridinium ester and
reemission of a detectable form of energy (e.g., "light"),
preferably of reemission of a detectable form of energy that can be
distinguished from the light emissions of the acridinium ester
(e.g., light of wavelengths different from those of the acridinium
ester) may be attached to the probe near the acridinium ester. The
just described energy acceptor may be a fluorophore moiety. The
just described energy acceptor may be at the 5' terminus of SEQ ID
NO:8. The just described energy acceptor may attached through an
internucleotidyl or terminal linker alternate to that used for the
acridinium ester, through a linker on a nucleotide base or as a
dedicated phosphoramidite. The fluorophore may be a fluorescein or
tetramethylrhodamine moiety. The probe may also have an attached
quencher moiety that accepts the energy from the acridinium ester
and/or from the energy acceptor attached near the acridinium ester
but does not reemit the energy as light. The quencher may attached
through an internucleotidyl or terminal linker alternate to those
used for the acridinium ester or above described energy acceptor,
through a linker on a nucleotide base or as a dedicated
phosphoramidite. The quencher may be from the precursor 3'-BHQ-2
CPG (part number 20-5932-01) or 3'-Dabcyl CPG (part number
20-5912-01) from Glen Research Corporation, Sterling, Va. The
quencher may be at the 3' terminus of SEQ ID NO:8.
[0207] SEQ ID NO:9 is a sequence of a 116-nucleotide amplicon. It
may be comprised of one or more ribonucleotides. Nucleotides 1-5
are from an RNA polymerase promoter sequence, and nucleotides 6-116
are complementary to a region of SEQ ID NO:4. Probes of SEQ ID NOS:
5 and 7 are at least partially complementary to a region of SEQ ID
NO:9. SEQ ID NO:10 is a sequence of a 215-nucleotide amplicon. It
may be comprised of one or more ribonucleotides. Nucleotides 1-5
are from an RNA polymerase promoter sequence, and nucleotides 6-215
are complementary to a region of SEQ ID NO:4. The sequence of
nucleotides 1-116 is shared with SEQ ID NO:9. Probes of SEQ ID
NOS:5 and 7 are at least partially complementary to a region of SEQ
ID NO:10, and probes of SEQ ID NOS:6 and 8 are at least partially
complementary to a different region of SEQ ID NO:10.
[0208] All publications and patents mentioned in the above
specification are herein incorporated by reference in their
entirety for all purposes whatsoever. Various modifications and
variations of the described method and system of the invention will
be apparent to those skilled in the art without departing from the
scope and spirit of the invention. Although the invention has been
described in connection with specific preferred embodiments, it
should be understood that the invention as claimed should not be
unduly limited to such specific embodiments. Indeed, various
modifications of the described modes for carrying out the invention
that are obvious to those skilled in the relevant fields are
intended to be within the scope of the following claims.
Sequence CWU 1
1
10150DNAArtificial SequenceSynthetic
Oligomerpromoter(1)..(27)Promoter Sequence 1aatttaatac gactcactat
agggagagtt tgtatgtctg ttgctattat 50219DNAArtificial
SequenceSynthetic Oligomer 2acagcagtac aaatggcag 19324DNAArtificial
SequenceSynthetic Oligomer 3attccctaca atccccaaag tcaa
2441016RNAArtificial SequenceSynthetic
Oligomermisc_feature(1)..(51)nucleotides from cloning vector,
including portions of the cloning vector's promoter sequence.
4gggagacaag cuugcaugcc ugcaggucga cucuagagga uccccgggua ccagcacaca
60aaggaauugg aggaaaugaa caaguagaua aauuagucag ugcuggaauc aggaaaauac
120uauuuuuaga uggaauagau aaggcccaag augaacauga gaaauaucac
aguaauugga 180gagcaauggc uagugauuuu aaccugccac cuguaguagc
aaaagaaaua guagccagcu 240gugauaaaug ucagcuaaaa ggagaagcca
ugcauggaca aguagacugu aguccaggaa 300uauggcaacu agauuguaca
cauuuagaag gaaaaguuau ccugguagca guucauguag 360ccaguggaua
uauagaagca gaaguuauuc cagcagaaac agggcaggaa acagcauauu
420uucuuuuaaa auuagcagga agauggccag uaaaaacaau acauacagac
aauggcagca 480auuucaccag ugcuacgguu aaggccgccu guuggugggc
gggaaucaag caggaauuug 540gaauucccua caauccccaa agucaaggag
uaguagaauc uaugaauaaa gaauuaaaga 600aaauuauagg acagguaaga
gaucaggcug aacaucuuaa gacagcagua caaauggcag 660uauucaucca
caauuuuaaa agaaaagggg ggauuggggg guacagugca ggggaaagaa
720uaguagacau aauagcaaca gacauacaaa cuaaagaauu acaaaaacaa
auuacaaaaa 780uucaaaauuu ucggguuuau uacagggaca gcagaaaucc
acuuuggaaa ggaccagcaa 840agcuccucug gaaaggugaa ggggcaguag
uaauacaaga uaauagugac auaaaaguag 900ugccaagaag aaaagcaaag
aucauuaggg auuauggaaa acagauggca ggugaugauu 960guguggcaag
uagacaggau gaggauuaga acauggaaaa guuuaguaaa acacca
1016522RNAArtificial SequenceSynthetic Oligomer 5ccacaauuuu
aaaagaaaag gg 22622RNAArtificial SequenceSynthetic Oligomer
6agaaaauuau aggacaggua ag 22732RNAArtificial SequenceSynthetic
Oligomer 7cucguccaca auuuuaaaag aaaagggacg ag 32832RNAArtificial
SequenceSynthetic Oligomer 8ccucuagaaa auuauaggac agguaagaga gg
329116RNAArtificial SequenceSynthetic Oligomer 9gggagaguuu
guaugucugu ugcuauuaug ucuacuauuc uuuccccugc acuguacccc 60ccaauccccc
cuuuucuuuu aaaauugugg augaauacug ccauuuguac ugcugu
11610215RNAArtificial SequenceSynthetic Oligomer 10gggagaguuu
guaugucugu ugcuauuaug ucuacuauuc uuuccccugc acuguacccc 60ccaauccccc
cuuuucuuuu aaaauugugg augaauacug ccauuuguac ugcugucuua
120agauguucag ccugaucucu uaccuguccu auaauuuucu uuaauucuuu
auucauagau 180ucuacuacuc cuugacuuug gggauuguag ggaau 215
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