High-sensitivity real-time polymerase chain reaction for detection of nucleic acids
First Claim
1. A method of determining an amount of a target nucleic acid in a sample, said method comprising the steps of:
- a) providing said sample;
b) contacting an aliquot of said sample with a solid support, wherein nucleic acid in said aliquot binds to said solid support;
c) eluting said nucleic acid bound to said solid support with at least two sequential volumes of 5-25 μ
l to produce a concentrated nucleic acid sample;
d) contacting said concentrated nucleic acid sample of step (c) with oligonucleotide primers capable of amplifying said target nucleic acid under appropriate conditions, a first probe labeled with a donor fluorophore, and a second probe labeled with an acceptor fluorophore to produce an amplification sample, wherein said first and second probes hybridize proximally to one another on said target nucleic acid, and wherein energy transferred from said donor fluorophore induces fluorescence from said acceptor fluorophore; and
e) performing an amplification on said amplification sample to produce an amplification product, wherein said amplification comprises a series of step-down cycles and a series of fluorescence acquisition cycles, wherein each of said fluorescence acquisition cycles comprises detection of fluorescence from said acceptor fluorophore, wherein the kinetics of an increase in intensity of fluorescence from said acceptor fluorophore are indicative of the amount of said target nucleic acid in said sample.
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Accused Products
Abstract
The invention features methods based on PCR that are capable of detecting single target molecules in a sample input volume of, e.g., 5 μl, and of quantifying organismal, e.g., chlamydial, DNA with high accuracy. Desirably, these methods employ a single tube format coupled with real-time fluorescent detection of amplicons. This approach facilitates the application of quantitative PCR (qPCR) to microbiological diagnosis in clinical settings. The invention also features primers and probes for the detection of Chlamidia. The use of specific hybridization probes with qPCR amplification provides the ability for identification of individual species or strains of microorganisms.
15 Citations
26 Claims
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1. A method of determining an amount of a target nucleic acid in a sample, said method comprising the steps of:
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a) providing said sample;
b) contacting an aliquot of said sample with a solid support, wherein nucleic acid in said aliquot binds to said solid support;
c) eluting said nucleic acid bound to said solid support with at least two sequential volumes of 5-25 μ
l to produce a concentrated nucleic acid sample;
d) contacting said concentrated nucleic acid sample of step (c) with oligonucleotide primers capable of amplifying said target nucleic acid under appropriate conditions, a first probe labeled with a donor fluorophore, and a second probe labeled with an acceptor fluorophore to produce an amplification sample, wherein said first and second probes hybridize proximally to one another on said target nucleic acid, and wherein energy transferred from said donor fluorophore induces fluorescence from said acceptor fluorophore; and
e) performing an amplification on said amplification sample to produce an amplification product, wherein said amplification comprises a series of step-down cycles and a series of fluorescence acquisition cycles, wherein each of said fluorescence acquisition cycles comprises detection of fluorescence from said acceptor fluorophore, wherein the kinetics of an increase in intensity of fluorescence from said acceptor fluorophore are indicative of the amount of said target nucleic acid in said sample. - View Dependent Claims (7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19)
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2. A method of determining an amount of a target nucleic acid in a sample, said method comprising the steps of:
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a) providing said sample;
b) contacting an aliquot of said sample with a solid support, wherein nucleic acid in said aliquot binds to said solid support;
c) eluting said nucleic acid bound to said solid support in step (b) to produce a volume of eluate and reducing said volume by centrifugal ultrafiltration to produce a concentrated nucleic acid sample;
d) contacting said concentrated nucleic acid sample of step (c) with oligonucleotide primers capable of amplifying said target nucleic acid under appropriate conditions, a first probe labeled with a donor fluorophore, and a second probe labeled with an acceptor fluorophore to produce an amplification sample, wherein said first and second probes hybridize proximally to one another on said target nucleic acid, and wherein energy transferred from said donor fluorophore induces fluorescence from said acceptor fluorophore; and
e) performing an amplification on said amplification sample to produce an amplification product, wherein said amplification comprises a series of step-down cycles and a series of fluorescence acquisition cycles, wherein each of said fluorescence acquisition cycles comprises detection of fluorescence from said acceptor fluorophore, wherein the kinetics of an increase intensity of fluorescence from said acceptor fluorophore are indicative of the amount of said target nucleic acid in said sample.
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3. A method of determining an amount of a target nucleic acid in a sample, said method comprising the steps of:
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a) providing a sample;
b) contacting a plurality of aliquots of said sample with a plurality of solid supports, wherein nucleic acid in said plurality of aliquots binds to said plurality of solid supports;
c) eluting said nucleic acid bound to each of said plurality of solid supports in step (b) to produce a plurality of volumes of eluate;
d) combining said volumes of (c) to produce a combined volume;
e) reducing said combined volume by centrifugal ultrafiltration to produce a concentrated nucleic acid sample;
f) contacting said concentrated nucleic acid sample of step (e) with oligonucleotide primers capable of amplifying said target nucleic acid under appropriate conditions, a first probe labeled with a donor fluorophore, and a second probe labeled with an acceptor fluorophore to produce an amplification sample, wherein said first and second probes hybridize proximally to one another on said target nucleic acid, and wherein energy transferred from said donor fluorophore induces fluorescence from said acceptor fluorophore; and
g) performing an amplification on said amplification sample to produce an amplification product, wherein said amplification comprises a series of step-down cycles and a series of fluorescence acquisition cycles, wherein each of said fluorescence acquisition cycles comprises detection of fluorescence from said acceptor fluorophore, wherein the kinetics of an increase in intensity of fluorescence from said acceptor fluorophore are indicative of the amount of said target nucleic acid in said sample.
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4. A method of diagnosing a microbial infection in a mammal, said method comprising the steps of:
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a) providing a sample of a biological material from said mammal;
b) preparing said sample for nucleic acid extraction to produce a nucleic acid sample;
c) contacting an aliquot of said nucleic acid sample with a solid support, wherein nucleic acid in said aliquot binds to said solid support;
d) eluting said nucleic acid from said solid support with at least two sequential volumes of 5-25 μ
l to produce a concentrated nucleic acid sample;
e) contacting said concentrated nucleic acid sample of step (d) with oligonucleotide primers capable of amplifying a target nucleic acid under appropriate conditions, a first probe labeled with a donor fluorophore, and a second probe labeled with an acceptor fluorophore to produce an amplification sample, wherein said first and second probes hybridize proximally to one another on said target nucleic acid, and wherein energy transferred from said donor fluorophore induces fluorescence from said acceptor fluorophore; and
f) performing an amplification on said amplification sample to produce an amplification product, wherein said amplification comprises a series of step-down cycles and a series of fluorescence acquisition cycles, wherein each of said fluorescence acquisition cycles comprises detection of fluorescence from said acceptor fluorophore, wherein fluorescence from said acceptor fluorophore is indicative of a presence of said microbial infection, and an absence of fluorescence from said acceptor fluorophore is indicative of an absence of said microbial infection. - View Dependent Claims (20)
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5. A method of diagnosing a microbial infection in a mammal, said method comprising the steps of:
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a) providing a sample of a biological material from said mammal;
b) preparing said sample for nucleic acid extraction to produce a nucleic acid sample;
c) contacting an aliquot of said nucleic acid sample with a solid support, wherein nucleic acid in said aliquot binds to said solid support;
d) eluting said nucleic acid bound to said solid support in step (b) to produce a volume of eluate and reducing said volume by centrifugal ultrafiltration to produce said concentrated nucleic acid sample;
e) contacting said concentrated nucleic acid sample of step (d) with oligonucleotide primers capable of amplifying a target nucleic acid under appropriate conditions, a first probe labeled with a donor fluorophore, and a second probe labeled with an acceptor fluorophore to produce an amplification sample, wherein said first and second probes hybridize proximally to one another on said target nucleic acid, and wherein energy transferred from said donor fluorophore induces fluorescence from said acceptor fluorophore; and
f) performing an amplification on said amplification sample to produce an amplification product, wherein said amplification comprises a series of step-down cycles and a series of fluorescence acquisition cycles, wherein each of said fluorescence acquisition cycles comprises detection of fluorescence from said acceptor fluorophore, wherein fluorescence from said acceptor fluorophore is indicative of a presence of said microbial infection, and an absence of fluorescence from said acceptor fluorophore is indicative of an absence of said microbial infection.
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6. A method of diagnosing a microbial infection in a mammal, said method comprising the steps of:
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a) providing a sample of a biological material from said mammal;
b) preparing said sample for nucleic acid extraction to produce a nucleic acid sample;
c) contacting a plurality of aliquots of said sample with a plurality of solid supports, wherein nucleic acid in said plurality of aliquots binds to said plurality of solid supports;
d) eluting said nucleic acid bound to each of said plurality of solid supports in step (c) to produce a plurality of volumes of eluate;
e) combining said volumes of (d) to produce a combined volume;
fi) reducing said combined volume by centrifugal ultrafiltration to produce a concentrated nucleic acid sample;
g) contacting said concentrated nucleic acid sample of step (f) with oligonucleotide primers capable of amplifying a target nucleic acid under appropriate conditions, a first probe labeled with a donor fluorophore, and a second probe labeled with an acceptor fluorophore to produce an amplification sample, wherein said first and second probes hybridize proximally to one another on said target nucleic acid, and wherein energy transferred from said donor fluorophore induces fluorescence from said acceptor fluorophore; and
h) performing an amplification on said amplification sample to produce an amplification product, wherein said amplification comprises a series of step-down cycles and a series of fluorescence acquisition cycles, wherein each of said fluorescence acquisition cycles comprises detection of fluorescence from said acceptor fluorophore, wherein fluorescence from said acceptor fluorophore is indicative of a presence of said microbial infection, and an absence of fluorescence from said acceptor fluorophore is indicative of an absence of said microbial infection.
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21. A primer having a nucleic acid sequence consisting of 5′
- -GGGGTTGTAGGGTYGAGRAIAWRRGATC-3′
(SEQ ID NO;
6);
5′
-GAGAGTGGTCTCCCCAGATTCARACTA-3′
(SEQ ID NO;
7);
5′
-TGACTAGGTTGRGCAAGYRTYT-3′
(SEQ ID NO;
13);
or 5′
-AAAGACAIATAYTCTTAAACGTCTATTATTAT-3′
(SEQ ID NO;
14), wherein I is inosine;
K is G or T;
M is C or A;
R is G or A;
W is A or T; and
Y is C or T.
- -GGGGTTGTAGGGTYGAGRAIAWRRGATC-3′
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22. A probe having a nucleic acid sequence consisting of 5′
- -AACGTTKARTTCTTGAACGCGAGGTTT-3′
(SEQ ID NO;
5);
5′
-GRAYGAHACAGGGTGATAGTCCCGTA-3′
(SEQ ID NO;
9);
5′
-ACGAAARAACAARAGACKCTAWTCGAT-3′
(SEQ ID NO;
10);
5′
-ACGAAAAAACAAAAGACGCTAATCGAT-3′
(SEQ ID NO;
11);
5′
-ACGAAAGGAGAKMAAGACYGACCTCAAC-3′
(SEQ ID NO;
12);
or 5′
-CGTAAACTAAATGTTTTGGAAACAA-3′
(SEQ ID NO;
16), wherein H is A or C or T;
I is inosine;
K is G or T;
M is C or A;
R is G or A;
W is A or T; and
Y is C or T. - View Dependent Claims (23, 24)
- -AACGTTKARTTCTTGAACGCGAGGTTT-3′
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25. A probe having a nucleic acid sequence consisting of 5′
- -CCTGAGTAGRRCTAGACACGTGAAAC-3′
(SEQ ID NO;
8) or 5′
-CTTAACAAIRCAAAWGAAATAGAAT-3′
(SEQ ID NO;
15), wherein I is inosine;
R is G or A; and
W is A or T. - View Dependent Claims (26)
- -CCTGAGTAGRRCTAGACACGTGAAAC-3′
Specification