Multiplex probes
First Claim
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1. A method of detecting a target nucleic acid sequence, comprising:
- a) providingi) a downstream oligonucleotide probe, comprising at least 10 base pairs, having a sequence that is complementary to a first sequence of a target oligonucleotide and that has a cleavable sequence, andii) an upstream oligonucleotide primer, comprising at least 10 base pairs, having a sequence that is complementary to a second sequence of the target oligonucleotide and that has an initial nucleic acid polymerase binding site, andiii) a downstream oligonucleotide primer, wherein the downstream oligonucleotide probe is configured for a polymerase to cleave mononucleotides or small oligonucleotides at its 5′
end, wherein the Tm of the downstream oligonucleotide probe, the Tm of the downstream oligonucleotide primer, and the Tm of the upstream oligonucleotide primer are each within about 15°
C. of the target nucleic acid Tm, and wherein the downstream oligonucleotide primer and the upstream oligonucleotide primer are designed to allow thermal cycling to be conducted within a 15°
C. temperature range;
b) denaturing DNA having the target sequence;
c) hybridizing the upstream oligonucleotide primer and downstream oligonucleotide probe to the target oligonucleotide;
d) binding a polymerase to the initial nucleic acid polymerase binding site;
e) extending the upstream oligonucleotide primer via polymerization with the polymerase toward the downstream oligonucleotide probe;
f) cleaving nucleotides or small oligonucleotides of the downstream oligonucleotide probe; and
g) detecting a signal resulting from said cleaving, wherein thermal cycling is conducted at least in part within said 15°
C. temperature range.
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Abstract
Methods and reagents suitable for conducing polymerase chain reaction are described. In particular, the disclosure provides probes and primers that are suitable in dynamic flux amplification procedures. In aspects, the disclosure provides long oligonucleotide probes and primers, as well as triplex forming probes and primers, which function within the narrow Tm ranges used with dynamic flux amplification. However, embodiments are also provided wherein the probes and primers taught herein can be utilized in standard PCR.
62 Citations
15 Claims
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1. A method of detecting a target nucleic acid sequence, comprising:
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a) providing i) a downstream oligonucleotide probe, comprising at least 10 base pairs, having a sequence that is complementary to a first sequence of a target oligonucleotide and that has a cleavable sequence, and ii) an upstream oligonucleotide primer, comprising at least 10 base pairs, having a sequence that is complementary to a second sequence of the target oligonucleotide and that has an initial nucleic acid polymerase binding site, and iii) a downstream oligonucleotide primer, wherein the downstream oligonucleotide probe is configured for a polymerase to cleave mononucleotides or small oligonucleotides at its 5′
end, wherein the Tm of the downstream oligonucleotide probe, the Tm of the downstream oligonucleotide primer, and the Tm of the upstream oligonucleotide primer are each within about 15°
C. of the target nucleic acid Tm, and wherein the downstream oligonucleotide primer and the upstream oligonucleotide primer are designed to allow thermal cycling to be conducted within a 15°
C. temperature range;b) denaturing DNA having the target sequence; c) hybridizing the upstream oligonucleotide primer and downstream oligonucleotide probe to the target oligonucleotide; d) binding a polymerase to the initial nucleic acid polymerase binding site; e) extending the upstream oligonucleotide primer via polymerization with the polymerase toward the downstream oligonucleotide probe; f) cleaving nucleotides or small oligonucleotides of the downstream oligonucleotide probe; and g) detecting a signal resulting from said cleaving, wherein thermal cycling is conducted at least in part within said 15°
C. temperature range. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
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Specification