Methods of using FET labeled oligonucleotides that include a 3'-5' exonuclease resistant quencher domain and compositions for practicing the same
First Claim
1. A method for detecting the production of a primer extension product in a primer extension reaction mixture, said method comprising:
- (a) producing a primer extension mixture that includes a nucleic acid polymerase, a FET labeled oligonucleotide that includes a 3′
→
5′
exonuclease resistant quencher domain, and at least one of;
(i) a nucleic acid intercalator, and (ii) a minor groove binder;
(b) subjecting said primer extension mixture to primer extension reaction conditions;
(c) detecting a change in a fluorescent signal from said FET labeled oligonucleotide probe to obtain an assay result; and
(d) employing said assay result to determine whether a primer extension product is present in said mixture.
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Abstract
Methods and compositions are provided for detecting a primer extension product in a reaction mixture. In the subject methods, a primer extension reaction is conducted in the presence of a polymerase having 3′→5′ exonuclease activity and at least one FET labeled oligonucleotide probe that includes a 3′→5′ exonuclease resistant quencher domain. Also provided are systems and kits for practicing the subject methods. The subject invention finds use in a variety of different applications, and are particularly suited for use in high fidelity PCR based reactions, including SNP detection applications, allelic variation detection applications, and the like.
53 Citations
54 Claims
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1. A method for detecting the production of a primer extension product in a primer extension reaction mixture, said method comprising:
-
(a) producing a primer extension mixture that includes a nucleic acid polymerase, a FET labeled oligonucleotide that includes a 3′
→
5′
exonuclease resistant quencher domain, and at least one of;
(i) a nucleic acid intercalator, and (ii) a minor groove binder;
(b) subjecting said primer extension mixture to primer extension reaction conditions;
(c) detecting a change in a fluorescent signal from said FET labeled oligonucleotide probe to obtain an assay result; and
(d) employing said assay result to determine whether a primer extension product is present in said mixture. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
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- 29. A FET labeled probe comprising nucleic acid intercalator bonded to a FET labeled oligonucleotide.
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42. A method of monitoring of a PCR amplification reaction, said method comprising:
(a) preparing a PCR amplification reaction mixture by combining;
(i) a template nucleic acid;
(ii) forward and reverse nucleic acid primers;
(iii) deoxyribonucleotides;
(iv) a nucleic acid polymerase;
(v) a FET labeled oligonucleotide that includes;
a 3′
→
5′
exonuclease resistant quencher domain comprising a dark quencher, a fluorescent reporter, domain comprising a fluorophore and a PCR product complementary domain; and
(vi) (vi) at least one of;
(A) a nucleic acid intercalator, and (B) a minor groove binder;
(b) subjecting said PCR amplification reaction mixture to PCR amplification conditions;
(c) monitoring said reaction mixture for a fluorescent signal from said FET labeled oligonucleotide probe to obtain an assay result; and
(d) employing said assay result to monitor said PCR amplification reaction. - View Dependent Claims (44, 45)
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46. A method for screening a nucleic acid sample for the presence of first and second nucleic acids that differ from each other by a single nucleotide, said method comprising:
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(a) producing a primer extension mixture that includes;
(i) said nucleic acid sample;
(ii) a nucleic acid polymerase;
(iii) first and second FET labeled oligonucleotide probes that are complementary to said first and second nucleic acids, respectively, wherein each of said first and second FET labeled oligonucleotides includes a 3′
→
5′
exonuclease resistant quencher domain; and
;
(iv) at least one of;
(A) a nucleic acid intercalator, and (B) a minor groove binder (b) subjecting said primer extension mixture to primer extension reaction conditions;
(c) detecting a change in a fluorescent signal, if any, from said first and second FET labeled oligonucleotide probes to obtain an assay result; and
(d) employing said assay result to determine the presence or absence of said first and second nucleic acids in said sample. - View Dependent Claims (47)
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48. A system for use in detecting the production of a primer extension product in a primer extension reaction mixture, said system comprising:
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(a) a FET labeled oligonucleotide that includes a 3′
→
5′
exonuclease resistant quencher domain;
(b) a nucleic acid polymerase; and
(c) at least one of;
(i) a nucleic acid intercalator; and
(ii) a minor groove binder.
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49. A kit for use in detecting the production of a primer extension product in a primer extension reaction mixture, said kit comprising:
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(a) a FET labeled oligonucleotide that includes a 3′
→
5′
exonuclease resistant quencher domain;
(b) at least one of;
(i) a nucleic acid intercalator; and
(ii) a minor groove binder. - View Dependent Claims (50, 51, 52, 53)
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54. In a method comprising employing fluorescently labeled nucleic acid detector and a polymerase, the improvement comprising:
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employing a FET labeled oligonucleotide that includes a 3′
→
5′
exonuclease resistant quencher domain as said fluorescently labeled nucleic acid detector, and at least one of;
(a) a nucleic acid intercalator; and
(b) a minor groove binder.
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Specification