Use of base-modified deoxynucleoside triphosphates to improve nucleic acid detection
First Claim
1. A method for the detection of a target nucleic acid in a sample, comprising:
- providing a reaction mixture comprising a target nucleic acid, at least one oligonucleotide primer, a DNA polymerase, and a mixture of deoxynucleoside 5′
-triphosphates containing at least one base-modified duplex-stabilizing dNTP;
amplifying the target nucleic acid, wherein the at least one base-modified duplex-stabilizing dNTP incorporates into amplicons providing copies of a modified DNA with enhanced hybridization properties;
providing at least one oligonucleotide probe and hybridizing the at least one oligonucleotide probe to the modified DNA to form a complex; and
detecting the complex, wherein presence of the complex is indicative of the presence of the target nucleic acid in the sample.
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Abstract
Aspects of the invention provide novel and surprisingly effective methods for the detection of nucleic acids, comprising nucleic acid amplification using base-modified deoxynucleoside 5′-triphosphates (dNTPs). Particular aspects relate to methods for enhancing hybridization properties of oligonucleotide primers and probes in assays detecting nucleic acids, comprise amplifying target DNAs in presence of base-modified duplex-stabilizing deoxyribonucleoside 5′-triphosphates to provide for modified target DNAs, and thereby considerably improving performance of the detection assays. The disclosed methods allow for increasing of the reaction temperature in PCR-based detection systems or, alternatively, reducing the length of the oligonucleotide primers and probes. Certain aspects relates to improvement of real time PCR assays, wherein nucleic acids of interest are detected as the reaction proceeds using fluorescent agents or oligonucleotide FRET probes.
42 Citations
57 Claims
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1. A method for the detection of a target nucleic acid in a sample, comprising:
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providing a reaction mixture comprising a target nucleic acid, at least one oligonucleotide primer, a DNA polymerase, and a mixture of deoxynucleoside 5′
-triphosphates containing at least one base-modified duplex-stabilizing dNTP;amplifying the target nucleic acid, wherein the at least one base-modified duplex-stabilizing dNTP incorporates into amplicons providing copies of a modified DNA with enhanced hybridization properties; providing at least one oligonucleotide probe and hybridizing the at least one oligonucleotide probe to the modified DNA to form a complex; and detecting the complex, wherein presence of the complex is indicative of the presence of the target nucleic acid in the sample. - 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, 29, 30, 31, 32, 33, 34, 35, 36)
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37. A method for the detection of a target nucleic acid in a sample, comprising:
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amplifying the target nucleic acid using detection PCR in a reaction mixture comprising; a target nucleic acid, at least two oligonucleotide primers to provide for exponential amplification of the target nucleic acid, a DNA polymerase, and a mixture of deoxynucleoside 5′
-triphosphates containing at least one base-modified duplex-stabilizing dNTP, wherein the at least one base-modified duplex-stabilizing dNTP incorporates into amplicons providing copies of a modified DNA with enhanced hybridization properties; anddetecting said modified DNA using at least one oligonucleotide probe that hybridizes to said modified DNA to form a complex, and detecting the complex, wherein presence of the complex is indicative of the presence of the target nucleic acid in the sample. - View Dependent Claims (38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57)
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Specification