Patent ID: 9051608
Filing Date: 2015-06-09
Classification: C12Q

Abstract:
1. An amplification method of detecting the presence or absence of a target nucleic acid sequence in a sample, comprising the steps of: (a) contacting a sample comprising a target nucleic acid sequence with a set of oligonucleotide primers comprising a 3′ end and a 5′ end, wherein a first primer comprises a sequence complementary to a region in one strand of the target nucleic acid sequence, and a second primer comprises a sequence complementary to a region in a second strand of the target nucleic acid sequence; (b) further contacting the sample with at least one detector oligonucleotide, comprising a 3′ end and a 5′ end, and comprising a sequence complementary to a region of the target nucleic acid between the region of the target sequence complementary to the sequence of the first primer and the region of the target sequence complementary to the sequence of the second primer, which comprises a non-cleavable nucleotide incorporated at its 5′ end and a contiguous nucleotide sequence that is non-complementary to the target nucleic acid sequence linked to the 5′ end of the sequence complementary the target nucleic acid sequence, thereby forming a mixture of duplexes under hybridization conditions, wherein the duplexes comprise the target nucleic acid annealed to the primer oligonucleotides and to the detector oligonucleotide such that the 3′ end of each primer oligonucleotide is upstream of the 5′ end of the detector oligonucleotide annealed to the same nucleic acid strand; (c) exposing the products of step (b) to a template-dependent polymerizing agent having 5′ to 3′ nuclease activity under conditions permissive for amplification, whereby the primer oligonucleotides are extended to produce extension products and the detector oligonucleotide is cleaved and releases a fragment comprising the nucleotide sequence that is non-complementary to the target nucleic acid sequence, thereby producing a mass-distinguishable product; and (d) detecting the presence or absence of the mass-distinguishable by mass spectrometry, thereby detecting the presence or absence of the target sequence in the sample.