Patent ID: 6875572

Claim:
A method for detecting the presence of a target nucleic acid molecule by detecting non-target cleavage products, comprising: a) providing: i) a cleavage agent; ii) a source of target nucleic acid, said target nucleic acid comprising a first region and a second region, said second region downstream of and contiguous to said first region; iii) a first oligonucleotide, wherein a first portion of said first oligonucleotide comprises at least one nucleotide analog and wherein said first portion is completely complementary to said first portion of said first target nucleic acid, and; iv) a second oligonucleotide comprising a 3′ portion and a 5′ portion, wherein said 5′ portion is completely complementary to said second region of said target nucleic acid; b) combining said cleavage agent, said target nucleic acid, said first oligonucleotide and said second oligonucleotide under reaction conditions such that at least said first portion of said first oligonucleotide is annealed to said first region of said target nucleic acid, and wherein at least said 5′ portion of said second oligonucleotide is annealed to said second region of said target nucleic acid so as to create a cleavage structure, and wherein cleavage of said cleavage structure occurs and cleaves said first oligonucleotide to generate a non-target cleavage product; and c) detecting the cleavage of said cleavage structure.