Patent ID: 7759062

Claim:
A method for detecting the presence or absence of a target nucleic acid in a sample comprising; a) incubating said sample with a stem oligonucleotide, an upstream oligonucleotide, a downstream probe, and a cleavage agent under conditions such that, if said target nucleic acid is present: i) a 3′ target specific region of said stem oligonucleotide hybridizes to said target nucleic acid, and a stem region of said stem oligonucleotide remains available for hybridization to a portion of said upstream oligonucleotide and said downstream probe, ii) a 5′ target specific region of said upstream oligonucleotide hybridizes to said target nucleic acid, and a stem specific region of said upstream oligonucleotide hybridizes to a portion of said stem region of said stem oligonucleotide, iii) a 3′ region of said downstream probe hybridizes to a portion of said stem region of said stem oligonucleotide, and a 5′ region of said downstream probe does not hybridize to said stem region of said stem oligonucleotide, wherein said downstream probe forms an invasive cleavage structure with said upstream oligonucleotide and said stem region of said stem oligonucleotide, and iv) said cleavage agent cleaves said downstream probe in said invasive cleavage structure thereby generating a 5′ cleaved portion; and b) detecting the presence or absence of said target nucleic acid in said sample.