Patent ID: 7195871

Claim:
A method for detecting a target sequence, comprising: a) providing: i) a sample containing synthetic DNA amplified from genomic DNA, said genomic DNA suspected of containing said target sequence, wherein said synthetic DNA comprises a first region and a second region, said second region downstream of and contiguous to said first region; ii) oligonucleotides capable of forming an invasive cleavage structure with said synthetic DNA when said genomic DNA contains said target sequence, wherein said oligonucleotides comprise first and second oligonucleotides, wherein at least a portion of said first oligonucleotide is completely complementary to said first region of said synthetic DNA and wherein said second oligonucleotide comprises a 3′ portion and a 5′ portion, wherein said 5′ portion is completely complementary to said second region of said synthetic DNA; and iii) an agent for cleaving an invasive cleavage structure, wherein said agent is a thermostable FEN nuclease; and b) exposing said sample to said oligonucleotides and said agent under conditions wherein said oligonucleotides form an invasive cleavage structure with said synthetic DNA when said genomic DNA contains said target sequence, wherein said invasive cleavage structure is cleaved by said agent; c) detecting cleavage of an invasive cleavage structure by said agent, thereby detecting the presence of said target sequence.