Methods of detection of a target nucleic acid sequence

1. A method of generating a signal indicative of the presence of a target nucleic acid in a sample, comprising:

in the same reaction vessel, forming a cleavage structure comprising duplex and single-stranded nucleic acid by incubating a sample comprising a target nucleic acid with a thermostable nucleic acid polymerase substantially lacking 5′ to 3′ exonuclease activity and cleaving said cleavage structure with a thermostable Fen nuclease lacking 5′ to 3′ synthetic activity to generate a signal, wherein generation of said signal is indicative of the presence of a target nucleic acid in said sample.

2. A method of detecting and/or measuring a target nucleic acid in a sample, comprising:

in the same reaction vessel, forming a cleavage structure comprising duplex and single-stranded nucleic acid, wherein said single stranded nucleic acid comprises a 5′ flap, by incubating a sample comprising a target nucleic acid with a thermostable nucleic acid polymerase substantially lacking 5′ to 3′ exonuclease activity and cleaving said cleavage structure with a thermostable Fen nuclease substantially lacking 5′ to 3′ synthetic activity to release a nucleic acid fragment, anti detecting and/or measuring the release of said fragment as an indication of the presence of the target in the sample.

3. The method of claim 1 or 2 , wherein said method comprises, in said reaction vessel, a pair of amplification primers complementary with said target nucleic acid to permit amplification of a sequence of said target nucleic acid between said primers.

4. The method of claim 3 , wherein said method comprises, in said reaction vessel, one or more dNTPs.

5. The method of claim 3 , wherein said method comprises, in said reaction vessel, an oligonucleotide that specifically hybridizes to a region of the target nucleic acid between said amplification primers.

6. The method of claims 1 or 2 , wherein said method comprises, in said reaction vessel, said thermostable Fen nuclease selected from the group consisting of Fen nuclease enzyme of Archaeglobus fulgidus, Methanococcus jannaschii, Pyrococcus furiosus, and Pyrococcus horikoshii.

7. The method of claims 1 or 2 , wherein said method comprises, in said reaction vessel, a thermostable polymerase selected from the group consisting of Pfu, Pfu-exo, Taq, Taq-exo, Deep vent and Deep vent exo.

8. The method of claims 1 or 2 , wherein a cleavage structure is formed prior to the addition of said Fen nuclease, said cleavage structure comprising a 5′ flap, and said Fen nuclease cleaves said 5′ flap of said cleavage structure.

9. The method of claim 8 , wherein said 5′ flap comprises a label comprising a first member of a pair of interactive labels effectively positioned to quench the generation of a detectable signal, the first and second members of said pair being separable by a site susceptible to Fen nuclease cleavage, thereby allowing the nuclease activity of the Fen nuclease to separate the first interactive signal generating labeled moiety from the second interactive signal generating labeled moiety by cleaving at said site susceptible to Fen nuclease, thereby generating a signal.

10. The method of claim 9 , wherein said pair of interactive labels comprises a quencher moiety and a fluorescent moiety.

11. The method of claim 3 , wherein said amplification primers are between about 10 to 100 nucleotides in length.

12. The method of claim 3 , wherein said amplification primers are between about 17-50 nucleotides in length.

13. The method of claim 3 , wherein said amplification primers are between about 17-45 nucleotides in length.

14. The method of claim 1 , wherein said Fen nuclease is a Fen-1 nuclease.