Compositions and methods for the detection of a nucleic acid using a cleavage reaction

1. A method for the detection of a target nucleic acid, said method comprising:

a. subjecting a reaction mixture to conditions which permit nucleic acid polymerization and cleavage of a cleavage structure, wherein said reaction mixture comprises: a first oligonucleotide, a second oligonucleotide comprising a 5′ region and a 3′ region, wherein said 3′ region is complementary to the first oligonucleotide, a target nucleic acid, a nucleic acid polymerase, and a 5′ nuclease;

b. forming a cleavage structure comprising said second oligonucleotide in duplex with an extension product of said first oligonucleotide, wherein said 5′ region of said second oligonucleotide is non-complementary to said extension product and is cleaved by said 5′ nuclease; and

c. detecting cleavage of said cleavage structure, wherein detecting cleavage of said cleavage structure is indicative of the presence and/or amount of the target nucleic acid.

2. The method of claim 1 , wherein said fast oligonucleotide comprises a 5′ region and a 3′ region and wherein said 3′ region of said first oligonucleotide is non-complementary to said second oligonucleotide and is complementary to said first strand of said target.

3. The method of claim 1 , wherein said 5′ region of said second oligonucleotide is non-complementary to said first oligonucleotide.

4. The method of claim 1 , wherein said second oligonucleotide comprises a detectable label.

5. The method of claim 1 , wherein said second oligonucleotide comprises a pair of interactive signal generating moieties.

6. The method of claim 5 , wherein a first member of said pair of interactive signal generating moieties is operatively coupled to the 5′ region of said second oligonucleotide and a second member of said pair of interactive signal generating moieties is operatively coupled to the 3′ region of said second oligonucleotide.

7. The method of claim 5 , wherein said pair of interactive signal generating moieties comprises a quencher moiety and a fluorescent moiety.

8. The method of claim 5 , wherein said pair of interactive signal generating moieties are effectively positioned to separate upon cleavage of a non-overlapping cleavage structure.

9. The method of claim 5 , wherein a first member of said pair of interactive signal generating moieties is operatively coupled to a 5′ flap of said second oligonucleotide and a second member of said pair of interactive signal generating moieties is operatively coupled to position +1 of said second oligonucleotide.

10. The method of claim 1 , wherein said second oligonucleotide further comprises a 3′ tail of nucleotides that are non-complementary to said first oligonucleotide.

11. The method of claim 10 , wherein said 3′ tail is complementary to a region of the second strand of said target nucleic acid that is downstream of a region of the second strand of said target nucleic acid that is complementary to said second oligonucleotide.

12. The method of claim 1 , wherein said second oligonucleotide is a cleavage resistant probe.

13. The method of claim 12 , wherein said cleavage resistant probe comprises one or more modifications that renders the portion downstream of the +1 position not susceptible to cleavage.

14. The method of claim 12 , wherein said cleavage resistant probe comprises one or more modifications that renders the portion downstream of the +2 position not susceptible to cleavage.

15. The method of claim 1 , wherein said 5′ nuclease is a FEN.

16. The method of claim 1 , wherein said 5′ nuclease is a flap-specific nuclease.

17. The method of claim 1 , wherein said 5′ nuclease is FEN-1.

18. The method of claim 1 , wherein said 5′ nuclease is thermostable.

19. The method of claim 1 , wherein said 5′ nuclease substantially lacks 5′ to 3′ synthetic activity.

20. The method of claim 1 , wherein said nucleic acid polyrnerase substantially lacks 5′ to 3′ nuclease activity.

21. The method of claim 1 , wherein the nucleic acid polymerase is a thermostable DNA polymerase.

22. The method of claim 12 , wherein said cleavage resistant probe comprises a 5′ region and a 3′ region, wherein said 3′ region is at least partially complementary to said the second strand of said target nucleic acid and wherein said 5′ region is not complementary to said second stand of said target nucleic acid.

23. A method for the detection of a target nucleic acid, said method comprising:

a. subjecting a reaction mixture to conditions which permit nucleic acid polymerization, and cleavage of a cleavage structure, wherein said reaction mixture comprises: a first oligonucleotide, a second oligonucleotide comprising a 5′ region and a 3′ region, wherein said 3′ region is complementary to the first oligonucleotide, a cleavage oligonucleotide, a target nucleic acid, a nucleic acid polymerase, and a 5′ nuclease;

b. forming a cleavage structure comprising said second oligonucleotide and said cleavage oligonucleotide both in duplex with an extension product of said fast oligonucleotide, wherein said 5′ region of said second oligonucleotide is non-complementary to said extension product and is cleaved by said 5′ nuclease; and

c. detecting cleavage of said cleavage structure, wherein detecting cleavage of said cleavage structure is indicative of the presence and/or amount of the target nucleic acid.

24. The method of claim 23 , wherein said cleavage oligonucleotide comprises at least one 3′ terminal nucleotide which is non-complementary to the target nucleic acid.

25. A method for the detection of a target nucleic acid, said method comprising:

a. subjecting a reaction mixture to conditions which permit nucleic acid polymerization, and cleavage of a cleavage structure, wherein said reaction mixture comprises: a first oligonucleotide, a second oligonucleotide comprising a 5′ region and a 3′ region, wherein said 3′ region is complementary to the first oligonucleotide, a reverse oligonucleotide primer, a target nucleic acid, a nucleic acid polymerase, and a 5′ nuclease;

b. forming a cleavage structure comprising said second oligonucleotide and the extension product of said reverse oligonucleotide primer both in duplex with an extension product of said first oligonucleotide, wherein said 5′ region of said second oligonucleotide is non-complementary to said extension product and is cleaved by said 5′ nuclease; and

c. detecting cleavage of said cleavage structure, wherein detecting cleavage of said cleavage structure is indicative of the presence and/or amount of the target nucleic acid.

26. A method for the detection of a target nucleic acid, said method comprising:

a. subjecting a reaction mixture to conditions which permit nucleic acid polymerization and cleavage of a cleavage structure, wherein said reaction mixture comprises: a first oligonucleotide, a second oligonucleotide comprising a 5′ region and a 3′ region, wherein said 3′ region is complementary to the fast oligonucleotide, a cleavage oligonucleotide, a reverse primer, a target nucleic acid, a nucleic acid polymerase, and a 5′ nuclease;

b. forming a cleavage structure comprising said second oligonucleotide and said cleavage oligonucleotide both in duplex with an extension product of said first oligonucleotide, wherein said 5′ region of said second oligonucleotide is non-complementary to said extension product and is cleaved by said 5′ nuclease; and

c. detecting cleavage of said cleavage structure, wherein detecting cleavage of said cleavage structure is indicative of the presence and/or amount of the target nucleic acid.

27. The method of claim 26 , wherein said second oligonucleotide is complementary to a region of the second strand of the target nucleic acid that is adjacent to said region of the second strand of the target nucleic acid that is complementary to the cleavage oligonucleotide.

28. The method of claim 26 , wherein the second oligonucleotide and cleavage oligonucleotide ate separated by a gap when hybridized to the second strand of said target nucleic acid.

29. The method of claim 26 , wherein the second oligonucleotide and cleavage oligonucleotide are separated by a nick when hybridized to second stand of said target nucleic acid.