Detection of nucleic acids and proteins

1. A method of detecting protein in a sample, the method comprising the steps of:

obtaining a sample comprising a target protein;

introducing an aptamer that binds to the target protein in the sample;

removing unbound aptamer;

dissociating bound aptamer from the target protein; and

performing a sequencing reaction on the dissociated aptamer in the sample, thereby detecting the target protein.

2. The method according to claim 1 , further comprising

amplifying the aptamer; and

wherein the sequencing reaction comprises sequencing the amplified aptamer, thereby detecting the target protein in the sample.

3. The method according to claim 1 , further comprising quantifying the target protein.

4. The method according to claim 2 , wherein prior to sequencing, the aptamer is attached to a substrate.

5. The method according to claim 4 , wherein the aptamer is directly attached to the substrate.

6. The method according to claim 4 , wherein the aptamer is indirectly attached to the substrate.

7. The method according to claim 2 , wherein sequencing is sequencing by synthesis.

8. The method according to claim 7 , wherein the sequencing by synthesis is single molecule sequencing by synthesis.

9. The method according to claim 2 , wherein sequencing comprises:

hybridizing a primer to the aptamer to form an aptamer/primer duplex;

contacting the duplex with a polymerase enzyme in the presence of at least one detectably labeled nucleotide under conditions that permit the polymerase to add nucleotides to the primers in a template-dependent manner;

detecting a signal from the incorporated labeled nucleotide; and

sequentially repeating the contacting and detecting steps at least once, wherein sequential detection of incorporated labeled nucleotide determines the sequence of each the aptamer.

10. The method according to claim 9 , wherein the detectably labeled nucleotide is an optically labeled nucleotide.

11. The method according to claim 10 , wherein the optically labeled nucleotide is a fluorescently labeled nucleotides.

12. The method according to claim 1 , wherein the target protein is associated with a disease.

13. The method according to claim 12 , wherein the disease is cancer.

14. The method according to claim 13 , wherein the cancer is bladder or colorectal cancer.

15. The method according to claim 1 , wherein the protein is MMP-2.

16. A method of detecting MMP-2 protein in a sample, the method comprising the steps of:

obtaining a sample comprising MMP-2 protein;

introducing an aptamer that binds to the MMP-2 protein in the sample;

removing unbound aptamer;

dissociating bound aptamer from the target protein; and

performing a sequencing reaction on the dissociated aptamer in the sample, thereby detecting the MMP-2 protein.

17. The method according to claim 16 , further comprising

amplifying the aptamer; and

wherein the sequencing reaction comprises sequencing the amplified aptamer, thereby detecting the MMP-2 protein in the sample.

18. The method according to claim 16 , further comprising quantifying the target protein.

19. A method of detecting multiple analytes in a sample, the method comprising the steps of:

obtaining a sample comprising at least one target nucleic acid and MMP-2 protein;

introducing an aptamer that binds to the MMP-2 protein in the sample;

removing unbound aptamer;

dissociating the aptamer from the MMP-2 complex; and

conducting a single assay, comprising performing a sequencing reaction on the target nucleic acid and the dissociated aptamer, thereby detecting the target nucleic acid and MMP-2 protein in the sample.

20. The method according to claim 19 , wherein the assay further comprises:

amplifying the aptamer; and the sequencing reaction comprises sequencing the amplified aptamer, thereby detecting the MMP-2 protein in the sample.

21. The method according to claim 20 , wherein the assay further comprises:

amplifying the nucleic acid in the sample; and the sequencing reaction comprises sequencing the amplified nucleic acid, thereby detecting the nucleic acid in the sample.

22. The method according to claim 19 , further comprising quantifying the target nucleic acid.

23. The method according to claim 19 , further comprising quantifying the MMP-2 protein.

24. The method according to claim 19 , further comprising quantifying the target nucleic acid and the MMP-2 protein.

25. The method according to claim 21 , wherein prior to sequencing, the nucleic acid and the aptamer are attached to a substrate.

26. The method according to claim 25 , wherein the nucleic acid and the aptamer are directly attached to the substrate.

27. The method according to claim 25 , wherein the nucleic acid and the aptamer are indirectly attached to the substrate.

28. The method according to claim 21 , wherein sequencing is sequencing by synthesis.

29. The method according to claim 28 , wherein the sequencing by synthesis is single molecule sequencing by synthesis.

30. The method according to claim 21 , wherein sequencing comprises:

hybridizing a primer to each of the nucleic acid and the aptamer to form each of a nucleic acid/primer duplex and an aptamer/primer duplex;

contacting each of the duplexes with a polymerase enzyme in the presence of at least one detectably labeled nucleotide under conditions that permit the polymerase to add nucleotides to the primers in a template-dependent manner;

detecting a signal from the incorporated labeled nucleotide; and

sequentially repeating the contacting and detecting steps at least once, wherein sequential detection of incorporated labeled nucleotide determines the sequence of each of the nucleic acid and the aptamer.

31. The method according to claim 30 , wherein the detectably labeled nucleotide is an optically labeled nucleotide.

32. The method according to claim 31 , wherein the optically labeled nucleotide is a fluorescently labeled nucleotides.

33. The method according to claim 19 , wherein the target nucleic acid is associated with a disease.

34. The method according to claim 33 , wherein the disease is cancer.

35. The method according to claim 34 , wherein the target nucleic acid is selected from the group consisting of: FGFR3, K-ras, K-ras2, APC, DCC, TP53, PRC1, NUSAPI1, CAPZ, PFKP, EVER1, FLT1, ESPL1, AKAP2, CDC45L, RAMP, SYNGR2, NDRG1, ZNF533, and hypermethylated nucleic acid.

36. The method according to claim 19 , wherein the MMP-2 protein is associated with a disease.

37. The method according to claim 36 , wherein the disease is cancer.

38. The method according to claim 37 , wherein the cancer is bladder or colorectal cancer.