Multiaptamer target detection
Described herein are compositions comprising a first aptamer, second aptamer and a target that are capable of forming a ternary complex, and wherein the first aptamer and the second aptamer comprise C-5 pyrimidine modification schemes that are different, and methods of making and using such compositions.
1. A method for detecting a target in a sample, the method comprising:
a) contacting the sample with a first aptamer to form a mixture, wherein the first aptamer is capable of binding to the target to form a first complex;
b) incubating the mixture under conditions that allow for the first complex to form;
c) contacting the mixture with a second aptamer, wherein the second aptamer is capable of binding the first complex to form a second complex;
d) incubating the mixture under conditions that allow for the second complex to form;
e) detecting for the presence or absence of the first aptamer, the second aptamer, the target, the first complex or the second complex in the mixture, wherein the presence of the first aptamer, the second aptamer, the target, the first complex or the second complex indicates that the target is present in the sample; and
wherein, the first aptamer comprises a first C-5 pyrimidine modification scheme, the second aptamer comprises a second C-5 pyrimidine modification scheme, and wherein the first C-5 pyrimidine modification scheme and the second C-5 pyrimidine modification scheme are different,
further wherein the first C-5 pyrimidine modification scheme comprises a 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BndU).
2. The method of claim 1 , wherein the first aptamer has binding affinity for the target and not the second aptamer.
3. The method of claim 1 , wherein the second aptamer has binding affinity for the target and not the first aptamer.
4. The method of claim 1 , wherein the second aptamer has binding affinity for the first complex.
5. The method of claim 1 , wherein the first aptamer binding region of the target and the second aptamer binding region of the target are different regions.
6. The method of claim 1 , wherein the first aptamer and the second aptamer, independently, comprise RNA, DNA or a combination thereof.
7. The method of claim 1 , wherein each uracil or thymine of the first aptamer is a 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BndU).
8. The method of claim 1 , wherein the second C-5 pyrimidine modification scheme comprises a C-5 modified pyrimidine selected from the group consisting of 5-(N-tryptaminocarboxyamide)-2′-deoxyuridine (TrpdU), 5-[N-(1-naphthylmethyl)carboxyamide]-2′-deoxyuridine (NapdU), 5-[N-(2-naphthylmethyl)carboxyamide]-2′-deoxyuridine (2-NapdU), and a combination thereof.
9. The method of claim 1 , wherein each uracil or thymine of the second aptamer is a C-5 modified pyrimidine selected from the group consisting of 5-(N-tryptaminocarboxyamide)-2′-deoxyuridine (TrpdU), 5-[N-(1-naphthylmethyl)carboxyamide]-2′-deoxyuridine (NapdU), 5-[N-(2-naphthylmethyl)carboxyamide]-2′-deoxyuridine (2-NapdU), and a combination thereof.
10. The method of claim 1 , wherein the first aptamer and the second aptamer, independently, are each from 20 to 100 nucleotides in length.
11. The method of claim 1 , wherein the first aptamer and/or the second aptamer further comprise a detectable moiety.
12. The method of claim 11 , wherein the detectable moiety is selected from the group consisting of a dye, a quantum dot, a radiolabel, an electrochemical functional group, an enzyme, an enzyme substrate, a ligand and a receptor.
13. The method of claim 1 , wherein the target comprises a protein or a peptide.
14. The method of claim 13 , wherein the target is a protein selected from the group consisting ANGPT2, TSP2, CRDL1, MATN2, GPVI, ESAM, C7, PLG, MMP-12, NPS-PLA2 and CdtA.
15. The method of claim 1 , wherein the dissociation constant (K d ) for the second complex is at least 0.02 nM, or from about 0.01 nM to about 10 nM, or from about 0.02 nM to about 6 nM, or from about 0.02 nM to about 3 nM.
16. The method of claim 1 , wherein the dissociation constant (K d ) for the first complex is from about 0.04 nM to about 5 nM, or from about 0.04 nM to about 4.8 nM.
17. The method of claim 1 , wherein the dissociation constant (K d ) for the second aptamer and the target is from about 0.03 nM to about 14 nM.
18. A method comprising:
a) contacting a target with a first aptamer to form a mixture, wherein the first aptamer is capable of binding the target to form a first complex;
b) incubating the mixture under conditions that allow for the first complex to form;
c) contacting the mixture with a second aptamer, wherein the second aptamer is capable of binding the target to form a second complex;
d) incubating the mixture under conditions that allow for the second complex to form;
e) detecting for the presence or absence of the first aptamer and the second aptamer in the mixture, wherein the presence of both the first aptamer and second aptamer in the mixture indicates that the binding of the first aptamer to the target and the binding of the second aptamer to the target is non-competitive; and
wherein, the first aptamer comprises a first C-5 pyrimidine modification scheme, the second aptamer comprises a second C-5 pyrimidine modification scheme, and wherein the first C-5 pyrimidine modification scheme and the second C-5 pyrimidine modification scheme are different.
19. The method of claim 18 , wherein the first aptamer has binding affinity for the target and not the second aptamer.
20. The method of claim 18 , wherein the second aptamer has binding affinity for the target and not the first aptamer.
21. The method of claim 18 , wherein the second aptamer has binding affinity for the first complex.
22. The method of claim 18 , wherein the first aptamer binding region of the target and the second aptamer binding region of the target are different regions.
23. The method of claim 18 , wherein the first aptamer and the second aptamer, independently, comprise RNA, DNA or a combination thereof.
24. The method of claim 18 , wherein each uracil or thymine of the first aptamer is a 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BndU).
25. The method of claim 18 , wherein the second C-5 pyrimidine modification scheme comprises a C-5 modified pyrimidine selected from the group consisting of 5-(N-tryptaminocarboxyamide)-2′-deoxyuridine (TrpdU), 5-[N-(1-naphthylmethyl)carboxyamide]-2′-deoxyuridine (NapdU), 5-[N-(2-naphthylmethyl)carboxyamide]-2′-deoxyuridine (2-NapdU), and a combination thereof.
26. The method of claim 18 , wherein each uracil or thymine of the second aptamer is a C-5 modified pyrimidine selected from the group consisting of 5-(N-tryptaminocarboxyamide)-2′-deoxyuridine (TrpdU), 5-[N-(1-naphthylmethyl)carboxyamide]-2′-deoxyuridine (NapdU), 5-[N-(2-naphthylmethyl)carboxyamide]-2′-deoxyuridine (2-NapdU), and a combination thereof.
27. The method of claim 18 , wherein the first aptamer and the second aptamer, independently, are each from 20 to 100 nucleotides in length.
28. The method of claim 18 , wherein the first aptamer and/or the second aptamer further comprise a detectable moiety.
29. The method of claim 28 , wherein the detectable moiety is selected from the group consisting of a dye, a quantum dot, a radiolabel, an electrochemical functional group, an enzyme, an enzyme substrate, a ligand and a receptor.
30. The method of claim 18 , wherein the target comprises a protein or a peptide.
31. The method of claim 30 , wherein the target is a protein selected from the group consisting ANGPT2, TSP2, CRDL1, MATN2, GPVI, ESAM, C7, PLG, MMP-12, NPS-PLA2 and CdtA.
32. The method of claim 18 , wherein the dissociation constant (K d ) for the second complex is at least 0.02 nM, or from about 0.01 nM to about 10 nM, or from about 0.02 nM to about 6 nM, or from about 0.02 nM to about 3 nM.
33. The method of claim 18 , wherein the dissociation constant (K d ) for the first complex is from about 0.04 nM to about 5 nM, or from about 0.04 nM to about 4.8 nM.
34. The method of claim 18 , wherein the dissociation constant (K d ) for the second aptamer and the target is from about 0.03 nM to about 14 nM.
35. The method of claim 18 , wherein the first C-5 pyrimidine modification scheme comprises a C-5 modified pyrimidine selected from the group consisting of 5-(N-tryptaminocarboxyamide)-2′-deoxyuridine (TrpdU), 5-[N-(1-naphthylmethyl)carboxyamide]-2′-deoxyuridine (NapdU), 5-[N-(2-naphthylmethyl)carboxyamide]-2′-deoxyuridine (2-NapdU), and a combination thereof.