Assays

1. A method, comprising:

(a) providing: an amount of a reporter compound; a first binding member being configured to bind an anchor group of a capture molecule; a second binding member capable of capturing the reporter compound; an amount of a target nucleic acid capable of forming complexes with the reporter compound, the forming of complexes with the reporter compound inhibiting capturing of the reporter compound by the second binding member; and an amount of capture molecules wherein each capture molecule comprises a binding portion specific to a region of the target nucleic acid and an anchor group;

(b) forming complexes each comprising the target nucleic acid and the capture molecule;

(c) contacting the complexes with the first binding member to bind the complexes to the first binding member

(d) releasing at least a subset of the amount of target nucleic acid from the first binding member;

(e) forming complexes of a subset of the amount of reporter compound with at least a subset of the amount of target nucleic acid;

(f) capturing a remaining subset of the amount of reporter compound not in complex with the target nucleic acid on the second binding member:

(g) determining a value indicative of the amount of reporter compound captured on the second binding member; and

(h) determining a value indicative of the amount of target nucleic acid based on the value indicative of the amount of reporter compound captured on the second binding member; and

(i) wherein the value indicative of the amount of reporter compound captured on the second binding member is determined before forming complexes of the subset of the amount of reporter compound with at least the subset of the amount of target nucleic acid.

2. The method of claim 1 , further comprising determining a value indicative of the amount of target nucleic acid based on the value indicative of the amount of reporter compound captured on the binding member.

3. The method of claim 2 , wherein the value indicative of the amount of target nucleic acid is determined based on a calibration curve correlating the value indicative of the presence and/or amount of reporter compound with the value indicative of the presence and/or amount of target nucleic acid.

4. The method of claim 1 , further comprising releasing the remaining subset of the amount of reporter compound from the binding member after the steps of forming complexes of a subset of the amount of reporter compound with at least a subset of the amount of target nucleic acid, capturing a remaining subset of the amount of reporter compound not in complex with a target nucleic acid on the binding member, and determining the value indicative of the amount of reporter compound captured on the binding member.

5. The method of claim 4 , further comprising performing the steps of releasing, forming complexes, capturing, and determining a number N additional times, where N is an integer greater than or equal to 1.

6. The method of claim 4 , further comprising performing the steps of releasing, forming complexes, capturing, and determining a number N additional times, wherein N ≥5 .

7. The method of claim 4 , further comprising performing the steps of releasing, forming complexes, capturing, and determining a number N additional times, wherein N ≥10 .

8. The method of claim 4 , further comprising performing the steps of releasing, forming complexes, capturing, and determining a number N additional times, wherein N ≥20 .

9. The method of claim 1 , further comprising, prior to the step of forming complexes: capturing at least a subset of the amount of reporter compound on the binding member; determining a value indicative of the amount of reporter compound captured on the binding member; and releasing captured reporter compounds from the binding member.

10. The method of claim 1 , wherein the step of forming complexes of a subset of the amount of reporter compound with at least a subset of the amount of target nucleic acid and the step of capturing a remaining subset of the amount of reporter compound not in complex with a target nucleic acid on the binding member are performed concomitantly.

11. The method of claim 1 , wherein the value indicative of the amount of reporter compound captured on the binding member is determined 1seconds to 120 seconds after initiating the steps of forming complexes of a subset of the amount of reporter compound with at least a subset of the amount of target nucleic acid and of capturing a remaining subset of the amount of reporter compound not in complex with a target nucleic acid on the binding member.

12. The method of claim 1 , wherein a reporter compound comprises one or more detectable labels.

13. The method of claim 12 , wherein the one or more detectable labels are fluorescent labels.

14. The method of claim 12 , wherein the label is a compound that includes a chemical substance that generates a detectable signal in a physical reaction.

15. The method of claim 12 , wherein the label is an enzyme that generates a detectable signal in an enzymatic reaction.

16. The method of claim 1 , wherein the reporter compounds are oligonucleotides.

17. The method of claim 1 , wherein forming a composition of matter comprises forming a composition of matter comprising: an amount of a first reporter compound, an amount of a first target nucleic acid capable of forming complexes with the first reporter compound, the forming of complexes with the first reporter compound inhibiting capturing of the first reporter compound by the binding member, an amount of a second reporter compound, and an amount of a second target nucleic acid capable of forming complexes with the second reporter compound, the forming of complexes with the second reporter compound inhibiting capturing of the second reporter compound by the binding member.

18. The method of claim 1 , wherein the binding member comprises one or more different capture molecules being capable of capturing a reporter compound on the binding member.

19. The method of claim 18 , wherein the capture molecules are oligonucleotides.

20. The method of claim 18 , wherein different capture molecules are arranged on different locations with respect to the binding member.

21. The method of claim 18 , wherein the reporter compound is captured on the binding member by forming complexes with the capture molecules.

22. The method of claim 1 , wherein determining the value indicative of the amount of reporter compound captured on the binding member comprises time-dependent monitoring of the indicative value.

23. The method of claim 1 , further comprising subjecting the target nucleic acid to thermal cyclic amplification.

24. The method of claim 23 , wherein the thermal cyclic amplification comprises at least 10 cycles.

25. The method of claim 23 , wherein the thermal cyclic amplification comprises at least 20cycles.

26. The method of claim 23 wherein the thermal amplification is a PCR.

27. The method of claim 26 , wherein performing the PCR comprises using a polymerase having exonuclease activity.