Methods of detecting target nucleic acids

1. A method of detecting a plurality of target polynucleotides, the method comprising:

a) contacting a population of coded molecules with a plurality of target polynucleotides, wherein the population of coded molecules comprises a plurality of subpopulations and each coded molecule of each subpopulation comprises:

(i) one or more block polymer regions and a target probe capable of hybridizing to a target polynucleotide, wherein the target probe of each subpopulation hybridizes to a different target polynucleotide; and

(ii) a detectable signal pattern distinguishable amongst the plurality of subpopulations;

b) modifying coded molecules of the population of coded molecules by modifying the target probe with a modifying agent following hybridizing the target probe with the different target polynucleotide, wherein the modified target probe is indicative of the different target polynucleotide;

c) translocating the modified coded molecules through a nanopore and detecting the signal pattern; and

d) associating the detected signal pattern to a specific subpopulation of coded molecules in the plurality of subpopulations, wherein a difference in the detected signal pattern compared to the signal pattern of the specific subpopulation indicates the presence of the different target polynucleotide.

2. The method of claim 1 , wherein associating includes comparing the detected signal pattern to a signal pattern of the specific subpopulation.

3. The method of claim 1 , in which the target polynucleotide comprises a 5-prime region and a 3-prime region, and the target probe comprises a 3-prime terminal sequence that hybridizes to the 5-prime region of the target polynucleotide, and wherein the modifying agent is a template-dependent polymerase and the modification is extension of the hybridized 3-prime region of the target probe.

4. The method of claim 3 , in which the 3-prime terminal sequence of the target probe comprises a 3-prime terminal nucleotide that interrogates a site of nucleotide polymorphism on the target polynucleotide.

5. The method of claim 3 , in which the target polynucleotide comprises a circular nucleic acid, wherein the circular nucleic acid is a ligated open circle probe (OCP).

6. The method of claim 1 , in which the target polynucleotide comprises adjacent first and second regions, and the method further comprises hybridizing a ligation probe to the target polynucleotide, wherein the ligation probe hybridizes to the first region and the target probe hybridizes to the second region of the target polynucleotide such that a terminus of the ligation probe and a terminus of the target probe are adjacent, and wherein the modifying agent is a ligase and the modification is ligation of the ligation probe to the target probe.

7. The method of claim 6 , in which the terminus of the target probe comprises a terminal nucleotide that interrogates a site of nucleotide polymorphism on the target polynucleotide.

8. The method of claim 6 , in which the terminus of the ligation probe comprises a terminal nucleotide that interrogates a site of nucleotide polymorphism on the target polynucleotide.

9. The method of claim 1 , in which the target polynucleotide comprises adjacent first and second regions, and the target probe comprises a 5-prime region and a 3-prime region, and wherein the method further comprises hybridizing a FLAP probe to the target polynucleotide, wherein the FLAP probe comprises a 3-prime segment that hybridizes to the first region, and the 3-prime region of the target probe hybridizes to the second region such that the 3-prime segment of the FLAP probe and the 3-prime region of the target probe are adjacently hybridized to the target polynucleotide to form a FLAP substrate, and wherein the modifying agent is a FLAP endonuclease and the modification is cleavage of the target probe.

10. The method of claim 9 , in which the 5-prime region of the target probe is non-complementary to the target polynucleotide.

11. The method of claim 9 , in which the FLAP probe further comprises a 3-prime unpaired segment that overlaps with the 5-prime region of the target probe in the FLAP substrate, thereby forming a double FLAP substrate.

12. The method of claim 9 , in which the target probe interrogates a site of nucleotide polymorphism on the target polynucleotide.

13. The method of claim 9 , in which the FLAP probe interrogates a site of nucleotide polymorphism on the target polynucleotide.

14. The method of claim 1 , in which the hybridization of the target probe to the target polynucleotide forms an endonuclease recognition site and a corresponding enodonuclease cleavage site, and wherein the modifying agent is an endonuclease that recognizes the recognition site and the modification is cleavage of the target probe.

15. The method of claim 14 , in which the endonuclease recognition site is a sequence-specific endonuclease recognition site and wherein the modifying agent is a sequence specific endonuclease active on the recognition site.

16. The method of claim 1 , in which the modifying agent is a double-stranded specific exonuclease suitable to act on the target probe hybridized to the target polynucleotide and the modification is degradation of all or a portion of the target probe.

17. The method of claim 1 , in which the coded molecule comprises a chimeric polymer.

18. The method of claim 17 , in which the chimeric polymer comprises nucleobase and non-nucleobase polymers.

19. The method of claim 1 , in which the coded molecule comprises at least two block polymers, and wherein the two block polymers are separated by a non-block polymer segment.

20. The method of claim 1 , in which the block polymer comprises dinucleotide repeats.