Encoded endonuclease assays

1 . A method of conducting an assay for nucleic acid targets, the method comprising:

(a) combining dual probes with a sample composition potentially comprising nucleic acid targets to form cleavable ternary nucleic acid complexes, wherein:

(i) each of the dual probes comprise two probes;

(ii) a first probe of each of the dual probes comprises a first targeting sequence that is complementary to a first portion of a nucleic acid target;

(iii) a second probe of each of the dual probes comprises:

(1) a second targeting sequence; and

(2) a non-targeting recognition element sequence,

wherein the second targeting sequence is complementary to a second portion of the nucleic acid target and wherein the second targeting sequence of the second probe overlaps by at least one nucleotide with the first targeting sequence of the first probe;

(iv) binding of the dual probe to the nucleic acid target with no mismatches between the nucleic acid target and the second targeting sequence of the second probe at a nucleic acid target site of interest results in a cleavable ternary nucleic acid complex, wherein the cleavable ternary nucleic acid complex comprises the non-targeting recognition element sequence of the second probe;

(v) binding of the dual probe to a non-target nucleic acid with mismatches between the non-target nucleic acid and the second targeting sequence of the second probe results in an uncleavable ternary nucleic acid complex;

(b) releasing from the cleavable ternary nucleic acid complex the non-targeting recognition element sequence, thereby forming a recognition element fragment;

(c) combining the released recognition element fragment with an additional nucleic acid sequence to create a circular nucleic acid, wherein the circular nucleic acid comprises a target-associated code and additional sequence elements, wherein the combining the released recognition element fragment with the additional nucleic acid sequence comprises ligating the released recognition element fragment to a coded oligonucleotide probe, wherein the coded oligonucleotide probe comprises a code comprising at least one segment encoding one or more symbols that correspond to a sequence of one or more nucleotides, and wherein the ligating comprises ligating ends of the released recognition element fragment to the coded oligonucleotide probe to produce a circular modified recognition element comprising the recognition element and the coded oligonucleotide probe; and

(d) performing a detection event to identify one or more detected codes of the target-associated code;

wherein the detected code indicates the presence of the nucleic acid target in the sample composition.

2 . The method of claim 1 , wherein the combining the released recognition element fragment with the additional nucleic acid sequence comprises circularizing the released recognition element fragment to produce a circular modified recognition element comprising the target-associated code.

3 . The method of claim 2 , wherein the circularizing the released recognition element fragment is by splint ligation.

4 . The method of claim 2 , wherein the circularizing the released recognition element fragment comprises contacting the released recognition element fragment with a splint oligonucleotide and performing a gap-fill extension and ligation reaction to produce the circular modified recognition element.

5 . The method of claim 1 , further comprising amplifying the nucleic acid targets in parallel with:

(a) binding of the dual probe to the nucleic acid target and the non-target nucleic acid; and

(b) releasing the recognition element fragment.

6 . The method of claim 1 , wherein:

(a) each of the dual probes comprises from 3 to 100 coded recognition elements; and

(b) each of the coded recognition elements comprises a soft decodable code.

7 . The method of claim 1 , wherein:

(a) each of the dual probes comprises from 100 to 10,000 coded recognition elements; and

(b) each of the coded recognition elements comprises a soft decodable code.

8 . The method of claim 1 , wherein the performing the detection event comprises:

(a) recording a signal produced in response to an interrogation of each segment of each of the codes; and

(b) determining, upon completion of the interrogation, a probability of the presence of each of the codes by applying a soft-decision probabilistic decoding algorithm to the recorded signal.

9 . The method of claim 1 , wherein the performing the detection event comprises determining whether the code is present without determining a nucleic acid sequence of the code.

10 . The method of claim 1 , wherein the performing the detection event comprises determining whether the code is present without making a specific base call for each nucleotide in the code.

11 . The method of claim 1 , wherein the releasing comprises cleaving the ternary nucleic acid complex using a flap endonuclease.

12 . The method of claim 1 , wherein the first probe and the second probe of each of the dual probes:

(a) hybridize to one of the nucleic acid targets; and

(b) overlap at the nucleic acid target site of interest, leaving the non-targeting recognition element sequence unhybridized.

13 . The method of claim 1 , further comprising:

(a) counting the one or more detected codes to produce a code count for each detected code; and

(b) estimating nucleic acid target quantities based on the code count.

14 . The method of claim 1 , wherein the at least one segment encoding one or more symbols has a length ranging from 3 to 150 nucleotides.

15 . The method of claim 1 , wherein each code is selected to avoid interaction with other assay components.

16 . The method of claim 1 , wherein each of the dual probes or the coded oligonucleotide probes is unique for a specific nucleic acid target and comprises a code that is unique within a set of codes.

17 . The method of claim 1 , further comprising amplifying the circular modified recognition element, wherein the amplifying the circular modified recognition element comprises a rolling circle amplification reaction to yield a nucleic acid concatemer comprising multiple copies of the code.

18 . The method of claim 1 , wherein the sample composition comprises nucleic acids extracted from one or a combination of any of whole blood, lymphatic fluid, serum, plasma, sweat, tear, saliva, sputum, cerebrospinal fluid, amniotic fluid, seminal fluid, vaginal excretion, serous fluid, synovial fluid, pericardial fluid, peritoneal fluid, pleural fluid, transudates, exudates, cystic fluid, bile, urine, gastric fluid, intestinal fluid, fecal samples, liquids containing single or multiple cells, liquids containing organelles, fluidized tissues, fluidized organisms, liquids containing multi-celled organisms, biological swabs or biological washes.

19 . The method of claim 1 , wherein the nucleic acid targets comprise wild-type and/or mutated nucleic acid sequences.

20 . The method of claim 1 , wherein the nucleic acid targets comprise point mutations.

21 . The method of claim 1 , wherein the nucleic acid targets comprise substitutions, insertions and/or deletions.

22 . The method of claim 1 , wherein the nucleic acid targets comprise copy number variations.

23 . The method of claim 1 , wherein the nucleic acid targets comprise extracellular DNA fragments selected for methylation patterns indicative of cancer.

24 . The method of claim 23 , wherein the extracellular DNA fragments comprise bases, wherein the bases are transformed prior to the performing of the detection event.

25 . The method of claim 1 , wherein the nucleic acid targets comprise methylated nucleotides.

26 . The method of claim 1 , wherein the nucleic acid targets comprise extracellular DNA fragments.

27 . The method of claim 1 , wherein the nucleic acid targets comprise RNA fragments.