Patent ID: 8586301

Claim:
A method for identifying a target nucleic acid sequence in a sample, the method comprising: contacting the target nucleic acid sequence with a capture probe under conditions that provide for selective hybridization of the capture probe to a first portion of the target nucleic acid sequence, wherein the capture probe comprises a reporter tether and a probe complementary to the first portion of the target nucleic acid sequence; ligating one or more nested probes to the capture probe under conditions that provide for transient hydridization of the one or more nested probes to a second portion of the target nucleic acid sequence adjacent to the first portion of the target nucleic acid sequence, wherein the one or more nested probes comprise probes complementary to the second portion of the target nucleic acid sequence, and wherein the one or more nested probes optionally comprise a reporter tether, provided that at least one of the one or more nested probes comprise a reporter tether in the form of a loop, and further comprising the step of opening the loop, prior to detection, to yield the reporter tether in linear form; ligating a terminal probe to the one or more nested probes under conditions that provide for transient hydridization of the terminal probe to a third portion of the target nucleic acid sequence adjacent to the second portion of the target nucleic acid sequence to form a target identifier, wherein the terminal probe comprises a reporter tether and a probe complementary to the third portion of the target nucleic acid sequence; and detecting the target identifier and thereby identifying the target nucleic acid sequence in the sample.