Multiplexed identification of nucleic acid sequences

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 probe complementary to the first portion of the target nucleic acid sequence;
• ligating a first terminal probe to the capture probe under conditions that provide for transient hydridization of the first terminal probe to a second portion of the target nucleic acid sequence adjacent to the first portion of the target nucleic acid sequence, wherein the first terminal probe comprises a reporter tether and a probe complementary to the second portion of the target nucleic acid sequence;
• ligating a second terminal probe to the capture probe under conditions that provide for transient hydridization of the second terminal probe to a third portion of the target nucleic acid sequence located adjacent to the first portion of the target nucleic acid sequence, but at the opposite end of the probe of the capture probe from the second portion of target nucleic acid sequence, to form a target identifier, wherein the second 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.

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;
• 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.

A method for identifying a target nucleic acid sequence in a sample, the method comprising:

• contacting the target nucleic acid sequence with a first capture probe and a second capture probe under conditions that provide for selective hybridization of the first capture probe and the second capture probe to a first portion and a second portion, respectively, of the target nucleic acid sequence, wherein the first capture probe and the second capture probe comprise a reporter tether and a probe complementary to the first portion and the second portion, respectively, of the target nucleic acid sequence;
• ligating one or more nested probes to the first capture probe and the second capture probe under conditions that provide for transient hydridization of the one or more nested probes to a portion of the target nucleic acid sequence located between the first and second portions of the target nucleic acid sequence to form a target identifier, wherein the one or more nested probes comprise probes complementary to the nucleic acid sequence located between the first and second portions of the target nucleic acid sequence, and wherein the one or more nested probes optionally comprise a reporter tether;
• and
• detecting the target identifier and thereby identifying the target nucleic acid sequence in the sample.