Multiplex systems, methods, and kits for detecting and identifying nucleic acids

A system for determining the presence or absence of at least one target nucleic acid sequence in a sample, comprising a plurality of subsystems, wherein each subsystem comprises:

• (a) a capture nucleic acid that is capable of binding to a first region of a target nucleic acid sequence in the sample;
• (b) a reporter agent that is capable of binding to a second region of the same target nucleic acid sequence in the sample, comprising at least one reporter nucleic acid;
• and
• (c) a solid support capable of specifically binding to the capture nucleic acid.

A system for determining the presence or absence of a target nucleic acid sequence in a sample, comprising:

• (a) a capture nucleic acid that is capable of binding to a first region of the target nucleic acid sequence;
• (b) a reporter agent that is capable of binding to a second region of the target nucleic acid sequence, comprising at least one reporter nucleic acid;
• and
• (c) a solid support capable of specifically binding to the capture nucleic acid.

A method for determining the presence or absence of at least one target nucleic acid sequence in a sample, comprising the steps of:

• (a) obtaining a detecting system comprising a plurality of subsystems, wherein each subsystem comprises:
• (i) a capture nucleic acid that is bound to a solid support and is capable of binding to a first region of a target nucleic acid sequence in the sample;
• and
• (ii) a reporter agent that is capable of binding to a second region of the same target nucleic acid sequence in the sample, comprising at least one reporter nucleic acid;
• (b) contacting the sample with the detecting system, under conditions suitable for formation of at least one complex comprising a capture nucleic acid, a reporter agent, and a target nucleic acid sequence;
• (c) isolating, if any, at least one complex comprising a target nucleic acid sequence, a capture nucleic acid, and a reporter nucleic acid;
• (d) amplifying the reporter nucleic acid or a portion thereof in the at least one complex;
• and
• (e) determining the presence or absence of the reporter nucleic acid or portion thereof;
• wherein the target nucleic acid sequence is present in the sample if the reporter nucleic acid or portion thereof is present, and the target nucleic acid sequence is absent from the sample if the reporter nucleic acid or portion thereof is absent.

A method for determining the presence or absence of at least one target nucleic acid sequence in a sample, comprising the steps of:

• (a) obtaining a detecting system comprising a plurality of subsystems, wherein each subsystem comprises:
• (i) a capture nucleic acid that is capable of binding to a first region of a target nucleic acid sequence in the sample;
• (ii) a reporter agent that is capable of binding to a second region of the same target nucleic acid sequence in the sample, comprising at least one reporter nucleic acid;
• and
• (iii) a solid support capable of specifically binding to the capture nucleic acid;
• (b) contacting the sample with the detecting system, under conditions suitable for formation of at least one complex comprising a capture nucleic acid, a reporter agent, and a target nucleic acid sequence;
• (c) isolating, if any, at least one complex comprising a target nucleic acid sequence, a capture nucleic acid, and a reporter nucleic acid;
• (d) amplifying the reporter nucleic acid or a portion thereof in the at least one complex;
• (e) binding the capture nucleic acid in each subsystem to the solid support of each subsystem;
• and
• (f) determining the presence or absence of the reporter nucleic acid or portion thereof;
• wherein the target nucleic acid sequence is present in the sample if the reporter nucleic acid or portion thereof is present, and the target nucleic acid sequence is absent from the sample if the reporter nucleic acid or portion thereof is absent.

A method for determining the presence or absence of a target nucleic acid sequence in a sample, comprising the steps of:

• (a) obtaining a detecting system comprising:
• (i) a capture nucleic acid that is bound to a solid support and is capable of binding to a first region of the target nucleic acid sequence;
• and
• (ii) a reporter agent that is capable of binding to a second region of the target nucleic acid sequence, comprising at least one reporter nucleic acid;
• (b) contacting the sample with the capture nucleic acid and the reporter agent, under conditions suitable for formation of a complex comprising the capture nucleic acid, the reporter agent, and the target nucleic acid sequence;
• (c) isolating, if any, a complex comprising the target nucleic acid sequence, the capture nucleic acid, and the reporter nucleic acid;
• (d) amplifying the reporter nucleic acid or a portion thereof in the complex;
• and
• (e) determining the presence or absence of the reporter nucleic acid or portion thereof;
• wherein the target nucleic acid sequence is present in the sample if the reporter nucleic acid or portion thereof is present, and the target nucleic acid sequence is absent from the sample if the reporter nucleic acid or portion thereof is absent.

A method for determining the presence or absence of a target nucleic acid sequence in a sample, comprising the steps of:

• (a) obtaining a detecting system comprising:
• (i) a capture nucleic acid that is capable of binding to a first region of the target nucleic acid sequence;
• (ii) a reporter agent that is capable of binding to a second region of the target nucleic acid sequence, comprising at least one reporter nucleic acid;
• and
• (iii) a solid support capable of specifically binding to the capture nucleic acid;
• (b) contacting the sample with the capture nucleic acid and the reporter agent, under conditions suitable for formation of a complex comprising the capture nucleic acid, the reporter agent, and the target nucleic acid sequence;
• (c) isolating, if any, a complex comprising the target nucleic acid sequence, the capture nucleic acid, and the reporter nucleic acid;
• (d) amplifying the reporter nucleic acid or a portion thereof in the complex;
• (e) binding the capture nucleic acid to the solid support;
• and
• (f) determining the presence or absence of the reporter nucleic acid or portion thereof,
• wherein the target nucleic acid sequence is present in the sample if the reporter nucleic acid or portion thereof is present, and the target nucleic acid sequence is absent from the sample if the reporter nucleic acid or portion thereof is absent.