Methods and compositions to detect nucleic acids in a biological sample

A method of detecting the presence of a target nucleic acid in a sample comprising the steps of:

• providing a sample containing a target nucleic acid,
• mixing the sample with a nucleic acid capture probe that forms under hybridizing conditions a partially double-stranded hairpin structure made up of
• an internal target-complementary sequence, flanked by
• a capture region, and
• a terminal region that binds to the capture region to form a double-stranded stem portion of the hairpin structure in which the target-complementary region forms a substantially single-stranded loop portion,
• specifically hybridizing the target-complementary sequence of the capture probe to a target sequence in the target nucleic acid,
• binding the capture region to an immobilized probe attached to a capture support by binding together members of a specific binding pair, thereby forming a capture hybrid made up of the target nucleic acid, the capture probe, and the immobilized probe attached to the capture support,
• separating the capture hybrid attached to the capture support from sample components,
• releasing the target nucleic acid from the capture hybrid,
• then specifically hybridizing a detection probe to the target nucleic to form a detection hybrid, and
• detecting a signal produced from the detection hybrid to indicate the presence of the target nucleic acid in the sample.