Photo-triggered nucleic acid constructs and methods for molecular detection

A method for detecting a presence or absence of an analyte nucleic acid in a solution, comprising:

• directing the solution to a device comprising a reaction chamber configured to receive the solution comprising the analyte nucleic acid, and further comprising a temperature control system capable of changing the temperature of the solution in the reaction chamber, wherein the reaction chamber:
• (i) the analyte nucleic acid comprising a first inner sequence flanked by a first outer sequence and a second outer sequence,
• (ii) a first pair of primers comprising one or more first photocleavable moieties, wherein said first pair of primers are configured to:
• (1) bind to said first outer sequence and/or said second outer sequence, (2) be elongated to amplify said analyte nucleic acid in a first amplification reaction to generate a first amplified nucleic acid sequence comprising the first inner sequence, and (3) be deactivated following said first amplification reaction when said one or more first photocleavable moieties are irradiated by light, and
• (iii) a second pair of primers comprising one or more second photocleavable moieties, wherein said second pair of primers are configured to:
• (1) be activated when said one or more second photocleavable moieties are irradiated by said light, (2) bind to said first inner sequence, and (3) be elongated to amplify said first amplified nucleic acid sequence in a second amplification reaction to generate a second amplified nucleic acid sequence;
• applying a time-varying temperature profile to the reaction chamber;
• applying an optical excitation pulse to the reaction chamber within a first time period;
• and
• detecting periodically a fluorescent signal from the reaction chamber during a second time period subsequent to the first time period
• wherein the fluorescent signal is indicative of the presence or absence of the analyte nucleic acid.