Multiplexed analysis of nucleic acid hybridization thermodynamics using integrated arrays

A method for assaying a presence of a target nucleic acid molecule in a sample, comprising:

• (a) providing (i) a surface comprising a probe coupled to an energy donor, wherein said probe is configured to selectively couple to said target nucleic acid molecule, and (ii) an optical detector below said surface, wherein said optical detector is configured to detect at least one optical signal generated upon energy transfer between an energy acceptor coupled to said target nucleic acid molecule and said energy donor and wherein said optical detector and said surface are integrated with a chip;
• (b) bringing said sample containing or suspected of containing said target nucleic acid molecule in contact with said surface under conditions sufficient to permit said probe to selectively couple to said target nucleic acid molecule;
• (c) using said optical detector to measure said at least one optical signal in real-time while subjecting said surface to a temperature change, wherein said at least one optical signal is indicative of an interaction between said energy acceptor and said energy donor pair, and wherein said energy acceptor quenches optical activity of said energy donor;
• and
• (d) generating signal versus temperature data using measurements of said at least one optical signal with said temperature change, thereby assaying said presence of said target nucleic acid molecule in said sample.