Square wave thermal cycling

A system for determining the melting temperature of a duplex nucleic acid molecule, said system comprising

• a programmable thermal cycling apparatus;
• a detector;
• and
• a program for square wave thermal cycling, said program comprising instructions for:
• subjecting a solution comprising a double-stranded nucleic acid molecule to a square wave temperature gradient, said gradient comprising a range of temperatures that causes at least one transition of said double-stranded nucleic acid molecule to a single-stranded nucleic acid molecules;
• and
• detecting said at least one transition over the course of said square wave temperature gradient.

A method of determining melting temperature of a double-stranded nucleic acid molecule, said method comprising:

• providing a sample comprising double-stranded nucleic acid molecules and a reporter moiety having a signature detectable signal in the presence of duplex nucleic acid;
• subjecting said sample to a series of temperature pulses, wherein at least a plurality of said pulses cause said double-stranded nucleic acid molecules to transition to single-stranded molecules and back to double-stranded molecules;
• and
• detecting, using the signal produced by said reporter moiety, the melting temperature of said double-stranded nucleic acid molecule.