Methods and devices for measuring duplex unwinding or strand exchange efficiency

A method for detecting unwinding or strand exchange of a double stranded nucleic acid, the method comprising:

• providing a sample comprising a pre-annealed duplex, wherein the pre-annealed duplex comprises a target nucleic acid and a synthetic nucleic acid comprising an optional first detectable label;
• a primer comprising a second detectable label;
• an amplifying enzyme for amplifying nucleic acids;
• and an unwinding enzyme for unwinding or strand exchange double stranded nucleic acids;
• incubating the sample under an isothermal amplification condition and for a time sufficient for nucleic acid amplification;
• and
• detecting the second detectable label and, optionally, the first detectable label, if present,
• wherein a ratio of the primer to the pre-annealed duplex is from 1:1 to 50:1.