Page "Temperature gradient gel electrophoresis" Paragraph 6

However, in TGGE, there is also a temperature gradient across the gel.

At room temperature, the DNA will exist stably in a double-stranded form.

As the temperature is increased, the strands begin to separate ( melting ), and the speed at which they move through the gel decreases drastically.

Critically, the temperature at which melting occurs depends on the sequence ( GC basepairs are more stable then AT due to stacking interactions, not, as commonly thought, due to the difference in hydrogen bonds ( there are three hydrogen bonds between a cytosine and guanine base pair, but only two between adenine and thymine )), so TGGE provides a " sequence dependent, size independent method " for separating DNA molecules.

TGGE not only separates molecules, but gives additional information about melting behavior and stability ( Biometra, 2000 ).