DNA usually consists of a double-stranded chain, antisense and sense strands of polynucleotides. The double strand is stabilized by hydrogen bonds between adenine and thymine and between guanine and cytosine. This stability depends on temperature and concentration of denaturing agents. If a base pair substitution occurs in a DNA segment, stability changes. A more drastic change occurs when a mismatched base pair is present in the segment.

Suppose that normal double stranded DNAs (described here as B:D, where B is the sense and D is the antisense strand) and DNAs carrying a single base pair substitution (B’:D’) are mixed, denatured and annealed. The original B:D and B’:D’ pairings and new B’:D and B:D’ pairings occur. The latter two contain a single mismatched base pair, i.e., base pairings other than A to T and G to C, and are more unstable than matched DNA strands, i.e., B:D, B’:D’.

The DGGE method consists of gel electrophoresis of previously mixed DNA, i.e., normal and test DNAs mixed, denatured and annealed, in the presence of increasing amounts of denaturing agent. Double-stranded DNAs bearing a mismatched base pair start to dissociate into partially single stranded forms of DNAs earlier, i.e., at lower concentrations of the denaturing agent, and such DNAs move far slower than normal DNAs in the gel–an indication of a variant DNA.