Denaturing Gradient Gel Electrophoresis (DGGE) allows the separation, and thus detection, of DNA molecules that differ by as little as a single nucleotide. The electrophoretic separation is based upon the melting properties of the double-stranded DNA molecule. The two complimentary strands of DNA separate (melt-out) under conditions of increased temperature or under the influence of certain chemicals (termed denaturants). If a DNA sample is heterozygous for a point mutation, the PCR reaction will generate a mixture of double-stranded molecules and up to four bands will be visible after running the DGGE gel. There will be homoduplexes from the wild and the mutant sequences and in addition there will be two types of heteroduplex DNA molecules (which migrate at a slower rate), representing hybridised mismatched wild-type and mutant DNA strands.

DGGE is not a method for the direct characterization of point mutations. However, it is extremely useful for localizing point mutations or polymorphisms in a nucleoride sequence for further identification by sequencing, or for prenatal diagnosis of -thalassaemia genotypes when analysed alongside positive and negative controls for the known parental mutations.