Abstract: A method for distinguishing fragments of DNA which contain single base mismatches from their perfectly paired homologues is disclosed. Single stranded regions within a duplex fragment are modified with carbodiimide, which reacts with unpaired guanine (G) and thymine (T) residues in DNA. Linear duplex DNA molecules do not react, while DNA molecules with single base mismatches react quantitatively with carbodiimide. Following reaction with carbodiimide, the DNA molecules are fractionated on high percentage polyacrylamide gels such that modified and unmodified fragments can be clearly distinguished. Application of this technique in order to located and purify DNA sequence differences responsible for phenotype variation and inherited disease is disclosed.