Abstract: The present invention relates to a method for detecting base sequence differences within homologous regions of two DNA molecules comprising the steps of contacting at least one strand of the first DNA molecule with the complementary strand of the second DNA molecule under conditions such that base pairing occurs, contacting the resulting DNA duplexes with a protein that recognizes substantially all base pair mismatches under conditions such that the protein forms specific complexes with its cognate mispairs, and detecting the resulting DNA:protein complexes by a suitable analytical method. Also disclosed are protein components of DNA mismatch correction systems and the use of these components in methods for genetic mapping.