Affinity of mismatch-binding protein MutS for heteroduplexes containing different mismatches

Abstract

We have used bandshift analysis to measure the interaction between the Escherichia coli mismatch-binding protein MutS and synthetic DNA fragments containing all possible DNA mismatches as well as an unpaired T (∆T). The order of affinity is found to be ∆T > GT > GG > AA ≈ TT ≈ TC>CA>GA > CC>GC. We find that the affinity for GT mismatches is affected by the flanking sequence and decreases in the order GnCn>(GC)n>AnTn>(AT)n. Studies with base analogues show good binding to φT (where φ represents 1′,2′-dideoxyribose), but much weaker binding to Gφ.