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

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 (DeltaT). The order of affinity is found to be DeltaT > GT > GG > AA approximate to TT approximate to TC > CA > GA > CC > GC, We find that the affinity for GT mismatches is affected by the flanking sequence and decreases in the order G(n)C(n) > (GC)(n) > A(n)T(n) > (AT)(n). Studies with base analogues show good binding to phiT (where phi represents 1',2'-dideoxy-ribose), but much weaker binding to G phi.