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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;GT&gt;GG&gt;AA approximately TT approximately TC&gt;CA&gt;GA&gt;CC&gt;GC. We find that the affinity for GT mismatches is affected by the flanking sequence and decreases in the order G(n)C(n)&gt;(GC)(n)&gt;A(n)T(n)&gt;(AT)(n). Studies with base analogues show good binding to phiT (where phi represents 1',2'-dideoxyribose), but much weaker binding to Gphi.

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