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

We have used bandshift analysis to measure the interaction between the Esch erichia coli mismatch-binding protein MutS and synthetic DNA fragments cont aining all possible DNA mismatches as well as an unpaired T (DeltaT). The o rder of affinity is found to be DeltaT > GT > GG > AA approximate to TT app roximate to TC > CA > GA > CC > GC, We find that the affinity for GT mismat ches 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 bi nding to phiT (where phi represents 1',2'-dideoxy-ribose), but much weaker binding to G phi.