Single molecule FRET reveals distinct MutS conformational dynamics on different DNA mismatches.

Abstract

DNA mismatch repair (MMR) is an essential biological process that is common to all living organisms. The proteins involved in the MMR pathway identify and correct base mismatch errors and small insertion/deletions that are made during replication as well as some types of DNA damage. MutS is the MMR protein that scans DNA and locates mismatches. Previous single molecule fluorescent resonant energy transfer (smFRET) studies have found that binding to a GT mismatch or T-insert loop in DNA induces Thermus aquaticus MutS to undergo ATP-dependent conformational changes that convert it to a long-lived sliding clamp. This post-mismatch-recognition state of MutS is associated with downstream repair signaling in many models. Because different mismatches are repaired with the varying efficiencies, here we extend the smFRET studies to characterize the interactions between MutS and several additional mismatches. We further examine some mismatches in different local sequence contexts. Our results reproduce the binding affinities expected for these mismatches and characterize a range of tendencies for sliding clamps to result from MutS interacting with them. We compare our results to reported repair efficiencies to correlate the conversion to sliding clamp with eventual mismatch repair.