Single molecule studies reveal that MutS's binding characteristics are mismatch type and context dependent and correlate with mismatch repair efficiency in vivo

During DNA replication, DNA polymerases can incorrectly incorporate a non-complementary nucleotide against the parental DNA strand, leading to mutations and ultimately debilitating diseases if left unrepaired. All organisms possess a mismatch repair system that scans, recognizes, and repairs DNA mismatches. MutS is one of the first repair proteins to arrive at a mismatch. Upon recognition, MutS exchanges bound ADP molecules to ATP, and undergoes a conformational change to form a sliding clamp and slide away from the mismatch. MutS will then recruit other repair proteins to the site and resolve the error. Previous in vivo studies from our lab suggest that the mismatch repair efficiency in E. coli is hypervariable not only for different mismatched bases, but also for their local sequence context. Deletion studies showed that MutS is responsible for the observed hypervariability. To understand the molecular mechanism underlying sequence dependence of MutS, we employed single molecule FRET (fluorescence resonance energy transfer) to directly detect MutS binding to a mismatch, sliding clamp formation, and dissociation. The binding characteristics of E. coli MutS showed a striking dependence of the mismatch type and the overall residence time of MutS on a mismatch-containing DNA in vitro was strongly correlated with the in vivo mismatch repair efficiencies. Furthermore, the sliding clamp formation yield in the presence of ATP was correlated with in vivo mismatch repair efficiencies. These data support in vivo repair trends and help clarify mechanistic basis by which mismatches are differentially repaired. Future experiments will be conducted using additional DNA mismatches with different sequence contexts to understand the generalizability of this observation.