Massively parallel single molecule tracking of sequence-dependent DNA mismatch repair in vivo

Whether due to mutagens or replication errors, DNA mismatches arise spontaneously in vivo. Unrepaired mismatches are sources of genetic variation and point mutations which can alter cellular phenotype and cause dysfunction, diseases, and cancer. To understand how diverse mismatches in various sequence contexts are recognized and repaired, we developed a high-throughput sequencing-based approach to track single mismatch repair outcomes in vivo and determined the mismatch repair efficiencies of 5682 distinct singly mispaired sequences in E. coli. We found that CC mismatches are always poorly repaired, whereas local sequence context is a strong determinant of the hypervariable repair efficiency of TT, AG, and CT mismatches. Single molecule FRET analysis of MutS interactions with mismatched DNA showed that well-repaired mismatches have a higher effective rate of sliding clamp formation. The hypervariable repair of TT mismatches can cause selectively enhanced mutability if a failure to repair would result in synonymous codon change or a conservative amino acid change. Sequence-dependent repair efficiency in E. coli can explain the patterns of substitution mutations in mismatch repair-deficient tumors, human cells, and C. elegans. Comparison to biophysical and biochemical analyses indicate that DNA physics is the primary determinant of repair efficiency by its impact on the mismatch recognition by MutS.