Search and repair of bona fide base‐pair mismatches in DNA

Abstract

The DNA mismatch repair system (MMR) helps maintain genome integrity by correcting base‐pair mismatches and insertion/deletion loops in DNA. MMR proteins are thus critical for limiting mutagenesis, and their malfunction is linked to sporadic cancers and the HNPCC syndrome. MutS proteins perform the challenging task of finding a few errors against a background of millions of correct base pairs in DNA, and initiate repair. In order to understand the mechanism by which MutS proteins locate these errors, we measured the movement of S. cerevisiae MutS (Msh2‐6), between near Watson‐Crick (2‐Aminopurine:T) and mismatched (G:T) base‐pair sites on DNA. We found that Msh2‐6 binds both sites at equally high rates (2x107 M−1s−1), but it leaves the matched site ~50‐fold faster than the mismatched site (t1/2 ~ 0.4 versus 18 s, respv). These data suggest that while Msh2‐6 makes similar initial contacts with various base pairs, it recognizes mismatches by forming stable contacts specifically at these sites. Notably, Msh2‐6 leaves the matched site and arrives at the mismatched site without dissociating from DNA, which suggests that the protein slides on DNA, probing base pairs via transient contacts until it is trapped at a bona fide mismatch. A sliding mechanism likely enables MutS proteins to scan long stretches of DNA rapidly, thereby ensuring efficient repair of infrequent aberrations in the double helix. Research support: NSF.