DNA mismatch repair (MMR) is critical for the maintenance of genomic stability. MMR is initiated by recognition of DNA mismatches by the protein, MutS, which subsequently recruits downstream repair factors. To better understand the mechanism by which MutS identifies and specifically binds mismatched basepairs embedded in random DNA sequences, we monitored the interaction between MutS and DNA substrates using atomic force microscopy (AFM). An alpha-shaped DNA loop formed by the interaction between MutS and DNA, which was independent of whether or not a mismatch was present in the DNA substrate. These data indicate that MutS associates with DNA non-specifically and forms an alpha-loop interaction with the DNA substrate. in this conformation, MutS is able to scan two arms of DNA simultaneously for each MutS dimer formed. (C) 2008 Elsevier Inc. All rights reserved.