Base Triplet Stepping by the Rad51/RecA Family of Recombinases during Strand Exchange

Homologous recombination (HR) is an important biological phenomenon because it repairs DNA double-strand break in an error-free way and rearranges genetic information during meiosis promoting genetic diversity. HR is mediated by the Rad51/RecA family of recombinases. The essential roles of the recombinases are searching for the homologous sequence and then exchanging DNA strands. Despite decades of work, the physical basis of the homology search and strand-exchange is not well-defined. Using the single-molecule DNA curtain technique, we reveal that the strand exchange occurs in precise 3-nucleotide (nt) steps for prokaryotic RecA and eukaryotic Rad51 and Dmc1. The free energy difference between the steps is ∼0.3 kBT, which is also conserved from bacteria to human. Molecular dynamics simulation suggests that Watson-Crick basepairing of base triplets is the molecular basis of the triplet stepping. We also show that all the recombinases can step over an internal mismatched base in the strand exchange. But only the meiosis-specific recombinase Dmc1 can step over a mismatched base without any destabilization of base-triplets, which enhances more genetic exchange during meiosis.