DNA Sequence Alignment by Microhomology Sampling during Homologous Recombination

Homologous recombination (HR) mediates the exchange of genetic information between sister or homologous chromatids. During HR, members of the RecA/Rad51 family of recombinases must somehow search through vast quantities of DNA sequence to align and pair single-strand DNA (ssDNA) with a homologous double-strand DNA (dsDNA) template. Here, we use single-molecule imaging to visualize Rad51 as it aligns and pairs homologous DNA sequences in real time. We show that Rad51 uses a length-based recognition mechanism while interrogating dsDNA, enabling robust kinetic selection of 8-nucleotide (nt) tracts of microhomology, which kinetically confines the search to sites with a high probability of being a homologous target. Successful pairing with a ninth nucleotide coincides with an additional reduction in binding free energy, and subsequent strand exchange occurs in precise 3-nt steps, reflecting the base triplet organization of the presynaptic complex. These findings provide crucial new insights into the physical and evolutionary underpinnings of DNA recombination. [Display omitted] •Single-molecule imaging reveals how Rad51 presynaptic complexes interrogate dsDNA•Rad51 quickly samples and rejects any DNA lacking 8-nt tracts of microhomology•Rad51 stably captures DNA harboring 8 nt of microhomology•Subsequent strand invasion occurs in precise 3-nt steps Single-molecule imaging with ssDNA curtains reveals how the Rad51/RecA family of DNA recombinases make use of short tracts of microhomology to interrogate and align homologous DNA sequences.