The central step in eukaryotic homologous recombination (HR) is ATP-dependent DNA strand exchange mediated by the Rad51 recombinase. In this process, Rad51 assembles on single-stranded DNA (ssDNA) to yield a helical filament that is able to search for and invade a homologous double-stranded DNA (dsDNA), leading to strand separation in the dsDNA and formation of new base pairs between the initiating ssDNA and the complementary strand in the duplex partner. Here we have used cryo-electron microscopy (cryo-EM) to solve the structures of human RAD51 in complex with DNA molecules in their presynaptic and post-synaptic states at near atomic resolution. Our structures revealed both conserved and distinct structural features of the RAD51-DNA complexes in comparison with its prokaryotic counterpart. Importantly, we have also captured the structure of an arrested synaptic complex. The results provide insights into the molecular mechanism of DNA homology search and strand exchange processes.
Homologous recombination (HR) is a primary DNA double-strand breaks (DSBs) repair mechanism. The recombinases Rad51 and Dmc1 are highly conserved in the RecA family; Rad51 is mainly responsible for DNA repair in somatic cells during mitosis while Dmc1 only works during meiosis in germ cells. This spatiotemporal difference is probably due to their distinctive mismatch tolerance during HR: Rad51 does not permit HR in the presence of mismatches, whereas Dmc1 can tolerate certain mismatches. Here, the cryo-EM structures of Rad51–DNA and Dmc1–DNA complexes revealed that the major conformational differences between these two proteins are located in their Loop2 regions, which contain invading single-stranded DNA (ssDNA) binding residues and double-stranded DNA (dsDNA) complementary strand binding residues, stabilizing ssDNA and dsDNA in presynaptic and postsynaptic complexes, respectively. By combining molecular dynamic simulation and single-molecule FRET assays, we identified that V273 and D274 in the Loop2 region of human RAD51 (hRAD51), corresponding to P274 and G275 of human DMC1 (hDMC1), are the key residues regulating mismatch tolerance during strand exchange in HR. This HR accuracy control mechanism provides mechanistic insights into the specific roles of Rad51 and Dmc1 in DNA double-strand break repair and may shed light on the regulatory mechanism of genetic recombination in mitosis and meiosis.
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