Smc5/6’s multifaceted DNA binding capacities stabilize branched DNA structures (Chang et al., Nature Commun 2022)
Smc5/6 stabilizes DNA junctions. (A) Representative kymograph of a λ DNA tether alternating between LF and HF in the presence of 10 nM LD650-RPA (red), 20 nM Cy3-Smc5/6 (green), and 2 mM ATP. The RPA signals remained on the DNA throughout pulling-relaxation cycles (examples indicated by white arrows). (B) (Top) Summary of the different Smc5/6 binding behaviors on DNA observed in our study. (Bottom) Working model for Smc5/6 binding modes on different types of DNA.
Structural maintenance of chromosomes (SMC) complexes are DNA-based protein machines essential for genome organization and maintenance. Compared to the well-studied cohesin and condensin, the Smc5/6 complex is uniquely involved in DNA replication and repair as well as in viral DNA restriction, but how it accomplishes these diverse functions has remained unclear. Here we use smCFFM to visualize the behavior of Smc5/6 on three different types of DNA that it encounters in vivo: double-stranded (ds) DNA, single-stranded (ss) DNA, and ss-ds DNA junctions. We find that Smc5/6 preferentially associates with junction DNA independent of ATP and accumulates on free ssDNA near the junctions. These interactions stabilize replication forks by preventing ssDNA annealing. On the other hand, we find that ATP binding, but not hydrolysis, enhances Smc5/6’s dynamic binding to dsDNA. These multifaceted DNA binding modes of Smc5/6 provide a molecular basis for understanding its physiological functions.