Fig. 4: Molecular dynamics (MD) simulations illustrating dsDNA conformational changes during RAD51-mediated D-loop initiation.

a The hydrogen bond distance variation between two specific nucleotide base pairs during the initiation of D-loop formation. The blue line indicates the distance variation for the base-pair 1 (A–T base pair hydrogen bond distance between the N1 atom of adenine and the N3 atom of thymine); the purple line indicated the distance variation for the base-pair 2 (A–T base pair hydrogen bond distance between the N1 atom of adenine and the N3 atom of thymine). Source data are provided as a Source Data file. b Snapshots of RAD51–dsDNA interaction at four key time points (1 ps, 10 ns, 19 ns, and 47 ns). The base-pair opening occurs around 19 ns. RAD51 is rendered as a surface colored by electrostatic potential (blue, positive; red, negative). dsDNA is shown in a cartoon representation. Regions of base-pair opening are highlighted with blue circles, and the positively charged Arg303–Arg306^N+7 region is outlined with a green dashed box. c–f Top panels: Cartoon schematic representations showing nucleotide base-pair interactions at key simulation time points (1 ps, 10 ns, 19 ns, and 47 ns), depicting the progressive disruption of base pairs during dsDNA bending. Bottom panels: Structural snapshots illustrating the corresponding dsDNA bending conformations at 1 ps, 10 ns, 19 ns, and 47 ns, respectively.