Extended Data Fig. 6: Molecular simulations of the untwisted region of DNA.
From: Cutting antiparallel DNA strands in a single active site
a, b, Unbiased simulations were run starting from the base-flipped out structure (PDB 6DBR) (a), and the zipper structure (b) using the Amber 14 force field. Plotted in each case are the all-atom RMSD to the base-flipped out structure (black) and the zippered structure (red). The structures at the start and end of each run are shown above the RMSD plots. c, d, The analogous results are given for simulations with the CHARMM 36 force field. e, Biased simulations were run from a canonical B-DNA form, in which the terminal residues were driven to mimic the stretched and untwisted DNA observed in the mouse and zebrafish NFC structures. The RMSD and initial and final structures are shown as before.
