Figure 4.

Mechanistic insights from molecular simulations. (A) Long timescale molecular dynamics (MD) simulations reporting a large-scale opening of the Nuc (indicated by the arrow in green). (B) Outward bending of Nuc along ∼4 μs MD trajectories (in two replicates), shown through the time evolution of the center of mass distance between the REC2 and Nuc domains (top), and the angle of Nuc with respect to the RuvC domain (bottom). (C) Comparison of the binding free energy between the association of the stem loop (green) and linear ssDNA (purple) with Cas12a using the MM-GBSA solvation method.