Figure 4: Close contacts give rise to strong internucleosomal interactions.

(A) Illustration of the simulation protocol employed to mimic the nucleosome unbinding pathway dictated by the DNA origami device.⁴⁴ The three configurations, A1, A2, and A3, corresponding to the three cyan dots in part B at distances 62.7, 80.2, and 96.3Å. For comparison, a tightly bound configuration uncovered in simulations without any restraints of nucleosome movement is shown as A1’. The number of contacts formed by histone tails and DNA (Htail-DNA) and by histone core and DNA (Hcore-DNA) from different nucleosomes are shown for A1 and A1’. (B) Free energy profile as a function of the distance between the geometric centers of the two nucleosomes, computed from unrestrained (black) and DNA origami-restrained simulations (red). Error bars were computed as the standard deviation of three independent estimates. (C) Average inter-nucleosomal contacts between DNA and histone tail (orange) and core (blue) residues, computed from unrestrained and DNA origami-restrained simulations. Error bars were computed as the standard deviation of three independent estimates.