Asymmetric dynamics in 601 nucleosomes.

(A) Free energy curves of DNA wrapping for the left (in red) and right (in blue) halves of assembled nucleosome at 400 mM. Only the structural ensemble corresponding to the state N, i.e., complete nucleosome, in the MSM ( Fig 2 ) is used. The free energy at the complete wrapping of 70 bp is set to zero. (B) For the tetrasome states including T, T R and T L , we plot the probability of the positions of the unbound H2A/H2B dimers on the left (in red) and the right (in blue) sides of the 601 DNA. The DNA position corresponds to the base pair of the phosphate group that is closest to residue ARG29 on the H2A histone (as described in Methods). On the left side the dimer has a much higher probability to be localized at the same position as when bound to the H3/H4 tetramer (indicated by the black dotted line), facilitating successful assembly. On top of the graph, we align each side of the 601 sequence to the DNA position axis (left side in red, right side in blue).