Modeling DNA-bending in the nucleosome: Role of AA periodicity

This paper uses atomistic molecular mechanics within the framework of the JUMNA model to study the bending properties of DNA segments, with emphasis on understanding the role of the 10 bp periodicity associated with AA repeats that has been found to dominate in nucleosomal DNA. The calculations impose a bending potential on 18 bp segments that is consistent with nucleosome structures (i.e., radius of curvature of 4.1 nm), and then determine the energies of the minimum energy structures for different values of the rotational register (a measure of the direction of bending of the DNA) subject to forces derived from the Amber force field (parm99bsc0). The results show that sequences that contain the 10 bp repeats but are otherwise random have a narrow distribution of rotational register values that minimize the energy such that it is possible to combine several minimized structures to give the 147 bp nearly planar loop structure of the nucleosome. The rotational register values that lead to minimum bending energy with 10 bp AA repeats have a narrower minor groove, which points toward the histone interior at the positions of the AA repeats, which is a result that matches the experiments. The calculations also show that these sequences have a relatively flat potential energy landscape for bending to a 4.1 nm radius of curvature. Random sequences that do not have the 10 bp AA repeats have less stable bent structures, and a flat rotational register distribution, such that low energy nearly planar loops are less likely.