Transient DNA wrapping process from local contact deformation

The transient process of DNA wrapping of a nanoparticle as a simplified model of nucleosomal DNA can offer the necessary condition to access the reversible and stimuli-responsive helical buckling conformation. Elaborating Marko and Shiggia model applied to this simplified wrapping conformation explains the role of coupling elasticity between 3DNA variables and the range of the artificial thermal fluctuation, which is quantitatively shown as one of the necessary conditions for the wrapping process in coarse-grained molecular dynamics (CGMD) simulation whose small random energy is found to be quintessential to form wrapping conformation. The activation of wrapping and its propagation along the dsDNA strand is analyzed using each type of bend-twist coupling based on how much energy is consumed to draw a curvature for 1.7 turns. The spatiotemporal distribution from each type of rotational and translational variables from the trajectory calculated by CGMD perceives the role of major-minor groove to form 1.7 turns and the mechanism of the relatively slow wrapping speed caused by several sequence components in dsDNA strand parallel to the importance of curvature coupling for forming superhelix.