Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics
Fig 4
Conformational combinations of facing phosphate linkages illustrated with CHARMM36.
In C-MDs, the BII-rich facing phosphate linkages adopt three conformational combinations, BI•BI (grey), BI•BII|BII•BI (green) and BII•BII (violet). The course of these combinations versus time (ns) is illustrated for facing phosphate groups of Oligo 4, two BII-rich steps, C5pG6•C19pG20 and T7pA8•T17pA18, and one BI-rich step, G6pT7•A18pC19. For clarity, only a small part of the trajectory is shown here.