Double-stranded DNA is among the stiffest biopolymers, whose bending propensity crucially influences many vital biological processes. It is not fully understood which among the two most likely forces, electrostatic self-repulsion or base pair stacking, plays a dominant role in determining the DNA's unique rigidity. Different theoretical and experimental studies to date have yielded contradictory results on this issue. We address this important question by means of Molecular Dynamics (MD) simulations using both atomistic and coarse-grained force fields. Particularly, our accurate coarse-grained model for the double-stranded DNA with explicit mobile ions, derived systematically from underlying atomistic MD simulations, is utilized in the present study. Using two independent sets of calculations, we found that electrostatic and non-electrostatic effects play a comparable role in maintaining DNA's stiffness. Our findings differ  substantially from predictions from existing theories for DNA rigidity and may indicate that a new conceptual understanding needs to be developed.

Understanding the physical mechanisms controlling DNA rigidity: Coarse-grained Molecular Dynamics simulation study

244th National Meeting (2012)

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