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arXiv · 1703.02598

DNA elasticity from coarse-grained simulations: the effect of groove asymmetry

Enrico Skoruppa·Michiel Laleman·Stefanos Nomidis·Enrico Carlon
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Abstract

It is well-established that many physical properties of DNA at sufficiently long length scales can be understood by means of simple polymer models. One of the most widely used elasticity models for DNA is the twistable worm-like chain (TWLC), which describes the double helix as a continuous elastic rod with bending and torsional stiffness. An extension of the TWLC, which has recently received some attention, is the model by Marko and Siggia, who introduced an additional twist-bend coupling, expected to arise from the groove asymmetry. By performing computer simulations of two available versions of oxDNA, a coarse-grained model of nucleic acids, we investigate the microscopic origin of twist-bend coupling. We show that this interaction is negligible in the oxDNA version with symmetric grooves, while it appears in the oxDNA version with asymmetric grooves. Our analysis is based on the calculation of the covariance matrix of equilibrium deformations, from which the stiffness parameters are obtained. The estimated twist-bend coupling coefficient from oxDNA simulations is $G=30\pm1$~nm. The groove asymmetry induces a novel twist length scale and an associated renormalized twist stiffness $\kappa_{\rm t} \approx 80$~nm, which is different from the intrinsic torsional stiffness $C \approx 110$~nm. This naturally explains the large variations on experimental estimates of the intrinsic stiffness performed in the past.

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Enrico Skoruppa, Michiel Laleman, Stefanos Nomidis, Enrico Carlon. 2017-03-07. DNA elasticity from coarse-grained simulations: the effect of groove asymmetry. https://doi.org/10.1063/1.4984039

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