Coarse-grained modeling of DNA curvature
GS Freeman and DM Hinckley and JP Lequieu and JK Whitmer and JJ de Pablo, JOURNAL OF CHEMICAL PHYSICS, 141, 165103 (2014).
The interaction of DNA with proteins occurs over a wide range of length scales, and depends critically on its local structure. In particular, recent experimental work suggests that the intrinsic curvature of DNA plays a significant role on its protein-binding properties. In this work, we present a coarse grained model of DNA that is capable of describing base-pairing, hybridization, major and minor groove widths, and local curvature. The model represents an extension of the recently proposed 3SPN.2 description of DNA D.M. Hinckley, G.S. Freeman, J.K. Whitmer, and J.J. de Pablo, J. Chem. Phys. 139, 144903 (2013), into which sequence-dependent shape and mechanical properties are incorporated. The proposed model is validated against experimental data including melting temperatures, local flexibilities, dsDNA persistence lengths, and minor groove width profiles. (C) 2014 AIP Publishing LLC.
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