Coarse-grained modeling of DNA curvature
Abstract
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.
- Publication:
-
Journal of Chemical Physics
- Pub Date:
- October 2014
- DOI:
- 10.1063/1.4897649
- arXiv:
- arXiv:1404.7726
- Bibcode:
- 2014JChPh.141p5103F
- Keywords:
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- Physics - Biological Physics;
- Physics - Chemical Physics;
- Quantitative Biology - Biomolecules
- E-Print:
- 9 pages, 6 figures