title: 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.
authors.affiliation: Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Gordon S
authors.initials: GS
authors.lastname: Freeman
authors.affiliation: Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Hinckley
authors.affiliation: Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Joshua P
authors.initials: JP
authors.lastname: Lequieu
authors.affiliation: Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.
authors.forename: Jonathan K
authors.initials: JK
authors.lastname: Whitmer
authors.affiliation: Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA and Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Juan J
authors.initials: JJ
authors.lastname: de Pablo
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D009691:Nucleic Acid Denaturation; D044366:Transition Temperature
chemical_list: D004247:DNA