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Journal article
Coarse-grained modeling of DNA curvature
The Journal of chemical physics, v 141(16), pp 165103-165103
28 Oct 2014
PMID: 25362344
Featured in Collection : UN Sustainable Development Goals @ Drexel
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. (C) 2014 AIP Publishing LLC.
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Details
- Title
- Coarse-grained modeling of DNA curvature
- Creators
- Gordon S. Freeman - Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USADaniel M. Hinckley - Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USAJoshua P. Lequieu - University of ChicagoJonathan K. Whitmer - Argonne Natl Lab, Div Mat Sci, Argonne, IL 60439 USAJuan J. de Pablo - Argonne Natl Lab, Div Mat Sci, Argonne, IL 60439 USAArgonne National Lab. (ANL), Argonne, IL (United States)
- Publication Details
- The Journal of chemical physics, v 141(16), pp 165103-165103
- Publisher
- Amer Inst Physics
- Number of pages
- 8
- Grant note
- National Science Foundation; National Science Foundation (NSF) U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division; United States Department of Energy (DOE) Wisconsin Alumni Research Foundation University of Chicago Research Computing Center U.S. Department of Energy's Office of Science; United States Department of Energy (DOE) DMR-0832760 / NSF-funded University of Wisconsin Nanoscale Science and Engineering Center UW-Madison DGE-1256259 / Graduate Research Fellowship from the National Science Foundation
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Chemical and Biological Engineering
- Web of Science ID
- WOS:000344589700081
- Scopus ID
- 2-s2.0-84908464352
- Other Identifier
- 991020950707904721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Chemistry, Physical
- Physics, Atomic, Molecular & Chemical