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• W2018205479 abstract "Restricted accessMoreSectionsView PDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmail Cite this article Balaeff A., Koudella C. R., Mahadevan L. and Schulten K. 2004Modelling DNA loops using continuum and statistical mechanics One contribution of 16 to a Theme ‘The mechanics of DNA’Phil. Trans. R. Soc. A.3621355–1371http://doi.org/10.1098/rsta.2004.1384SectionRestricted accessModelling DNA loops using continuum and statistical mechanics One contribution of 16 to a Theme ‘The mechanics of DNA’ A. Balaeff A. Balaeff Beckman Institute and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Google Scholar Find this author on PubMed Search for more papers by this author , C. R. Koudella C. R. Koudella Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK () Google Scholar Find this author on PubMed Search for more papers by this author , L. Mahadevan L. Mahadevan Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK () Google Scholar Find this author on PubMed Search for more papers by this author and K. Schulten K. Schulten Beckman Institute and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Google Scholar Find this author on PubMed Search for more papers by this author A. Balaeff A. Balaeff Beckman Institute and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Google Scholar Find this author on PubMed Search for more papers by this author , C. R. Koudella C. R. Koudella Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK () Google Scholar Find this author on PubMed Search for more papers by this author , L. Mahadevan L. Mahadevan Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK () Google Scholar Find this author on PubMed Search for more papers by this author and K. Schulten K. Schulten Beckman Institute and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Google Scholar Find this author on PubMed Search for more papers by this author Published:15 July 2004https://doi.org/10.1098/rsta.2004.1384AbstractThe classical Kirchhoff elastic–rod model applied to DNA is extended to account for sequence–dependent intrinsic twist and curvature, anisotropic bending rigidity, electrostatic force interactions, and overdamped Brownian motion in a solvent. The zero–temperature equilibrium rod model is then applied to study the structural basis of the function of the lac repressor protein in the lac operon of Escherichia coli. The structure of a DNA loop induced by the clamping of two distant DNA operator sites by lac repressor is investigated and the optimal geometries for the loop of length 76 bp are predicted. Further, the mimicked binding of catabolite gene activator protein (CAP) inside the loop provides solutions that might explain the experimentally observed synergy in DNA binding between the two proteins. Finally, a combined Monte Carlo and Brownian dynamics solver for a worm–like chain model is described and a preliminary analysis of DNA loop–formation kinetics is presented. Previous ArticleNext Article VIEW FULL TEXT DOWNLOAD PDF FiguresRelatedReferencesDetailsCited by Biton Y (2018) Effects of Protein-Induced Local Bending and Sequence Dependence on the Configurations of Supercoiled DNA Minicircles, Journal of Chemical Theory and Computation, 10.1021/acs.jctc.7b01090, 14:4, (2063-2075), Online publication date: 10-Apr-2018. Chatzieleftheriou S, Adendorff M and Lagaros N (2016) Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures, Journal of Chemical Information and Modeling, 10.1021/acs.jcim.6b00356, 56:10, (1963-1978), Online publication date: 24-Oct-2016. Maghsoodi A, Chatterjee A, Andricioaei I and Perkins N (2016) A First Model of the Dynamics of the Bacteriophage T4 Injection Machinery, Journal of Computational and Nonlinear Dynamics, 10.1115/1.4033554, 11:4, Online publication date: 1-Jul-2016. 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Aksimentiev A, Heng J, Timp G and Schulten K (2004) Microscopic Kinetics of DNA Translocation through Synthetic Nanopores, Biophysical Journal, 10.1529/biophysj.104.042960, 87:3, (2086-2097), Online publication date: 1-Sep-2004. Villa E, Balaeff A, Mahadevan L and Schulten K (2004) Multiscale Method for Simulating Protein-DNA Complexes, Multiscale Modeling & Simulation, 10.1137/040604789, 2:4, (527-553), Online publication date: 1-Jan-2004. Towles K, Beausang J, Garcia H, Phillips R and Nelson P (2009) First-principles calculation of DNA looping in tethered particle experiments, Physical Biology, 10.1088/1478-3975/6/2/025001, 6:2, (025001) Kim Y, Kim D and Mayer C (2016) Structural Basis for Elastic Mechanical Properties of the DNA Double Helix, PLOS ONE, 10.1371/journal.pone.0153228, 11:4, (e0153228) This Issue15 July 2004Volume 362Issue 1820Theme Issue ‘The mechanics of DNA’ compiled by J. M. T. Thompson Article InformationDOI:https://doi.org/10.1098/rsta.2004.1384Published by:Royal SocietyPrint ISSN:1364-503XOnline ISSN:1471-2962History: Published online15/07/2004Published in print15/07/2004 License: Citations and impact KeywordsBrownian DynamicsCatabolite Gene Activator Protein (Cap)Lac RepressorElastic–Rod ModelDna LoopsLoop–Formation Kinetics" @default.
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