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A Coarse-Grained Simulation Study of the Structures, Energetics, and Dynamics of Linear and Circular DNA with Its Ions
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). University of Namur, Belgium.
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). Stellenbosch University, South Africa.
Number of Authors: 3
2015 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 6, 2813-2826 p.Article in journal (Refereed) Published
Abstract [en]

We have studied the structural, energetics, and dynamical properties of a variety of linear and circular DNA fragments using a solvent-mediated coarse-grained (CG) model of DNA with explicit ions recently developed by us [Naome et al., J. Chem. Theory Comput., 2014, 10, 3541-3549]. We particularly examined the treatment of electrostatics and determined that a large cutoff is necessary to properly reproduce the DNA flexibility. Moreover, it is crucial to include long-ranged electrostatic interactions: a Particle Mesh Ewald scheme at low resolution is sufficient to avoid structural artifacts. We calculated the ring closure probabilities, as a j-factors, for DNA fragments of different lengths from equilibrium, as well. as restrained molecular dynamics (MD) simulations. The latter force integration method provided accurate results without model fitting. We generated topology and energy maps for DNA minicircles of various lengths and helical densities, at low and high ion concentrations. A general trend for structure compaction is observed, driven by an increase in writhing as the ionic concentration increases. Finally, we applied a reconstruction procedure to generate detailed molecular structures from the various superhelical conformations generated by the CG MD of the DNA minicircles. These pre-equilibrated reconstructed atomistic structures can serve as starting material for atomistic simulations.

Place, publisher, year, edition, pages
2015. Vol. 11, no 6, 2813-2826 p.
National Category
Chemical Sciences Physical Sciences
Identifiers
URN: urn:nbn:se:su:diva-119181DOI: 10.1021/acs.jctc.5b00113ISI: 000356201700040OAI: oai:DiVA.org:su-119181DiVA: diva2:844924
Available from: 2015-08-10 Created: 2015-07-29 Last updated: 2017-12-04Bibliographically approved

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Naome, AymericLaaksonen, Aatto
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