title: A coarse-grained simulation study of the structures, energetics, and dynamics of linear and circular DNA with its ions.
abstract: 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 [Naômé 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 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.
authors.affiliation: Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, University of Namur , 5000 Namur, Belgium.|Namur Medicine & Drug Innovation Center (NAMEDIC), University of Namur , 5000 Namur, Belgium.|Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University , 10691 Stockholm, Sweden.|Science for Life Laboratory, 17121 Solna, Sweden.
authors.forename: Aymeric
authors.initials: A
authors.lastname: Naômé
authors.affiliation: Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University , 10691 Stockholm, Sweden.|Science for Life Laboratory, 17121 Solna, Sweden.|Stellenbosch Institute of Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University , 7600 Stellenbosch, South Africa.
authors.forename: Aatto
authors.initials: A
authors.lastname: Laaksonen
authors.affiliation: Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, University of Namur , 5000 Namur, Belgium.|Namur Medicine & Drug Innovation Center (NAMEDIC), University of Namur , 5000 Namur, Belgium.
authors.forename: Daniel P
authors.initials: DP
authors.lastname: Vercauteren
mesh_terms: D004247:DNA / Q000737:chemistry*; D004270:DNA, Circular / Q000737:chemistry; D007477:Ions / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation
chemical_list: D004270:DNA, Circular; D007477:Ions; D004247:DNA