A Coarse-Grained Simulation Study of the Structures, Energetics, and Dynamics of Linear and Circular DNA with Its Ions

• Published in: Journal of chemical theory and computation 2015-06, Vol.11 (6), p.2813-2826
• Main Authors: Naômé, Aymeric, Laaksonen, Aatto, Vercauteren, Daniel P
• Format: Article
• Language: English
• Subjects: DNA - chemistry; DNA, Circular - chemistry; Ions - chemistry; Molecular Dynamics Simulation; Nucleic Acid Conformation
• ISSN: 1549-9618; 1549-9626; 1549-9626
• DOI: 10.1021/acs.jctc.5b00113

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.