title: Analyzing ion distributions around DNA.
abstract: We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact with the nucleic and are coupled to its conformational fluctuations. The data from this approach is presented as ion populations or ion densities (in units of molarity) and can be analyzed in radial, angular and longitudinal coordinates using 1D or 2D graphics. It is also possible to regenerate 3D densities in Cartesian space. This approach makes it easy to understand and compare ion distributions and also allows the calculation of average ion populations in any desired zone surrounding a nucleic acid without requiring references to its constituent atoms. The method is illustrated using microsecond molecular dynamics simulations for two different DNA oligomers in the presence of 0.15 M potassium chloride. We discuss the results in terms of convergence, sequence-specific ion binding and coupling with DNA conformation.
authors.affiliation: Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UMR 5086/Univ. Lyon I, IBCP, 7 Passage du Vercors, 69367 Lyon, France richard.lavery@ibcp.fr.
authors.forename: Richard
authors.initials: R
authors.lastname: Lavery
authors.affiliation: Section de Mathématiques, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland.
authors.forename: John H
authors.initials: JH
authors.lastname: Maddocks
authors.affiliation: Section de Mathématiques, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland.
authors.forename: Marco
authors.initials: M
authors.lastname: Pasi
authors.affiliation: Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UMR 5086/Univ. Lyon I, IBCP, 7 Passage du Vercors, 69367 Lyon, France.
authors.forename: Krystyna
authors.initials: K
authors.lastname: Zakrzewska
mesh_terms: D002712:Chlorides / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D007477:Ions / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D010758:Phosphorus / Q000737:chemistry; D011188:Potassium / Q000737:chemistry
chemical_list: D002712:Chlorides; D007477:Ions; D010758:Phosphorus; D004247:DNA; D011188:Potassium