title: Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics.
abstract: Microsecond molecular dynamics simulations of B-DNA oligomers carried out in an aqueous environment with a physiological salt concentration enable us to perform a detailed analysis of how potassium ions interact with the double helix. The oligomers studied contain all 136 distinct tetranucleotides and we are thus able to make a comprehensive analysis of base sequence effects. Using a recently developed curvilinear helicoidal coordinate method we are able to analyze the details of ion populations and densities within the major and minor grooves and in the space surrounding DNA. The results show higher ion populations than have typically been observed in earlier studies and sequence effects that go beyond the nature of individual base pairs or base pair steps. We also show that, in some special cases, ion distributions converge very slowly and, on a microsecond timescale, do not reflect the symmetry of the corresponding base sequence.
authors: Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UM 5086/Université Lyon I, IBCP, 7 passage du Vercors, 69367 Lyon, France.
authors: Marco
authors: M
authors: Pasi
authors: Section de Mathématiques, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland.
authors: John H
authors: JH
authors: Maddocks
authors: Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UM 5086/Université Lyon I, IBCP, 7 passage du Vercors, 69367 Lyon, France richard.lavery@ibcp.fr.
authors: Richard
authors: R
authors: Lavery
mesh_terms: D001483:Base Sequence; D002414:Cations, Monovalent / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011188:Potassium / Q000737:chemistry*
chemical_list: D002414:Cations, Monovalent; D004247:DNA; D011188:Potassium