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Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics

Pasi, Marco ; Maddocks, John H. ; Lavery, Richard

In: Nucleic Acids Research, 2015, vol. 43, no. 4, p. 2412-2423

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    Titre
    • Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics
    Auteur
    • Pasi, Marco. Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UM 5086/Université Lyon I, IBCP, 7 passage du Vercors, 69367 Lyon, France
    • Maddocks, John H.. Section de Mathématiques, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
    • Lavery, Richard. Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UM 5086/Université Lyon I, IBCP, 7 passage du Vercors, 69367 Lyon, France
    Type de document
    • Postprint
    Langue
    • Anglais
    Publié dans
    • Nucleic Acids Research, 2015, vol. 43, no. 4, p. 2412-2423. Oxford University Press
    Autre version électronique
    Classification
    • Santé
    Identifiant OAI-PMH
    • oai:doc.rero.ch:296750
    Summary
    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