Representation of DNA environment : Spiral staircase distribution function

© 2018 Wiley Periodicals, Inc.

Bibliographische Detailangaben
Veröffentlicht in:Journal of computational chemistry. - 1984. - 39(2018), 27 vom: 15. Okt., Seite 2300-2306
1. Verfasser: Silanteva, Irina (VerfasserIn)
Weitere Verfasser: Komolkin, Andrei V
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2018
Zugriff auf das übergeordnete Werk:Journal of computational chemistry
Schlagworte:Journal Article distribution function hydration shell ionic atmosphere molecular dynamics nucleotides DNA 9007-49-2 Sodium 9NEZ333N27 mehr... Magnesium I38ZP9992A
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520 |a In the present study, we investigated the local structure of DNA and its environment using a new visualization technique. The spiral staircase distribution function (SSDF) is determined as two-dimensional density distribution of atoms of water and ligands in local reference frames linked with each base pair of poly-DNA molecule, either GC or AT. This property of SSDF provides opportunity to study sequence-specific binding of ions, peptides, and other agents derived from a molecular dynamics computer simulation. The spatial structure of double-stranded DNA environment in water solution containing either Mg2+ or Na+ ions was investigated using of SSDF. The distributions of ions around GC and AT base pairs are shown separately. It is observed that Mg2+ ions interact with DNA atoms by means of the layer of water molecules and penetrate into the major groove only. Na+ ions have a direct contact with DNA atoms and penetrate both into the major and minor grooves of DNA. © 2018 Wiley Periodicals, Inc 
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