Representation of DNA environment : Spiral staircase distribution function
© 2018 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 39(2018), 27 vom: 15. Okt., Seite 2300-2306 |
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| Format: | Online-Aufsatz |
| Sprache: | English |
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2018
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| 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... |
| Zusammenfassung: | © 2018 Wiley Periodicals, Inc. 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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| Beschreibung: | Date Completed 17.09.2019 Date Revised 17.09.2019 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.25549 |