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231225s2018 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.25549
|2 doi
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|a pubmed24n0964.xml
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|a eng
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|a Silanteva, Irina
|e verfasserin
|4 aut
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|a Representation of DNA environment
|b Spiral staircase distribution function
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|c 2018
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
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|a Date Completed 17.09.2019
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|a Date Revised 17.09.2019
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|a published: Print-Electronic
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|a Citation Status MEDLINE
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|a © 2018 Wiley Periodicals, Inc.
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|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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|a Journal Article
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|a distribution function
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|a hydration shell
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|a ionic atmosphere
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|a molecular dynamics
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|a nucleotides
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|a DNA
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|a Magnesium
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|a Komolkin, Andrei V
|e verfasserin
|4 aut
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 39(2018), 27 vom: 15. Okt., Seite 2300-2306
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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|g volume:39
|g year:2018
|g number:27
|g day:15
|g month:10
|g pages:2300-2306
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|u http://dx.doi.org/10.1002/jcc.25549
|3 Volltext
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