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Similarities and differences in interaction of K(+) and Na(+) with condensed ordered DNA. A molecular dynamics computer simulation study

Four 20 ns molecular dynamics simulations have been performed with two counterions, K(+) or Na(+), at two water contents, 15 or 20 H(2)O per nucleotide. A hexagonal simulation cell comprised of three identical DNA decamers [d(5′-ATGCAGTCAG) × d(5′-TGACTGCATC)] with periodic boundary condition along...

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Autores principales: Cheng, Yuhua, Korolev, Nikolay, Nordenskiöld, Lars
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1356527/
https://www.ncbi.nlm.nih.gov/pubmed/16449204
http://dx.doi.org/10.1093/nar/gkj434
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author Cheng, Yuhua
Korolev, Nikolay
Nordenskiöld, Lars
author_facet Cheng, Yuhua
Korolev, Nikolay
Nordenskiöld, Lars
author_sort Cheng, Yuhua
collection PubMed
description Four 20 ns molecular dynamics simulations have been performed with two counterions, K(+) or Na(+), at two water contents, 15 or 20 H(2)O per nucleotide. A hexagonal simulation cell comprised of three identical DNA decamers [d(5′-ATGCAGTCAG) × d(5′-TGACTGCATC)] with periodic boundary condition along the DNA helix was used. The simulation setup mimics the DNA state in oriented DNA fibers or in crystals of DNA oligomers. Variation of counterion nature and water content do not alter averaged DNA structure. K(+) and Na(+) binding to DNA are different. K(+) binds to the electronegative sites of DNA bases in the major and the minor grooves, while Na(+) interacts preferentially with the phosphate groups. Increase of water causes a shift of both K(+) and Na(+) from the first hydration shell of O1P/O2P and of the DNA bases in the minor groove with lesser influence for the cation binding to the bases in the major groove. Mobility of both water and cations in the K–DNA systems is faster than in the Na–DNA systems: Na(+) organizes and immobilizes water structure around itself and near DNA while for K(+) water is less organized and more dynamic.
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spelling pubmed-13565272006-02-01 Similarities and differences in interaction of K(+) and Na(+) with condensed ordered DNA. A molecular dynamics computer simulation study Cheng, Yuhua Korolev, Nikolay Nordenskiöld, Lars Nucleic Acids Res Article Four 20 ns molecular dynamics simulations have been performed with two counterions, K(+) or Na(+), at two water contents, 15 or 20 H(2)O per nucleotide. A hexagonal simulation cell comprised of three identical DNA decamers [d(5′-ATGCAGTCAG) × d(5′-TGACTGCATC)] with periodic boundary condition along the DNA helix was used. The simulation setup mimics the DNA state in oriented DNA fibers or in crystals of DNA oligomers. Variation of counterion nature and water content do not alter averaged DNA structure. K(+) and Na(+) binding to DNA are different. K(+) binds to the electronegative sites of DNA bases in the major and the minor grooves, while Na(+) interacts preferentially with the phosphate groups. Increase of water causes a shift of both K(+) and Na(+) from the first hydration shell of O1P/O2P and of the DNA bases in the minor groove with lesser influence for the cation binding to the bases in the major groove. Mobility of both water and cations in the K–DNA systems is faster than in the Na–DNA systems: Na(+) organizes and immobilizes water structure around itself and near DNA while for K(+) water is less organized and more dynamic. Oxford University Press 2006 2006-01-30 /pmc/articles/PMC1356527/ /pubmed/16449204 http://dx.doi.org/10.1093/nar/gkj434 Text en © The Author 2006. Published by Oxford University Press. All rights reserved
spellingShingle Article
Cheng, Yuhua
Korolev, Nikolay
Nordenskiöld, Lars
Similarities and differences in interaction of K(+) and Na(+) with condensed ordered DNA. A molecular dynamics computer simulation study
title Similarities and differences in interaction of K(+) and Na(+) with condensed ordered DNA. A molecular dynamics computer simulation study
title_full Similarities and differences in interaction of K(+) and Na(+) with condensed ordered DNA. A molecular dynamics computer simulation study
title_fullStr Similarities and differences in interaction of K(+) and Na(+) with condensed ordered DNA. A molecular dynamics computer simulation study
title_full_unstemmed Similarities and differences in interaction of K(+) and Na(+) with condensed ordered DNA. A molecular dynamics computer simulation study
title_short Similarities and differences in interaction of K(+) and Na(+) with condensed ordered DNA. A molecular dynamics computer simulation study
title_sort similarities and differences in interaction of k(+) and na(+) with condensed ordered dna. a molecular dynamics computer simulation study
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1356527/
https://www.ncbi.nlm.nih.gov/pubmed/16449204
http://dx.doi.org/10.1093/nar/gkj434
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