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Similarities and differences in interaction of K + and Na + with condensed ordered DNA. A molecular dynamics computer simulation study
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| Zeitschriftentitel: | Nucleic Acids Research |
|---|---|
| Personen und Körperschaften: | , , |
| In: | Nucleic Acids Research, 34, 2006, 2, S. 686-696 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Oxford University Press (OUP)
|
| Schlagwörter: |
| author_facet |
Cheng, Yuhua Korolev, Nikolay Nordenskiöld, Lars Cheng, Yuhua Korolev, Nikolay Nordenskiöld, Lars |
|---|---|
| author |
Cheng, Yuhua Korolev, Nikolay Nordenskiöld, Lars |
| spellingShingle |
Cheng, Yuhua Korolev, Nikolay Nordenskiöld, Lars Nucleic Acids Research Similarities and differences in interaction of K + and Na + with condensed ordered DNA. A molecular dynamics computer simulation study Genetics |
| author_sort |
cheng, yuhua |
| spelling |
Cheng, Yuhua Korolev, Nikolay Nordenskiöld, Lars 1362-4962 0305-1048 Oxford University Press (OUP) Genetics http://dx.doi.org/10.1093/nar/gkj434 <jats:title>Abstract</jats:title><jats:p>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.</jats:p> Similarities and differences in interaction of K + and Na + with condensed ordered DNA. A molecular dynamics computer simulation study Nucleic Acids Research |
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| title |
Similarities and differences in interaction of K + and Na + with condensed ordered DNA. A molecular dynamics computer simulation study |
| title_unstemmed |
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 |
Genetics |
| url |
http://dx.doi.org/10.1093/nar/gkj434 |
| publishDate |
2006 |
| physical |
686-696 |
| description |
<jats:title>Abstract</jats:title><jats:p>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.</jats:p> |
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| author | Cheng, Yuhua, Korolev, Nikolay, Nordenskiöld, Lars |
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| description | <jats:title>Abstract</jats:title><jats:p>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.</jats:p> |
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| imprint_str_mv | Oxford University Press (OUP), 2006 |
| institution | DE-Brt1, DE-Zwi2, DE-D161, DE-Gla1, DE-Zi4, DE-15, DE-Pl11, DE-Rs1, DE-105, DE-14, DE-Ch1, DE-L229, DE-D275, DE-Bn3 |
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| physical | 686-696 |
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| spelling | Cheng, Yuhua Korolev, Nikolay Nordenskiöld, Lars 1362-4962 0305-1048 Oxford University Press (OUP) Genetics http://dx.doi.org/10.1093/nar/gkj434 <jats:title>Abstract</jats:title><jats:p>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.</jats:p> Similarities and differences in interaction of K + and Na + with condensed ordered DNA. A molecular dynamics computer simulation study Nucleic Acids Research |
| spellingShingle | Cheng, Yuhua, Korolev, Nikolay, Nordenskiöld, Lars, Nucleic Acids Research, Similarities and differences in interaction of K + and Na + with condensed ordered DNA. A molecular dynamics computer simulation study, Genetics |
| 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 |
| title_unstemmed | Similarities and differences in interaction of K + and Na + with condensed ordered DNA. A molecular dynamics computer simulation study |
| topic | Genetics |
| url | http://dx.doi.org/10.1093/nar/gkj434 |