Solvent-Induced DNA Conformational Transition

by: B Gu, FS Zhang, ZP Wang, HY Zhou

Physical Review Letters, Vol. 100, No. 8. (2008)

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Abstract

Modified water models with scaled charges are used to investigate solvent polarity effects on DNA structure. Several intensive molecular dynamics simulations of the DNA EcoRI dodecamer d(CGCGAATTCGCG) in different model solvents are performed. When the polarity of the solvent molecule decreases, from overpolarized to less polarized, DNA experiences the conformational transitions of constrainedB form(A-B)mixA form. We demonstrate that one important cause of these structure changes is the competition between hydration and direct cation coupling to the free oxygen atoms in the phosphate groups on DNA backbones.

@article{citeulike:2767689, abstract = {Modified water models with scaled charges are used to investigate solvent polarity effects on DNA structure. Several intensive molecular dynamics simulations of the DNA EcoRI dodecamer d(CGCGAATTCGCG) in different model solvents are performed. When the polarity of the solvent molecule decreases, from overpolarized to less polarized, DNA experiences the conformational transitions of constrainedB form(A-B)mixA form. We demonstrate that one important cause of these structure changes is the competition between hydration and direct cation coupling to the free oxygen atoms in the phosphate groups on DNA backbones.}, author = {Gu, B. and Zhang, F. S. and Wang, Z. P. and Zhou, H. Y. }, citeulike-article-id = {2767689}, doi = {10.1103/PhysRevLett.100.088104}, journal = {Physical Review Letters}, keywords = {2008, biology, people}, number = {8}, posted-at = {2008-05-08 00:29:02}, priority = {2}, publisher = {APS}, title = {Solvent-Induced DNA Conformational Transition}, url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal\&id=PRLTAO000100000008088104000001\&idtype=cvips\&gifs=yes}, volume = {100}, year = {2008} }

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TY - JOUR ID - citeulike:2767689 TI - Solvent-Induced DNA Conformational Transition JF - Physical Review Letters VL - 100 IS - 8 PB - APS N2 - Modified water models with scaled charges are used to investigate solvent polarity effects on DNA structure. Several intensive molecular dynamics simulations of the DNA EcoRI dodecamer d(CGCGAATTCGCG) in different model solvents are performed. When the polarity of the solvent molecule decreases, from overpolarized to less polarized, DNA experiences the conformational transitions of constrainedB form(A-B)mixA form. We demonstrate that one important cause of these structure changes is the competition between hydration and direct cation coupling to the free oxygen atoms in the phosphate groups on DNA backbones. KW - 2008 KW - biology KW - people AU - Gu, B AU - Zhang, FS AU - Wang, ZP AU - Zhou, HY PY - 2008/// UR - http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PRLTAO000100000008088104000001&idtype=cvips&gifs=yes ER -

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