A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions.
Advances in computer power, methodology, and empirical force fields now allow routine "stable" nanosecond-length molecular dynamics simulations of DNA in water. The accurate representation of environmental influences on structure remains a major, unresolved issue. In contrast to simulations of A-DNA in water (where an A-DNA to B-DNA transition is observed) and in pure ethanol (where disruption of the structure is observed), A-DNA in approximately 85% ethanol solution remains in a canonical A-DNA geometry as expected. The stabilization of A-DNA by ethanol is likely due to disruption of the spine of hydration in the minor groove and the presence of ion-mediated interhelical bonds and extensive hydration across the major groove.
Cheatham
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Pittsburgh Supercomputing Center, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.
Crowley
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Fox
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Kollman
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D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D000431:Ethanol; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D014867:Water
D014867:Water; D000431:Ethanol; D004247:DNA