A molecular dynamics simulation of double-helical B-DNA including counterions and water.
- 1 October 1985
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 82 (19) , 6537-6540
- https://doi.org/10.1073/pnas.82.19.6537
Abstract
We present the results of an atomic level molecular dynamical simulation of a 5-base-pair fragment of double-helical DNA with inclusion of water and sodium counterions and a complete description of their electrostatic interactions. The shape of the double helix is preserved throughout the simulation, and the helix repeat is calculated to be 10.0, in reasonable agreement with experimental results. The most flexible conformational angles in the structure are the glycosidic angle and the sugar pucker.Keywords
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