Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics

Journal of the American Chemical Society vol. 117  p. 5001-5002  DOI: 10.1021/ja00122a034  Published: 1995-05-01 

Darrin M. York [ ] , Weitao Yang, Hsing Lee, Tom A. Darden, Lee G. Pedersen

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The relationship between DNA structure and function is fundamental to the understanding of biological processes. Currently, the most reliable source of biomolecular structural information comes from X-ray crystallographic data. Recent advances in theoretical modeling techniques have allowed molecular simulations to approach the accuracy obtainable from X-ray crystallography for proteins. We report the results of a 2.2 ns simulation of the B-DNA dodecamer d[CGCGAATTCGCG12 in a crystal unit cell, and demonstrate that, with rigorous accommodation of long-range forces, molecular simulation may be extended to provide atomic level accuracy of polynucleotide structures.