This Article Full Text Full Text (PDF) Supplement Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Reddy, S. Y. Articles by Karplus, M. Search for Related Content PubMed PubMed Citation Articles by Reddy, S. Y. Articles by Karplus, M.

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids

Swarnalatha Y. Reddy^*, Fabrice Leclerc^*,, and Martin Karplus^*,

^* Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138 USA; Laboratoire de Maturation des ARN et Enzymologie Moléculaire, CNRS-UHP Nancy I UMR 7567, Université Henri Poincaré, Faculté des Sciences, B.P. 239, 54506 Vandoeuvre-lès-Nancy, France; and Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur, 4 rue Blaise Pascal, 67000, Strasbourg, France

Correspondence: Address reprint requests to Martin Karplus, Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138 USA. Tel.: 617-495-1768; Fax: 617-496-3204; E-mail: marci{at}tammy.harvard.edu.

The improvements of the force fields and the more accurate treatment of long-range interactions are providing more reliable molecular dynamics simulations of nucleic acids. The abilities of certain nucleic acid force fields to represent the structural and conformational properties of nucleic acids in solution are compared. The force fields are AMBER 4.1, BMS, CHARMM22, and CHARMM27; the comparison of the latter two is the primary focus of this paper. The performance of each force field is evaluated first on its ability to reproduce the B-DNA decamer d(CGATTAATCG)₂ in solution with simulations in which the long-range electrostatics were treated by the particle mesh Ewald method; the crystal structure determined by Quintana et al. (1992) is used as the starting point for all simulations. A detailed analysis of the structural and solvation properties shows how well the different force fields can reproduce sequence-specific features. The results are compared with data from experimental and previous theoretical studies.

This article has been cited by other articles:

				A. V. Vargiu, P. Ruggerone, A. Magistrato, and P. Carloni Sliding of Alkylating Anticancer Drugs along the Minor Groove of DNA: New Insights on Sequence Selectivity Biophys. J., January 15, 2008; 94(2): 550 - 561. [Abstract] [Full Text] [PDF]

				S. Piana Structure and energy of a DNA dodecamer under tensile load Nucleic Acids Res., December 14, 2005; 33(22): 7029 - 7038. [Abstract] [Full Text] [PDF]

				N. Pastor The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface Biophys. J., May 1, 2005; 88(5): 3262 - 3275. [Abstract] [Full Text] [PDF]

				D. L. Beveridge, G. Barreiro, K. S. Byun, D. A. Case, T. E. Cheatham III, S. B. Dixit, E. Giudice, F. Lankas, R. Lavery, J. H. Maddocks, et al. Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(CpG) Steps Biophys. J., December 1, 2004; 87(6): 3799 - 3813. [Abstract] [Full Text] [PDF]

				P. Varnai and K. Zakrzewska DNA and its counterions: a molecular dynamics study Nucleic Acids Res., August 10, 2004; 32(14): 4269 - 4280. [Abstract] [Full Text] [PDF]