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Biophys J, July 2002, p. 382-406, Vol. 83, No. 1

Accurate Representation of B-DNA Double Helical Structure with Implicit Solvent and Counterions

Lihua Wang,* Brian E. Hingerty,dagger A. R. Srinivasan,Dagger Wilma K. Olson,Dagger and Suse Broyde*

 *Biology Department, New York University, New York, New York 10003,  dagger Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830-6480, and  Dagger Department of Chemistry, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08903 USA

High-resolution nuclear magnetic resonance (NMR) and crystallographic data have been taken to refine the force field used in the torsion angle space nucleic acids molecular mechanics program DUPLEX. The population balance deduced from NMR studies of two carcinogen-modified DNA conformers in equilibrium was used to fine tune a sigmoidal, distance-dependent dielectric function so that reasonable relative energies could be obtained. In addition, the base-pair and backbone geometry from high-resolution crystal structures of the Dickerson-Drew dodecamer was used to re-evaluate the deoxyribose pseudorotation profile and the Lennard-Jones nonbonded energy terms. With a modified dielectric function that assumes a very steep distance-dependent form, a deoxyribose pseudorotation profile with reduced energy barriers between C2'- and C3'-endo minima, and a shift of the Lennard-Jones potential energy minimum to a distance ~0.4 Å greater than the sum of the van der Waals' radii, the sequence-dependent conformational features of the Dickerson-Drew dodecamer in both the solid state and the aqueous liquid crystalline phase are well reproduced. The robust performance of the revised force field, in conjunction with its efficiency through implicit treatment of solvent and counterions, provides a valuable tool for elucidating conformations and structure-function relationships of DNA, including those of molecules modified by carcinogens and other ligands.

Biophys J, July 2002, p. 382-406, Vol. 83, No. 1
© 2002 by the Biophysical Society   0006-3495/02/07/382/25  $2.00


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Copyright © 2002 by the Biophysical Society.