title: The electrostatic contribution to DNA base-stacking interactions.
abstract: Base-stacking and phosphate-phosphate interactions in B-DNA are studied using the finite difference Poisson-Boltzmann equation. Interaction energies and dielectric constants are calculated and compared to the predictions of simple dielectric models. No extant simple dielectric model adequately describes phosphate-phosphate interactions. Electrostatic effects contribute negligibly to the sequence and conformational dependence of base-stacking interactions. Electrostatic base-stacking interactions can be adequately modeled using the Hingerty screening function. The repulsive and dispersive Lennard-Jones interactions dominate the dependence of the stacking interactions on roll, tilt, twist, and propellor. The Lennard-Jones stacking energy in ideal B-DNA is found to be essentially independent of sequence.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032.
authors.forename: R A
authors.initials: RA
authors.lastname: Friedman
authors.forename: B
authors.initials: B
authors.lastname: Honig
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004563:Electrochemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA