The electrostatic contribution to DNA base‐stacking interactions

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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 propeller. The Lennard–Jones stacking energy in ideal B‐DNA is found to be essentially independent of sequence.