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The electrostatic contribution to DNA base‐stacking interactions
Author(s) -
Friedman Richard A.,
Honig Barry
Publication year - 1992
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360320205
Subject(s) - stacking , chemistry , electrostatics , dielectric , base pair , chemical physics , molecular physics , base (topology) , poisson–boltzmann equation , static electricity , computational chemistry , dna , ion , physics , quantum mechanics , mathematical analysis , biochemistry , mathematics , organic chemistry
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.