Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps.

TitleNature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps.
Publication TypeJournal Article
Year of Publication2006
AuthorsSponer, Jiri, Jurecka Petr, Marchán Ivan, F Luque Javier, Orozco Modesto, and Hobza Pavel
Date Published2006 Mar 20
KeywordsBase Pairing, Crystallography, DNA, Hydrogen Bonding, Nucleic Acid Conformation, Quantum Theory, Solvents, Static Electricity, Thermodynamics, X-Ray

Base-stacking energies in ten unique B-DNA base-pair steps and some other arrangements were evaluated by the second-order Møller-Plesset (MP2) method, complete basis set (CBS) extrapolation, and correction for triple (T) electron-correlation contributions. The CBS(T) calculations were compared with decade-old MP2/6-31G*(0.25) reference data and AMBER force field. The new calculations show modest increases in stacking stabilization compared to the MP2/6-31G*(0.25) data and surprisingly large sequence-dependent variation of stacking energies. The absolute force-field values are in better agreement with the new reference data, while relative discrepancies between quantum-chemical (QM) and force-field values increase modestly. Nevertheless, the force field provides good qualitative description of stacking, and there is no need to introduce additional pair-additive electrostatic terms, such as distributed multipoles or out-of-plane charges. There is a rather surprising difference of about 0.1 A between the vertical separation of base pairs predicted by quantum chemistry and derived from crystal structures. Evaluations of different local arrangements of the 5’-CG-3’ step indicate a sensitivity of the relative stacking energies to the level of calculation. Thus, describing quantitative relations between local DNA geometrical variations and stacking may be more complicated than usually assumed. The reference calculations are complemented by continuum-solvent assessment of solvent-screening effects.