Intra-strand stacking interactions in B-DNA crystals characterized by post-SCF quantum chemistry computations

Abstract

The distributions of intermolecular interaction energies (IIE) of all possible 5′-X/Y-3′ (X, Y = A, G, T, C) stacked pairs in conformations exactly matching to intra-strand orientations occurring in crystallographic B-DNA double strands were characterized by quantum chemistry calculations on MP2/aug-cc-pvDZ level. The essential feature of this approach is sampling over meaningful conformations and getting statistically significant data on the energetics of stacking interactions in B-DNA crystals. Based on the most frequently occurring IIE values (in kcal mol⁻¹) the following order of the intra-strand stacking interactions in B-DNA solids is concluded: G/A −10.2 ± 1.1 > A/G −9.2 ± 1.0 ≈ G/C −8.7 ± 1.2 > A/A −8.3 ± 1.0 > A/T −7.7 ± 0.9 > C/G −7.2 ± 0.9 > T/G −6.5 ± 1.3 ≈ A/C −6.2 ± 0.8 ≈ G/T −6.2 ± 1.3 > T/A −5.6 ± 0.9 > G/G −5.1 ± 1.1 > T/C −4.9 ± 0.7 > C/T −4.8 ± 1.1 > T/T −4.7 ± 0.5 > C/A −3.8 ± 0.8 > C/C −1.0 ± 1.0 (standard deviations are provided in parenthesis). Sequence-related structural diversities and SCF and correlation contributions to the stacking interactions are also discussed. The most representative structures of stacked dimers were found based on a clustering protocol.