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

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 super(-1)) the following order of the intra-strand stacking interactions in B-DNA solids is concluded: G/A -10.2 plus or minus 1.1 > A/G -9.2 plus or minus 1.0 approximately G/C -8.7 plus or minus 1.2 > A/A -8.3 plus or minus 1.0 > A/T -7.7 plus or minus 0.9 > C/G -7.2 plus or minus 0.9 > T/G -6.5 plus or minus 1.3 approximately A/C -6.2 plus or minus 0.8 approximately G/T -6.2 plus or minus 1.3 > T/A -5.6 plus or minus 0.9 > G/G -5.1 plus or minus 1.1 > T/C -4.9 plus or minus 0.7 > C/T -4.8 plus or minus 1.1 > T/T -4.7 plus or minus 0.5 > C/A -3.8 plus or minus 0.8 > C/C -1.0 plus or minus 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.