The post-SCF quantum chemistry characteristics of the energetic heterogeneity of stacked guanine-guanine pairs found in B-DNA and A-DNA crystals

The energies of homo-guanine pairs (5'G/G-3') in stacked conformations found in crystallographic B-DNA and A-DNA were estimated by means of DF-MP2/aDZ method with inclusion of the correction for basis superposition error. The significant heterogeneity was noticed related to the structural properties, the intermolecular interaction enemies, the values of the ionization potential and the localization of the HOMO densities. The direct consequence of polymorphism of DNA is the variation of only two structural parameters defining guanine-guanine stacking. These two distinguishing variables are slide and roll. The rest of base step parameters exhibit similar variability for both A-DNA and B-DNA helices. Besides, the polymorphism of nucleic acid directly influences the stabilization of the guanine stacked pairs favoring slightly attractions in B-DNA. The most frequently occurring intermolecular interaction energies correspond to -4.87 kcal/mol and -4.20 kcal/mol for B-DNA and A-DNA forms, respectively. On the contrary, there are no significant differences in electro-donating properties of G/G pairs found in A-DNA and B-DNA since the most frequently occurring structures are characterized by almost identical IP values for both studied polymorphic forms. Most of G/G stacked complexes (>85%) are characterized by IP values belonging to the interval from 7.6 to 7.8 eV. Finally, the localization of the HOMO densities on guanine pairs was analyzed. Interestingly, irrespectively of the polymorphic form of DNA all three possible situation may take place. One may find such G/G pairs for which HOMO is located mostly on 5'-G, on 3'-G or spread out over both guanine molecules in stacked complex. The N-7 centre of 3'-G is supposed to be the source of such diversity. (C) 2008 Elsevier B.V. All rights reserved.