Possible configuration of dimers of Gua-Cyt bases. Computation by molecular mechanic models and density functional theory

The energies of interactions between guanine and cytosine in various mutual positions were calculated by the methods of molecular mechanics with refined atom-atom potential functions and the quantum mechanics theory of density functional. Both methods indicate three types of mutual positions of bases in local energy minima. These types correspond to (1) nearly coplanar base positions with intermolecular hydrogen bond formation (base pairing); (2) arrangements of two bases in nearly parallel planes one above another (base stacking); and (3) nearly perpendicular positions of base planes. According to the calculations, the global energy minimum corresponds to the Watson-Crick base pair with three hydrogen bonds. A specific feature of the pair is a transition from many positions of type (2) to positions of type (1) without any energy barrier. This feature is revealed by both methods. Another special feature of this pair is a deviation, for most of mutual base positions, of the amine group atoms from the ring plane, the deviation being more pronounced for Gua. These features are important for understanding the conformational behavior of DNA fragments and the RNA structure.