[Eight types of stacking interaction in dinucleotides. Conformational analysis of ApA, ApC, CpA, CpC, GpG]

On the basis of general stereochemical considerations the classification of the stacking state of dinucleoside phosphate (DNP) including eight types of stacks of nucleic bases has been suggested. With the use of the algorithm, which makes possible determination of the backbone conformation for the given nucleic bases arrangement, the stacking conformes of DNP were analysed by atom-atom potential method. For all compounds different types of stacking conformes were obtained with energy values lower than that for the unstacking state. It follows from the results of calculations that for description of the conformational situation of DNP in solution the "non-canonical" conformers should be born in mind. In particular the forms having different sugar conformations in Np- and in pN-parts of the dimers are of interest. The effect of choice of the atom-atom potential functions on optimal conformation of DNP is discussed. For single-stranded RNA several regular and non-regular structures are proposed.