Simulation of DNA conformation possibilities by means of nonbonded interaction energy calculations of complementary dinucleoside phosphate complexes.

Nonbonded interaction energy calculations were performed for complementary deoxydinucleoside phosphate complexes dApdA with dUpdU and dUpdA with dUpdA. All dihedral and bond angles but nitrogen base angles were the variables in minimization of energy. Complex conformations resembling A- and B-family double-helical conformations were recieved as a result of calculations when intramolecular interaction energy approach minima. Dihedral angles of one molecule of the complex may differ from corresponding angles of another by several degrees. Energy optimal complex conformations in other space regions of conformation parameters were found. Biological consequences of possible dihedral and bond angle changes of double stranded nucleic acids at interactions with other molecules are discussed.