Block-units method for conformational calculations of large nucleic acid chains. I. Block-units approximation of atomic structure and conformational energy of polynucleotides.
A new block-units method for rapid conformational calculation of large nucleic acid fragments has been developed. Atomic structure of polynucleotides has been approximated by the block-units structure. Each monomer of the polynucleotide consists of three one-center block units: phosphate, ribose, and nucleic base. Full conformational energy of the polynucleotide is separated into two parts. The first part is the energy of the short-range interactions between adjacent block units and is calculated on the basis of the potential energy surface model of the dinucleotide fragment pXp (where X = A, G, T, U, C). The second part is the energy of the middle- and long-range interactions between separated block units, and is calculated as a sum of the effective interaction energies between centers of the block units. The present block-units method is in agreement within the range of +/- 0.5 kcal/mol with the method of the atom-atom potentials, but the former is 30-100-fold faster. The block-units method is recommended for screening of the probable conformations of the large polynucleotide systems.
Vorobjev YuN
Institute of Bioorganic Chemistry, Siberian Division, USSR Academy of Sciences, Novosibirsk.
D055598:Chemical Phenomena; D002627:Chemistry, Physical; D008722:Methods; D009690:Nucleic Acid Conformation; D010710:Phosphates; D011119:Polynucleotides; D012266:Ribose
D010710:Phosphates; D011119:Polynucleotides; D012266:Ribose