PARALLEL DOUBLE-HELICAL DNA - CONFORMATIONAL-ANALYSIS OF REGULAR POLY(DA).POLY(DT) HELICES WITH SEVERAL VARIATIONS OF INTERBASE BONDING

Our conformational analysis of homopolymeric poly(dA).poly(dT) double-helical DNA with a parallel orientation of the sugar-phosphate backbone is consistent with a heteronomic model. We investigated all possible models of helical base stacking and all variations of basepair orientation in the context of the sugar-phosphate backbone. Dihedral angles of the sugar-phosphate backbone and helical parameters of DNA at the conformational energy minimum were determined by potential energy optimization, calculated using atom-atom potentials. The dependence of conformational energy on the type of hydrogen bonding of the bases and the direction of sugar-phosphate linkages is evaluated.