PARALLEL RNA HELICES - CONFORMATIONAL-ANALYSIS OF DOUBLE-STRANDED PARALLEL AND 4-STRANDED REGULAR HELICES COMPOSED OF POLY(RA) AND POLY(RU)WITH SEVERAL BASE-BINDING TYPES

Conformational analysis was carried out for parallel homopolymeric RNA helices poly(A).poly(U) in the framework of the heteronomic model, an d for four-stranded poly(U).poly(A).poly(A). poly(U) helices in which the chains with the same bases are parallel and related by a twofold s ymmetry axis. All possible models of base binding into a symmetrical f our-stranded complex and all variants of base orientation relative to the ribose-phosphate backbone were considered. Optimization of potenti al energy calculated using atom-atom potentitals was performed to dete rmine the dihedral angles and the helix parameters corresponding to mi nimal conformational energies of parallel two- and four-stranded RNA h elices. The possibility of stabilization of four-stranded RNA structur es by intramolecular hydrogen bonding was discussed. The results of ca lculations for parallel double-stranded RNA helices were compared with the spectroscopic and X-ray data on parallel poly(A).poly(U) in solut ion and in crystalline fibers, as well as with the earlier analogous c alculations for DNA helical complexes. Such a comparison allowed a num ber of conclusions concerning the structural properties of triple-stra nded complexes poly(dA).2poly(dT) and poly(A).2poly(U), which contain fragments corresponding to parallel heteronomic helices.