STRUCTURE OF THE PURINE-PYRIMIDINE ALTERNATING RNA DOUBLE HELIX, R(GUAUAUA)D(C), WITH A 3'-TERMINAL DEOXY RESIDUE

The crystal structure of the purine-pyrimidine alternating octameric R NA helix, r(GUAUAUA)d(C), carrying a 3'-terminal deoxycytidine residue , has been determined at 2.2 Angstrom resolution. The molecule crystal lizes in the rhombohedral space group R3 (hexagonal cell constants: a = b = 43.07, c = 59.36 Angstrom;alpha = beta = 90, gamma = 120 degrees ) with one duplex in an asymmetric unit. The structure was solved by m olecular replacement and refined with 83 and 2/3 solvent molecules and 2/3 sodium ions to a final R factor of 15.6% using 1775 reflections ( 86%). The duplexes are approximately linear, their global helix axes a re inclined by 10 degrees with respect to the 3(2)-screw axes, and the y are stacked on top of each other in a head-to-tail fashion. The twis t between the junction base pairs of the stacked duplexes is negligibl e resulting in a discontinuity of the helix backbones and grooves. The sodium ions on the threefold axis play a significant role in the orga nization of the packing network. The helical parameters, particularly the twist and the roll, of this alternating sequence are in accord wit h Calladine's rules. Almost all the 2'-hydroxyl groups are involved in specific hydrogen-bonding interactions, either directly to the sugar ring oxygens O4' on the 3' side, or, through water bridges, to the sug ars, phosphates, or bases. This hydrogen bonding of the 2'-hydroxyl gr oups restrains the conformation of the sugar-phosphate backbone and th e glycosidic torsion angles of this RNA fragment. The lack of intermol ecular packing contacts in the grooves provides a clear picture of the groove solvation.