Crystal Structure of an RNA Duplex [r(gugcaca)dC]₂ with 3′-Dinucleoside Overhangs Forming a Superhelix

Abstract

Crystal structure of the RNA octamer duplex, [r(gugcaca)dC] ₂, with space group I2₁2₁2₁ and the cell constants a=24.29, b=45.25 and c=73.68Å, has been determined and refined. The structural and packing architecture of the molecule consist of a highly bent six base paired duplex forming a right-handed superhelix stacked in tandem compared to an infinite pseudo- continuous column as is usually present in RNA crystal structures. The super helix could be formed by the head-to-head stacking (g1 over g1 and g9 over g9), the large bend and the twists at the junctions may also be responsible. The sugar-phosphate backbones of the 3′-end dinucleoside overhangs snuggly fit into the minor grooves of adjacent double helical stacks. The 3′-terminal deoxycytidines form antiparallel hemiprotonated trans (C·C)⁺ pairs with symmetry related deoxycytidines, while the penultimate adenines form base triples (a*g·c) with the capping g·c base pairs of the hexamer duplex with the adenine (a7) at one end being syn and at the other anti. These triple interactions are the same as those found in the tetrahymena ribozyme and group I intron.