Conversation 11: No. 2

category image Volume: Conversation 11
Issue Number 2
May 2000
ISBN 0-940030-81-0

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

Crystal structure of the RNA octamer duplex, [r(gugcaca)dC]2, with space group I21212 1 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 pseudocontinuous 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.

Shome Nath Mitra
Roopa Biswas
Ke Shi
Muttaiya Sundaralingam

Biological Macromolecular Structure Center
Departments of Chemistry and Biochemistry
The Ohio State University
012 Rightmire Hall
1060 Carmack Road
Columbus, OH 43210


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