CRYSTAL-STRUCTURE OF AN ALTERNATING OCTAMER R(GUAUGUA)DC WITH ADJACENT G-CENTER-DOT-U WOBBLE PAIRS

The crystal structure of the RNA duplex, r(GUAUGUA)dC, with a 3'-termi nal deoxy C residue, has been determined at 1.38 Angstrom resolution. The r(GUAUGU) hexameric consensus sequence is present at the exon-intr on junction in pre-mRNAs of yeast and higher eukaryotic organisms. The crystal belongs to the rhombohedral space group R3. The hexagonal uni t cell dimensions are a = b = 39.71 Angstrom, c = 68.15 Angstrom and g amma = 120 degrees with one duplex in the asymmetric unit. The structu re was solved using the molecular replacement method. The final model contains 332 atoms of the duplex and 67 solvent molecules. The R-facto r is 17.6% (R-free of 23.1%) for 4035 reflections with F greater than or equal to 1.5 sigma(F) in the resolution range 10.0 to 1.38 Angstrom . The duplex is of the A-type with a pseudodyad relating the two stran ds. The RNA helix is slightly distorted, in spite of the presence of t wo adjacent G . U wobble base-pairs located at the center of the helix . The twist angle between the wobble pairs, 38.1 degrees, is above the average value and those between the wobble base-pairs and the flankin g Watson-Crick base-pairs, 26.7 degrees and 26.3 degrees, respectively , are lower than the average values. The twist between the junction ba se-pairs are about 24 degrees. The G . U wobble pairs are bridged by w ater molecules and solvated iri the grooves. G . U base-pairs are as s table as the Watson-Crick A . U pairs and only slightly less stable th an the G . C pairs accounting for their frequent occurrence in RNA. (C ) 1997 Academic Press Limited.