Crystal structure of an alternating octamer r(GUAUGUA)dC with adjacent G·U wobble pairs

The crystal structure of the RNA duplex, r(GUAUGUA)dC, with a 3'-terminal deoxy C residue, has been determined at 1.38 Å resolution. The r(GUAUGU) hexameric consensus sequence is present at the exon-intron junction in pre-mRNAs of yeast and higher eukaryotic organisms. The crystal belongs to the rhombohedral space group R3. The hexagonal unit cell dimensions are a = b = 39.71 Å, c = 68.15 Å and γ = 120°with one duplex in the asymmetric unit. The structure was solved using the molecular replacement method. The final model contains 332 atoms of the duplex and 67 solvent molecules. The R-factor is 17.6% (R(free) of 23.1%) for 4035 reflections with F ≤ 1.5σ(F) in the resolution range 10.0 to 1.38 Å. The duplex is of the A-type with a pseudodyad relating the two strands. The RNA helix is slightly distorted, in spite of the presence of two adjacent G·U wobble base-pairs located at the center of the helix. The twist angle between the wobble pairs, 38.1°, is above the average value and those between the wobble base-pairs and the flanking Watson-Crick base-pairs, 26.7°and 26.3°, respectively, are lower than the average values. The twist between the junction base-pairs are about 24°. The G·U wobble pairs are bridged by water molecules and solvated in the grooves. G·U base-pairs are as stable as the Watson-Crick A·U pairs and only slightly less stable than the G·C pairs accounting for their frequent occurrence in RNA.