Crystal structure of a 14 bp RNA duplex with non-symmetrical tandem G center dot U wobble base pairs

Adjacent G . U wobble base pairs are frequently found in rRNA, Atomic struc tures of small RNA motifs help to provide a better understanding of the eff ects of various tandem mismatches on duplex structure and stability, thereb y providing better rules for RNA structure prediction and validation. The c rystal structure of an RNA duplex containing the sequence r(GGUA<(UU)under bar>GC-<(GG)under bar>UACC)(2) has been solved at 2.1 Angstrom resolution u sing experimental phases. Novel refinement strategies were needed for build ing the correct solvent model. At present, this is the only short RNA duple x structure containing 5'-U-U-3'/3'-G-G-5' non-symmetric tandem G . U wobbl e base pairs. In the 14mer duplex, the six central base pairs are all displ aced away from the helix axis, yielding significant changes in local backbo ne conformation, helix parameters and charge distribution that may provide specific recognition sites for biologically relevant ligand binding, The gr eatest deviations from A-form helix occur where the guanine of a wobble bas e pair stacks over a purine from the opposite strand. In this vicinity, the intra-strand phosphate distances increase significantly, and the major gro ove width increases up to 3 Angstrom. Structural comparisons with other sho rt duplexes containing symmetrical tandem G . U or G . T wobble base pairs show that nearest-neighbor sequence dependencies govern helical twist and t he occurrence of cross-strand purine stacks.