Crystal structure of an RNA duplex r(G GCGC CC)(2) with non-adjacent G center dot U base pairs

The crystal structure of a self-complementary RNA duplex r(G (G) under bar GCGC<(U)Yunder bar>CC)(2) with non-adjacent G . U and U . G wobble pairs se parated by four Watson-Crick base pairs has been determined to 2.5 Angstrom resolution. Crystals belong to the space group R3; a = 33.09 Angstrom, alp ha = 87.30 degrees with a pseudodyad related duplex in the asymmetric unit. The structure was refined to a final R-work Of 17.5% and R-free of 24.0%. The duplexes stack head-to-tail forming infinite columns with virtually no twist at the junction steps. The 3'-terminal cytosine nucleosides are disor dered and there are no electron densities, but the 3' penultimate phosphate s are observed. As expected, the wobble pairs are displaced with guanine to wards the minor groove and uracil towards the major groove. The largest twi st angles (37.70 and 40.57 degrees) are at steps G1 . C17/G2 . U16 and U7 . G11/C8 . G10, while the smallest twist angles (28.24 and 27.27 degrees) ar e at G2 . U16/G3 . C15 and C6 . G12/U7 . G11 and conform to the pseudo-dyad symmetry of the duplex. The molecule has two unequal kinks (17 and 11 degr ees) at the wobble sites and a third kink at the central G5 site which may be attributed to trans alpha (O5'-P), trans gamma (C4'-C5') backbone confor mations. The 2'-hydroxyl groups in the minor groove form inter-column hydro gen bonding, either directly or through water molecules.