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

Abstract

The crystal structure of a self-complementary RNA duplex r(GGGCGCUCC)2 with non-adjacent G·U and U·G wobble pairs separated by four Watson-Crick base pairs has been determined to 2.5 Å resolution. Crystals belong to the space group R3; a = 33.09 Å, α = 87.30°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 disordered and there are no electron densities, but the 3' penultimate phosphates are observed. As expected, the wobble pairs are displaced with guanine towards the minor groove and uracil towards the major groove. The largest twist angles (37.70 and 40.57°) are at steps G1·C17/G2·U16 and U7·G11/C8·G10, while the smallest twist angles (28.24 and 27.27°) are 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°) at the wobble sites and a third kink at the central G5 site which may be attributed to trans α (O5'-P), trans γ (C4'-C5') backbone conformations. The 2'-hydroxyl groups in the minor groove form inter-column hydrogen bonding, either directly or through water molecules.