Structure of an RNA duplex with an unusual G·C pair in wobble-like conformation at 1.6 Å resolution

The structure of the RNA duplex r(CUGGGCGG)·r(CCGCCUGG) has been determined at 1.6 A resolution and refined to a final R factor of 18.3% (Rfree = 24.1%). The sequence of the RNA fragment resembles domain E of Thermus flavus 5S rRNA. A previously undescribed wobble-like G·C base-pair formation is found. Owing to the observed hydrogen-bond network, it is proposed that the cytosine is protonated at position N3. The unusual base-pair formation is presumably strained by intermolecular interactions. In this context, crystal packing and particular intermolecular contacts may have direct influence on the three-dimensional structure. Furthermore, this structure includes two G·U wobble base pairs in tandem conformation, with the purines forming a so-called `cross-strand G stack'.