Structure of an RNA duplex with an unusual G center dot C pair in wobble-like conformation at 1.6 angstrom resolution

The structure of the RNA duplex r(CUGGGCGG).r(CCGCCUGG) has been determined at 1.6 Angstrom resolution and refined to a final R factor of 18.3% (R-fre e = 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 formatio n is found. Owing to the observed hydrogen-bond network, it is proposed tha t the cytosine is protonated at position N3. The unusual base-pair formatio n is presumably strained by intermolecular interactions. In this context, c rystal packing and particular intermolecular contacts may have direct influ ence on the three-dimensional structure. Furthermore, this structure includ es two G.U wobble base pairs in tandem conformation, with the purines formi ng a so-called 'cross-strand G stack'.