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Updated: Oct 9, 2026

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes
Published on: November 1, 2012
Structure of an RNA duplex with an unusual G.C pair in wobble-like conformation at 1.6 A resolution
M Perbandt1, M Vallazza, C Lippmann
1Institute of Medical Biochemistry and Molecular Biology, University Hospital Eppendorf, c/o DESY Building 22a, Notkestrasse 85, 22603 Hamburg, Germany.
Abstract:
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% (R(free) = 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'.
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