Structure of an RNA duplex with an unusual G.C pair in wobble-like conformation at 1.6 A 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% (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'.
Perbandt
M
M
Institute of Medical Biochemistry and Molecular Biology, University Hospital Eppendorf, c/o DESY Building 22a, Notkestrasse 85, 22603 Hamburg, Germany.
Vallazza
M
M
Lippmann
C
C
Betzel
C
C
Erdmann
V A
VA
D020029:Base Pairing; D001483:Base Sequence; D018360:Crystallography, X-Ray; D003596:Cytosine; D006147:Guanine; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry*; D012329:RNA, Bacterial / Q000737:chemistry; D012330:RNA, Double-Stranded / Q000737:chemistry*; D012341:RNA, Ribosomal, 5S / Q000737:chemistry*; D013824:Thermus
D009843:Oligoribonucleotides; D012329:RNA, Bacterial; D012330:RNA, Double-Stranded; D012341:RNA, Ribosomal, 5S; D006147:Guanine; D003596:Cytosine