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

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'.

Structural basis for recognition ofS-adenosylhomocysteine by riboswitches

“…These nucleotides form a noncanonical G:C wobble as previously observed in domain E of the Thermus flavus 5S rRNA (Perbandt et al 2001). …”

Diversity of Base-pair Conformations and their Occurrence in rRNA Structure and RNA Structural Motifs

“…The C:G Wb conformation was previously observed with C84:G92 in the 1.6 Å resolution crystal structure for domain E in the Thermus flavus 5 S rRNA (PDB, 439D). 46 Interestingly, while C:G Wb is isosteric to U:G Wb, U:G Wb * should be flipped horizontally to be isosteric to U:G Wb (Figure 14(b)). G647:G724 (Ec: G664:G741) in the 16 S rRNA also adopts the conformational arrangement similar to that of the U:G Wb conformation (Figure 14(b)).…”

RNA-Binding Potential of Protoberberine Alkaloids: Spectroscopic and Calorimetric Studies on the Binding of Berberine, Palmatine, and Coralyne to Protonated RNA Structures

“…Importance of cytidine protonation in RNA functions is also known (Oyelere and Strobel, 2000). Few studies on pH-dependent change of RNA structure are also available in the literature ( Jang et al, 1998;Perbandt et al, 2001;Reiter et al, 2004;Sinha et al, 2006). Our laboratory has demonstrated previously that at low ionic strength and low temperature, protonation in RNAs and DNAs with CG sequences leads to a unique structure designated as H L -form (Suresh Kumar et al, 2003;Sinha et al, 2006;Maiti and Suresh Kumar, 2007).…”