NMR structures of EMCV IRES RNA motifs solved
Sadia Mohammed, Marie M. Phelan, Usman Rasul and Vasudevan Ramesh
(2014) NMR elucidation of the role of Mg2+ in the structure and stability of the conserved RNA motifs of the EMCV IRES element, Organic & Biomolecular Chemistry DOI: 10.1039/c3ob41840e c3ob41840e
The three dimensional solution structures of a highly conserved 16mer RNA, endowed with a classic 'GNRA' tetraloop motif, and a 17mer RNA containing a cytosine-rich heptaloop which is predicted to be a potential receptor for the former RNA, of the I-domain of Encephalomyocarditis virus internal ribosomal entry site (EMCV IRES) RNA element have been determined by NMR spectroscopy. As Mg2+ play important role in the activity of the IRES, the corresponding NMR structures of the Mg2+ bound RNA complexes have also been determined. These RNA NMR structures were calculated to a high degree of precision with low RMSDs and low clash scores and represent the first structures of a type II picornavirus IRES. Analysis of the NMR structures demonstrate that the role of Mg2+ is principally to confer enhanced stability to the RNAs whereby the tetra- and heptaloops can achieve optimum conformation for any RNA-RNA interactions which are crucial for understanding the structure-function relationship of the IRES.