NMR structures of EMCV IRES RNA motifs solved

Sadia Mohammed, Marie M. Phelan, Usman Rasul and Vasudevan Ramesh

NMR structure of the high conserved and functionally significant 16mer RNA motif endowed with a classic “GNRA” tetraloop of the novel EMCV IRES element.

(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. 

       

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