The structure, kinetics, and interactions of the conserved 16mer and 15mer RNA motifs of the internal ribosome entry site (IRES) of the Foot-and-Mouth Disease virus (FMDV), have been investigated by homonuclear and heteronuclear NMR techniques. The 16mer RNA is endowed with a classic GNRA tetraloop motif, which is essential for IRES activity and the 15mer RNA motif is a potential tetraloop receptor. We have determined three high resolution NMR solution structures of the 16mer apo-RNA, the 16mer Mg2+ RNA complex and the 15mer apo-RNA with RMSDs of 0.17Å, 0.16Å and 0.35Å, respectively. The high precision of these NMR structures was achieved by including a large number of NMR experimental restraints, derived from NOEs and coupling constants, and validating them using the MolProbity program. The 16mer RNA structure comprised of six base pairs with a GUAA tetraloop and the 15mer RNA structure comprised of four base pairs and a large heptaloop; this is the first heptaloop to be studied by NMR.Addition of Mg2+ to the 16mer apo-RNA caused selective chemical shift changes to the stem G177 and loop G178 imino proton resonances, suggesting Mg2+-induced conformational change to the GUAA tetraloop. This was supported by a significant chemical shift change to the selectively 19F-labelled loop U179 in the 5-FU 16mer RNA. Furthermore, variable temperature experiments revealed retarded imino proton exchange for the stem and loop imino protons, demonstrating the enhanced thermodynamic stability conferred by Mg2+. This enhancement in stability was confirmed by measuring the imino proton exchange rates for the 16mer apo-RNA and the 16mer Mg2+ RNA complex. Analysis of the 16mer apo-RNA and its Mg2+ RNA complex NMR solution structures revealed that Mg2+-induced structural changes to the GUAA tetraloop act to stabilise the loop via stronger base stacking and intramolecular interactions. Fascinatingly, we discovered that Mg2+ ions provide increased stability required for the formation of a G.A sheared base pair in the GUAA tetraloop. RNA-RNA interactions between the 16mer and 15mer RNAs and their fluorinated analogues were studied by NMR spectroscopy. Small changes to chemical shift and linewidth of proton peaks in the non-fluorinated RNA-RNA complex provided evidence for a weak interaction between the loop of the 16mer RNA and the stem of the 15mer RNA. 19F-NMR experiments revealed additional peaks for the 19F-labelled U179 of the fluorinated 16mer/15mer RNA complex providing further good evidence of RNA-RNA interaction. The NMR structures of the conserved RNA motifs and their interactions have yielded important information in understanding the properties and behaviour of RNA. This will provide the first stepping stone in understanding the IRES mechanism and its use in antiviral therapy and biotechnology.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:554174 |
| Date | January 2012 |
| Creators | Rasul, Usman Anawar |
| Contributors | Ramesh, Vasudevan |
| Publisher | University of Manchester |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | https://www.research.manchester.ac.uk/portal/en/theses/nmr-studies-of-the-structure-kinetics-and-interactions-of-the-conserved-rna-motifs-in-the-fmdv-ires(be21f327-53e1-48aa-bf9c-c4bd2d028417).html |
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