The structure and Mg(2+) binding properties of a conserved 75mer RNA motif of the internal ribosome entry site (IRES) element of encephalomyocarditis virus picornavirus have been investigated by (1)H-NMR and UV melting experiments. The assignment of the imino proton resonances with characteristic chemical shift dispersion for canonical and non-canonical base pairs confirmed the predicted secondary structure of the 75mer and its fragments. Addition of Mg(2+) resulted in a dramatic increase in apparent melting temperature, with the 75mer RNA registering the biggest increase, from 63 to 80 degrees C, thus providing evidence for enhanced stability arising from Mg(2+) binding. Similarly, addition of Mg(2+) induced selective changes to the chemical shifts of the imino protons of a GCGA tetraloop in the 75mer, that is essential for IRES activity, thereby highlighting a possible structural role for Mg(2+) in the folding of the 75mer. Significantly, the same protons show retarded exchange to water solvent, even at elevated temperature, which suggest that Mg(2+) induces a conformational rearrangement of the 75mer. Thus, we propose that Mg(2+) serves two important roles: (i) enhancing thermodynamic stability of the 75mer RNA (and its submotifs) via non-specific interactions with the phosphate backbone and (ii) promoting the folding of the 75mer RNA by binding to the GCGA tetraloop.

The interaction of a highly conserved secondary structural RNA motif of Halobacterium halobium and Escherichia coli 23S ribosomal RNAs with the peptidyl transferase inhibitor antibiotic amicetin has been investigated by proton NMR spectroscopy and molecular modelling. The NMR spectra of the synthetic 35mer RNA motifs revealed spectral features characteristic of a stable, well folded A-RNA type tertiary conformation, including resolved resonances assigned to unpaired bases located in the middle of the motif strongly implicated in amicetin binding. Addition of amicetin to the 35mer RNA samples was accompanied by significant and discrete changes to the spectra which can be qualitatively interpreted to the changes induced to the local conformation of the RNA motifs arising from the formation of a specific complex with amicetin. These results are also supported by the unconstrained molecular model of RNAamicetin complex which highlights potential interactions between the two molecular components.