Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch

Eichhorn, Catherine D.; Feng, Jun; Suddala, Krishna C.; Walter, Nils G.; Brooks, Charles L.; Al-Hashimi, Hashim M.

The NMR spectra suggest that the unbound 36 nt queC minimal aptamer domain is highly disordered and that the ssRNA tail is not involved significantly in any tertiary interactions. To test this hypothesis further, we compared NMR spectra of the isolated 12 nt ssRNA tail with the corresponding spectra of the unbound queC aptamer. Remarkably, NMR spectra of the isolated 12 nt ssRNA tail overlay almost perfectly with the queC aptamer domain and specifically onto the highly intense resonances corresponding to highly disordered residues ( Figure 1B ). The only significant deviations are observed for A25 and U26, which are located at the junction site between the hairpin and the tail ( Figure 1B ). This indicates that in the absence of ligand, the ssRNA tail is not involved in any significant tertiary interactions under the NMR conditions (1 mM RNA, 25 mM sodium chloride, 15 mM sodium phosphate, pH 6.4, 0.1 mM EDTA, 298 K).