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.

Finally, our results suggest that the conformational properties of the ssRNA tail are optimized to allow the queC riboswitch to efficiently bind ligands within the short commitment time available to this kinetic switch. In particular, the pre-stacked ssRNA tail can efficiently rotate about a flexible hinge against the hairpin loop, and explore conformational space efficiently for rapid ligand binding. This pre-stacking about dynamic hinges may be a general feature of many ssRNAs that can play different architectural roles in a variety of RNA contexts.