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 data clearly show the absence of any pre-existing tertiary interactions involving the ssRNA tail in the unbound queC aptamer domain. This together with our findings regarding the conformational behavior of the unbound ssRNA tail suggests the following model for ligand binding ( Figure 5 ). In the absence of ligand, the ssRNA tail is disordered but on average forms an A-form helix-like conformation, which can efficiently explore conformational space about a highly flexible junction. The ligand may transiently form encounter complexes when the tail is close in space to the P1 hairpin, and possibly with the help of divalent ions such as calcium (27, 73) , triggering the necessary conformational changes required to form the pseudoknot and binding pocket. This finding is consistent with computational modeling of the ligand binding mechanism in which A-minor tertiary interactions form first, followed by pseudoknot formation (30) and may explain the fast ligand binding rate observed in the related F. nucleatum queC riboswitch (52). Our results, including the observation of greater dynamics in the mutant, provide a framework for more rigorous testing of this proposed model with future in vitro and in vivo studies.