The pbuE adenine riboswitch undergoes metal ion-dependent folding that involves a loop-loop interaction. Binding of 2-aminopurine to the aptamer domain strongly correlates with the ability of the loops to interact, and single-molecule FRET studies reveal that folding proceeds via a discrete intermediate. Folding occurs in the absence of adenine ligand, but ligand binding stabilizes the folded structure by increasing the folding rate and decreasing the unfolding rate, and it lowers the magnesium ion concentration required to promote the loop-loop interaction. Individual aptamer molecules exhibit great heterogeneity in folding and unfolding rates, but this is reduced in the presence of adenine. In the full riboswitch, the adenine binding domain fails to fold because of conformational competition by the terminator stem. Thus, riboswitch function should depend on the relative rates of ligand binding and the transcriptional process.

Excited-state proton transfer in aqueous and ethanolic solutions of 2-(2′-hydroxyphenyl)benzimidazole (HBI) was investigated by means of UV-vis absorption and fluorescence spectroscopy. The behavior of HBI in water differed from its behavior in ethanol, and in both solvents fluorescence behavior depended on acidity. In both neutral water and neutral ethanol, ground-state HBI exhibits conformational equilibrium between a cis-enol form with an intramolecular hydrogen bond and a trans-enol form that is hydrogen-bonded to the solvent; the ground-state keto tautomer is also present in water but was not detected in ethanol. The excited cis-enol conformer always undergoes ultrafast intramolecular proton transfer to afford the excited keto tautomer. The excited trans-enol form fluoresces in both solvents, and in water it also loses its hydroxyl proton to the solvent, leaving the excited anion. In both acidic aqueous solution and acidic ethanol, excited protonated HBI loses its hydroxyl proton to give the excited keto form, but this process is faster in water than in ethanol, in which fluorescence by the cation is also observed.

S-adenosylmethionine (SAM) riboswitches are widespread in bacteria, and up to five different SAM riboswitch families have been reported, highlighting the relevance of SAM regulation. On the basis of crystallographic and biochemical data, it has been postulated, but never demonstrated, that ligand recognition by SAM riboswitches involves key conformational changes in the RNA architecture. We show here that the aptamer follows a two-step hierarchical folding selectively induced by metal ions and ligand binding, each of them leading to the formation of one of the two helical stacks observed in the crystal structure. Moreover, we find that the anti-antiterminator P1 stem is rotated along its helical axis upon ligand binding, a mechanistic feature that could be common to other riboswitches. We also show that the nonconserved P4 helical domain is used as an auxiliary element to enhance the ligand-binding affinity. This work provides the first comprehensive characterization, to our knowledge, of a ligand-controlled riboswitch folding pathway.

It has been shown that the activity of the hammerhead ribozyme at µM magnesium ion concentrations is markedly increased by the inclusion of loops in helices I and II. We have studied the effect of such loops on the magnesium ion-induced folding of the ribozyme, using fluorescence resonance energy transfer. We find that with the loops in place, folding into the active conformation occurs in a single step, in the µM range of magnesium ion concentration. Disruption of the loop-loop interaction leads to a reversion to two-step folding, with the second stage requiring mM concentrations of magnesium ion. Sodium ions also promote the folding of the natural form of the ribozyme at high concentrations, but the folding occurs as a two-stage process. The loops clearly act as important auxiliary elements in the function of the ribozyme, permitting folding to occur efficiently under physiological conditions.