Observation of preQ 1 -II riboswitch dynamics using single-molecule FRET.

PreQ ₁ riboswitches regulate the synthesis of the hypermodified tRNA base queuosine by sensing the pyrrolopyrimidine metabolite preQ ₁ . Here, we use single-molecule FRET to interrogate the structural dynamics of apo and preQ ₁ -bound states of the preQ ₁ -II riboswitch from Lactobacillus rhamnosus . We find that the apo-form of the riboswitch spontaneously samples multiple conformations. Magnesium ions and preQ ₁  stabilize conformations that sequester the ribosome-binding site of the mRNA within the pseudoknotted structure, thus inhibiting translation initiation. Our results reveal that folding of the preQ ₁ -II riboswitch is complex and provide evidence favoring a conformational selection model of effector binding by riboswitches of this class.