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

PreQ1 riboswitches regulate the synthesis of the hypermodified tRNA base queuosine by sensing the pyrrolopyrimidine metabolite preQ1 . Here, we use single-molecule FRET to interrogate the structural dynamics of apo and preQ1 -bound states of the preQ1 -II riboswitch from Lactobacillus rhamnosus. We find that the apo-form of the riboswitch spontaneously samples multiple conformations. Magnesium ions and preQ1  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 preQ1 -II riboswitch is complex and provide evidence favoring a conformational selection model of effector binding by riboswitches of this class.