Riboswitch ligand binding occurs at
A canonical riboswitch comprises two functionally separable domains fused in single transcript. The 5' aptamer domain folds into highly specific pocket with conserved nucleotides and tertiary interactions that selectively bind metabolite via hydrogen bonding and stacking with nanomolar to micromolar affinity. Aptamer architecture often pre-organized to reduce entropic cost of binding. Ligand recognition stabilizes alternative base-pairing pattern in adjacent expression platform downstream. As sensor module, aptamer itself does not regulate but communicates ligand occupancy through allosteric s
Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 6: RNA Regulation, Riboswitch Aptamer Domain