Structure-based insights into the ligand specificity tuning of 2′-dG-III riboswitch

Riboswitches are conserved non-coding RNA domains predominantly located at the 5′-end of the bacterial mRNAs, serving as gene expression regulators. Recently, a third class of 2′-deoxyguanosine riboswitch (2′-dG-III) has been identified from guanine riboswitch family, exhibiting comparable binding affinity toward 2′-dG, guanine, and guanosine. To elucidate the unique ligand recognition mechanism of this riboswitch, we solved its crystal structures in complex with different purine derivatives, including 2′-dG, guanine, and guanosine. The tertiary structure reveals a typical tuning-fork-like architecture, with three stems converging at a central three-way junction. The bound ligand, 2′-dG, is anchored within the junctional core through specific molecular interactions involving certain critical nucleotides. Through systemic comparative analysis of the binding pocket across different ligand-bound states, as well as related guanine family riboswitches, including 2′-dG-I, 2′-dG-II, and Guanine-I riboswitches, we identified subtle yet significant structural variations that modulate binding affinity and specificity. Leveraging these findings, we further engineered RNA biosensors by fusing the 2′-dG-III riboswitch with Pepper fluorogenic RNA aptamer, which exhibits a robust, positive correlation between fluorescence intensity and 2′-dG levels in vitro. Together, this work not only advances our understanding of the ligand recognition mechanisms underlying the 2′-dG-III riboswitch and related guanine riboswitch family but also lays the groundwork for fine-tuning riboswitch specificity, paving the way for the development of highly specific RNA-based biosensors.