Magnesium mediates local and global conformation changes of the 2'-deoxyguanosine riboswitch

In prokaryotes, 2-3% of the genes were found to be regulated by a class of mRNAs named riboswitches, usually residing in 5' untranslated region of genes, and control expression mainly by premature transcription termination or inhibition of translation initiation via binding to certain metabolite. To date, a family of purine-sensing riboswitches, which share similar secondary and tertiary structures, have been discovered and studied for their structures and mechanistic basis of gene regulation. The 2'-deoxyguanosine (2'-dG) riboswitch is classified as a close variant of the guanine-sensing riboswitches. When it binds the 2'-dG molecule, it induces the termination of the transcription process. Thus, it is important to understand how the ligand-binding region (aptamer domain) of the riboswitch is affected. In general, positively charged metal ions (specially Mg²⁺) aid in neutralization of the highly negative RNA backbone, permitting the formation of complex bends, folds, and long-range contacts characteristic of complex RNA structures. In this work, we used explicit solvent molecular dynamics simulation and explored the combined effects of ligand binding and Mg²⁺ on the 2'-dG riboswitch at atomic level. We revealed how the absence of ligand and Mg²⁺ weaken the terminal P1 helix and lead to conformation transformation, and how ligand binding and Mg²⁺ affect the stability of other secondary and tertiary motifs of the riboswitch that may also contributes to the reorganization of the riboswitch. The findings are also supported by our SHAPE (Selective 2' Hydroxyl Acylation analyzed by Primer Extension) probing experiments.