2'-deoxyguanosine riboswitch motion regulated by ligand and magnesium

Riboswitch, often found in bacteria, is a family of untranslated message RNA regions located at 5' end. Acting like a switch, it regulates the transcription or translation process, and thus metabolism, by binding to certain metabolite. As an example, the 2'-deoxyguanosine (dG) riboswitch is able to bind the 2'-deoxyguanosine molecule. When the binding is formed, the transcription process is terminated (OFF state), however, when there is no ligand binding, the riboswitch takes a conformation change during RNA elongation, hence enabling the process (ON state). So, it is important to understand how the ligand-binding (aptamer) region of the riboswitch works and how the ligand affect it. Since RNA is negatively charged, cations, especially magnesiums, also play a very important role in stablizing RNA molecule. In this work, we used all atom simulation to study how ligand and magnesium affect the motion of the aptamer region of 2' dG ribowitch and how we relate RNA motion from simulaiton to the result from selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiment, which measures RNA backbone flexibility.