Influence of Mg2+ and THF on THF-II riboswitch based on molecular dynamics simulations

The study of RNA binding to ligands and conformational changes in the presence of ions is of particular importance. We investigate the process of THF-II-loti_TL RNA both with and without ligand, and in the absence or presence of Mg²⁺, using molecular dynamics simulation. It is found that the THF-II-loti_TL conformation is more stable in the presence of Mg²⁺, and the THF-II-loti_TL shows a more stable structure with ligand than it is without ligand. Thus, Mg²⁺ plays a significant role in the stabilization of the THF-II-loti_TL RNA structure. These investigations offer new perspectives into the dynamical folding of the THF-II riboswitch.