Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements

Global RMSD for the first four of eight replicas with different conditions at 300 K. (A) Case without Mg²⁺ (0 mM Mg²⁺) and without ligand (dG[−]). (B) Case without Mg²⁺ (0 mM Mg²⁺) and with ligand (dG[+]). (C) Case with Mg²⁺ (5 mM Mg²⁺) and without ligand (dG[−]). (D) Case with Mg²⁺ (5 mM Mg²⁺) and with ligand (dG[+]). In general, the fluctuations of the system become lower with the addition of either the ligand or Mg²⁺. Metastable states with larger fluctuation exist without Mg²⁺ or ligand but are not heavily populated. However, in the absence of both ligand and Mg²⁺, these partially disordered states emerge in the overall population.