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

Abstract

Residing in the 5′ untranslated region of the mRNA, the 2′-deoxyguanosine (2′-dG) riboswitch mRNA element adopts an alternative structure upon binding of the 2′-dG molecule, which terminates transcription. RNA conformations are generally strongly affected by positively charged metal ions (especially Mg2+). We have quantitatively explored the combined effect of ligand (2′-dG) and Mg2+binding on the energy landscape of the aptamer domain of the 2′-dG riboswitch with both explicit solvent all-atom molecular dynamics simulations (99 μsec aggregate sampling for the study) and selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) experiments. We show that both ligand and Mg2+are required for the stabilization of the aptamer domain; however, the two factors act with different modalities. The addition of Mg2+remodels the energy landscape and reduces its frustration by the formation of additional contacts. In contrast, the binding of 2′-dG eliminates the metastable states by nucleating a compact core for the aptamer domain. Mg2+ions and ligand binding are required to stabilize the least stable helix, P1 (which needs to unfold to activate the transcription platform), and the riboswitch core formed by the backbone of the P2 and P3 helices. Mg2+and ligand also facilitate a more compact structure in the three-way junction region.