Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering

• Published in: Journal of molecular biology 2023-10, Vol.435 (20), p.168253-168253, Article 168253
• Main Authors: Kaiser, Christoph, Vogel, Marc, Appel, Bettina, Weigand, Julia, Müller, Sabine, Suess, Beatrix, Wachtveitl, Josef
• Format: Article
• Language: English
• Subjects: conformational dynamics; kinetic modelling; magnesium-driven folding; riboswitch engineering; tetracycline-binding aptamer
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2023.168253

[Display omitted] •Magnesium ion-dependent functional folding of Tetracycline binding RNA aptamer.•Propagation of conformational changes from binding pocket to expression platform.•Dynamic magnesium acquisition drives interaction between core and closing stem. Engineering in vitro selected RNA aptamers into in vivo functional riboswitches represents a long-standing challenge in molecular biology. The highly specific aptamer domain of the riboswitch undergoes a conformational adjustment in response to ligand sensing, which in turn exerts the regulatory function. Besides essential factors like structural complexity and ligand binding kinetics, the active role of magnesium ions in stabilizing RNA tertiary structures and assisting in ligand binding can be a vital criterion. We present spectroscopic studies on the magnesium ion-driven folding of the Tetracycline binding aptamer. Using fluorescent labels, the aptamer pre-folding and subsequent ligand binding is monitored by magnesium titration experiments and time-resolved stopped-flow measurements. A minimum concentration of 0.5 mM magnesium is required to fold into a magnesium ion-stabilized binding-competent state with a preformed binding pocket. Tetracycline binding causes a pronounced conformational change that results in the establishment of the triple helix core motif, and that further propagates towards the closing stem. By a dynamic acquisition of magnesium ions, a kink motif is formed at the intersection of the triple helix and closing stem regions. This ultimately entails a stabilization of the closing stem which is discussed as a key element in the regulatory function of the Tetracycline aptamer.