Influence of Mg2+ on the conformational flexibility of a tetracycline aptamer

  • The tetracycline-binding RNA aptamer (TC-aptamer) is a synthetic riboswitch that binds the antibiotic tetracycline (TC) with exceptionally high affinity. Although a crystal structure exists of the TC-bound state, little is known about the conformational dynamics and changes upon ligand binding. In this study, pulsed electron paramagnetic resonance techniques for measuring distances (PELDOR) in combination with rigid nitroxide spin labels (Çm spin label) were used to investigate the conformational flexibility of the TC-aptamer in the presence and absence of TC at different Mg2+ concentrations. TC was found to be the essential factor for stabilizing the tertiary structure at intermediate Mg2+ concentrations. At higher Mg2+ concentrations, Mg2+ alone is sufficient to stabilize the tertiary structure. In addition, the orientation of the two spin-labeled RNA helices with respect to each other was analyzed with orientation-selective PELDOR and compared to the crystal structure. These results demonstrate for the first time the unique value of the Çm spin label in combination with PELDOR to provide information about conformational flexibilities and orientations of secondary structure elements of biologically relevant RNAs.

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Author:Thilo Hetzke, Marc Vogel, Dnyaneshwar B. Gophane, Julia E. WeigandORCiDGND, Beatrix SüßGND, Snorri Thor SigurdssonORCiD, Thomas F. PrisnerORCiD
Pubmed Id:
Parent Title (English):RNA
Publisher:Laboratory Press ; HighWire Press
Place of publication:Cold Spring Harbor, NY ; Stanford, Calif.
Document Type:Article
Year of Completion:2018
Date of first Publication:2018/10/18
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2019/10/21
Tag:DEER; PELDOR; conformational flexibility; divalent metal ions; synthetic riboswitches; tetracycline aptamer
Page Number:11
First Page:158
Last Page:167
This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at
Institutes:Biochemie, Chemie und Pharmazie / Biochemie und Chemie
Wissenschaftliche Zentren und koordinierte Programme / Zentrum für Biomolekulare Magnetische Resonanz (BMRZ)
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 54 Chemie / 540 Chemie und zugeordnete Wissenschaften
Licence (English):License LogoCreative Commons - Namensnennung-Nicht kommerziell 4.0