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

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

Title: Influence of Mg2+ on the conformational flexibility of a tetracycline aptamer
Author: Hetzke, Thilo
Vogel, Marc
Gophane, Dnyaneshwar B.
Weigand, Julia E.
Suess, Beatrix
Sigurdsson, Snorri   orcid.org/0000-0003-2492-1456
Prisner, Thomas F.
Date: 2018-10-18
Language: English
Scope: 158-167
University/Institute: Háskóli Íslands
University of Iceland
School: Verkfræði- og náttúruvísindasvið (HÍ)
School of Engineering and Natural Sciences (UI)
Department: Raunvísindadeild (HÍ)
Faculty of Physical Sciences (UI)
Raunvísindastofnun (HÍ)
Science Institute (UI)
Series: RNA;25(1)
ISSN: 1355-8382
1469-9001 (eISSN)
DOI: 10.1261/rna.068684.118
Subject: Molecular Biology; Tetracycline aptamer; Conformational flexibility; Divalent metal ions; PELDOR; Synthetic riboswitches; Sameindalíffræði; Kjarnsýrur
URI: https://hdl.handle.net/20.500.11815/1945

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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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