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

Hetzke, Thilo and Vogel, Marc and Gophane, Dnyaneshwar B. and Weigand, Julia E. and Suess, Beatrix and Sigurdsson, Snorri Th. and Prisner, Thomas F. (2019):
Influence of Mg2+ on the conformational flexibility of a tetracycline aptamer.
In: RNA (New York, N.Y.), 25 (1), pp. 158-167. ISSN 1469-9001,
DOI: 10.1261/rna.068684.118,
[Article]

Abstract

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), was used to investigate the conformational flexibility of the TC aptamer in the presence and absence of TC at different Mg concentrations. TC was found to be the essential factor for stabilizing the tertiary structure at intermediate Mg concentrations. At higher Mg concentrations, Mg 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.

Item Type: Article
Erschienen: 2019
Creators: Hetzke, Thilo and Vogel, Marc and Gophane, Dnyaneshwar B. and Weigand, Julia E. and Suess, Beatrix and Sigurdsson, Snorri Th. and Prisner, Thomas F.
Title: Influence of Mg2+ on the conformational flexibility of a tetracycline aptamer.
Language: English
Abstract:

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), was used to investigate the conformational flexibility of the TC aptamer in the presence and absence of TC at different Mg concentrations. TC was found to be the essential factor for stabilizing the tertiary structure at intermediate Mg concentrations. At higher Mg concentrations, Mg 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.

Journal or Publication Title: RNA (New York, N.Y.)
Journal volume: 25
Number: 1
Divisions: 10 Department of Biology
10 Department of Biology > Synthetic Genetic Circuits
10 Department of Biology > RNA Biochemistry
Date Deposited: 22 Oct 2018 10:51
DOI: 10.1261/rna.068684.118
Identification Number: pmid:30337459
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