TY  - JOUR
A1  - Hetzke, Thilo
A1  - Vogel, Marc
A1  - Gophane, Dnyaneshwar B.
A1  - Weigand, Julia E.
A1  - Süß, Beatrix
A1  - Sigurdsson, Snorri Thor
A1  - Prisner, Thomas F.
T1  - Influence of Mg2+ on the conformational flexibility of a tetracycline aptamer
T2  - RNA
N2  - 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.
KW  - tetracycline aptamer
KW  - conformational flexibility
KW  - divalent metal ions
KW  - PELDOR
KW  - DEER
KW  - synthetic riboswitches
Y1  - 2018
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/48673
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-486734
SN  - 1469-9001
SN  - 1355-8382
N1  - This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
VL  - 25
IS  - 1
SP  - 158
EP  - 167
PB  - Laboratory Press ; HighWire Press
CY  - Cold Spring Harbor, NY ; Stanford, Calif.
ER  -