dc.contributor |
Háskóli Íslands |
dc.contributor |
University of Iceland |
dc.contributor.author |
Hetzke, Thilo |
dc.contributor.author |
Vogel, Marc |
dc.contributor.author |
Gophane, Dnyaneshwar B. |
dc.contributor.author |
Weigand, Julia E. |
dc.contributor.author |
Suess, Beatrix |
dc.contributor.author |
Sigurdsson, Snorri |
dc.contributor.author |
Prisner, Thomas F. |
dc.date.accessioned |
2020-08-10T11:25:17Z |
dc.date.available |
2020-08-10T11:25:17Z |
dc.date.issued |
2018-10-18 |
dc.identifier.issn |
1355-8382 |
dc.identifier.issn |
1469-9001 (eISSN) |
dc.identifier.uri |
https://hdl.handle.net/20.500.11815/1945 |
dc.description |
Publisher's version (útgefin gerin) |
dc.description.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) 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. |
dc.description.sponsorship |
We thank Dr. Alice Bowen and Dr. Philipp Spindler for help in setting up initial Q-band and X-band PELDOR measurements. We also thank Dr. Claudia Grytz, Nicole Erlenbach, and Dr. Andriy Marko for help with PELDOR X-band simulations. S.Th.S. acknowledges financial support from the Icelandic Research Fund (141062-051). T.F.P., B.S., and J.E.W. acknowledge financial support from the Collaborative Research Center 902 - Molecular Principles of RNA-based regulation of the German Research Foundation (3214020004). |
dc.format.extent |
158-167 |
dc.language.iso |
en |
dc.publisher |
Cold Spring Harbor Laboratory |
dc.relation.ispartofseries |
RNA;25(1) |
dc.rights |
info:eu-repo/semantics/openAccess |
dc.subject |
Molecular Biology |
dc.subject |
Tetracycline aptamer |
dc.subject |
Conformational flexibility |
dc.subject |
Divalent metal ions |
dc.subject |
PELDOR |
dc.subject |
Synthetic riboswitches |
dc.subject |
Sameindalíffræði |
dc.subject |
Kjarnsýrur |
dc.title |
Influence of Mg2+ on the conformational flexibility of a tetracycline aptamer |
dc.type |
info:eu-repo/semantics/article |
dcterms.license |
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/ |
dc.description.version |
Peer reviewed |
dc.identifier.journal |
RNA |
dc.identifier.doi |
10.1261/rna.068684.118 |
dc.relation.url |
https://syndication.highwire.org/content/doi/10.1261/rna.068684.118 |
dc.contributor.department |
Raunvísindadeild (HÍ) |
dc.contributor.department |
Faculty of Physical Sciences (UI) |
dc.contributor.department |
Raunvísindastofnun (HÍ) |
dc.contributor.department |
Science Institute (UI) |
dc.contributor.school |
Verkfræði- og náttúruvísindasvið (HÍ) |
dc.contributor.school |
School of Engineering and Natural Sciences (UI) |