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Flexibility and conformation of the cocaine aptamer studied by PELDOR

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dc.contributor Háskóli Íslands
dc.contributor University of Iceland
dc.contributor.author Grytz, C. M.
dc.contributor.author Marko, A.
dc.contributor.author Cekan, P.
dc.contributor.author Sigurdsson, Snorri
dc.contributor.author Prisner, Thomas F.
dc.date.accessioned 2020-08-10T11:29:57Z
dc.date.available 2020-08-10T11:29:57Z
dc.date.issued 2016
dc.identifier.issn 1463-9076
dc.identifier.issn 1463-9084 (eISSN)
dc.identifier.uri https://hdl.handle.net/20.500.11815/1946
dc.description Publisher's version (útgefin grein)
dc.description.abstract The cocaine aptamer is a DNA three-way junction that binds cocaine at its helical junction. We studied the global conformation and overall flexibility of the aptamer in the absence and presence of cocaine by pulsed electron-electron double resonance (PELDOR) spectroscopy, also called double electronelectron resonance (DEER). The rigid nitroxide spin label C was incorporated pairwise into two helices of the aptamer. Multi-frequency 2D PELDOR experiments allow the determination of the mutual orientation and the distances between two Cs. Since C is rigidly attached to double-stranded DNA, it directly reports on the aptamer dynamics. The cocaine-bound and the non-bound states could be differentiated by their conformational flexibility, which decreases upon binding to cocaine. We observed a small change in the width and mean value of the distance distribution between the two spin labels upon cocaine binding. Further structural insights were obtained by investigating the relative orientation between the two spin-labeled stems of the aptamer. We determined the bend angle between this two stems. By combining the orientation information with a priori knowledge about the secondary structure of the aptamer, we obtained a molecular model describing the global folding and flexibility of the cocaine aptamer.
dc.description.sponsorship This work was supported by the Deutsche Forschungsgemeinschaft DFG (SFB 902 Molecular Principles of RNA-based Regulation, Cluster of Excellence Frankfurt Macromolecular Complexes) and the Icelandic Research Fund [120001022]. T. F. Prisner and C. M. Grytz gratefully acknowledge support by the Fond der Chemischen Industrie. We thank Dnyaneshwar B. Gophane for help in sample preparation.
dc.format.extent 2993-3002
dc.language.iso en
dc.publisher Royal Society of Chemistry (RSC)
dc.relation.ispartofseries Physical Chemistry Chemical Physics;18(4)
dc.rights info:eu-repo/semantics/openAccess
dc.subject Kjarnsýrur
dc.subject Spectroscopy
dc.subject Litrófsgreining
dc.subject DNA-rannsóknir
dc.title Flexibility and conformation of the cocaine aptamer studied by PELDOR
dc.type info:eu-repo/semantics/article
dcterms.license This journal is available under a Creative Commons License (Attribution 3.0 Unported (CC BY 3.0)), as described at https://creativecommons.org/licenses/by/3.0/
dc.description.version Peer reviewed
dc.identifier.journal Physical Chemistry Chemical Physics
dc.identifier.doi 10.1039/c5cp06158j
dc.relation.url http://pubs.rsc.org/en/content/articlepdf/2016/CP/C5CP06158J
dc.contributor.department Raunvísindadeild (HÍ)
dc.contributor.department Faculty of Physical Sciences (UI)
dc.contributor.school Verkfræði- og náttúruvísindasvið (HÍ)
dc.contributor.school School of Engineering and Natural Sciences (UI)

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