Opin vísindi

Flexibility and conformation of the cocaine aptamer studied by PELDOR

Flexibility and conformation of the cocaine aptamer studied by PELDOR

Title: Flexibility and conformation of the cocaine aptamer studied by PELDOR
Author: Grytz, C. M.
Marko, A.
Cekan, P.
Sigurdsson, Snorri
Prisner, Thomas F.
Date: 2016
Language: English
Scope: 2993-3002
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)
Series: Physical Chemistry Chemical Physics;18(4)
ISSN: 1463-9076
1463-9084 (eISSN)
DOI: 10.1039/c5cp06158j
Subject: Kjarnsýrur; Spectroscopy; Litrófsgreining; DNA-rannsóknir
URI: https://hdl.handle.net/20.500.11815/1946

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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.


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