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Issue 4, 2016
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Flexibility and conformation of the cocaine aptamer studied by PELDOR

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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 electron–electron resonance (DEER). The rigid nitroxide spin label Ç 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 Çs. Since Ç 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.

Graphical abstract: Flexibility and conformation of the cocaine aptamer studied by PELDOR

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Supplementary files

Article information


Submitted
12 Oct 2015
Accepted
18 Dec 2015
First published
18 Dec 2015

This article is Open Access

Phys. Chem. Chem. Phys., 2016,18, 2993-3002
Article type
Paper
Author version available

Flexibility and conformation of the cocaine aptamer studied by PELDOR

C. M. Grytz, A. Marko, P. Cekan, S. Th. Sigurdsson and T. F. Prisner, Phys. Chem. Chem. Phys., 2016, 18, 2993
DOI: 10.1039/C5CP06158J

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