Daems, E, Dewaele, D, Barylyuk, K et al. (2 more authors) (2021) Aptamer-ligand recognition studied by native ion mobility-mass spectrometry. Talanta, 224. 121917. ISSN 0039-9140
Abstract
The range of applications for aptamers, small oligonucleotide-based receptors binding to their targets with high specificity and affinity, has been steadily expanding. Our understanding of the mechanisms governing aptamer-ligand recognition and binding is however lagging, stymieing the progress in the rational design of new aptamers and optimization of the known ones. Here we demonstrate the capabilities and limitations of native ion mobility-mass spectrometry for the analysis of their higher-order structure and non-covalent interactions. A set of related cocaine-binding aptamers, displaying a range of folding properties and ligand binding affinities, was used as a case study in both positive and negative electrospray ionization modes. Using carefully controlled experimental conditions, we probed their conformational behavior and interactions with the high-affinity ligand quinine as a surrogate for cocaine. The ratios of bound and unbound aptamers in the mass spectra were used to rank them according to their apparent quinine-binding affinity, qualitatively matching the published ranking order. The arrival time differences between the free aptamer and aptamer-quinine complexes were consistent with a small ligand-induced conformational change, and found to inversely correlate with the affinity of binding. This mass spectrometry-based approach provides a fast and convenient way to study the molecular basis of aptamer-ligand recognition.
Metadata
Item Type: | Article |
---|---|
Authors/Creators: |
|
Copyright, Publisher and Additional Information: | © 2020, Elsevier B.V. All rights reserved. This is an author produced version of an article published in Talanta. Uploaded in accordance with the publisher's self-archiving policy. |
Keywords: | Oligonucleotide structure; Aptamers; Ligand affinity; Native mass spectrometry; Ion mobility |
Dates: |
|
Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Biological Sciences (Leeds) > School of Molecular and Cellular Biology (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 25 Jan 2021 15:58 |
Last Modified: | 02 Dec 2021 01:38 |
Status: | Published |
Publisher: | Elsevier BV |
Identification Number: | 10.1016/j.talanta.2020.121917 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:170296 |