1. Truncations and in silico docking to enhance the analytical response of aptamer-based biosensors.
- Author
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Nguyen MD, Osborne MT, Prevot GT, Churcher ZR, Johnson PE, Simine L, and Dauphin-Ducharme P
- Subjects
- Electrochemical Techniques methods, Theophylline analysis, Theophylline chemistry, Methotrexate chemistry, Glucose analysis, Glucose chemistry, SELEX Aptamer Technique methods, Computer Simulation, Biosensing Techniques methods, Aptamers, Nucleotide chemistry, Cocaine analysis, Molecular Docking Simulation
- Abstract
Aptamers are short oligonucleotides capable of binding specifically to various targets (i.e., small molecules, proteins, and whole cells) which have been introduced in biosensors such as in the electrochemical aptamer-based (E-AB) sensing platform. E-AB sensors are comprised of a redox-reporter-modified aptamer attached to an electrode that undergoes, upon target addition, a binding-induced change in electron transfer rates. To date, E-AB sensors have faced a limitation in the translatability of aptamers into the sensing platform presumably because sequences obtained from Systematic Evolution of Ligands by Exponential Enrichment (SELEX) are typically long (>80 nucleotides) and that obtaining structural information remains time and resource consuming. In response, we explore the utility of aptamer base truncations and in silico docking to improve their translatability into E-AB sensors. Here, we first apply this to the glucose aptamer, which we characterize in solution using NMR methods to guide design and translate truncated variants in E-AB biosensors. We further investigated the applicability of the truncation and computational approaches to four other aptamer systems (vancomycin, cocaine, methotrexate and theophylline) from which we derived functional E-AB sensors. We foresee that our strategy will increase the success rate of translating aptamers into sensing platforms to afford low-cost measurements of molecules directly in undiluted complex matrices., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Philippe Dauphin Ducharme reports financial support was provided by Natural Sciences and Engineering Research Council of Canada. Philippe Dauphin reports financial support was provided by Quebec Research Fund Nature and Technology. If there are other authors, they declare that they have no known Competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2024
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