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Docking Simulation and Sandwich Assay for Aptamer-Based Botulinum Neurotoxin Type C Detection
Aptamers are biomaterials that bind to a target molecule through a unique structure, and have high applicability in the diagnostic and medical fields. To effectively utilize aptamers, it is important to analyze the structure of the aptamer binding to the target molecule; however, there are difficult...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7460441/ https://www.ncbi.nlm.nih.gov/pubmed/32806662 http://dx.doi.org/10.3390/bios10080098 |
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author | Oh, In-Hwan Park, Dae-Young Cha, Ji-Man Shin, Woo-Ri Kim, Ji Hun Kim, Sun Chang Cho, Byung-Kwan Ahn, Ji-Young Kim, Yang-Hoon |
author_facet | Oh, In-Hwan Park, Dae-Young Cha, Ji-Man Shin, Woo-Ri Kim, Ji Hun Kim, Sun Chang Cho, Byung-Kwan Ahn, Ji-Young Kim, Yang-Hoon |
author_sort | Oh, In-Hwan |
collection | PubMed |
description | Aptamers are biomaterials that bind to a target molecule through a unique structure, and have high applicability in the diagnostic and medical fields. To effectively utilize aptamers, it is important to analyze the structure of the aptamer binding to the target molecule; however, there are difficulties in experimentally identifying this structure. In the modern pharmaceutical industry, computer-driven docking simulations that predict intermolecular binding models are used to select candidates that effectively bind target molecules. Botulinum toxin (BoNT) is the most poisonous neurotoxin produced from the Clostridium botulinum bacteria, and BoNT/C, one of the eight serotypes, causes paralysis in livestock. In this study, the aptamers that bound to BoNT/C were screened via the systematic evolution of ligands by exponential enrichment, and the binding affinity analysis and binding model were evaluated to select optimal aptamers. Based on surface plasmon resonance analysis and molecular operating environment docking simulation, a pair of aptamers that had high binding affinity to BoNT/C and were bound to different BoNT/C sites were selected. A sandwich assay based on this aptamer pair detected the BoNT/C protein to a concentration as low as ~0.2 ng Ml(−1). These results show that docking simulations are a useful strategy for screening aptamers that bind to specific targets. |
format | Online Article Text |
id | pubmed-7460441 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-74604412020-09-03 Docking Simulation and Sandwich Assay for Aptamer-Based Botulinum Neurotoxin Type C Detection Oh, In-Hwan Park, Dae-Young Cha, Ji-Man Shin, Woo-Ri Kim, Ji Hun Kim, Sun Chang Cho, Byung-Kwan Ahn, Ji-Young Kim, Yang-Hoon Biosensors (Basel) Article Aptamers are biomaterials that bind to a target molecule through a unique structure, and have high applicability in the diagnostic and medical fields. To effectively utilize aptamers, it is important to analyze the structure of the aptamer binding to the target molecule; however, there are difficulties in experimentally identifying this structure. In the modern pharmaceutical industry, computer-driven docking simulations that predict intermolecular binding models are used to select candidates that effectively bind target molecules. Botulinum toxin (BoNT) is the most poisonous neurotoxin produced from the Clostridium botulinum bacteria, and BoNT/C, one of the eight serotypes, causes paralysis in livestock. In this study, the aptamers that bound to BoNT/C were screened via the systematic evolution of ligands by exponential enrichment, and the binding affinity analysis and binding model were evaluated to select optimal aptamers. Based on surface plasmon resonance analysis and molecular operating environment docking simulation, a pair of aptamers that had high binding affinity to BoNT/C and were bound to different BoNT/C sites were selected. A sandwich assay based on this aptamer pair detected the BoNT/C protein to a concentration as low as ~0.2 ng Ml(−1). These results show that docking simulations are a useful strategy for screening aptamers that bind to specific targets. MDPI 2020-08-12 /pmc/articles/PMC7460441/ /pubmed/32806662 http://dx.doi.org/10.3390/bios10080098 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Oh, In-Hwan Park, Dae-Young Cha, Ji-Man Shin, Woo-Ri Kim, Ji Hun Kim, Sun Chang Cho, Byung-Kwan Ahn, Ji-Young Kim, Yang-Hoon Docking Simulation and Sandwich Assay for Aptamer-Based Botulinum Neurotoxin Type C Detection |
title | Docking Simulation and Sandwich Assay for Aptamer-Based Botulinum Neurotoxin Type C Detection |
title_full | Docking Simulation and Sandwich Assay for Aptamer-Based Botulinum Neurotoxin Type C Detection |
title_fullStr | Docking Simulation and Sandwich Assay for Aptamer-Based Botulinum Neurotoxin Type C Detection |
title_full_unstemmed | Docking Simulation and Sandwich Assay for Aptamer-Based Botulinum Neurotoxin Type C Detection |
title_short | Docking Simulation and Sandwich Assay for Aptamer-Based Botulinum Neurotoxin Type C Detection |
title_sort | docking simulation and sandwich assay for aptamer-based botulinum neurotoxin type c detection |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7460441/ https://www.ncbi.nlm.nih.gov/pubmed/32806662 http://dx.doi.org/10.3390/bios10080098 |
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