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Wei K, Ye Z, Dong W, Zhang L, Wang W, Li J, Eltzov E, Wang S, Mao X. Generating robust aptamers for food analysis by sequence-based configuration optimization. Talanta 2024; 275:126044. [PMID: 38626500 DOI: 10.1016/j.talanta.2024.126044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/18/2024]
Abstract
Advanced analytical techniques are emerging in the food industry. Aptamer-based biosensors achieve rapid and highly selective analysis, thus drawing particular attention. Aptamers are oligonucleotide probes screened via in vitro Systematic Evolution of Ligands by EXponential Enrichment (SELEX), which can bind with their specific targets by folding into three-dimensional configurations and accept various modifications to be incorporated into biosensors, showing great potential in food analysis. Unfortunately, aptamers obtained by SELEX may not possess satisfactory affinity. Post-SELEX strategies were proposed to optimize aptamers' configuration and enhance the binding affinity, with specificity confirmed. Sequence-based optimization strategies exhibit great advantages in simple operation, good generalization, low cost, etc. This review summarizes the latest study (2015-2023) on generating robust aptamers for food targets by sequence-based configuration optimization, as well as the generated aptamers and aptasensors, with an expectation to provide inspirations for developing aptamer and aptasensors with high performance for food analysis and to safeguard food quality and safety.
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Affiliation(s)
- Kaiyue Wei
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Ziyang Ye
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Wenhui Dong
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Ling Zhang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Wenjing Wang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Jiao Li
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Evgeni Eltzov
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Center, Agricultural Research Organization, Bet Dagan, 50250, Israel
| | - Sai Wang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China.
| | - Xiangzhao Mao
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
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Higuera-Rodriguez RA, De Pascali MC, Aziz M, Sattler M, Rant U, Kaiser W. Kinetic FRET Assay to Measure Binding-Induced Conformational Changes of Nucleic Acids. ACS Sens 2023; 8:4597-4606. [PMID: 38060303 PMCID: PMC10749467 DOI: 10.1021/acssensors.3c01527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/27/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
The interaction of small molecules or proteins with RNA or DNA often involves changes in the nucleic acid (NA) folding and structure. A biophysical characterization of these processes helps us to understand the underlying molecular mechanisms. Here, we propose kinFRET (kinetics Förster resonance energy transfer), a real-time ensemble FRET methodology to measure binding and folding kinetics. With kinFRET, the kinetics of conformational changes of NAs (DNA or RNA) upon analyte binding can be directly followed via a FRET signal using a chip-based biosensor. We demonstrate the utility of this approach with two representative examples. First, we monitored the conformational changes of different formats of an aptamer (MN19) upon interaction with small-molecule analytes. Second, we characterized the binding kinetics of RNA recognition by tandem K homology (KH) domains of the human insulin-like growth factor II mRNA-binding protein 3 (IMP3), which reveals distinct kinetic contributions of the two KH domains. Our data demonstrate that kinFRET is well suited to study the kinetics and conformational changes of NA-analyte interactions.
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Affiliation(s)
- R. Anahi Higuera-Rodriguez
- TUM
School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching 85748, Germany
- Dynamic
Biosensors GmbH, Perchtinger Str. 8/10, Munich 81379, Germany
| | - Mareike C. De Pascali
- TUM
School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching 85748, Germany
- Dynamic
Biosensors GmbH, Perchtinger Str. 8/10, Munich 81379, Germany
| | - Masood Aziz
- TUM
School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching 85748, Germany
- Helmholtz
Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg 85764, Germany
| | - Michael Sattler
- TUM
School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching 85748, Germany
- Helmholtz
Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg 85764, Germany
| | - Ulrich Rant
- Dynamic
Biosensors GmbH, Perchtinger Str. 8/10, Munich 81379, Germany
| | - Wolfgang Kaiser
- Dynamic
Biosensors GmbH, Perchtinger Str. 8/10, Munich 81379, Germany
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Bennett HA, Li Y, Yan H. Thermal treatment affects aptamers' structural profiles. Bioorg Med Chem Lett 2023; 82:129150. [PMID: 36693483 DOI: 10.1016/j.bmcl.2023.129150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Using anion-exchange high performance liquid chromatography under non-denaturing conditions, the conformational flexibility of adenosine-, ampicillin-, and quinine aptamers were studied. It was found that all three aptamers showed more than one species when not subjected to thermal anneal. Addition of ligand to untreated aptamers did not significantly change the structural distribution. Upon heating followed by slow cooling, however, all three aptamers were found to exist virtually solely in one structure, presumably the partial hairpin species. It was also found that sonication of quinine aptamer, but not adenosine and ampicillin aptamer, led to its elution off HPLC as virtually a single species. These changes in conformational distribution as a result of thermal anneal or sonication were further confirmed by UV/vis and circular dichroism spectroscopy, as well as melt curves. The findings provided basis for future optimization of aptamer selection and preparation, where thermal anneal can help optimize selection efficiency and improve the consistency in the interpretation of results.
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Affiliation(s)
- Hayley-Ann Bennett
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada
| | - Yifeng Li
- Department of Computer Science and Department of Biological Sciences, Brock University, Canada.
| | - Hongbin Yan
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada.
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DNA binding by the antimalarial compound artemisinin. Sci Rep 2022; 12:133. [PMID: 34997002 PMCID: PMC8741894 DOI: 10.1038/s41598-021-03958-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Artemisinin (ART) is a vital medicinal compound that is used alone or as part of a combination therapy against malaria. ART is thought to function by attaching to heme covalently and alkylating a range of proteins. Using a combination of biophysical methods, we demonstrate that ART is bound by three-way junction and duplex containing DNA molecules. Binding of ART by DNA is first shown for the cocaine-binding DNA aptamer and extensively studied using this DNA molecule. Isothermal titration calorimetry methods show that the binding of ART is both entropically and enthalpically driven at physiological NaCl concentration. Native mass spectrometry methods confirm DNA binding and show that a non-covalent complex is formed. Nuclear magnetic resonance spectroscopy shows that ART binds at the three-way junction of the cocaine-binding aptamer, and that binding results in the folding of the structure-switching variant of this aptamer. This structure-switching ability was exploited using the photochrome aptamer switch assay to demonstrate that ART can be detected using this biosensing assay. This study is the first to demonstrate the DNA binding ability of ART and should lay the foundation for further work to study implications of DNA binding for the antimalarial activity of ART.
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Shoara AA, Churcher ZR, Slavkovic S, Johnson PE. Weak Binding of Levamisole by the Cocaine-Binding Aptamer Does Not Interfere with an Aptamer-Based Detection Assay. ACS OMEGA 2021; 6:24209-24217. [PMID: 34568699 PMCID: PMC8459413 DOI: 10.1021/acsomega.1c03781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Indexed: 05/05/2023]
Abstract
Levamisole is a common and harmful adulterant of street samples of cocaine and can cause electrochemical tests for cocaine to give false negative results. To see if levamisole would interfere with aptamer-based bioassays, we analyzed the binding of levamisole to the cocaine-binding DNA aptamer. At low aptamer concentrations (0.5 to 20 μM) using isothermal titration calorimetry methods and thermal stability measurements, no binding of levamisole to the cocaine-binding aptamer was observed. At higher levamisole concentrations (500 μM), weak binding to the cocaine-binding aptamer was detected using nuclear magnetic resonance (NMR) spectroscopy chemical shift perturbations. NMR-detected titrations show that levamisole binding is competitive with cocaine binding, indicating that both ligands share a common binding site. Finally, we show that the presence of levamisole does not interfere with the photochrome aptamer switch binding assay for cocaine. We conclude that assays using low concentrations of cocaine, and consequently low concentration of levamisole as an adulterant, should be unaffected by the weak binding of levamisole.
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Van Riesen AJ, Le J, Slavkovic S, Churcher ZR, Shoara AA, Johnson PE, Manderville RA. Visible Fluorescent Light-up Probe for DNA Three-Way Junctions Provides Host–Guest Biosensing Applications. ACS APPLIED BIO MATERIALS 2021; 4:6732-6741. [DOI: 10.1021/acsabm.1c00431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Abigail J. Van Riesen
- Departments of Chemistry and Toxicology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jennifer Le
- Departments of Chemistry and Toxicology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Sladjana Slavkovic
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Zachary R. Churcher
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Aron A. Shoara
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Philip E. Johnson
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Richard A. Manderville
- Departments of Chemistry and Toxicology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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