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Jiang M, Fang X, Diao H, Lv S, Zhang Z, Zhang X, Chen Z, Luo Z. Semi-automated and efficient parallel SELEX of aptamers for multiple targets. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:2039-2043. [PMID: 37066673 DOI: 10.1039/d3ay00367a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In this study, we constructed and optimized a semi-automatic instrument to perform aptamer SELEX targeting multiple proteins simultaneously. Our work provides a simple SELEX platform characterized by real-time feedback, which is time efficient and can reduce human intervention. A number of aptamers were rapidly screened by this method. Moreover, the binding affinities of these aptamers were verified by various methods, including SPR and flow cytometry, which supports the applicability and reliability of our newly established aptamer SELEX system.
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Affiliation(s)
- Meng Jiang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049, China.
| | - Xiaona Fang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Han Diao
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Shaokang Lv
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Zheng Zhang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Xiang Zhang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Zhiwei Chen
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049, China.
- Institute of Food and Nutrition Science, Shandong University of Technology, Zibo, 255049, P. R. China
- School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255049, P. R. China
| | - Zhaofeng Luo
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
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Dong Y, Xu Y, Yong W, Chu X, Wang D. Aptamer and its potential applications for food safety. Crit Rev Food Sci Nutr 2014; 54:1548-61. [PMID: 24580557 DOI: 10.1080/10408398.2011.642905] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Accompanied by industrial globalization, rapid urbanization, and population increment, mass production and staple trading for food consumption are upsoaring continuously, foodborne disease resulted from various food safety issues is currently a crucial public health concern worldwide, which has not only created a great burden on both economy and society, but also greatly threatened the sustainability of mankind's livelihood and human reproduction. In order to better ensure food safety and thus effectively curb the occurrence of foodborne diseases, the development and evolving of inspection strategies are indispensable measures for quality assurance and conformity assessment. Nowadays, as complementary measures to and with advantageous merits over classic analytical methods, highly specific and selective aptamer-based assays have found their increasingly important roles in various domains of food analysis. This critical review summarizes the advantages of aptamer as compared with antibody, introduces important evolving variants of systematic evolution of ligands by exponential enrichment (SELEX), and presents an overview of potential aptamer applications for food safety.
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Affiliation(s)
- Yiyang Dong
- a Beijing Key Laboratory of Bioprocess, College of Life Science and Technology , Beijing University of Chemical Technology , Beijing , P.R. China
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Nikolaus N, Strehlitz B. DNA-aptamers binding aminoglycoside antibiotics. SENSORS 2014; 14:3737-55. [PMID: 24566637 PMCID: PMC3958260 DOI: 10.3390/s140203737] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/20/2014] [Accepted: 01/30/2014] [Indexed: 02/05/2023]
Abstract
Aptamers are short, single stranded DNA or RNA oligonucleotides that are able to bind specifically and with high affinity to their non-nucleic acid target molecules. This binding reaction enables their application as biorecognition elements in biosensors and assays. As antibiotic residues pose a problem contributing to the emergence of antibiotic-resistant pathogens and thereby reducing the effectiveness of the drug to fight human infections, we selected aptamers targeted against the aminoglycoside antibiotic kanamycin A with the aim of constructing a robust and functional assay that can be used for water analysis. With this work we show that aptamers that were derived from a Capture-SELEX procedure targeting against kanamycin A also display binding to related aminoglycoside antibiotics. The binding patterns differ among all tested aptamers so that there are highly substance specific aptamers and more group specific aptamers binding to a different variety of aminoglycoside antibiotics. Also the region of the aminoglycoside antibiotics responsible for aptamer binding can be estimated. Affinities of the different aptamers for their target substance, kanamycin A, are measured with different approaches and are in the micromolar range. Finally, the proof of principle of an assay for detection of kanamycin A in a real water sample is given.
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Affiliation(s)
- Nadia Nikolaus
- Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, Leipzig 04318, Germany.
| | - Beate Strehlitz
- Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, Leipzig 04318, Germany.
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Challenges and opportunities for small molecule aptamer development. J Nucleic Acids 2012; 2012:748913. [PMID: 23150810 PMCID: PMC3488411 DOI: 10.1155/2012/748913] [Citation(s) in RCA: 286] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/08/2012] [Indexed: 12/14/2022] Open
Abstract
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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Derbyshire N, White SJ, Bunka DHJ, Song L, Stead S, Tarbin J, Sharman M, Zhou D, Stockley PG. Toggled RNA aptamers against aminoglycosides allowing facile detection of antibiotics using gold nanoparticle assays. Anal Chem 2012; 84:6595-602. [PMID: 22793869 PMCID: PMC3413241 DOI: 10.1021/ac300815c] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 07/12/2012] [Indexed: 11/28/2022]
Abstract
We have used systematic evolution of ligands by exponential enrichment (SELEX) to isolate RNA aptamers against aminoglycoside antibiotics. The SELEX rounds were toggled against four pairs of aminoglycosides with the goal of isolating reagents that recognize conserved structural features. The resulting aptamers bind both of their selection targets with nanomolar affinities. They also bind the less structurally related targets, although they show clear specificity for this class of antibiotics. We show that this lack of aminoglycoside specificity is a common property of aptamers previously selected against single compounds and described as "specific". Broad target specificity aptamers would be ideal for sensors detecting the entire class of aminoglycosides. We have used ligand-induced aggregation of gold-nanoparticles coated with our aptamers as a rapid and sensitive assay for these compounds. In contrast to DNA aptamers, unmodified RNA aptamers cannot be used as the recognition ligand in this assay, whereas 2'-fluoro-pyrimidine derivatives work reliably. We discuss the possible application of these reagents as sensors for drug residues and the challenges for understanding the structural basis of aminoglycoside-aptamer recognition highlighted by the SELEX results.
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Affiliation(s)
- Nicola Derbyshire
- Astbury
Centre for Structural Molecular Biology and School of Chemistry, University of Leeds, Leeds, LS2 9JT,
United Kingdom
| | - Simon J. White
- Astbury
Centre for Structural Molecular Biology and School of Chemistry, University of Leeds, Leeds, LS2 9JT,
United Kingdom
| | - David H. J. Bunka
- Astbury
Centre for Structural Molecular Biology and School of Chemistry, University of Leeds, Leeds, LS2 9JT,
United Kingdom
| | - Lei Song
- Astbury
Centre for Structural Molecular Biology and School of Chemistry, University of Leeds, Leeds, LS2 9JT,
United Kingdom
| | - Sara Stead
- The Food and Environmental
Research Agency, Sand Hutton, Yorkshire, YO41 1LZ, United
Kingdom
| | - Jonathan Tarbin
- The Food and Environmental
Research Agency, Sand Hutton, Yorkshire, YO41 1LZ, United
Kingdom
| | - Matthew Sharman
- The Food and Environmental
Research Agency, Sand Hutton, Yorkshire, YO41 1LZ, United
Kingdom
| | - Dejian Zhou
- Astbury
Centre for Structural Molecular Biology and School of Chemistry, University of Leeds, Leeds, LS2 9JT,
United Kingdom
| | - Peter G. Stockley
- Astbury
Centre for Structural Molecular Biology and School of Chemistry, University of Leeds, Leeds, LS2 9JT,
United Kingdom
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González-Fernández E, de-los-Santos-Álvarez N, Miranda-Ordieres AJ, Lobo-Castañón MJ. SPR evaluation of binding kinetics and affinity study of modified RNA aptamers towards small molecules. Talanta 2012; 99:767-73. [PMID: 22967622 DOI: 10.1016/j.talanta.2012.07.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 06/25/2012] [Accepted: 07/05/2012] [Indexed: 12/01/2022]
Abstract
Establishing an efficient method for evaluating the affinity changes after post-SELEX modification of aptamers is essential for broadening the application of these oligonucleotides in biosensing. This is especially challenging when the ligand is a small molecule. Changes in affinity upon partial or total replacement of 2'-OH with 2'-OMe groups in the ribose moieties of a tobramycin binding RNA aptamer are described. The kinetic profile and binding properties of the different anti-tobramycin aptamers were measured by surface plasmon resonance (SPR) experiments through a real-time binding assay with the antibiotic covalently coupled to the gold sensor. This configuration maximizes the changes associated to the recognition event, which is otherwise undetectable. The results indicated that the modification slightly affects the binding characteristics of the parent RNA, while conferring biological stability to the aptamers against nucleases.
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Affiliation(s)
- Eva González-Fernández
- Universidad de Oviedo, Departamento de Química Física y Analítica, Av. Julian Claveria 8, 33006 Oviedo, Spain
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Codrea V, Hayner M, Hall B, Jhaveri S, Ellington A. In vitro selection of RNA aptamers to a small molecule target. ACTA ACUST UNITED AC 2010; Chapter 9:Unit 9.5.1-23. [PMID: 20201029 DOI: 10.1002/0471142700.nc0905s40] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This unit describes the selection of aptamers from a single-stranded RNA pool that bind to small molecule targets. Aptamers generated by this type of selection experiment can potentially function as receptors for small molecules in numerous applications, including medical diagnostics, therapeutics, and environmental monitoring. This unit describes two modes of selection, one by column filtration and one by batch selection.
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Affiliation(s)
- Vlad Codrea
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas, USA
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Paul DJ, Seedhouse SJ, Disney MD. Two-dimensional combinatorial screening and the RNA Privileged Space Predictor program efficiently identify aminoglycoside-RNA hairpin loop interactions. Nucleic Acids Res 2009; 37:5894-907. [PMID: 19726586 PMCID: PMC2761267 DOI: 10.1093/nar/gkp594] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Herein, we report the identification of RNA hairpin loops that bind derivatives of kanamycin A, tobramycin, neamine, and neomycin B via two-dimensional combinatorial screening, a method that screens chemical and RNA spaces simultaneously. An arrayed aminoglycoside library was probed for binding to a 6-nucleotide RNA hairpin loop library (4096 members). Members of the loop library that bound each aminoglycoside were excised from the array, amplified and sequenced. Sequences were analyzed with our newly developed RNA Privileged Space Predictor (RNA-PSP) program, which analyzes selected sequences to identify statistically significant trends. RNA-PSP identified the following unique trends: 5'UNNNC3' loops for the kanamycin A derivative (where N is any nucleotide); 5'UNNC3' loops for the tobramycin derivative; 5'UNC3' loops for the neamine derivative; and 5'UNNG3' loops for the neomycin B derivative. The affinities and selectivities of a subset of the ligand-hairpin loop interactions were determined. The selected interactions have K(d) values ranging from 10 nM to 605 nM. Selectivities ranged from 0.4 to >200-fold. Interestingly, the results from RNA-PSP are able to qualitatively predict specificity based on overlap between the RNA sequences selected for the ligands. These studies expand the information available on small molecule-RNA motif interactions, which could be useful to design ligands targeting RNA.
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Affiliation(s)
- Dustin J Paul
- Department of Chemistry and Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, 657 Natural Sciences Complex, Buffalo, NY 14260, USA
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