1
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Chen J, Zhou J, Peng Y, Xie Y, Xiao Y. Aptamers: A prospective tool for infectious diseases diagnosis. J Clin Lab Anal 2022; 36:e24725. [PMID: 36245423 PMCID: PMC9701868 DOI: 10.1002/jcla.24725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 12/05/2022] Open
Abstract
It is well known that people's health is seriously threatened by various pathogens (such as Mycobacterium tuberculosis, Treponema pallidum, Novel coronavirus, HIV, Mucor, etc.), which leads to heavy socioeconomic burdens. Therefore, early and accurate pathogen diagnosis is essential for timely and effective therapies. Up to now, diagnosing human contagious diseases at molecule and nano levels is remarkably difficult owing to insufficient valid probes when it comes to determining the biological markers of pathogens. Aptamers are a set of high‐specificity and high‐sensitivity plastic oligonucleotides screened in vitro via the selective expansion of ligands by exponential enrichment (SELEX). With the advent of aptamer‐based technologies, their merits have aroused mounting academic interest. In recent years, as new detection and treatment tools, nucleic acid aptamers have been extensively utilized in the field of biomedicine, such as pathogen detection, new drug development, clinical diagnosis, nanotechnology, etc. However, the traditional SELEX method is cumbersome and has a long screening cycle, and it takes several months to screen out aptamers with high specificity. With the persistent development of SELEX‐based aptamer screening technologies, the application scenarios of aptamers have become more and more extensive. The present research briefly reviews the research progress of nucleic acid aptamers in the field of biomedicine, especially in the diagnosis of contagious diseases.
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Affiliation(s)
- Jiayi Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jiahuan Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yunchi Peng
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yafeng Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yongjian Xiao
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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2
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Yılmaz D, Muslu T, Parlar A, Kurt H, Yüce M. SELEX against whole-cell bacteria resulted in lipopolysaccharide binding aptamers. J Biotechnol 2022; 354:10-20. [PMID: 35700936 DOI: 10.1016/j.jbiotec.2022.06.001] [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: 02/16/2022] [Revised: 05/11/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022]
Abstract
Nucleic acid aptamers are target-specific oligonucleotides selected from combinatorial libraries through an iterative in vitro screening process known as Systemic Evolution of Ligands by Exponential Enrichment (SELEX). In this report, the selection of bacteria differentiating ssDNA aptamer candidates from a combinatorial library through the whole-cell SELEX method was performed. The enriched SELEX pool was sequenced using Illumina Next-Generation Sequencing (NGS) technology and analyzed for the most abundant sequences using CLC Genomics Workbench. The sequencing data resulted in several oligonucleotide families from which three individual sequences were chosen per SELEX based on the copy numbers. The binding performance of the selected aptamers was assessed by flow cytometry and fluorescence spectroscopy, and the binding constants were estimated using binding saturation curves. Varying results were obtained from two independent SELEX procedures where the SELEX against the model gram-negative bacterium Escherichia coli provided more selective sequences while the SELEX library used against gram-positive bacterium Listeria monocytogenes did not evolve as expected. The sequences that emerged from E. coli SELEX were shown to bind Lipopolysaccharide residues (LPS) and inhibit LPS-induced macrophage polarization. Thus, it can be said that, performed whole-cell SELEX could be resulted as the selection of aptamers which can bind LPS and inhibit LPS induced inflammation response and thus can be candidates for the inhibition of bacterial infections. In future studies, the selected aptamer sequences could be structurally and chemically modified and exploited as potential diagnostic tools and therapeutic agents as LPS antagonists.
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Affiliation(s)
- Deniz Yılmaz
- Sabanci University SUNUM Nanotechnology Research and Application Centre, Tuzla 34956, Istanbul, Turkey
| | - Tuğdem Muslu
- Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla 34956, Istanbul, Turkey
| | - Ayhan Parlar
- Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla 34956, Istanbul, Turkey
| | - Hasan Kurt
- School of Engineering and Natural Sciences, Istanbul Medipol University, Beykoz, 34810 Istanbul, Turkey; Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Beykoz, 34810 Istanbul, Turkey; Nanosolar Plasmonics Ltd., Gebze, 41400 Kocaeli, Turkey
| | - Meral Yüce
- Sabanci University SUNUM Nanotechnology Research and Application Centre, Tuzla 34956, Istanbul, Turkey.
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Liu M, Yue F, Kong Q, Liu Z, Guo Y, Sun X. Aptamers against Pathogenic Bacteria: Selection Strategies and Apta-assay/Aptasensor Application for Food Safety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5477-5498. [PMID: 35471004 DOI: 10.1021/acs.jafc.2c01547] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Pathogenic bacteria are primarily kinds of detrimental agents that cause mankind illness via contaminated food with traits of multiple types, universality, and low content. In view of the detection demands for rapidity, aptamer recognition factors emerged as a substitution for antibodies, which are short single strands of nucleic acid selected via in vitro. They display certain superiorities over antibodies, such as preferable stability, liable modification, and cost-efficiency. Taking advantage of the situation, numerous aptamers against pathogenic bacteria have been successfully selected and applied, yet there are still restrictions on commercial availability. In this review, the strategies/approaches to key sections in pathogen aptamers SELEX and post-SELEX are summarized and sorted out. Recently, optical, electrochemical, and piezoelectric aptamer-based assays or sensors dedicated to pathogen detection have been critically reviewed. Ultimately, the existing challenges and future trends in this field are proposed to further promote development prospects.
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Affiliation(s)
- Mengyue Liu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
| | - Fengling Yue
- School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
| | - Qianqian Kong
- School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
| | - Zhanli Liu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
| | - Yemin Guo
- School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
| | - Xia Sun
- School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
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4
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Sorgenfrei M, Hürlimann LM, Remy MM, Keller PM, Seeger MA. Biomolecules capturing live bacteria from clinical samples. Trends Biochem Sci 2022; 47:673-688. [PMID: 35487808 DOI: 10.1016/j.tibs.2022.03.018] [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: 11/23/2021] [Revised: 02/04/2022] [Accepted: 03/22/2022] [Indexed: 10/18/2022]
Abstract
Rapid phenotypic antimicrobial susceptibility testing (AST) requires the enrichment of live bacteria from patient samples, which is particularly challenging in the context of life-threatening bloodstream infections (BSIs) due to low bacterial titers. Over two decades, an extensive array of pathogen-specific biomolecules has been identified to capture live bacteria. The prevailing biomolecules are immune proteins of the complement system, antibodies, aptamers, phage proteins, and antimicrobial peptides. These biomolecules differ by their binder generation technologies and exhibit highly variable specificities, ranging from bacterial strains to most pathogenic bacteria. Here, we summarize how these diverse biomolecules were identified, list examples of successfully reported capture assays, and provide an outlook on the use of nanobodies raised against conserved surface-accessible proteins as promising biomolecules for pathogen capture.
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Affiliation(s)
- Michèle Sorgenfrei
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Lea M Hürlimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Mélissa M Remy
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Peter M Keller
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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Xiong L, Xia M, Wang Q, Meng Z, Zhang J, Yu G, Dong Z, Lu Y, Sun Y. DNA aptamers specific for Legionella pneumophila: systematic evolution of ligands by exponential enrichment in whole bacterial cells. Biotechnol Lett 2022; 44:777-786. [PMID: 35416565 DOI: 10.1007/s10529-022-03252-z] [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: 12/13/2021] [Accepted: 03/31/2022] [Indexed: 11/30/2022]
Abstract
Legionella pneumophila is the major causative agent of Legionnaires' disease and Pontiac fever, which pose major public health problems. Rapid detection of L. pneumophila is important for global control of these diseases. Aptamers, short oligonucleotides that bind to targets with high affinity and specificity, have great potential for use in pathogenic bacterium detection, diagnostics, and therapy. Here, we used a whole-cell SELEX (systematic evolution of ligands by exponential enrichment) method to isolate and characterize single-stranded DNA (ssDNA) aptamers against L. pneumophila. A total of 60 ssDNA sequences were identified after 17 rounds of selection. Other bacterial species (Escherichia coli, Bacillus subtilis, Pseudomonas syringae, Staphylococcus aureus, Legionella quateirensis, and Legionella adelaidensis) were used for counterselection to enhance the specificity of ssDNA aptamers against L. pneumophila. Four ssDNA aptamers showed strong affinity and high selectivity for L. pneumophila, with Kd values in the nanomolar range. Bioinformatic analysis of the most specific aptamers revealed predicted conserved secondary structures that might bind to L. pneumophila cell walls. In addition, the binding of these four fluorescently labeled aptamers to the surface of L. pneumophila was observed directly by fluorescence microscopy. These aptamers identified in this study could be used in the future to develop medical diagnostic tools and public environmental detection assays for L. pneumophila.
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Affiliation(s)
- Lina Xiong
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Mingchen Xia
- Guangzhou Saite Testing Co., LTD, Guangzhou, China
| | - Qinglin Wang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhen Meng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China.,College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China
| | - Jie Zhang
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China.,College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Guohui Yu
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China.,College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China
| | - Zhangyong Dong
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China.,College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China
| | - Yongjun Lu
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yunhao Sun
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China. .,College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China.
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6
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Saad M, Faucher SP. Aptamers and Aptamer-Coupled Biosensors to Detect Water-Borne Pathogens. Front Microbiol 2021; 12:643797. [PMID: 33679681 PMCID: PMC7933031 DOI: 10.3389/fmicb.2021.643797] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Aptamers can serve as efficient bioreceptors for the development of biosensing detection platforms. Aptamers are short DNA or RNA oligonucleotides that fold into specific structures, which enable them to selectively bind to target analytes. The method used to identify aptamers is Systematic Evolution of Ligands through Exponential Enrichment (SELEX). Target properties can have an impact on aptamer efficiencies. Therefore, characteristics of water-borne microbial targets must be carefully considered during SELEX for optimal aptamer development. Several aptamers have been described for key water-borne pathogens. Here, we provide an exhaustive overview of these aptamers and discuss important microbial aspects to consider when developing such aptamers.
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Affiliation(s)
- Mariam Saad
- Department of Natural Resources, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Faculté de Médecine Vétérinaire, Saint-Hyacinthe, QC, Canada
| | - Sebastien P. Faucher
- Department of Natural Resources, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Faculté de Médecine Vétérinaire, Saint-Hyacinthe, QC, Canada
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7
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Ning Y, Hu J, Lu F. Aptamers used for biosensors and targeted therapy. Biomed Pharmacother 2020; 132:110902. [PMID: 33096353 PMCID: PMC7574901 DOI: 10.1016/j.biopha.2020.110902] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 01/07/2023] Open
Abstract
Aptamers are single-stranded nucleic acid sequences that can bind to target molecules with high selectivity and affinity. Most aptamers are screened in vitro by a combinatorial biology technique called systematic evolution of ligands by exponential enrichment (SELEX). Since aptamers were discovered in the 1990s, they have attracted considerable attention and have been widely used in many fields owing to their unique advantages. In this review, we present an overview of the advancements made in aptamers used for biosensors and targeted therapy. For the former, we will discuss multiple aptamer-based biosensors with different principles detected by various signaling methods. For the latter, we will focus on aptamer-based targeted therapy using aptamers as both biotechnological tools for targeted drug delivery and as targeted therapeutic agents. Finally, challenges and new perspectives associated with these two regions were further discussed. We hope that this review will help researchers interested in aptamer-related biosensing and targeted therapy research.
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Affiliation(s)
- Yi Ning
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, PR China
| | - Jue Hu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, PR China
| | - Fangguo Lu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, PR China.
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8
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Xu L, Jiang B, Zhou W, Yuan R, Xiang Y. Coupling strand extension/excision amplification with target recycling enables highly sensitive and aptamer-based label-free sensing of ATP in human serum. Analyst 2019; 145:434-439. [PMID: 31793560 DOI: 10.1039/c9an02000d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Detection of aberrant ATP concentrations with high sensitivity and selectivity is of critical importance for monitoring many biological processes and disease stages. By coupling extension/excision amplification with target recycling, we have established an aptamer-based method for label-free fluorescence ATP detection in human serum with high sensitivity. The ATP target molecules associate with the aptamer-containing double hairpin probes and cause conformational changes of the probes to initiate the cyclic strand extension/excision processes in the presence of polymerase, endonuclease and assistance sequences for the recycling of ATP and the production of a large number of G-quadruplex sequences. The organic dye thioflavin T subsequently binds these G-quadruplex sequences to yield substantially enhanced fluorescence emission for achieving highly sensitive detection of ATP down to 2.2 nM in the range of 5 to 200 nM without using any labels. The developed aptamer sensing method also exhibits high selectivity and allows the monitoring of ATP at low concentrations in diluted real samples, which offers promising opportunities to establish effective signal magnification means for the detection of various biomolecules at trace levels.
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Affiliation(s)
- Lin Xu
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
| | - Bingying Jiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
| | - Wenjiao Zhou
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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Wang HX, Zhao YW, Li Z, Liu BS, Zhang D. Development and Application of Aptamer-Based Surface-Enhanced Raman Spectroscopy Sensors in Quantitative Analysis and Biotherapy. SENSORS (BASEL, SWITZERLAND) 2019; 19:E3806. [PMID: 31484403 PMCID: PMC6749344 DOI: 10.3390/s19173806] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/16/2019] [Accepted: 08/31/2019] [Indexed: 12/16/2022]
Abstract
Surface-enhanced Raman scattering (SERS) is one of the most special and important Raman techniques. An apparent Raman signal can be observed when the target molecules are absorbed onto the surface of the SERS substrates, especially on the "hot spots" of the substrates. Early research focused on exploring the highly active SERS substrates and their detection applications in label-free SERS technology. However, it is a great challenge to use these label-free SERS sensors for detecting hydrophobic or non-polar molecules, especially in complex systems or at low concentrations. Therefore, antibodies, aptamers, and antimicrobial peptides have been used to effectively improve the target selectivity and meet the analysis requirements. Among these selective elements, aptamers are easy to use for synthesis and modifications, and their stability, affinity and specificity are extremely good; they have been successfully used in a variety of testing areas. The combination of SERS detection technology and aptamer recognition ability not only improved the selection accuracy of target molecules, but also improved the sensitivity of the analysis. Variations of aptamer-based SERS sensors have been developed and have achieved satisfactory results in the analysis of small molecules, pathogenic microorganism, mycotoxins, tumor marker and other functional molecules, as well as in successful photothermal therapy of tumors. Herein, we present the latest advances of the aptamer-based SERS sensors, as well as the assembling sensing platforms and the strategies for signal amplification. Furthermore, the existing problems and potential trends of the aptamer-based SERS sensors are discussed.
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Affiliation(s)
- Hai-Xia Wang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yu-Wen Zhao
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zheng Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Bo-Shi Liu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Di Zhang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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Application of Aptamer-Based Biosensor for Rapid Detection of Pathogenic Escherichia coli. SENSORS 2018; 18:s18082518. [PMID: 30071682 PMCID: PMC6111995 DOI: 10.3390/s18082518] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 12/17/2022]
Abstract
Pathogenic Escherichia coli (E. coli) widely exist in Nature and have always been a serious threat to the human health. Conventional colony forming units counting-based methods are quite time consuming and not fit for rapid detection for E. coli. Therefore, novel strategies for improving detection efficiency and sensitivity are in great demand. Aptamers have been widely used in various sensors due to their extremely high affinity and specificity. Successful applications of aptamers have been found in the rapid detection of pathogenic E. coli. Herein, we present the latest advances in screening of aptamers for E. coli, and review the preparation and application of aptamer-based biosensors in rapid detection of E. coli. Furthermore, the problems and new trends in these aptamer-based biosensors for rapid detection of pathogenic microorganism are also discussed.
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11
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Yan YL, Gänzle MG. Structure and function relationships of the binding of β- and ɑ-galactosylated oligosaccharides to K88 fimbriae of enterotoxigenic Escherichia coli. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2018.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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12
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Pan Q, Luo F, Liu M, Zhang XL. Oligonucleotide aptamers: promising and powerful diagnostic and therapeutic tools for infectious diseases. J Infect 2018; 77:83-98. [PMID: 29746951 PMCID: PMC7112547 DOI: 10.1016/j.jinf.2018.04.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 01/02/2018] [Accepted: 04/08/2018] [Indexed: 12/21/2022]
Abstract
The entire human population is at risk of infectious diseases worldwide. Thus far, the diagnosis and treatment of human infectious diseases at the molecular and nanoscale levels have been extremely challenging tasks because of the lack of effective probes to identify and recognize biomarkers of pathogens. Oligonucleotide aptamers are a class of small nucleic acid ligands that are composed of single-stranded DNA (ssDNA) or RNA and act as affinity probes or molecular recognition elements for a variety of targets. These aptamers have an exciting potential for diagnose and/or treatment of specific diseases. In this review, we highlight areas where aptamers have been developed as diagnostic and therapeutic agents for both bacterial and viral infectious diseases as well as aptamer-based detection.
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Affiliation(s)
- Qin Pan
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Fengling Luo
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Min Liu
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China.
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13
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Renders M, Miller E, Lam CH, Perrin DM. Whole cell-SELEX of aptamers with a tyrosine-like side chain against live bacteria. Org Biomol Chem 2018; 15:1980-1989. [PMID: 28009914 DOI: 10.1039/c6ob02451c] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In an effort to expand the binding and recognition capabilities of aptamers, a nucleoside triphosphate modified with a phenol that mimics the side chain of tyrosine was used in the selection of DNA aptamers against live bacteria. Of multiple modified aptamers that were isolated against Escherichia coli DH5α cells, one aptamer displays high selectivity and affinity for the target cells and is greatly enriched for phenol-modified dU nucleotides (dUy, 47.5%). When the same sequences are synthesized with TTP, no binding is observed. Taken together, these findings highlight the value of using modified nucleotide triphosphates in aptamer selections and portends success in SELEX against an array of whole cells as targets.
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Affiliation(s)
- Marleen Renders
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
| | - Emily Miller
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
| | - Curtis H Lam
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
| | - David M Perrin
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
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14
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Whole-bacterium SELEX of DNA aptamers for rapid detection of E.coli O157:H7 using a QCM sensor. J Biotechnol 2017; 266:39-49. [PMID: 29242148 DOI: 10.1016/j.jbiotec.2017.12.011] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/27/2017] [Accepted: 12/10/2017] [Indexed: 12/21/2022]
Abstract
The rapid detection of foodborne pathogens is critical to ensure food safety. The objective of this study is to select aptamers specifically bound to Escherichia coli O157:H7 using the whole-bacterium SELEX (Systematic Evolution of Ligands by Exponential Enrichment) and apply the selected aptamer to a QCM (quartz crystal microbalance) sensor for rapid and sensitive detection of target bacteria. A total of 19 rounds of selection against live E. coli O157:H7 and 6 rounds of counter selection against a mixture of Staphylococcus aureus, Listeria monocytogenes, and Salmonella Typhimurium, were performed. The aptamer pool from the last round was cloned and sequenced. One sequence S1 that appeared 16 times was characterized and a dissociation constant (Kd) of 10.30nM was obtained. Subsequently, a QCM aptasensor was developed for the rapid detection of E. coli O157:H7. The limit of detection (LOD) and the detection time of the aptasensor was determined to be 1.46×103 CFU/ml and 50min, respectively. This study demonstrated that the ssDNA aptamer selected by the whole-bacterium SELEX possessed higher sensitivity than previous work and the potential use of the constructed QCM aptasensor in rapid screening of foodborne pathogens.
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Yan L, Da H, Zhang S, López VM, Wang W. Bacterial magnetosome and its potential application. Microbiol Res 2017; 203:19-28. [PMID: 28754204 DOI: 10.1016/j.micres.2017.06.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/08/2017] [Accepted: 06/17/2017] [Indexed: 01/01/2023]
Abstract
Bacterial magnetosome, synthetized by magnetosome-producing microorganisms including magnetotactic bacteria (MTB) and some non-magnetotactic bacteria (Non-MTB), is a new type of material comprising magnetic nanocrystals surrounded by a phospholipid bilayer. Because of the special properties such as single magnetic domain, excellent biocompatibility and surface modification, bacterial magnetosome has become an increasingly attractive for researchers in biology, medicine, paleomagnetism, geology and environmental science. This review briefly describes the general feature of magnetosome-producing microorganisms. This article also highlights recent advances in the understanding of the biochemical and magnetic characteristics of bacterial magnetosome, as well as the magnetosome formation mechanism including iron ions uptake, magnetosome membrane formation, biomineralization and magnetosome chain assembly. Finally, this review presents the potential applications of bacterial magnetosome in biomedicine, wastewater treatment, and the significance of mineralization of magnetosome in biology and geology.
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Affiliation(s)
- Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, PR China.
| | - Huiyun Da
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, PR China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, PR China
| | - Viviana Morillo López
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV 89154, USA
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, PR China
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Pathania P, Sharma A, Kumar B, Rishi P, Raman Suri C. Selective identification of specific aptamers for the detection of non-typhoidal salmonellosis in an apta-impedimetric sensing format. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2098-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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17
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Tarditto LV, Arévalo FJ, Zon MA, Ovando HG, Vettorazzi NR, Fernández H. Electrochemical sensor for the determination of enterotoxigenic Escherichia coli in swine feces using glassy carbon electrodes modified with multi-walled carbon nanotubes. Microchem J 2016. [DOI: 10.1016/j.microc.2016.03.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Rasoulinejad S, Gargari SLM. Aptamer-nanobody based ELASA for specific detection of Acinetobacter baumannii isolates. J Biotechnol 2016; 231:46-54. [PMID: 27234880 DOI: 10.1016/j.jbiotec.2016.05.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/12/2016] [Accepted: 05/19/2016] [Indexed: 11/26/2022]
Abstract
Acinetobacter baumannii has turned into an important threat in nosocomial outbreak infections and multidrug resistance leading to high mortality rates in the 21st century. In recent years its mortality has increased by 15% which in part could be due to lack of a rapid and sensitive diagnostic test. In this work we introduced a new detection test for A. baumannii with two highly specific aptamer and nanobody molecules. High binding affinity DNA oligonucleotide aptamers toward A. baumannii were selected through 12 rounds of whole cell System Evolution of Ligands by EXponential enrichment process (SELEX). The SELEX procedures was monitored by flow cytometry. The dissociation constant and binding efficiency of the selected aptamer Aci49 was 7.547±1:353pM and 47.50%, respectively. A sandwich enzyme linked aptamer sorbent assay (ELASA) was designed with the biotinylated Aci49 aptamer and our previously developed nanobody against biofilm associated protein (Bap). The assay system was optimized with A. baumannii (ATCC 19606) and 47 clinical isolates of A. baumannii were tested. The threshold of detection in sandwich ELASA process was10(3) CFU/ml. The sensitivity of test toward the clinical isolates was 95.47%. Our results reveal that the sandwich ELASA is sensitive and specific enough for the rapid detection of A. baumannii from clinical isolates.
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Marton S, Cleto F, Krieger MA, Cardoso J. Isolation of an Aptamer that Binds Specifically to E. coli. PLoS One 2016; 11:e0153637. [PMID: 27104834 PMCID: PMC4841571 DOI: 10.1371/journal.pone.0153637] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/01/2016] [Indexed: 01/24/2023] Open
Abstract
Escherichia coli is a bacterial species found ubiquitously in the intestinal flora of animals, although pathogenic variants cause major public health problems. Aptamers are short oligonucleotides that bind to targets with high affinity and specificity, and have great potential for use in diagnostics and therapy. We used cell-based Systematic Evolution of Ligands by EXponential enrichment (cell-SELEX) to isolate four single stranded DNA (ssDNA) aptamers that bind strongly to E. coli cells (ATCC generic strain 25922), with Kd values in the nanomolar range. Fluorescently labeled aptamers label the surface of E. coli cells, as viewed by fluorescent microscopy. Specificity tests with twelve different bacterial species showed that one of the aptamers–called P12-31—is highly specific for E. coli. Importantly, this aptamer binds to Meningitis/sepsis associated E. coli (MNEC) clinical isolates, and is the first aptamer described with potential for use in the diagnosis of MNEC-borne pathologies.
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Affiliation(s)
- Soledad Marton
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
| | - Fernanda Cleto
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
| | - Marco Aurélio Krieger
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil.,Instituto Carlos Chagas, Laboratório de Genomica Functional, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
| | - Josiane Cardoso
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
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Bai W, Zhu C, Liu J, Yan M, Yang S, Chen A. Gold nanoparticle-based colorimetric aptasensor for rapid detection of six organophosphorous pesticides. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2015; 34:2244-2249. [PMID: 26031388 DOI: 10.1002/etc.3088] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/22/2015] [Accepted: 05/25/2015] [Indexed: 06/04/2023]
Abstract
Fast immunoassay-based screening methods are unavailable for most small-molecule pesticides because of a lack of immunogenicity and the difficulty in obtaining antibodies by animal immunization. Aptamers are single-stranded DNA molecules selected through an in vitro process, which can bind to any target including nonimmunogenic small molecules with high affinity and specificity. Although various aptamer-based sensing methods have been developed for antibiotics, microorganisms, heavy metal ions, and biotoxins, there are few reports on aptamer-based methods for quick detection of organophosphorous pesticides. The gold (Au) nanoparticle (AuNP) colorimetric assay is a widely utilized rapid detection method because of properties such as easy operation and visualized results. In the present study, organophosphorous pesticide aptamers were adsorbed on the surface of AuNPs to stabilize the AuNP solution against high concentrations of salt to prevent AuNP aggregation. After the addition of targets, the aptamers binding to the targets are detached from the AuNPs, resulting in aggregation of AuNPs and a color change from red to purple-blue. The proposed method can detect 6 organophosphorous pesticides with good recoveries from 72% to 135% in environmental river water samples. The present study provides a new way for simple, rapid, and multiplex detection of organophosphorous pesticides.
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Affiliation(s)
- Wenhui Bai
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Chao Zhu
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Jinchuan Liu
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Mengmeng Yan
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Shuming Yang
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Ailiang Chen
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing, China
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Ling M, Peng Z, Cheng L, Deng L. Rapid Fluorescent Detection of Enterotoxigenic Escherichia coli (ETEC) K88 Based on Graphene Oxide-Dependent Nanoquencher and Klenow Fragment-Triggered Target Cyclic Amplification. APPLIED SPECTROSCOPY 2015; 69:1175-1181. [PMID: 26449811 DOI: 10.1366/15-07881] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Based on Klenow fragment (KF)-assisted target recycling amplification and graphene oxide (GO), a novel aptasensor, containing a capture probe (CP) and a signal probe (SP), was constructed and applied for the rapid detection of enterotoxigenic Escherichia coli (ETEC) K88. The CP was constructed of regions I and II, where the region I is aptamer sequence of ETEC K88 and the region II can form a double-stranded DNA structure with the SP. The SP was labeled with carboxyfluorescein (FAM) and acted as the primer sequence of the polymerization reaction. Before the targets were added, the two probes formed a partial double-strand junction (PDSJ) on the surface of the GO and the fluorescence was completely quenched. In the presence of the targets, the fluorescence was recovered due to the formation of the target-aptamer complex and its separation from the surface of the GO. Following this, the target-aptamer complex initiated the polymerization of the DNA strand in the presence of deoxynucleotides (dNTPs) and the KF. The displaced target then combined into another PDSJ, and the cycle started anew, leading to the formation of numerous complementary double-stranded DNAs. Meanwhile, the fluorescence signal was significantly enhanced. The results indicated that the established sensor has higher sensitivity specificity to its target bacteria in a wide range of 1 × 10(2) to 1 × 10(8) colony-forming units (CFU) mL(-1). The detection limit based on a signal-to-noise ratio (S/N) of 3 is 1 × 10(2) CFU mL(-1). More important, this rapid detection method is superior to other methods, having not only a short detection time but also a low fluorescence background, and is cheaper and has a wider applicability because its probes are easily designed and synthesized. Given these factors, our detection system has great prospects as a potential alternative to conventional ETEC K88 detection.
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Affiliation(s)
- Min Ling
- Hunan Normal University, Department of Microbiology, College of Life Science, Changsha 410081, China
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Davydova A, Vorobjeva M, Pyshnyi D, Altman S, Vlassov V, Venyaminova A. Aptamers against pathogenic microorganisms. Crit Rev Microbiol 2015; 42:847-65. [PMID: 26258445 PMCID: PMC5022137 DOI: 10.3109/1040841x.2015.1070115] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. One of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. Such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. The present review summarizes various modern SELEX techniques used in this field, and of several currently identified aptamers against viral particles and unicellular organisms, and their applications. The prospects of applying nucleic acid aptamers for the development of novel detection systems and antibacterial and antiviral drugs are discussed.
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Affiliation(s)
- Anna Davydova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Maria Vorobjeva
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Dmitrii Pyshnyi
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Sidney Altman
- b Department of Molecular, Cellular and Developmental Biology , Yale University , New Haven , CT , USA
| | - Valentin Vlassov
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Alya Venyaminova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
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Study on Electrochemical Insulin Sensing Utilizing a DNA Aptamer-Immobilized Gold Electrode. MATERIALS 2015; 8:4710-4719. [PMID: 28793466 PMCID: PMC5455528 DOI: 10.3390/ma8084710] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/14/2015] [Accepted: 07/21/2015] [Indexed: 11/25/2022]
Abstract
We investigated an insulin-sensing method by utilizing an insulin-binding aptamer IGA3, which forms an anti-parallel G-quadruplex with folded single strands. Spectroscopic observation indicates that some anti-parallel G-quadruplex bind hemin and show peroxidase activity. In this study, the peroxidase activity of IGA3 with hemin was confirmed by spectrophotometric measurements, i.e., the activity was three-times higher than hemin itself. IGA3 was then immobilized onto a gold electrode to determine its electrochemical activity. The peroxidase activity of the immobilized IGA3-hemin complex was determined by cyclic voltammetry, and a cathodic peak current of the electrode showed a dependence on the concentration of H2O2. The cathodic peak current of the IGA3-hemin complex decreased by binding it to insulin, and this decrease depended on the concentration of insulin.
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Single-Stranded DNA Aptamers against Pathogens and Toxins: Identification and Biosensing Applications. BIOMED RESEARCH INTERNATIONAL 2015. [PMID: 26199940 PMCID: PMC4493287 DOI: 10.1155/2015/419318] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Molecular recognition elements (MREs) can be short sequences of single-stranded DNA, RNA, small peptides, or antibody fragments. They can bind to user-defined targets with high affinity and specificity. There has been an increasing interest in the identification and application of nucleic acid molecular recognition elements, commonly known as aptamers, since they were first described in 1990 by the Gold and Szostak laboratories. A large number of target specific nucleic acids MREs and their applications are currently in the literature. This review first describes the general methodologies used in identifying single-stranded DNA (ssDNA) aptamers. It then summarizes advancements in the identification and biosensing application of ssDNA aptamers specific for bacteria, viruses, their associated molecules, and selected chemical toxins. Lastly, an overview of the basic principles of ssDNA aptamer-based biosensors is discussed.
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Niemirowicz K, Swiecicka I, Wilczewska AZ, Markiewicz KH, Surel U, Kułakowska A, Namiot Z, Szynaka B, Bucki R, Car H. Growth arrest and rapid capture of select pathogens following magnetic nanoparticle treatment. Colloids Surf B Biointerfaces 2015; 131:29-38. [PMID: 25942700 DOI: 10.1016/j.colsurfb.2015.04.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 03/06/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
Abstract
Thorough understanding of magnetic nanoparticle (MNP) properties is essential for developing new theranostics. In this study, we provide evidence that non-modified magnetic iron oxide nanoparticles and their functionalized derivatives may be used to restrict growth and capture different pathogens. Coprecipitation of Fe(2+) and Fe(3+) ions in an alkaline solution was used to synthesize MNPs that subsequently were functionalized by gold and aminosilane coating. Transmission electron microscopy (TEM), differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopy (FT-IR) were used to assess their physicochemical properties. A significant decrease of Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa and Candida albicans outgrown from medium after addition of MNPs or their derivatives was observed during 24h culture. Measurement of optical density revealed that using MNPs, these pathogens can be quickly captured and removed (with efficiency reaching almost 100%) from purposely infected saline buffer and body fluids such as human blood plasma, serum, abdominal fluids and cerebrospinal fluids. These effects depend on nanoparticle concentration, surface chemistry, the type of pathogen, as well as the surrounding environment.
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Affiliation(s)
- Katarzyna Niemirowicz
- Department of Microbiological and Nanobiomedical Engineering, Medical University of Białystok, Mickiewicza 2c, 15-222 Białystok, Poland; Department of Experimental Pharmacology, Medical University of Białystok, Szpitalna 37, 15-295 Białystok, Poland.
| | - Izabela Swiecicka
- Department of Microbiology, University of Białystok, J. K. Ciołkowski Street 1, 15-245 Białystok, Poland; Laboratory of Applied Microbiology, University of Białystok, J. K. Ciołkowski Street 1, 15-245 Białystok, Poland
| | | | - Karolina H Markiewicz
- Institute of Chemistry, University of Białystok, Hurtowa 1, 15-399 Białystok, Poland
| | - Urszula Surel
- Department of Microbiological and Nanobiomedical Engineering, Medical University of Białystok, Mickiewicza 2c, 15-222 Białystok, Poland
| | - Alina Kułakowska
- Department of Neurology, Medical University of Białystok, M. Skłodowskiej - Curie 24A, 15-276 Białystok, Poland
| | - Zbigniew Namiot
- Department of Physiology, Medical University of Białystok, Mickiewicza 2C, 15-222 Białystok, Poland
| | - Beata Szynaka
- Department of Histology and Embryology, Medical University of Białystok, Waszyngtona 13, 15-269 Białystok, Poland
| | - Robert Bucki
- Department of Microbiological and Nanobiomedical Engineering, Medical University of Białystok, Mickiewicza 2c, 15-222 Białystok, Poland; The Faculty of Health Sciences of the Jan Kochanowski University in Kielce, IX WiekówKielc 19, 25-317 Kielce, Poland
| | - Halina Car
- Department of Experimental Pharmacology, Medical University of Białystok, Szpitalna 37, 15-295 Białystok, Poland
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Bruno JG, Phillips T, Montez T, Garcia A, Sivils JC, Mayo MW, Greis A. Development of a fluorescent enzyme-linked DNA aptamer-magnetic bead sandwich assay and portable fluorometer for sensitive and rapid listeria detection. J Fluoresc 2014; 25:173-83. [PMID: 25511112 DOI: 10.1007/s10895-014-1495-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 12/05/2014] [Indexed: 12/14/2022]
Abstract
A fluorescent DNA aptamer-magnetic bead sandwich assay was developed to detect listeriolysin O (LLO) protein from pathogenic Listeria bacteria using a peroxidase-linked system, Amplex Ultra Red (AUR; derivatized resazurin) substrate, and a custom-designed handheld fluorometer. The assay is highly sensitive with demonstrated limits of detection (LODs) in the range of 4 to 61 L. monocytogenes cells or the equivalent LLO produced by 4 to 61 cells on average in separate titration trials. Total assay processing and analysis time was approximately 30 mins. The assay has demonstrated the ability to detect 6 species of Listeria as desired by the USDA's Food Safety Inspection Service (FSIS). The portable system was designed to be used primarily with surface swab samples from fomites, but it can also be used to assess enrichment cultures. The minimal time to detect a positive enrichment culture in our hands from an initial 10 cell inoculum in 200 ml of broth has been 8 h post-incubation at 37 °C in shaker flask cultures. An optional automated magnetic bead assay processing and wash device capable of simultaneously processing 6 samples with low and consistent fluorescence background for higher volume central laboratories is also described.
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Affiliation(s)
- John G Bruno
- Pronucleotein Biotechnologies Corporation, 4100 NW Loop 410, Suite 110, San Antonio, TX, 78229, USA,
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