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Léguillier V, Heddi B, Vidic J. Recent Advances in Aptamer-Based Biosensors for Bacterial Detection. BIOSENSORS 2024; 14:210. [PMID: 38785684 PMCID: PMC11117931 DOI: 10.3390/bios14050210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
The rapid and sensitive detection of pathogenic bacteria is becoming increasingly important for the timely prevention of contamination and the treatment of infections. Biosensors based on nucleic acid aptamers, integrated with optical, electrochemical, and mass-sensitive analytical techniques, have garnered intense interest because of their versatility, cost-efficiency, and ability to exhibit high affinity and specificity in binding bacterial biomarkers, toxins, and whole cells. This review highlights the development of aptamers, their structural characterization, and the chemical modifications enabling optimized recognition properties and enhanced stability in complex biological matrices. Furthermore, recent examples of aptasensors for the detection of bacterial cells, biomarkers, and toxins are discussed. Finally, we explore the barriers to and discuss perspectives on the application of aptamer-based bacterial detection.
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Affiliation(s)
- Vincent Léguillier
- INRAE, AgroParisTech, Micalis Institut, Université Paris-Saclay, UMR 1319, 78350 Jouy-en-Josas, France;
- ENS Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, 91190 Gif-sur-Yvette, France
| | - Brahim Heddi
- ENS Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, 91190 Gif-sur-Yvette, France
| | - Jasmina Vidic
- INRAE, AgroParisTech, Micalis Institut, Université Paris-Saclay, UMR 1319, 78350 Jouy-en-Josas, France;
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2
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Córdova-Espinoza MG, González-Vázquez R, Barron-Fattel RR, Gónzalez-Vázquez R, Vargas-Hernández MA, Albores-Méndez EM, Esquivel-Campos AL, Mendoza-Pérez F, Mayorga-Reyes L, Gutiérrez-Nava MA, Medina-Quero K, Escamilla-Gutiérrez A. Aptamers: A Cutting-Edge Approach for Gram-Negative Bacterial Pathogen Identification. Int J Mol Sci 2024; 25:1257. [PMID: 38279257 PMCID: PMC10817072 DOI: 10.3390/ijms25021257] [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: 11/03/2023] [Revised: 01/04/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
Early and accurate diagnoses of pathogenic microorganisms is essential to correctly identify diseases, treating infections, and tracking disease outbreaks associated with microbial infections, to develop precautionary measures that allow a fast and effective response in epidemics and pandemics, thus improving public health. Aptamers are a class of synthetic nucleic acid molecules with the potential to be used for medical purposes, since they can be directed towards any target molecule. Currently, the use of aptamers has increased because they are a useful tool in the detection of specific targets. We present a brief review of the use of aptamers to detect and identify bacteria or even some toxins with clinical importance. This work describes the advances in the technology of aptamers, with the purpose of providing knowledge to develop new aptamers for diagnoses and treatment of different diseases caused by infectious microorganisms.
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Affiliation(s)
- María Guadalupe Córdova-Espinoza
- Immunology Laboratory, Escuela Militar de Graduados de Sanidad, SEDENA, Mexico City 11200, Mexico;
- National School of Biological Sciences, National Polytechnic Institute, Laboratory of Medical Bacteriology, Mexico City 11350, Mexico; (R.G.-V.); (R.R.B.-F.)
- Mexican Social Security Institute, Unidad Medica de Alta Especialidad, Hospital de Especialidades, “Dr. Antonio Fraga Mouret”, National Medical Center La Raza, Mexico City 02990, Mexico
| | - Rosa González-Vázquez
- National School of Biological Sciences, National Polytechnic Institute, Laboratory of Medical Bacteriology, Mexico City 11350, Mexico; (R.G.-V.); (R.R.B.-F.)
- Mexican Social Security Institute, Unidad Medica de Alta Especialidad, Hospital de Especialidades, “Dr. Antonio Fraga Mouret”, National Medical Center La Raza, Mexico City 02990, Mexico
| | - Rolando Rafik Barron-Fattel
- National School of Biological Sciences, National Polytechnic Institute, Laboratory of Medical Bacteriology, Mexico City 11350, Mexico; (R.G.-V.); (R.R.B.-F.)
| | - Raquel Gónzalez-Vázquez
- Laboratory of Biotechnology, Department of Biological Systems, Metropolitana Campus Xochimilco, CONAHCYT—Universidad Autonoma, Calzada del Hueso 1100, Col. Villa Quietud, Alcaldia Coyoacan, Mexico City 04960, Mexico;
| | - Marco Antonio Vargas-Hernández
- Research Department, Escuela Militar de Graduados de Sanidad, SEDENA, Mexico City 11200, Mexico; (M.A.V.-H.); (E.M.A.-M.)
| | - Exsal Manuel Albores-Méndez
- Research Department, Escuela Militar de Graduados de Sanidad, SEDENA, Mexico City 11200, Mexico; (M.A.V.-H.); (E.M.A.-M.)
| | - Ana Laura Esquivel-Campos
- Laboratory of Biotechnology, Department of Biological Systems, Universidad Autonoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Alcaldia Coyoacan, Mexico City 04960, Mexico; (A.L.E.-C.); (F.M.-P.); (L.M.-R.)
| | - Felipe Mendoza-Pérez
- Laboratory of Biotechnology, Department of Biological Systems, Universidad Autonoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Alcaldia Coyoacan, Mexico City 04960, Mexico; (A.L.E.-C.); (F.M.-P.); (L.M.-R.)
| | - Lino Mayorga-Reyes
- Laboratory of Biotechnology, Department of Biological Systems, Universidad Autonoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Alcaldia Coyoacan, Mexico City 04960, Mexico; (A.L.E.-C.); (F.M.-P.); (L.M.-R.)
| | - María Angélica Gutiérrez-Nava
- Laboratory of Microbial Ecology, Department of Biological Systems, Universidad Autonoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Coyoacan, Mexico City 04960, Mexico;
| | - Karen Medina-Quero
- Immunology Laboratory, Escuela Militar de Graduados de Sanidad, SEDENA, Mexico City 11200, Mexico;
| | - Alejandro Escamilla-Gutiérrez
- National School of Biological Sciences, National Polytechnic Institute, Laboratory of Medical Bacteriology, Mexico City 11350, Mexico; (R.G.-V.); (R.R.B.-F.)
- Mexican Social Security Institute, Unidad Medica de Alta Especialidad, Microbiology Laboratory, Hospital General “Dr. Gaudencio González Garza”, National Medical Center La Raza, Mexico City 02990, Mexico
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3
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Manfredini A, Malusà E, Canfora L. Aptamer-based technology for detecting Bacillus subtilis in soil. Appl Microbiol Biotechnol 2023; 107:6963-6972. [PMID: 37698608 DOI: 10.1007/s00253-023-12765-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/12/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
The uncertainty associated with the impact of a bioinoculant on soil microbial community and, as a consequence, on soil quality, as well as the need to define its persistence, has prompted the demand for an accurate detection and tracking of the presence and the quantification of a target microbial inoculant in soil. Although DNA or RNA-based molecular detection are well established and commonly applied in this regard, alternative ligands such as DNA-aptamers have several advantages over them, such as low cost, ease of modification, ease of immobilisation on lab-on-chip or nanosensors, high stability and not thermolability. In this study, we used a toggle-cell SELEX method to isolate, select and characterise ssDNA (single-strand DNA) aptamers to detect a Bacillus subtilis strain which is being tested as a plant growth promoting rhizobacteria (PGPR) formulation. Two ssDNA aptamers (patenting application n.102022000022590) showed strong affinity and specificity for B. subtilis strains, with values of the kinetic parameters Kd (dissociation constant) in the nanomolar range and Bmax (maximum intensity of binding) around 1. Validation of the suitability of the aptamers was validated on three inoculated soils characterised by different chemical-physical features and in soil from a field trial with the formulated B. subtilis PCM/B 00105 strain. These are considered significant features to monitor B. subtilis strains in soil, practical to optimise bioinoculant application methods, support regulatory processes and foster the shift of agricultural production toward more sustainable cropping systems. KEY POINTS: • First DNA aptamers binding a B. subtilis strain included in a bioinoculum formulation. • First DNA aptamer binding B. subtilis in soil. • Aptamer may be a method for microbial inoculant detection in soil.
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Affiliation(s)
| | - Eligio Malusà
- CREA Centro di Ricerca Viticoltura ed Enologia, 31015, Conegliano, Italy
- National Institute of Horticultural Research, 96-100, Skierniewice, Poland
| | - Loredana Canfora
- CREA Centro di Ricerca Agricoltura e Ambiente, 00184, Rome, Italy
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4
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Ma N, Sun M, Shi H, Xue L, Zhang M, Yang W, Dang Y, Qiao Z. A Colorimetric/Fluorescent Dual-Mode Aptasensor for Salmonella Based on the Magnetic Separation of Aptamers and a DNA-Nanotriangle Programmed Multivalent Aptamer. Foods 2023; 12:3853. [PMID: 37893744 PMCID: PMC10606715 DOI: 10.3390/foods12203853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Salmonella infection has emerged as a global health threat, causing death, disability, and socioeconomic disruption worldwide. The rapid and sensitive detection of Salmonella is of great significance in guaranteeing food safety. Herein, we developed a colorimetric/fluorescent dual-mode method based on a DNA-nanotriangle programmed multivalent aptamer for the sensitive detection of Salmonella. In this system, aptamers are precisely controlled and assembled on a DNA nanotriangle structure to fabricate a multivalent aptamer (NTri-Multi-Apt) with enhanced binding affinity and specificity toward Salmonella. The NTri-Multi-Apt was designed to carry many streptavidin-HRPs for colorimetric read-outs and a large load of Sybr green I in the dsDNA scaffold for the output of a fluorescent signal. Therefore, combined with the magnetic separation of aptamers and the prefabricated NTri-Multi-Apt, the dual-mode approach achieved simple and sensitive detection, with LODs of 316 and 60 CFU/mL for colorimetric and fluorescent detection, respectively. Notably, the fluorescent mode provided a self-calibrated and fivefold-improved sensitivity over colorimetric detection. Systematic results also revealed that the proposed dual-mode method exhibited high specificity and applicability for milk, egg white, and chicken meat samples, serving as a promising tool for real bacterial sample testing. As a result, the innovative dual-mode detection method showed new insights for the detection of other pathogens.
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Affiliation(s)
- Na Ma
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo 315800, China
| | - Mengni Sun
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo 315800, China
| | - Hanxing Shi
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo 315800, China
| | - Liangliang Xue
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo 315800, China
| | - Min Zhang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo 315800, China
| | - Wenge Yang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo 315800, China
| | - Yali Dang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo 315800, China
| | - Zhaohui Qiao
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo 315800, China
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5
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A review: Construction of aptamer screening methods based on improving the screening rate of key steps. Talanta 2023. [DOI: 10.1016/j.talanta.2022.124003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Nikam PS, Palachandra S, Kingston JJ. In vitro selection and characterization of ssDNA aptamers by cross-over SELEX and its application for detection of S. Typhimurium. Anal Biochem 2022; 656:114884. [DOI: 10.1016/j.ab.2022.114884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/10/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022]
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Mohamad N, Azizan NI, Mokhtar NFK, Mustafa S, Mohd Desa MN, Hashim AM. Future perspectives on aptamer for application in food authentication. Anal Biochem 2022; 656:114861. [PMID: 35985482 DOI: 10.1016/j.ab.2022.114861] [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: 02/23/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022]
Abstract
Food fraudulence and food contamination are major concerns, particularly among consumers with specific dietary, cultural, lifestyle, and religious requirements. Current food authentication methods have several drawbacks and limitations, necessitating the development of a simpler, more sensitive, and rapid detection approach for food screening analysis, such as an aptamer-based biosensor system. Although the use of aptamer is growing in various fields, aptamer applications for food authentication are still lacking. In this review, we discuss the limitations of existing food authentication technologies and describe the applications of aptamer in food analyses. We also project several potential targets or marker molecules to be targeted in the SELEX process. Finally, this review highlights the drawbacks of current aptamer technologies and outlines the potential route of aptamer selection and applications for successful food authentication. This review provides an overview of the use of aptamer in food research and its potential application as a molecular reporter for rapid detection in food authentication process. Developing databases to store all biochemical profiles of food and applying machine learning algorithms against the biochemical profiles are urged to accelerate the identification of more reliable biomarker molecules as aptamer targets for food authentication.
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Affiliation(s)
- Nornazliya Mohamad
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nur Inani Azizan
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nur Fadhilah Khairil Mokhtar
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Shuhaimi Mustafa
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Nasir Mohd Desa
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Faculty of Medicine and Health Science, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor, Malaysia
| | - Amalia Mohd Hashim
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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8
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Banu K, Mondal B, Rai B, Monica N, Hanumegowda R. Prospects for the application of aptamer based assay platforms in pathogen detection. Biocybern Biomed Eng 2022. [DOI: 10.1016/j.bbe.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Chen W, Lai Q, Zhang Y, Liu Z. Recent Advances in Aptasensors For Rapid and Sensitive Detection of Staphylococcus Aureus. Front Bioeng Biotechnol 2022; 10:889431. [PMID: 35677308 PMCID: PMC9169243 DOI: 10.3389/fbioe.2022.889431] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/12/2022] [Indexed: 12/30/2022] Open
Abstract
The infection of Staphylococcus aureus (S.aureus) and the spread of drug-resistant bacteria pose a serious threat to global public health. Therefore, timely, rapid and accurate detection of S. aureus is of great significance for food safety, environmental monitoring, clinical diagnosis and treatment, and prevention of drug-resistant bacteria dissemination. Traditional S. aureus detection methods such as culture identification, ELISA, PCR, MALDI-TOF-MS and sequencing, etc., have good sensitivity and specificity, but they are complex to operate, requiring professionals and expensive and complex machines. Therefore, it is still challenging to develop a fast, simple, low-cost, specific and sensitive S. aureus detection method. Recent studies have demonstrated that fast, specific, low-cost, low sample volume, automated, and portable aptasensors have been widely used for S. aureus detection and have been proposed as the most attractive alternatives to their traditional detection methods. In this review, recent advances of aptasensors based on different transducer (optical and electrochemical) for S. aureus detection have been discussed in details. Furthermore, the applications of aptasensors in point-of-care testing (POCT) have also been discussed. More and more aptasensors are combined with nanomaterials as efficient transducers and amplifiers, which appears to be the development trend in aptasensors. Finally, some significant challenges for the development and application of aptasensors are outlined.
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Affiliation(s)
- Wei Chen
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, China
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
- *Correspondence: Wei Chen, ; Zhengchun Liu,
| | - Qingteng Lai
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, China
| | - Yanke Zhang
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, China
| | - Zhengchun Liu
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, China
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
- *Correspondence: Wei Chen, ; Zhengchun Liu,
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10
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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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11
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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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12
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Tabb JS, Rapoport E, Han I, Lombardi J, Green O. An antigen-targeting assay for Lyme disease: Combining aptamers and SERS to detect the OspA protein. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2022; 41:102528. [PMID: 35104673 DOI: 10.1016/j.nano.2022.102528] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 12/25/2022]
Abstract
Lyme disease is the fastest growing vector-borne disease in the United States. However, current testing modalities are ill suited to detection of Lyme disease, leading to the diagnosis of many cases after treatment is effective. We present an improved, direct method Lyme disease diagnosis, where the Lyme specific biomarker Outer Surface Protein A (OspA) in clinical serum samples is identified using a diagnostic platform combining surface enhanced Raman scattering (SERS) and aptamers. Employing orthogonal projections to latent structures discriminant analysis, the system accurately identified 91% of serum samples from Lyme patients, and 96% of serum samples from symptomatic controls. In addition, the OspA limit-of-detection, determined to be 1 × 10-4 ng/mL, is greater than four orders of magnitude lower than that found in serum samples from early Lyme disease patients. The application of this platform to detect this difficult-to-diagnose disease suggests its potential for detecting other diseases that present similar difficulties.
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Affiliation(s)
| | | | - Il Han
- Ionica Sciences, Ithaca, NY, USA
| | - John Lombardi
- Department of Chemistry, The City College of New York, New York, NY, USA
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13
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Devi S, Sharma N, Ahmed T, Huma ZI, Kour S, Sahoo B, Singh AK, Macesic N, Lee SJ, Gupta MK. Aptamer-based diagnostic and therapeutic approaches in animals: Current potential and challenges. Saudi J Biol Sci 2021; 28:5081-5093. [PMID: 34466086 PMCID: PMC8381015 DOI: 10.1016/j.sjbs.2021.05.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 01/19/2023] Open
Abstract
Fast and precise diagnosis of infectious and non-infectious animal diseases and their targeted treatments are of utmost importance for their clinical management. The existing biochemical, serological and molecular methods of disease diagnosis need improvement in their specificity, sensitivity and cost and, are generally not amenable for being used as points-of-care (POC) device. Further, with dramatic changes in environment and farm management practices, one should also arm ourselves and prepare for emerging and re-emerging animal diseases such as cancer, prion diseases, COVID-19, influenza etc. Aptamer – oligonucleotide or short peptides that can specifically bind to target molecules – have increasingly become popular in developing biosensors for sensitive detection of analytes, pathogens (bacteria, virus, fungus, prions), drug residues, toxins and, cancerous cells. They have also been proven successful in the cellular delivery of drugs and targeted therapy of infectious diseases and physiological disorders. However, the in vivo application of aptamer-mediated biosensing and therapy in animals has been limited. This paper reviews the existing reports on the application of aptamer-based biosensors and targeted therapy in animals. It also dissects the various modifications to aptamers that were found to be successful in in vivo application of the aptamers in diagnostics and therapeutics. Finally, it also highlights major challenges and future directions in the application of aptamers in the field of veterinary medicine.
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Affiliation(s)
- Sapna Devi
- Division of Veterinary Medicine, Faculty of Veterinary Sciences & A.H., Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, R.S. Pura, Jammu, J & K, India
| | - Neelesh Sharma
- Division of Veterinary Medicine, Faculty of Veterinary Sciences & A.H., Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, R.S. Pura, Jammu, J & K, India
- Corresponding author at: Division of Veterinary Medicine, Faculty of Veterinary Sciences & A.H., Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Jammu and Kashmir 181102, India.
| | - Touqeer Ahmed
- Division of Veterinary Medicine, Faculty of Veterinary Sciences & A.H., Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, R.S. Pura, Jammu, J & K, India
| | - Zul I. Huma
- Division of Veterinary Medicine, Faculty of Veterinary Sciences & A.H., Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, R.S. Pura, Jammu, J & K, India
| | - Savleen Kour
- Division of Veterinary Medicine, Faculty of Veterinary Sciences & A.H., Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, R.S. Pura, Jammu, J & K, India
| | - Bijayalaxmi Sahoo
- Gene Manipulation Laboratory, Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Odisha, India
| | - Amit Kumar Singh
- Experimental Animal Facility, National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Agra, U.P., India
| | - Nino Macesic
- Clinic for Reproduction and Theriogenology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Sung Jin Lee
- College of Animal Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Mukesh Kumar Gupta
- Gene Manipulation Laboratory, Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Odisha, India
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14
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Subjakova V, Oravczova V, Tatarko M, Hianik T. Advances in electrochemical aptasensors and immunosensors for detection of bacterial pathogens in food. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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15
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Xu Y, Jiang X, Zhou Y, Ma M, Wang M, Ying B. Systematic Evolution of Ligands by Exponential Enrichment Technologies and Aptamer-Based Applications: Recent Progress and Challenges in Precision Medicine of Infectious Diseases. Front Bioeng Biotechnol 2021; 9:704077. [PMID: 34447741 PMCID: PMC8383106 DOI: 10.3389/fbioe.2021.704077] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/26/2021] [Indexed: 02/05/2023] Open
Abstract
Infectious diseases are considered as a pressing challenge to global public health. Accurate and rapid diagnostics tools for early recognition of the pathogen, as well as individualized precision therapy are essential for controlling the spread of infectious diseases. Aptamers, which were screened by systematic evolution of ligands by exponential enrichment (SELEX), can bind to targets with high affinity and specificity so that have exciting potential in both diagnosis and treatment of infectious diseases. In this review, we provide a comprehensive overview of the latest development of SELEX technology and focus on the applications of aptamer-based technologies in infectious diseases, such as targeted drug-delivery, treatments and biosensors for diagnosing. The challenges and the future development in this field of clinical application will also be discussed.
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Affiliation(s)
- Yixin Xu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Jiang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yanhong Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ming Ma
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,The First People's Hospital of Shuangliu District, Chengdu/West China (Airport)Hospital Sichuan University, Chengdu, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
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16
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Song M, Lyu C, Duan N, Wu S, Khan IM, Wang Z. The isolation of high-affinity ssDNA aptamer for the detection of ribavirin in chicken. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:3110-3117. [PMID: 34156053 DOI: 10.1039/d1ay00606a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The abuse of ribavirin, an antiviral drug, in poultry breeding can cause quality degradation and drug resistance. So it is of great importance to establish a simple and effective method for detecting ribavirin in foods. In this work, aptamers that could especially bind to ribavirin with high affinity were obtained by the Capture-SELEX method. After 15 rounds of enrichment, ssDNA library pool was enriched and then analyzed by high-throughput sequencing. The seven most enriched sequences were selected as candidate aptamers for affinity and specificity characterization. Among the candidate aptamers, APT-1 was proved to be the optimal aptamer. The dissociation constant (Kd) values of APT-1 obtained by the two methods of colorimetric and fluorescence were 34.34 ± 6.038 nmol L-1, 61.19 ± 21.48 nmol L-1, respectively. To study the binding mechanism of the selected aptamer, molecular docking was conducted and results indicated that hydrogen bonds were formed at binding sites located at G37, T38, A40, T53 and A54. Furthermore, to confirm the practicability of the selected aptamer, a fluorescence assay was designed, showing the liner range within 1.0-50 ng mL-1 and the low detection limit of 0.67 ng mL-1. Besides, the aptamer was applied for the detection of ribavirin in chicken samples and the recoveries ranged from 87.26% to 105.57%, which showed great application potential in food safety.
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Affiliation(s)
- Mingyan Song
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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17
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Srivastava S, Abraham PR, Mukhopadhyay S. Aptamers: An Emerging Tool for Diagnosis and Therapeutics in Tuberculosis. Front Cell Infect Microbiol 2021; 11:656421. [PMID: 34277465 PMCID: PMC8280756 DOI: 10.3389/fcimb.2021.656421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) has been plaguing human civilization for centuries, and currently around one-third of the global population is affected with TB. Development of novel intervention tools for early diagnosis and therapeutics against Mycobacterium tuberculosis (M.tb) is the main thrust area in today's scenario. In this direction global efforts were made to use aptamers, the chemical antibodies as tool for TB diagnostics and therapeutics. This review describes the various aptamers introduced for targeting M.tb and highlights the need for development of novel aptamers to selectively target virulent proteins of M.tb for vaccine and anti-TB drugs. The objective of this review is to highlight the diagnostic and therapeutic application of aptamers used for tuberculosis. The discovery of aptamers, SELEX technology, different types of SELEX development processes, DNA and RNA aptamers reported for diseases and pathogenic agents as well have also been described in detail. But the emphasis of this review is on the development of aptamers which can block the function of virulent mycobacterial components for developing newer TB vaccine candidates and/or drug targets. Aptamers designed to target M.tb cell wall proteins, virulent factors, secretory proteins, or combination could orchestrate advanced diagnosis and therapeutic measures for tuberculosis.
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Affiliation(s)
- Shruti Srivastava
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Philip Raj Abraham
- Unit of OMICS, ICMR-Vector Control Research Centre (VCRC), Puducherry, India
| | - Sangita Mukhopadhyay
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
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18
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Chen M, Pan L, Tu K. A fluorescence biosensor for Salmonella typhimurium detection in food based on the nano-self-assembly of alendronic acid modified upconversion and gold nanoparticles. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2415-2423. [PMID: 33998617 DOI: 10.1039/d1ay00493j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A simple and quick-response fluorescent biosensor for Salmonella typhimurium detection based on the recognition of an aptamer coupled with alendronic acid (ADA)@upconversion nanoparticles (UCNPs) and gold nanoparticles (AuNPs) has been developed. Briefly, the aptamer can adsorb on the surfaces of the AuNPs via a "Au-S" bond to protect the AuNPs from aggregation in highly concentrated salt solution. Then, the AuNPs and UCNPs are linked by electrostatic adsorption, which leads to a decrease in the fluorescence peak at 541 nm based on fluorescence resonance energy transfer (FRET) between the UCNPs and AuNPs. In the presence of Salmonella typhimurium, the "Au-S" bond was broken, and the fluorescence intensity at 541 nm was recovered. Under optimal conditions, the correlation between the concentration of S. typhimurium and the intensity of the fluorescent biosensor signals was observed to be linear within the range of 1.16 × 102 to 1.16 × 107 CFU mL-1 (R2 = 0.9912), and the detection limit of the developed biosensor was observed to be 36 CFU mL-1. Furthermore, the proposed method was successfully used to detect the Salmonella typhimurium pathogen in food samples with satisfactory results.
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Affiliation(s)
- Min Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.
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19
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Kim DM, Park JS, Jung SW, Yeom J, Yoo SM. Biosensing Applications Using Nanostructure-Based Localized Surface Plasmon Resonance Sensors. SENSORS (BASEL, SWITZERLAND) 2021; 21:3191. [PMID: 34064431 PMCID: PMC8125509 DOI: 10.3390/s21093191] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 01/06/2023]
Abstract
Localized surface plasmon resonance (LSPR)-based biosensors have recently garnered increasing attention due to their potential to allow label-free, portable, low-cost, and real-time monitoring of diverse analytes. Recent developments in this technology have focused on biochemical markers in clinical and environmental settings coupled with advances in nanostructure technology. Therefore, this review focuses on the recent advances in LSPR-based biosensor technology for the detection of diverse chemicals and biomolecules. Moreover, we also provide recent examples of sensing strategies based on diverse nanostructure platforms, in addition to their advantages and limitations. Finally, this review discusses potential strategies for the development of biosensors with enhanced sensing performance.
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Affiliation(s)
- Dong Min Kim
- Center for Applied Life Science, Hanbat National University, Daejeon 34158, Korea;
| | - Jong Seong Park
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (J.S.P.); (S.-W.J.); (J.Y.)
| | - Seung-Woon Jung
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (J.S.P.); (S.-W.J.); (J.Y.)
| | - Jinho Yeom
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (J.S.P.); (S.-W.J.); (J.Y.)
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (J.S.P.); (S.-W.J.); (J.Y.)
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20
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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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21
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Binding Characteristics Study of DNA based Aptamers for E. coli O157:H7. Molecules 2021; 26:molecules26010204. [PMID: 33401561 PMCID: PMC7795876 DOI: 10.3390/molecules26010204] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 01/29/2023] Open
Abstract
E. coli O157:H7 is a pathogenic bacterium producing verotoxins that could lead to serious complications such as hemolytic uremia syndrome. Fast detection of such pathogens is important. For rapid detection, aptamers are quickly gaining traction as alternative biorecognition molecules besides conventional antibodies. Several DNA aptamers have been selected for E. coli O157:H7. Nonetheless, there has not been a comparative study of the binding characteristics of these aptamers. In this work, we present a comprehensive analysis of binding characteristics including binding affinity (Kd) and binding capacity (Bmax) of DNA-based aptamers for E. coli O157:H7 using qPCR. Our results show that aptamer E18R has the highest binding capacity to E. coli 157:H7 and the highest specificity over non-pathogenic E. coli strains K12 and DH5α. Our study also finds that the common biotin-tag modification at 5' end typically changes the binding capacity significantly. For most of the selected aptamers, the binding capacity after a biotin-tag modification decreases. There exists a discrepancy in the binding capability between the selected aptamer and the aptamer used for detection. Our study also shows that a lower concentration of Mg2+ ions in the binding buffer leads to a decrease in the binding capacity of E17F and E18R, while it does not affect the binding capacity of S1 and EcoR1.
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22
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Zhang W, Bu S, Bai H, Ma C, Ma L, Wei H, Liu X, Li Z, Wan J. A sensitive biosensor for determination of pathogenic bacteria using aldehyde dehydrogenase signaling system. Anal Bioanal Chem 2020; 412:7955-7962. [PMID: 32879993 DOI: 10.1007/s00216-020-02928-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/04/2020] [Accepted: 08/28/2020] [Indexed: 12/16/2022]
Abstract
Aldehyde dehydrogenase (ALDH) was first developed as an enzymatic signaling system of a biosensor for sensitive point-of-care detection of pathogenic bacteria. ALDH and specific aptamers to Salmonella typhimurium (S. typhimurium), as organic components, were embedded in organic-inorganic nanocomposites as a biosensor signal label, integrating the functions of signal amplification and target recognition. The biosensing mechanism is based on the fact that ALDH can catalyze rapid oxidation of acetaldehyde into acetic acid, resulting in pH change with portable pH meter readout. The altered pH exhibited a linear relationship with the logarithm of S. typhimurium from 102 to 108 CFU/mL and detection limit of 46 CFU/mL. Thus, the proposed biosensor has potential application in the diagnosis of pathogenic bacteria.
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Affiliation(s)
- Wenguang Zhang
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, Jilin, China
| | - Shengjun Bu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, Jilin, China
| | - Huasong Bai
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, Jilin, China
| | - Chengyou Ma
- College of Geo-Exploration Science and Technology, Jilin University, Changchun, 130026, Jilin, China
| | - Li Ma
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, Jilin, China
| | - Hongguo Wei
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, Jilin, China
| | - Xiu Liu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, Jilin, China
| | - Zehong Li
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China.
| | - Jiayu Wan
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, Jilin, China.
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23
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Huo B, Hu Y, Gao Z, Li G. Recent advances on functional nucleic acid-based biosensors for detection of food contaminants. Talanta 2020; 222:121565. [PMID: 33167261 DOI: 10.1016/j.talanta.2020.121565] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023]
Abstract
It has seen increasing development of reliable, robust, and flexible biosensors for rapid food-safety analysis in the past few decades. Recently, functional nucleic acid-based biosensors have attracted attention because of their programmability, bottom-up characteristics, and structural switches. However, few systematic reviews devoted to categorizing the potential of DNA nanostructures and devices were found for detecting food contaminants. Hence, the applications of functional nucleic acid-based biosensors were reviewed for analyzing food contaminants, including foodborne pathogen bacteria, biotoxins, heavy metals, and et al. In addition to categorizing the various biosensors, multiple signal readout strategies, such as optical, electrochemical, and mass-based signals were also examined. Finally, the future changes and potential opportunities, as well as practical applications of functional nucleic acid-based biosensors were discussed.
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Affiliation(s)
- Bingyang Huo
- School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuling Hu
- School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Gongke Li
- School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China.
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24
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Chen W, Teng J, Yao L, Xu J, Liu G. Selection of Specific DNA Aptamers for Hetero-Sandwich-Based Colorimetric Determination of Campylobacter jejuni in Food. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8455-8461. [PMID: 32663006 DOI: 10.1021/acs.jafc.0c02865] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Herein, a high-affinity single-stranded DNA aptamer (59 nt) against Campylobacter jejuni, defined as CJA1, was obtained using the whole-bacterium-based systemic evolution of ligands by exponential enrichment procedure. CJA1 was analyzed with a stable secondary structure and low dissociation constant (Kd) value of 1.37 ± 0.28 nM. The potential use of CJA1 was exemplified by the construction of a hetero-sandwich platform, in which C. jejuni was bound with a biotin-tagged CJA1 to perform a colorimetric reaction that is associated with visible color changes and detectable optical responses. Dependent upon this sensing platform, C. jejuni can be detected from 1.7 × 101 to 1.7 × 106 colony-forming units (CFU)/mL. The limit of detection (LOD) is obtained as 10 CFU/mL in PBS. The specificity study showed that the sensing platform is easy to distinguish C. jejuni from other common pathogens. Moreover, the C. jejuni-contaminated milk samples can also be accurately probed (LOD = 13 CFU/mL) without sacrificing its assay abilities, indicating the promising prospect of CJA1 in the fields of biosensing and diagnostics.
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Affiliation(s)
- Wei Chen
- Engineering Research Center of Food Bio-process, Ministry of Education (MOE), School of Food & Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, People's Republic of China
- Research Center for Biomedical and Health Science, School of Life and Health, Anhui Science & Technology University, Fengyang, Chuzhou, Anhui 233100, People's Republic of China
| | - Jun Teng
- Engineering Research Center of Food Bio-process, Ministry of Education (MOE), School of Food & Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, People's Republic of China
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58105, United States
| | - Li Yao
- Engineering Research Center of Food Bio-process, Ministry of Education (MOE), School of Food & Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, People's Republic of China
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58105, United States
| | - Jianguo Xu
- Engineering Research Center of Food Bio-process, Ministry of Education (MOE), School of Food & Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, People's Republic of China
| | - Guodong Liu
- Research Center for Biomedical and Health Science, School of Life and Health, Anhui Science & Technology University, Fengyang, Chuzhou, Anhui 233100, People's Republic of China
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25
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Hosseini SMH, Bassami MR, Haghparast A, Sankian M, Hashemi Tabar G. Identification of Aptamers that Specifically Bind to A 1 Antigen by Performing Cell-on Human Erythrocytes. Galen Med J 2020; 9:e1657. [PMID: 34466563 PMCID: PMC8343710 DOI: 10.31661/gmj.v9i0.1657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/12/2019] [Accepted: 11/10/2019] [Indexed: 11/16/2022] Open
Abstract
Background The apply of aptamers as a new generation's way to probe diagnostic for the detection of target molecules has gained ground. Aptamers can be used as alternatives to diagnostic antibodies for detection of blood groups due to their unique features. This study was aimed to produce DNA diagnostic aptamer detecting the antigen of A1 blood group using the Cell-Selex method. Materials and Methods DNA aptamer was isolated against A1 RBC antigen after ten stages of Cell-Selex and amplification by an asymmetric polymerase chain reaction. The progress of the stages of selection was evaluated using flow cytometry analysis, which the DNA aptamer isolated from the tenth cycle with an affinity of 70% fluorescent intensity, was selected from four positive colonies followed by determination of the sequences and secondary structures. Results The aptameric sequence obtained from C4 cloning was calculated with the highest binding affinity to A1 antigen having an apparent dissociation constant (Kd value) of at least 29.5 ± 4.3 Pmol, which was introduced as the selected aptamer-based on ΔG obtained from a colony of C4 equal to -13.13. Conclusion The aptamer obtained from using Cell-Selex method could be used as an example for the development of diagnostic tools such as biosensors for detecting A1 blood group antigens.
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Affiliation(s)
- Seyed Mohammad Hasan Hosseini
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Reza Bassami
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Alireza Haghparast
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mojtaba Sankian
- Immunology Research Center, Medical School, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gholamreza Hashemi Tabar
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Correspondence to: Gholamreza Hashemi Tabar, Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran Telephone Number: + 985118763851 Email Address:
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Aptamers Against Live Targets: Is In Vivo SELEX Finally Coming to the Edge? MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:192-204. [PMID: 32585627 PMCID: PMC7321788 DOI: 10.1016/j.omtn.2020.05.025] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/18/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022]
Abstract
Targeted therapeutics underwent a revolution with the entry of monoclonal antibodies in the medical toolkit. Oligonucleotide aptamers form another family of target agents that have been lagging behind in reaching the clinical arena in spite of their potential clinical translation. Some of the reasons for this might be related to the challenge in identifying aptamers with optimal in vivo specificity, and the nature of their pharmacokinetics. Aptamers usually show exquisite specificity, but they are also molecules that display dynamic structures subject to changing environments. Temperature, ion atmosphere, pH, and other variables are factors that could determine the affinity and specificity of aptamers. Thus, it is important to tune the aptamer selection process to the conditions in which you want your final aptamer to function; ideally, for in vivo applications, aptamers should be selected in an in vivo-like system or, ultimately, in a whole in vivo organism. In this review we recapitulate the implementations in systematic evolution of ligands by exponential enrichment (SELEX) to obtain aptamers with the best in vivo activity.
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Paniel N, Noguer T. Detection of Salmonella in Food Matrices, from Conventional Methods to Recent Aptamer-Sensing Technologies. Foods 2019; 8:E371. [PMID: 31480504 PMCID: PMC6770675 DOI: 10.3390/foods8090371] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/20/2019] [Accepted: 08/26/2019] [Indexed: 01/01/2023] Open
Abstract
Rapid detection of the foodborne pathogen Salmonella in food processing is of crucial importance to prevent food outbreaks and to ensure consumer safety. Detection and quantification of Salmonella species in food samples is routinely performed using conventional culture-based techniques, which are labor intensive, involve well-trained personnel, and are unsuitable for on-site and high-throughput analysis. To overcome these drawbacks, many research teams have developed alternative methods like biosensors, and more particularly aptasensors, were a nucleic acid is used as biorecognition element. The increasing interest in these devices is related to their high specificity, convenience, and relative rapid response. This review aims to present the advances made in these last years in the development of biosensors for the detection and the quantification of Salmonella, highlighting applications on meat from the chicken food chain.
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Affiliation(s)
- Nathalie Paniel
- Laboratoire BAE, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France.
- Unité EMaiRIT'S, Centre Technique de la Conservation des Produits Agricoles (CTCPA), Site Agroparc, 449 Avenue Clément Ader, BP21203, 84911 Avignon, France.
| | - Thierry Noguer
- Laboratoire BAE, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France.
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579, Sorbonne Universités (UPMC) Paris 6 et CNRS, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France.
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Optical biosensing of Streptococcus agalactiae based on core/shell magnetic nanoparticle-quantum dot. Anal Bioanal Chem 2019; 411:6733-6743. [PMID: 31402423 DOI: 10.1007/s00216-019-02046-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/14/2019] [Accepted: 07/22/2019] [Indexed: 01/01/2023]
Abstract
An immunomagnetic optical probe based on a core/shell magnetic nanoparticle-quantum dot was fabricated for detection of Streptococcus agalactiae, the causative agent of pneumonia and meningitis in newborns. The silica-coated magnetic nanoparticles conjugated with anti-S. agalactiae monoclonal antibody provided high specificity for pre-enrichment of bacteria from biological samples with a complex matrix such as milk. Compared with conventional methods such as culture and molecular techniques, the combination of fluorescent quantum dot and magnetic nanoparticle enhanced the sensitivity and speed of bacterial identification. The bio-functionalized fluorescent-magnetic nanoparticles were characterized by TEM, SEM, VSM, XRD, DLS, and FTIR and applied to the detection of S. agalactiae with a limit of 10 and 102 CFU/mL in PBS and milk, respectively. This immunomagnetic optical probe can be used for rapid isolation, sensitive, and specific detection of targeted bacteria without any treatment in clinical and animal samples in the presence of other infectious agents.
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Wu W, Yu C, Wang Q, Zhao F, He H, Liu C, Yang Q. Research advances of DNA aptasensors for foodborne pathogen detection. Crit Rev Food Sci Nutr 2019; 60:2353-2368. [PMID: 31298036 DOI: 10.1080/10408398.2019.1636763] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aptamers, referring to single-stranded DNA or RNA molecules can specifically recognize and bind to their targets. Based on their excellent specificity, sensitivity, high affinity, and simplicity of modification, aptamers offer great potential for pathogen detection and biomolecular screening. This article reviews aptamer screening technologies and aptamer application technologies, including gold-nanoparticle lateral flow assays, fluorescence assays, electrochemical assays, colorimetric assays, and surface-enhanced Raman assays, in the detection of foodborne pathogens. Although notable progress (more rapid, sensitive, and accurate) has been achieved in the field, challenges and drawbacks in their applications still remain to be overcome.
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Affiliation(s)
- Wei Wu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China.,State Key Laboratory of Bio-fibers and Eco-textiles, Institute of Biochemical Engineering, School of Materials Science and Engineering, Qingdao University, Qingdao, China
| | - Chundi Yu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Qi Wang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Fangyuan Zhao
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Hong He
- Clinical Laboratory, Affiliated Hospital to Qingdao University, Qingdao, China
| | - Chunzhao Liu
- State Key Laboratory of Bio-fibers and Eco-textiles, Institute of Biochemical Engineering, School of Materials Science and Engineering, Qingdao University, Qingdao, China.,State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Qingli Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
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Akki SU, Werth CJ. Critical Review: DNA Aptasensors, Are They Ready for Monitoring Organic Pollutants in Natural and Treated Water Sources? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:8989-9007. [PMID: 30016080 DOI: 10.1021/acs.est.8b00558] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
There is a growing need to monitor anthropogenic organic contaminants detected in water sources. DNA aptamers are synthetic single-stranded oligonucleotides, selected to bind to target contaminants with favorable selectivity and sensitivity. These aptamers can be functionalized and are used with a variety of sensing platforms to develop sensors, or aptasensors. In this critical review, we (1) identify the state-of-the-art in DNA aptamer selection, (2) evaluate target and aptamer properties that make for sensitive and selective binding and sensing, (3) determine strengths and weaknesses of alternative sensing platforms, and (4) assess the potential for aptasensors to quantify environmentally relevant concentrations of organic contaminants in water. Among a suite of target and aptamer properties, binding affinity is either directly (e.g., organic carbon partition coefficient) or inversely (e.g., polar surface area) correlated to properties that indicate greater target hydrophobicity results in the strongest binding aptamers, and binding affinity is correlated to aptasensor limits of detection. Electrochemical-based aptasensors show the greatest sensitivity, which is similar to ELISA-based methods. Only a handful of aptasensors can detect organic pollutants at environmentally relevant concentrations, and interference from structurally similar analogs commonly present in natural waters is a yet-to-be overcome challenge. These findings lead to recommendations to improve aptasensor performance.
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Affiliation(s)
- Spurti U Akki
- Department of Civil and Environmental Engineering , University of Illinois at Urbana-Champaign , 205 North Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Charles J Werth
- Department of Civil, Architecture, and Environmental Engineering , University of Texas at Austin , 301 East Dean Keeton Street , Austin , Texas 78712 , United States
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Suh SH, Choi SJ, Dwivedi HP, Moore MD, Escudero-Abarca BI, Jaykus LA. Use of DNA aptamer for sandwich type detection of Listeria monocytogenes. Anal Biochem 2018; 557:27-33. [PMID: 29649475 DOI: 10.1016/j.ab.2018.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 02/03/2023]
Abstract
A single stranded (ss) DNA aptamer, specific to members of Listeria genus, was used to develop a two-site binding sandwich assay for capture and detection of L. monocytogenes. Antibody-immobilized immunomagnetic beads were used to capture L. monocytogenes, followed by their exposure to the aptamer detector. Detection was achieved by amplification of cell-bound aptamers by qPCR. The lower limit of detection for the combined assay was 2.5 CFU L. monocytogenes in 500 μl buffer. This is juxtaposed to a detection limit of 2.4 log10 CFU in 500 μl buffer for immunomagnetic separation coupled with qPCR detection of L. monocytogenes targeting the hly gene. When applied to turkey deli meat, subjected to 24 h of non-selective enrichment, the two-site binding sandwich assay showed positive results at initial inoculum levels of 1-2 log10 CFU per 25 g sample. Because of its lower limit of detection, the assay reported here could be useful for detection of L. monocytogenes in foods and environmental samples.
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Affiliation(s)
- Soo Hwan Suh
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Soo Jung Choi
- Functional Food Research Center, Korea University, Seoul, South Korea.
| | - Hari P Dwivedi
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Matthew D Moore
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Blanca I Escudero-Abarca
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Lee-Ann Jaykus
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
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Neethirajan S, Ragavan K, Weng X. Agro-defense: Biosensors for food from healthy crops and animals. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2017.12.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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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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Zhang Y, Luo F, Zhang Y, Zhu L, Li Y, Zhao S, He P, Wang Q. A sensitive assay based on specific aptamer binding for the detection of Salmonella enterica serovar Typhimurium in milk samples by microchip capillary electrophoresis. J Chromatogr A 2017; 1534:188-194. [PMID: 29289340 DOI: 10.1016/j.chroma.2017.12.054] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/13/2017] [Accepted: 12/19/2017] [Indexed: 11/27/2022]
Abstract
The detection of Salmonella enterica serovar Typhimurium (S. Typhimurium) is very important for the prevention of food poisoning and other infectious diseases. Here we reported a simple and sensitive strategy to test S. Typhimurium by microchip capillary electrophoresis couple with laser-induced fluorescence (MCE-LIF) based on the specific reaction between the bacterium and corresponding aptamers. Based on the differences in charge to mass ratio between bacteria-aptamer complexes and free aptamers, a separation of the complexes and free aptamers could be obtained by MCE. The optimal parameters of the specific reaction including fluorescent dye concentration, Mg2+ concentration, incubation time, and pH of incubation solution were carefully investigated. Meanwhile, a non-specific DNA was exploited as a contrast for the detection of S. Typhimurium. Under the optimal conditions, a rapid separation of the bacteria-aptamer complex and free aptamers was achieved within 135 s with a limit of detection (S/N = 3) of 3.37 × 102 CFU mL-1. This method was applied for the detection of S. Typhimurium in fresh milk samples and a recovery rate of 95.8% was obtained. The experimental results indicated that the specific aptamers are of enough biostability and the established method could be used to analyze S. Typhimurium in foods.
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Affiliation(s)
- Yan Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Feifei Luo
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Yating Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Luqi Zhu
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Yi Li
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Shuangli Zhao
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Pingang He
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Qingjiang Wang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China.
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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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36
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Ramlal S, Mondal B, Lavu PS, N B, Kingston J. Capture and detection of Staphylococcus aureus with dual labeled aptamers to cell surface components. Int J Food Microbiol 2017; 265:74-83. [PMID: 29132030 DOI: 10.1016/j.ijfoodmicro.2017.11.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/22/2017] [Accepted: 11/04/2017] [Indexed: 11/18/2022]
Abstract
In the present study, a high throughput whole cell SELEX method has been applied successfully in selecting specific aptamers against whole cells of Staphylococcus aureus, a potent food poisoning bacterium. A total ten rounds of SELEX and three rounds of intermittent counter SELEX, was performed to obtain specific aptamers. Obtained oligonucleotide pool were cloned, sequenced and then grouped into different families based on their primary sequence homology and secondary structure similarity. FITC labeled sequences from different families were selected for further characterization via flow cytometry analysis. The dissociation constant (Kd) values of specific and higher binders ranged from 34 to 128nM. Binding assays to assess the selectivity of aptamer RAB10, RAB 20, RAB 28 and RAB 35 demonstrated high affinity against S. aureus and low binding affinity for other bacteria. To demonstrate the potential use of the aptamer a sensitive dual labeled sandwich detection system was developed using aptamer RAB10 and RAB 35 with a detection limit of 102CFU/mL. Furthermore detection from mixed cell population and spiked sample emphasized the robustness as well as applicability of the developed method. Altogether, the established assay could be a reliable detection tool for the routine investigation of Staphylococcus aureus in samples from food and clinical sources.
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Affiliation(s)
- Shylaja Ramlal
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka 570011, India.
| | - Bhairab Mondal
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka 570011, India
| | - Padma Sudharani Lavu
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka 570011, India
| | - Bhavanashri N
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka 570011, India
| | - Joseph Kingston
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka 570011, India
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Mirzakhani K, Gargari SLM, Rasooli I, Rasoulinejad S. Development of a DNA Aptamer for Screening Neisseria meningitidis Serogroup B by Cell SELEX. IRANIAN BIOMEDICAL JOURNAL 2017; 22:193-201. [PMID: 28941453 PMCID: PMC5889504 DOI: 10.22034/ibj.22.3.193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/26/2017] [Accepted: 07/30/2017] [Indexed: 02/07/2023]
Abstract
Background Artificial oligonucleotides like DNA or RNA aptamers can be used as biodiagnostic alternatives for antibodies to detect pathogens. Comparing to antibodies, artificial oligonucleotides are produced easily at lower costs and are more stable. Neisseria meningitidis, the causative agent of meningitis, is responsible for about 1% of infections in an epidemic period. Specific DNA aptamers that bind to N. meningitidis serogroup B were identified by whole-cell Systemic Evolution of Ligands by EXponential Enrichment (SELEX). Methods The SELEX begins with a library of labeled ssDNA molecules. After six rounds of selection and two rounds of counter-selection, 60 clones were obtained, of which the binding efficiency of 21 aptamers to the aforementioned bacterium was tested by flow cytometry. Results The aptamers K3 and K4 showed the highest affinity to N. meningitidis serogroup B and no affinity to N. meningitidis serogroups Y, A, and C, or to other meningitis causing bacteria. The dissociation constant (Kd value) for K3 and K4 were calculated as 28.3±8.9 pM and 39.1±8.6 pM, respectively. K3 aptamer with the lowest Kd was chosen as the main aptamer. K3 could detect N. meningitidis in patients’ cerebrospinal fluid (CSF) samples and in CSF from healthy volunteers inoculated with N. meningitidis serogroup B (ATCC 13090) at 200 and 100 CFU ml-1, respectively. Conclusion The findings suggest the application of the developed aptamer in specific detection of N. meningitidis serogroup B amongst a group of meningitis causing bacteria.
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Affiliation(s)
- Kimia Mirzakhani
- Faculty of Medicine, Institute of Human Genetics, Friedrich-Schiller University, Jena, Germany
| | | | - Iraj Rasooli
- Department of Biology, Shahed University, Tehran, Iran
- Molecular Microbiology Research Center, Shahed University, Tehran, Iran
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You Y, Lim S, Hahn J, Choi YJ, Gunasekaran S. Bifunctional linker-based immunosensing for rapid and visible detection of bacteria in real matrices. Biosens Bioelectron 2017; 100:389-395. [PMID: 28954255 DOI: 10.1016/j.bios.2017.09.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 08/27/2017] [Accepted: 09/18/2017] [Indexed: 10/18/2022]
Abstract
Detection of pathogens present in food and water is essential to help ensure food safety. Among the popular methods for pathogen detection are those based on culture and colony-counting and polymerase chain reaction (PCR). However, the time-consuming nature and/or the need for sophisticated instrumentation of those methods limit their on-site applications. We have developed a rapid and highly sensitive immunosensing method for visible detection of bacteria in real matrices based on the aggregation of AuNPs without requiring any readout device. We use biotinylated anti-bacteria antibodies as bifunctional linkers (BLs) to mediate the aggregation of streptavidin-functionalized gold nanoparticles (st-AuNPs) to produce visually recognizable color change, due to surface plasmon resonance (SPR), which occurs in about 30min of total assay time when the sample is mildly agitated or within three hours in quiescent conditions. The aggregation of st-AuNPs, which produces the indication signal, is achieved very differently than in visual detection methods reported previously and hence affords ultrahigh sensitivity. While BLs can both bind to the target and crosslink st-AuNPs, their latter function is essentially disabled when they bind to the target bacteria. By varying the amount of st-AuNPs used, we can tailor the assay effectiveness improving limit of detection (LOD) down to 10CFUmL-1 of E. coli and Salmonella. Test results obtained with tap water, lake water and milk samples show that assay performance is unaffected by matrix effects. Further, in a mixture of live and autoclaved E. coli cells our assay could detect only live cells. Therefore, our BL-based immunosensor is suitable for highly sensitive, rapid, and on-site detection of bacteria in real matrices.
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Affiliation(s)
- Youngsang You
- Department of Biological Systems Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Seokwon Lim
- Department of Food Science & Technology, Hoseo University, 79-20 Hoseoro, Asan, Chungnam 336-795, South Korea; Center for Natural Sciences, Hoseo University, 79-20 Hoseoro, Asan, Chungnam 336-795, South Korea
| | - Jungwoo Hahn
- Department of Agricultural Biotechnology, Seoul National University, 1 Gwanakro, Gwanakgu, Seoul 151-921, South Korea
| | - Young Jin Choi
- Department of Agricultural Biotechnology, Seoul National University, 1 Gwanakro, Gwanakgu, Seoul 151-921, South Korea; Center for Food and Bioconvergence, Seoul National University, 1 Gwanakro, Gwanakgu, Seoul 151-921, South Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanakro, Gwanakgu, Seoul 151-921, South Korea
| | - Sundaram Gunasekaran
- Department of Biological Systems Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Malekzad H, Jouyban A, Hasanzadeh M, Shadjou N, de la Guardia M. Ensuring food safety using aptamer based assays: Electroanalytical approach. Trends Analyt Chem 2017; 94:77-94. [PMID: 32287541 PMCID: PMC7112916 DOI: 10.1016/j.trac.2017.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Aptamers, are being increasingly employed as favorable receptors for constructing highly sensitive biosensors, for their remarkable affinities towards certain targets including a wide scope of biological or chemical substances, and their superiority over other biologic receptors. The selectivity and affinity of the aptamers have been integrated with the wise design of the assay, applying suitable modifications, such as nanomaterials on the electrode surface, employing oligonucleotide-specific amplification strategies or, their combinations. After successful performance of the electrochemical aptasensors for biomedical applications, the food sector with its direct implication for human health, which demands rapid and sensitive and economic analytical solutions for determination of health threatening contaminants in all stages of production process, is the next field of research for developing efficient electrochemical aptasensors. The aim of this review is to categorize and introduce food hazards and summarize the recent electrochemical aptasensors that have been developed to address these contaminants.
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Affiliation(s)
- Hedieh Malekzad
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolghasem Jouyban
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Kimia Idea Pardaz Azarbayjan (KIPA) Science Based Company, Tabriz University of Medical Sciences, Tabriz 51664, Iran
| | - Mohammad Hasanzadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasrin Shadjou
- Department of Nanochemistry, Nano Technology Research Center, Urmia University, Urmia, Iran
- Department of Nanochemistry, Faculty of Science, Urmia University, Urmia, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, Burjassot 46100, Valencia, Spain
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Tripathi P, Upadhyay N, Nara S. Recent advancements in lateral flow immunoassays: A journey for toxin detection in food. Crit Rev Food Sci Nutr 2017; 58:1715-1734. [PMID: 28071928 DOI: 10.1080/10408398.2016.1276048] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Biotechnology embraces various physical and chemical phenomena toward advancement of health diagnostics. Toward such advancement, detection of toxins plays an important role. Toxins produce severe health impacts on consumption with high mortality associated in acute cases. The most prominent route of infection and intoxication is through food matrices. Therefore, rapid detection of toxins at low concentrations is the need of modern diagnostics. Lateral flow immunoassays are one of the emergent and popularly used rapid detection technology developed for detecting various kinds of analytes. This review thus focuses on recent advancements in lateral flow immunoassays for detecting different toxins in agricultural food. Appropriate emphasis was given on how the labels, recognition elements, or detection strategy has laid an impact on improvement in immunochromatographic assays for toxins. The paper also discusses the gradual change in sensitivities and specificities of assays in accordance with the method of food processing used. The review concludes with the major challenges faced by this technology and provides an outlook and insight of ideas to improve it in the future.
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Affiliation(s)
- Pranav Tripathi
- a Department of Biotechnology , Motilal Nehru National Institute of Technology , Allahabad , Uttar Pradesh , India
| | - Neha Upadhyay
- a Department of Biotechnology , Motilal Nehru National Institute of Technology , Allahabad , Uttar Pradesh , India
| | - Seema Nara
- a Department of Biotechnology , Motilal Nehru National Institute of Technology , Allahabad , Uttar Pradesh , India
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41
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Chandola C, Kalme S, Casteleijn MG, Urtti A, Neerathilingam M. Application of aptamers in diagnostics, drug-delivery and imaging. J Biosci 2017; 41:535-61. [PMID: 27581942 DOI: 10.1007/s12038-016-9632-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aptamers are small, single-stranded oligonucleotides (DNA or RNA) that bind to their target with high specificity and affinity. Although aptamers are analogous to antibodies for a wide range of target recognition and variety of applications, they have significant advantages over antibodies. Since aptamers have recently emerged as a class of biomolecules with an application in a wide array of fields, we need to summarize the latest developments herein. In this review we will discuss about the latest developments in using aptamers in diagnostics, drug delivery and imaging. We begin with diagnostics, discussing the application of aptamers for the detection of infective agents itself, antigens/ toxins (bacteria), biomarkers (cancer), or a combination. The ease of conjugation and labelling of aptamers makes them a potential tool for diagnostics. Also, due to the reduced off-target effects of aptamers, their use as a potential drug delivery tool is emerging rapidly. Hence, we discuss their use in targeted delivery in conjugation with siRNAs, nanoparticles, liposomes, drugs and antibodies. Finally, we discuss about the conjugation strategies applicable for RNA and DNA aptamers for imaging. Their stability and self-assembly after heating makes them superior over protein-based binding molecules in terms of labelling and conjugation strategies.
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Affiliation(s)
- Chetan Chandola
- 1Center for Cellular and Molecular Platforms, NCBS-TIFR, Bangalore 560 065, India
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42
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An Update on Aptamer-Based Multiplex System Approaches for the Detection of Common Foodborne Pathogens. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-0814-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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43
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Tan J, Yang N, Hu Z, Su J, Zhong J, Yang Y, Yu Y, Zhu J, Xue D, Huang Y, Lai Z, Huang Y, Lu X, Zhao Y. Aptamer-Functionalized Fluorescent Silica Nanoparticles for Highly Sensitive Detection of Leukemia Cells. NANOSCALE RESEARCH LETTERS 2016; 11:298. [PMID: 27299653 PMCID: PMC4907968 DOI: 10.1186/s11671-016-1512-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 05/31/2016] [Indexed: 05/04/2023]
Abstract
A simple, highly sensitive method to detect leukemia cells has been developed based on aptamer-modified fluorescent silica nanoparticles (FSNPs). In this strategy, the amine-labeled Sgc8 aptamer was conjugated to carboxyl-modified FSNPs via amide coupling between amino and carboxyl groups. Sensitivity and specificity of Sgc8-FSNPs were assessed using flow cytometry and fluorescence microscopy. These results showed that Sgc8-FSNPs detected leukemia cells with high sensitivity and specificity. Aptamer-modified FSNPs hold promise for sensitive and specific detection of leukemia cells. Changing the aptamer may allow the FSNPs to detect other types of cancer cells.
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Affiliation(s)
- Juntao Tan
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Nuo Yang
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Zixi Hu
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Jing Su
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Jianhong Zhong
- Department of Oncologic Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yang Yang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yating Yu
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Jianmeng Zhu
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Dabin Xue
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Yingying Huang
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Zongqiang Lai
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Yong Huang
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China.
- Department of Thoracic Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China.
| | - Xiaoling Lu
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China.
| | - Yongxiang Zhao
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China.
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Wang L, Wang R, Chen F, Jiang T, Wang H, Slavik M, Wei H, Li Y. QCM-based aptamer selection and detection of Salmonella typhimurium. Food Chem 2016; 221:776-782. [PMID: 27979272 DOI: 10.1016/j.foodchem.2016.11.104] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/11/2016] [Accepted: 11/21/2016] [Indexed: 12/26/2022]
Abstract
In this study, quartz crystal microbalance (QCM) was used to select aptamers against Salmonella typhimurium. To increase the success rate of Systematic Evolution of Ligands Exponential Enrichment (SELEX), the affinity of DNA pool in each round was simultaneously tracked using QCM in order to avoid the loss of high-quality aptamers. When the frequency change reached a maximum value after several rounds of selection and counter-selection, the candidate pool was cloned and sequenced. Out of three aptamer candidates, aptamer B5 showed high specificity and binding affinity with dissociation constant (Kd value) of 58.5nM, and was chosen for further studies. Subsequently, a QCM-based aptasensor was developed to detect S. typhimurium. This aptasensor was able to detect 103CFU/mL of S. typhimurium with less than 1h. This study demonstrated QCM-based selection could be more effective selection of aptamers and QCM-based aptasensor could be more sensitive in detecting S. typhimurium.
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Affiliation(s)
- Lijun Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ronghui Wang
- Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Fang Chen
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Tieshan Jiang
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Hong Wang
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Michael Slavik
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Hua Wei
- Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, China
| | - Yanbin Li
- Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA; Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA.
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Alfavian H, Mousavi Gargari SL, Rasoulinejad S, Medhat A. Development of a DNA aptamer that binds specifically to group A Streptococcus serotype M3. Can J Microbiol 2016; 63:160-168. [PMID: 28121169 DOI: 10.1139/cjm-2016-0495] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Group A streptococcus (GAS) is an important Gram-positive pathogen that causes various human diseases ranging from peripheral lesions to invasive infections. The M protein is one of the main virulence factors present on the cell surface and is associated with invasive GAS infections. Compared with other M types, serotype M3 has a predominant role in lethal infections and demonstrates epidemic behaviors, including streptococcal toxic shock syndrome, bacteremia, and necrotizing fasciitis. Traditional methods for M typing are time-consuming, tedious, contradictory, and generally restricted to reference laboratories. Therefore, development of a new M-typing technique is needed. Aptamers with the ability to detect their target with a high degree of accuracy and specificity can be ideal candidates for specific M-typing of Streptococcus pyogenes. In this study DNA aptamers with a high binding affinity towards S. pyogenes serotype M3 were selected through 12 iterative rounds of the Systematic Evolution of Ligands by EXponential (SELEX) enrichment procedure using live cells as a target. We monitored the progress of the SELEX procedure by flow cytometry analysis. Of several aptamer sequences analyzed, 12L18A showed the highest binding efficiency towards S. pyogenes type M3, with an apparent dissociation constant (Kd) of 7.47 ± 1.72 pmol/L being the lowest. Therefore the isolated aptamer can be used in any tool, such as a biosensor, for the detection of S. pyogenes and can be used in the development of a novel M-typing system.
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Affiliation(s)
- Hanif Alfavian
- a Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran
| | | | - Samaneh Rasoulinejad
- a Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran
| | - Arvin Medhat
- b GENEXIR Biopharma, a knowledge-based company at Pasteur Institute of Iran Health Technology Park, Tehran, Iran
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Pashazadeh P, Mokhtarzadeh A, Hasanzadeh M, Hejazi M, Hashemi M, de la Guardia M. Nano-materials for use in sensing of salmonella infections: Recent advances. Biosens Bioelectron 2016; 87:1050-1064. [PMID: 27728896 DOI: 10.1016/j.bios.2016.08.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 12/22/2022]
Abstract
Salmonella infectious diseases spreading every day through food have become a life-threatening problem for millions of people and growing menace to society. Health expert's estimate that the yearly cost of all the food borne diseases is approximately $5-6 billion. Traditional methodologies for salmonella analysis provide high reliability and very low limits of detection. Among them immunoassays and Nucleic acid-based assays provide results within 24h, but they are expensive, tedious and time consuming. So, there is an urgent need for development of rapid, robust and cost-effective alternative technologies for real-time monitoring of salmonella. Several biosensors have been designed and commercialized for detection of this pathogen in food and water. In this overview, we have updated the literature concerning novel biosensing methods such as various optical and electrochemical biosensors and newly developed nano- and micro-scaled and aptamers based biosensors for detection of salmonella pathogen. Furthermore, attention has been focused on the principal concepts, applications, and examples that have been achieved up to diagnose salmonella. In addition, commercial biosensors and foreseeable future trends for onsite detecting salmonella have been summarized.
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Affiliation(s)
- Paria Pashazadeh
- Department of Biochemistry and Biophysics, Metabolic Disorders Research Center, Gorgan Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Golestan Province, Iran
| | - Ahad Mokhtarzadeh
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Biotechnology, Higher Education Institute of Rab-Rashid, Tabriz, Iran.
| | - Mohammad Hasanzadeh
- Drug Applied Research Center, Tabhriz University of Medical Sciences, Tabriz, 51664 Iran; Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, 51664 Iran
| | - Maryam Hejazi
- School of Medicine, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Maryam Hashemi
- Nanotechnology Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain.
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Lin X, Sun X, Luo S, Liu B, Yang C. Development of DNA-based signal amplification and microfluidic technology for protein assay: A review. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.02.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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48
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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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Visual detection technique for efficient screening and isolation of Salmonella based on a novel enrichment assay using chromatography membrane. Eur J Clin Microbiol Infect Dis 2016; 35:353-61. [PMID: 26796551 DOI: 10.1007/s10096-015-2543-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/29/2015] [Indexed: 10/22/2022]
Abstract
To detect Salmonella more efficiently and isolate strains more easily, a novel and simple detection method that uses an enrichment assay and two chromogenic reactions on a chromatography membrane was developed. Grade 3 chromatography paper is used as functionalized solid phase support (SPS), which contains specially optimized medium. One reaction for screening is based on the sulfate-reducing capacity of Salmonella. Hydrogen sulfide (H2S) generated by Salmonella reacts with ammonium ferric citrate to produce black colored ferrous sulfide. Another reaction is based on Salmonella C8 esterase that is unique for Enterobacteriaceae except Serratia and interacts with 4-methylumbelliferyl caprylate (MUCAP) to produce fluorescent umbelliferone, which is visible under ultraviolet light. A very low detection limit (10(1) CFU ml(-1)) for Salmonella was achieved on the background of 10(5) CFU ml(-1) Escherichia coli. More importantly, testing with more than 1,000 anal samples indicated that our method has a high positive detection rate and is relatively low cost, compared with the traditional culture-based method. It took only 1 day for the preliminary screening and 2 days to efficiently isolate the Salmonella cells, indicating that the new assay is specific, rapid, and simple for Salmonella detection. In contrast to the traditional culture-based method, this method can be easily used to screen and isolate targeted strains with the naked eye. The results of quantitative and comparative experiments showed that the visual detection technique is an efficient alternative method for the screening of Salmonella spp. in many applications of large-sized samples related to public health surveillance.
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