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Karthikeyan M, Rathinasabapathi P. A Label-Free Colorimetric AuNP-Aptasensor for the Rapid Detection of Vibrio cholerae O139. Cell Mol Bioeng 2024; 17:229-241. [PMID: 39050512 PMCID: PMC11263534 DOI: 10.1007/s12195-024-00804-3] [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: 12/19/2023] [Accepted: 05/28/2024] [Indexed: 07/27/2024] Open
Abstract
Purpose Waterborne pathogens pose a significant threat to public health, emphasizing the continuous necessity for advancing robust detection techniques, particularly in preventing outbreaks associated with these pathogens. This study focuses on cholera, an infectious disease caused by Vibrio cholerae, serogroups O1 and O139, often transmitted through contaminated water and food, raising significant public health concerns in areas with poor sanitation and limited access to clean water. Methods We developed a colorimetric biosensor using aptamer-functionalized gold nanoparticles to identify Vibrio cholerae O139 and address this issue. The detection mechanism relies on the color change of gold nanoparticles (AuNPs) from red to blue-purple induced by NaCl after the pathogen incubation and aptamer-target binding. Initial steps involved synthesizing and characterizing AuNPs, then exploring the impact of aptamer and NaCl concentrations on AuNP agglomeration. Optimization procedures for aptamer concentration and salt addition identified the optimal conditions for detection as 120 pM aptamers and 1 M NaCl. Results The aptasensor demonstrated a robust linear relationship, detecting V. cholerae concentrations from 103 to 108 CFU/mL, with a limit of detection (LOD) of 587 CFU/mL. Specificity tests and accurate sample analyses confirmed the efficiency of the AuNPs aptasensor, showcasing its reliability and speed compared to traditional culture examination methods. Moreover, we extended the aptasensor to a paper-based sensing platform with similar detection principles. Conclusion The change in color upon target binding was captured with a smartphone and analyzed using image processing software. The paper-based device detected the target in less than 2 min, demonstrating its convenience for on-field applications.
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Affiliation(s)
- Masilamani Karthikeyan
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603 203 India
| | - Pasupathi Rathinasabapathi
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603 203 India
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2
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Chen X, Chang Y, Ye M, Wang Z, Wu S, Duan N. Rational Design of a Robust G-Quadruplex Aptamer as an Inhibitor to Alleviate Listeria monocytogenes Infection. ACS APPLIED MATERIALS & INTERFACES 2024; 16:15946-15958. [PMID: 38519414 DOI: 10.1021/acsami.4c00496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Listeria monocytogenes (LM) is one of the most invasive foodborne pathogens that cause listeriosis, making it imperative to explore novel inhibiting strategies for alleviating its infection. The adhesion and invasion of LM within host cells are partly orchestrated by an invasin protein internalin A (InlA), which facilitates bacterial passage by interacting with the host cell E-cadherin (E-Cad). Hence, in this work, we proposed an aptamer blocking strategy by binding to the region on InlA that directly mediated E-Cad receptor engagement, thereby alleviating LM infection. An aptamer GA8 with a robust G-quadruplex (G4) structural feature was designed through truncation and base mutation from the original aptamer A8. The molecular docking and dynamics analysis showed that the InlA/aptamer GA8 binding interface was highly overlapping with the natural InlA/E-Cad binding interface, which confirmed that GA8 can tightly and stably bind InlA and block more distinct epitopes on InlA that involved the interaction with E-Cad. On the cellular level, it was confirmed that GA8 effectively blocked LM adhesion with an inhibition rate of 78%. Overall, the robust G4 aptamer-mediated design provides a new direction for the development of inhibitors against other wide-ranging and emerging pathogens.
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Affiliation(s)
- Xiaowan Chen
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Yuting Chang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Mingyue Ye
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Shijia Wu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Nuo Duan
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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3
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Sousa AM, Ferreira D, Rodrigues LR, Pereira MO. Aptamer-based therapy for fighting biofilm-associated infections. J Control Release 2024; 367:522-539. [PMID: 38295992 DOI: 10.1016/j.jconrel.2024.01.061] [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: 09/30/2023] [Revised: 01/06/2024] [Accepted: 01/27/2024] [Indexed: 02/06/2024]
Abstract
Biofilms are key players in the pathogenesis of most of chronic infections associated with host tissue or fluids and indwelling medical devices. These chronic infections are hard to be treated due to the increased biofilms tolerance towards antibiotics in comparison to planktonic (or free living) cells. Despite the advanced understanding of their formation and physiology, biofilms continue to be a challenge and there is no standardized therapeutic approach in clinical practice to eradicate them. Aptamers offer distinctive properties, including excellent affinity, selectivity, stability, making them valuable tools for therapeutic purposes. This review explores the flexibility and designability of aptamers as antibiofilm drugs but, importantly, as targeting tools for diverse drug and delivery systems. It highlights specific examples of application of aptamers in biofilms of diverse species according to different modes of action including inhibition of motility and adhesion, blocking of quorum sensing molecules, and dispersal of biofilm-cells to planktonic state. Moreover, it discusses the limitations and challenges that impaired an increased success of the use of aptamers on biofilm management, as well as the opportunities related to aptamers modifications that can significantly expand their applicability on the biofilm field.
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Affiliation(s)
- Ana Margarida Sousa
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal.
| | - Débora Ferreira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| | - Lígia Raquel Rodrigues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| | - Maria Olívia Pereira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal.
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4
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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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5
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Li D, Su Y, Li J, Liu R, Fang B, He J, Xu W, Zhu L. Applications and Challenges of Bacteriostatic Aptamers in the Treatment of Common Pathogenic Bacteria Infections. Biomacromolecules 2023; 24:4568-4586. [PMID: 37728999 DOI: 10.1021/acs.biomac.3c00634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The continuous evolution and spread of common pathogenic bacteria is a major challenge in diagnosis and treatment with current biotechnology and modern molecular medicine. To confront this challenge, scientists urgently need to find alternatives for traditional antimicrobial agents. Various bacteriostatic aptamers obtained through SELEX screening are one of the most promising strategies. These bacteriostatic aptamers can reduce bacterial infection by blocking bacterial toxin infiltration, inhibiting biofilm formation, preventing bacterial invasion of immune cells, interfering with essential biochemical processes, and other mechanisms. In addition, aptamers may also help enhance the function of other antibacterial materials/drugs when used in combination. This paper has reviewed the bacteriostatic aptamers in the treatment of common pathogenic bacteria infections. For this aspect, first, bacteriostatic aptamers and their screening strategies are summarized. Then, the effect of molecular tailoring and modification on the performance of the bacteriostatic aptamer is analyzed, and the antibacterial mechanism and antibacterial strategy based on aptamers are introduced. Finally, the key technical challenges and their development prospects in clinical treatment are also carefully discussed.
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Affiliation(s)
- Diandian Li
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Yuan Su
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jie Li
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Rong Liu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Bing Fang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jingjing He
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
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Huang Y, Doeven EH, Chen L, Yao Y, Wang Y, Lin B, Zeng Y, Li L, Qian Z, Guo L. Facial Preparation of Cyclometalated Iridium (III) Nanowires as Highly Efficient Electrochemiluminescence Luminophores for Biosensing. BIOSENSORS 2023; 13:bios13040459. [PMID: 37185534 PMCID: PMC10136454 DOI: 10.3390/bios13040459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/24/2023] [Accepted: 04/03/2023] [Indexed: 05/17/2023]
Abstract
In this study, highly efficient ECL luminophores composed of iridium complex-based nanowires (Ir-NCDs) were synthesized via covalently linking bis(2-phenylpyridine)-(4-carboxypropyl-2,2'-bipyridyl) iridium(III) hexafluorophosphate with nitrogen-doped carbon quantum dots (NCDs). The ECL intensity of the nanowires showed a five-fold increase in ECL intensity compared with the iridium complex monomer under the same experimental conditions. A label-free ECL biosensing platform based on Ir-NCDs was established for Salmonella enteritidis (SE) detection. The ECL signal was quenched linearly in the range of 102-108 CFU/mL for SE with a detection limit of 102 CFU/mL. Moreover, the relative standard deviations (RSD) of the stability within and between batches were 0.98% and 3.9%, respectively. In addition, the proposed sensor showed high sensitivity, selectivity and stability towards SE in sheep feces samples with satisfactory results. In summary, the excellent ECL efficiency of Ir-NCDs demonstrates the prospects for Ir(III) complexes in bioanalytical applications.
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Affiliation(s)
- Yueyue Huang
- College of Chemistry and Material Sciences, Zhejiang Normal University, Jinhua 321004, China
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
| | - Egan H Doeven
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds, VIC 3216, Australia
| | - Lifen Chen
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
| | - Yuanyuan Yao
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
| | - Yueliang Wang
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
| | - Bingyong Lin
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
| | - Yanbo Zeng
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
| | - Lei Li
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
| | - Zhaosheng Qian
- College of Chemistry and Material Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Longhua Guo
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
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7
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He J, Duan Q, Ran C, Fu T, Liu Y, Tan W. Recent progress of aptamer‒drug conjugates in cancer therapy. Acta Pharm Sin B 2023; 13:1358-1370. [PMID: 37139427 PMCID: PMC10150127 DOI: 10.1016/j.apsb.2023.01.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/18/2022] [Accepted: 12/15/2022] [Indexed: 01/28/2023] Open
Abstract
Aptamers are single-stranded DNA or RNA sequences that can specifically bind with the target protein or molecule via specific secondary structures. Compared to antibody-drug conjugates (ADC), aptamer‒drug conjugate (ApDC) is also an efficient, targeted drug for cancer therapy with a smaller size, higher chemical stability, lower immunogenicity, faster tissue penetration, and facile engineering. Despite all these advantages, several key factors have delayed the clinical translation of ApDC, such as in vivo off-target effects and potential safety issues. In this review, we highlight the most recent progress in the development of ApDC and discuss solutions to the problems noted above.
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Affiliation(s)
- Jiaxuan He
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Qiao Duan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunyan Ran
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Ting Fu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Yuan Liu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Weihong Tan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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8
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Paramithiotis S. Molecular Targets for Foodborne Pathogenic Bacteria Detection. Pathogens 2023; 12:pathogens12010104. [PMID: 36678453 PMCID: PMC9865778 DOI: 10.3390/pathogens12010104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The detection of foodborne pathogenic bacteria currently relies on their ability to grow on chemically defined liquid and solid media, which is the essence of the classical microbiological approach. Such procedures are time-consuming and the quality of the result is affected by the selectivity of the media employed. Several alternative strategies based on the detection of molecular markers have been proposed. These markers may be cell constituents, may reside on the cell envelope or may be specific metabolites. Each marker provides specific advantages and, at the same time, suffers from specific limitations. The food matrix and chemical composition, as well as the accompanying microbiota, may also severely compromise detection. The aim of the present review article is to present and critically discuss all available information regarding the molecular targets that have been employed as markers for the detection of foodborne pathogens. Their strengths and limitations, as well as the proposed alleviation strategies, are presented, with particular emphasis on their applicability in real food systems and the challenges that are yet to be effectively addressed.
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Affiliation(s)
- Spiros Paramithiotis
- Laboratory of Food Process Engineering, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
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9
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Schmitz FRW, Cesca K, Valério A, de Oliveira D, Hotza D. Colorimetric detection of Pseudomonas aeruginosa by aptamer-functionalized gold nanoparticles. Appl Microbiol Biotechnol 2022; 107:71-80. [DOI: 10.1007/s00253-022-12283-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/25/2022]
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10
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Chen J, Zhou J, Peng Y, Xie Y, Xiao Y. Aptamers: A prospective tool for infectious diseases diagnosis. J Clin Lab Anal 2022; 36:e24725. [PMID: 36245423 PMCID: PMC9701868 DOI: 10.1002/jcla.24725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 12/05/2022] Open
Abstract
It is well known that people's health is seriously threatened by various pathogens (such as Mycobacterium tuberculosis, Treponema pallidum, Novel coronavirus, HIV, Mucor, etc.), which leads to heavy socioeconomic burdens. Therefore, early and accurate pathogen diagnosis is essential for timely and effective therapies. Up to now, diagnosing human contagious diseases at molecule and nano levels is remarkably difficult owing to insufficient valid probes when it comes to determining the biological markers of pathogens. Aptamers are a set of high‐specificity and high‐sensitivity plastic oligonucleotides screened in vitro via the selective expansion of ligands by exponential enrichment (SELEX). With the advent of aptamer‐based technologies, their merits have aroused mounting academic interest. In recent years, as new detection and treatment tools, nucleic acid aptamers have been extensively utilized in the field of biomedicine, such as pathogen detection, new drug development, clinical diagnosis, nanotechnology, etc. However, the traditional SELEX method is cumbersome and has a long screening cycle, and it takes several months to screen out aptamers with high specificity. With the persistent development of SELEX‐based aptamer screening technologies, the application scenarios of aptamers have become more and more extensive. The present research briefly reviews the research progress of nucleic acid aptamers in the field of biomedicine, especially in the diagnosis of contagious diseases.
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Affiliation(s)
- Jiayi Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jiahuan Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yunchi Peng
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yafeng Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yongjian Xiao
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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11
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Ahmad Faris AN, Ahmad Najib M, Mohd Nazri MN, Hamzah ASA, Aziah I, Yusof NY, Mohamud R, Ismail I, Mustafa FH. Colorimetric Approach for Nucleic Acid Salmonella spp. Detection: A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10570. [PMID: 36078284 PMCID: PMC9518084 DOI: 10.3390/ijerph191710570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/09/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Water- and food-related health issues have received a lot of attention recently because food-poisoning bacteria, in particular, are becoming serious threats to human health. Currently, techniques used to detect these bacteria are time-consuming and laborious. To overcome these challenges, the colorimetric strategy is attractive because it provides simple, rapid and accurate sensing for the detection of Salmonella spp. bacteria. The aim of this study is to review the progress regarding the colorimetric method of nucleic acid for Salmonella detection. A literature search was conducted using three databases (PubMed, Scopus and ScienceDirect). Of the 88 studies identified in our search, 15 were included for further analysis. Salmonella bacteria from different species, such as S. Typhimurium, S. Enteritidis, S. Typhi and S. Paratyphi A, were identified using the colorimetric method. The limit of detection (LoD) was evaluated in two types of concentrations, which were colony-forming unit (CFU) and CFU per mL. The majority of the studies used spiked samples (53%) rather than real samples (33%) to determine the LoDs. More research is needed to assess the sensitivity and specificity of colorimetric nucleic acid in bacterial detection, as well as its potential use in routine diagnosis.
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Affiliation(s)
- Asma Nadia Ahmad Faris
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Mohamad Ahmad Najib
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Muhammad Najmi Mohd Nazri
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Amir Syahir Amir Hamzah
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Ismail Aziah
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Irneza Ismail
- Advanced Devices & System (ADS) Research Group, Department of Electrical & Electronic Engineering, Faculty of Engineering and Built Environment, Universiti Sains Islam Malaysia, Bandar Baru Nilai, Nilai 71800, Negeri Sembilan, Malaysia
| | - Fatin Hamimi Mustafa
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
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12
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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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13
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Carter E, Davis SA, Hill DJ. Rapid Detection of Neisseria gonorrhoeae Genomic DNA Using Gold Nanoprobes Which Target the Gonococcal DNA Uptake Sequence. Front Cell Infect Microbiol 2022; 12:920447. [PMID: 35873173 PMCID: PMC9304934 DOI: 10.3389/fcimb.2022.920447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid spread of antimicrobial resistant Neisseria gonorrhoeae continues to pose a serious threat to global health. To successfully treat and control gonococcal infections, rapid diagnosis is critical. Currently, nucleic acid amplification tests are the recommended diagnostic, however, these are both technically demanding and time consuming, making them unsuitable for resource-poor clinics. Consequently, there is a substantial need for an affordable, point-of-care diagnostic to use in these settings. In this study, DNA-functionalised gold nanoparticles (gold nanoprobes), with the ability to specifically detect the DNA Uptake Sequence (DUS) of Neisseria gonorrhoeae, were prepared. Using complementary annealing, the gold nanoprobes were shown to hybridise to genomic gonococcal DNA, causing a significant shift in their salt stability. By exploiting the shift in nanoprobe stability under the presence of target DNA, a solution-based colorimetric diagnostic for gonococcal DNA was prepared. Detection of purified genomic DNA was achieved in under 30 minutes, with a detection limit of 15.0 ng. Significantly, testing with DNA extracted from an off-target control organism suggested specificity for Neisseria. These results highlight the potential of DUS-specific gold nanoprobes in the rapid point-of-care diagnosis of gonococcal infections.
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Affiliation(s)
- Ella Carter
- School of Chemistry, University of Bristol, Bristol, United Kingdom
- Bristol Centre for Functional Nanomaterials, University of Bristol, Bristol, United Kingdom
| | - Sean A. Davis
- School of Chemistry, University of Bristol, Bristol, United Kingdom
- *Correspondence: Darryl Hill, ; Sean Davis,
| | - Darryl J. Hill
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- *Correspondence: Darryl Hill, ; Sean Davis,
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14
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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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15
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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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16
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Research progress of whole-cell-SELEX selection and the application of cell-targeting aptamer. Mol Biol Rep 2022; 49:7979-7993. [PMID: 35274201 DOI: 10.1007/s11033-022-07317-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Aptamers refer to the artificially synthesized nucleic acid sequences (DNA/RNA) that can bind to a wide range of targets with high affinity and specificity, which are generally generated from systematic evolution of ligands by exponential enrichment (SELEX). As a novel method of aptamers screening, whole-cell-SELEX (WC-SELEX) has gained more and more attention in many fields such as biomedicine, analytical chemistry, and molecular diagnostics due to its ability to screen multiple potential aptamers without knowing the detailed structural information of target molecules. METHODS AND RESULTS In recent years, with the deepening of research on application of aptamers, the traditional WC-SELEX cannot meet the practical application because of long experimental period, complicated operation process and low specificity, etc. Therefore, the development of more efficient methods for screening aptamer is always on the road. This paper summarizes the current research status of WC-SELEX for bacteria, parasites and animal cells, and reviews the latest advances of WC-SELEX techniques that are dependent on novel instruments, materials and microelectronics, including fluorescence-activated cell sorting-assisted SELEX, three-dimensional assisted WC-SELEX, and microfluidic chip system-assisted WC-SELEX. In addition, the application of aptamers targeting cells was discussed. CONCLUSION Taken together, this review is aimed at providing a reference for WC-SELEX selection and application of aptamer targeting cells.
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Li B, Feng D, Miao Y, Liang X, Gu L, Lan H, Gao S, Zhang Y, Deng Y, Geng L. The systemic characterization of aptamer cocktail for bacterial detection studied by graphene oxide-based fluorescence resonance energy transfer aptasensor. J Mol Recognit 2021; 34:e2934. [PMID: 34553439 DOI: 10.1002/jmr.2934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 08/12/2021] [Indexed: 12/15/2022]
Abstract
Aptamers have gained significant attention as the molecular recognition element to replace antibodies in sensor development and target delivery. Nevertheless, it is noteworthy that unlike the wide application of polyvalent antibodies, existing researches on the combined use of heterologous aptamers with similar recognition affinity and specificity for target detection were sporadic. Herein, first, the wide existence of polyaptamer for bacteria was revealed through the summary of existing literature. Furthermore, based on the establishment of a sensitive aptamer cocktail/graphene oxide fluorescence resonance energy transfer polyaptasensor with a detection limit as low as 10 CFU/ml, the systemic characterization of aptamer cocktails in bacterial detection was carried out by taking E. coli, Vi. parahemolyticus, S. typhimurium, and C. sakazakii as the assay targets. It was turned out that the polyaptasensors for C. sakazakii and S. typhimurium owned prevalence in the broader concentration range of target bacteria. While the polyaptasensors for E. coli and V. parahemolyticus outperformed monoaptasensor mainly in the lower concentration of target bacteria. The linear relationships between fluorescence recovery and the concentration of bacteria were also discussed. The different characteristics of the bacterial cellular membrane, including the binding affinity and the robustness to variation, are analyzed to be the main reason for the diverse detection performance of aptasensors. The study here enhances a sensor detection strategy with super sensitivity. More importantly, this systemic study on the aptamer cocktail in reference to antibodies will advance the in-depth understanding and rational design of aptamer based biological recognition, detection, and targeting.
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Affiliation(s)
- Baichang Li
- Department of Life, Beijing Institute of Technology, Beijing, China
| | - Dongwei Feng
- Department of Life, Beijing Institute of Technology, Beijing, China
| | - Yunfei Miao
- Department of Life, Beijing Institute of Technology, Beijing, China
| | - Xuewang Liang
- Department of Life, Beijing Institute of Technology, Beijing, China
| | - Le Gu
- Biological Detection Department, BOE Technology Group Co., Ltd., Beijing, China
| | - Hongying Lan
- Department of Life, Beijing Institute of Technology, Beijing, China
| | - Shimeng Gao
- College of Agriculture and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Yaxi Zhang
- Department of Life, Beijing Institute of Technology, Beijing, China
| | - Yulin Deng
- Department of Life, Beijing Institute of Technology, Beijing, China
| | - Lina Geng
- Department of Life, Beijing Institute of Technology, Beijing, China
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18
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Advancement in Salmonella Detection Methods: From Conventional to Electrochemical-Based Sensing Detection. BIOSENSORS-BASEL 2021; 11:bios11090346. [PMID: 34562936 PMCID: PMC8468554 DOI: 10.3390/bios11090346] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 02/07/2023]
Abstract
Large-scale food-borne outbreaks caused by Salmonella are rarely seen nowadays, thanks to the advanced nature of the medical system. However, small, localised outbreaks in certain regions still exist and could possess a huge threat to the public health if eradication measure is not initiated. This review discusses the progress of Salmonella detection approaches covering their basic principles, characteristics, applications, and performances. Conventional Salmonella detection is usually performed using a culture-based method, which is time-consuming, labour intensive, and unsuitable for on-site testing and high-throughput analysis. To date, there are many detection methods with a unique detection system available for Salmonella detection utilising immunological-based techniques, molecular-based techniques, mass spectrometry, spectroscopy, optical phenotyping, and biosensor methods. The electrochemical biosensor has growing interest in Salmonella detection mainly due to its excellent sensitivity, rapidity, and portability. The use of a highly specific bioreceptor, such as aptamers, and the application of nanomaterials are contributing factors to these excellent characteristics. Furthermore, insight on the types of biorecognition elements, the principles of electrochemical transduction elements, and the miniaturisation potential of electrochemical biosensors are discussed.
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19
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Lavu PS, Mondal B, Ramlal S. Selection and Characterization of Cell Surface Specific Aptamer and Development of Fluorescence Assay for Detection of Shigella flexneri from Water Samples. J Fluoresc 2021; 31:685-693. [PMID: 33582948 DOI: 10.1007/s10895-021-02691-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
The present study demonstrates, development of ssDNA aptamers against whole cell of S. flexneri employing a whole bacterium-based Systemic Evolution of Ligands by Exponential Enrichment (SELEX). After ten rounds of SELEX, cell surface specific aptamer pool was cloned, sequenced and divided based on sequence similarities and secondary structure. Binding affinity of FITC labelled aptamer from different group were carried out by flow cytometry analysis. The dissociation constant (Kd) values for specific and higher binder were evaluated to range from 144 to 329 nM. Six high binding aptamers with lower dissociation constant was chosen for selectivity study. Aptamer SHI 23, SHI 37 and SHI 42 showed higher selectivity towards S. flexneri in comparison with other related bacteria. Further applicability of selected aptamer was proven by fluorescence assay for convenience detection of target cell from spiked water sample and natural contaminated water samples. Altogether, aptamer generated in this study can be alternative DNA ligands for detection of S. flexneri compared to available ligands.
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Affiliation(s)
- Padma Sudharani Lavu
- Microbiology Division, Defence Food Research Laboratory, Siddharthanagar, Mysore, Karnataka, 570011, India
| | - Bhairab Mondal
- Microbiology Division, Defence Food Research Laboratory, Siddharthanagar, Mysore, Karnataka, 570011, India
| | - Shylaja Ramlal
- Microbiology Division, Defence Food Research Laboratory, Siddharthanagar, Mysore, Karnataka, 570011, India.
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20
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Kim CJ, Si Z, Reghu S, Guo Z, Zhang K, Li J, Chan-Park MB. DNA-derived nanostructures selectively capture gram-positive bacteria. Drug Deliv Transl Res 2021; 11:1438-1450. [PMID: 33880733 DOI: 10.1007/s13346-021-00975-w] [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] [Accepted: 03/31/2021] [Indexed: 10/21/2022]
Abstract
We report the first demonstration of the efficient bacteria targeting properties of DNA-based polymeric micelles with high-density DNA corona. Nanoscale polymer micelles derived from DNA-b-polystyrene (DNA-b-PS) efficiently selected most tested Gram-positive strains over Gram-negative strains; single-strand DNAs were 20-fold less selective. We demonstrate that these targeting properties were derived from the interaction between densely packed DNA strands of the micelle corona and the peptidoglycan layers of Gram-positive bacteria. DNA-b-PS micelles incorporating magnetic nanoparticles (MNPs) can efficiently capture and concentrate Gram-positive bacteria suggesting the simple applications of these DNA block copolymer micelles for concentrating bacteria. Adenine (A), thymine (T), cytosine (C), and guanine (G)-rich nanostructures were fabricated, respectively, for investigating the effect of sequence on Gram-selective bacteria targeting. T-rich micelles showed the most efficient targeting properties. The targeting properties of these DNA nanostructures toward Gram-positive bacteria may have applications as a targeted therapeutic delivery system.
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Affiliation(s)
- Chan-Jin Kim
- Centre for Antimicrobial Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Nanyang, 637459, Singapore
| | - Zhangyong Si
- Centre for Antimicrobial Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Nanyang, 637459, Singapore
| | - Sheethal Reghu
- Centre for Antimicrobial Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Nanyang, 637459, Singapore
| | - Zhong Guo
- Centre for Antimicrobial Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Nanyang, 637459, Singapore
| | - Kaixi Zhang
- Centre for Antimicrobial Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Nanyang, 637459, Singapore
| | - Jianghua Li
- Centre for Antimicrobial Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Nanyang, 637459, Singapore
| | - Mary B Chan-Park
- Centre for Antimicrobial Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Nanyang, 637459, Singapore. .,Lee Kong Chian School of Medicine, Nanyang Technological University, Nanyang, 636921, Singapore. .,School of Physical & Mathematical Sciences, Nanyang Technological University, Nanyang, 637371, Singapore.
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21
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Zhou Y, Xiong H, Chen R, Wan L, Kong Y, Rao J, Xie Y, Huang C, Zhang XL. Aptamer Detection of Mycobaterium tuberculosis Mannose-Capped Lipoarabinomannan in Lesion Tissues for Tuberculosis Diagnosis. Front Cell Infect Microbiol 2021; 11:634915. [PMID: 33791241 PMCID: PMC8006938 DOI: 10.3389/fcimb.2021.634915] [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: 12/08/2020] [Accepted: 01/18/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) is the leading infectious cause of mortality worldwide. However, the diagnosis of TB, especially extrapulmonary TB (EPTB) diagnosis from lesion tissues, remains a challenge. Nucleic acid aptamers are analogous to antibodies and have advantages of easier modification, high specificity, and affinity. Mannose-capped lipoarabinomannan (ManLAM) is a unique surface lipoglycan component or constantly released from mycobacterium tuberculosis (M.tb) cell wall, which makes it a perfect candidate biomarker for TB diagnosis. Our present study aims to establish M.tb ManLAM aptamer-based immunohistochemistry (IHC) method for TB diagnosis. We performed TB diagnosis using 263 formalin-fixed paraffin-embedded tissue samples including 213 TB samples (pulmonary TB (PTB) and EPTB), and 8 samples from latent TB infection (LTBI) high risk subjects, and 42 samples from other non-TB patients with ManLAM aptamer-based IHC and routine laboratory TB diagnostic methods parallelly. The sensitivity and specificity of the ManLAM aptamer-based IHC were 86.38% and 92.86%, with much higher sensitivity than those of mycobacterial culture (9.66%) and acid-fast staining (AFS) (43.01%) and comparability to Interferon-gamma Release Assay (IGRA) (84.38%) and GeneXpert (79.31%). High agreement between ManLAM based-IHC and IGRA or GeneXpert for TB diagnosis were observed. Furthermore, ManLAM aptamer-based IHC combination with other routine TB laboratory diagnostic methods significantly increased the sensitivity up to 88.64%–97.92%. As our knowledge, this is the first report about aptamer-based IHC for disease diagnosis. Thus, ManLAM aptamer-based IHC has potentials for TB diagnosis, including PTB, and EPTB, and assists the diagnosis of LTBI with high effectiveness, feasibility, and easy production.
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Affiliation(s)
- Yuanyuan Zhou
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Huan Xiong
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Rong Chen
- Department of Pathology, Medical Department, Jin Yin-Tan Hospital, Wuhan, China.,Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Wuhan, China
| | - Lixia Wan
- Department of Pathology, Medical Department, Jin Yin-Tan Hospital, Wuhan, China.,Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Wuhan, China
| | - Ying Kong
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Jianwei Rao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Yan Xie
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Chaolin Huang
- Department of Pathology, Medical Department, Jin Yin-Tan Hospital, Wuhan, China.,Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Wuhan, China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
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22
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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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23
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Pereira HS, Tagliaferri TL, Mendes TADO. Enlarging the Toolbox Against Antimicrobial Resistance: Aptamers and CRISPR-Cas. Front Microbiol 2021; 12:606360. [PMID: 33679633 PMCID: PMC7932999 DOI: 10.3389/fmicb.2021.606360] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
In the post-genomic era, molecular treatments and diagnostics have been envisioned as powerful techniques to tackle the antimicrobial resistance (AMR) crisis. Among the molecular approaches, aptamers and CRISPR-Cas have gained support due to their practicality, sensibility, and flexibility to interact with a variety of extra- and intracellular targets. Those characteristics enabled the development of quick and onsite diagnostic tools as well as alternative treatments for pan-resistant bacterial infections. Even with such potential, more studies are necessary to pave the way for their successful use against AMR. In this review, we highlight those two robust techniques and encourage researchers to refine them toward AMR. Also, we describe how aptamers and CRISPR-Cas can work together with the current diagnostic and treatment toolbox.
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Affiliation(s)
| | | | - Tiago Antônio de Oliveira Mendes
- Laboratory of Synthetic Biology and Modelling of Biological Systems, Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Brazil
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Wang P, Sun Y, Li X, Wang L, Xu Y, He L, Li G. Recent advances in dual recognition based surface enhanced Raman scattering for pathogenic bacteria detection: A review. Anal Chim Acta 2021; 1157:338279. [PMID: 33832584 DOI: 10.1016/j.aca.2021.338279] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 12/16/2022]
Abstract
Rapid and reliable detection of pathogenic bacteria at the early stage represents a highly topical research area for food safety and public health. Although culture based method is the gold standard method for bacteria detection, recent techniques have promoted the development of alternative methods, such as surface enhanced Raman scattering (SERS). SERS provides additional advantages of high speed, simultaneous detection and characterization, multiplex analysis, and comparatively low cost. However, conventional SERS methods for bacteria detection are facing limitations of low sensitivity, susceptible to matrix interference, and poor accuracy. In recent years, specific detection of pathogenic bacteria with dual recognition based SERS methods has attracted increasing attentions. These methods include two steps recognition of target bacteria, and integrate the functions of target separation and detection. Considering their merits of excellent specificity, ultrahigh sensitivity, multiplex detection capability, and potential for on-site applications, these methods are promising alternatives for rapid and reliable detection of pathogenic bacteria. Herein, this review aims to summarize the recent advances in dual recognition based SERS methods for specific detection of pathogenic bacteria. Their advantages and limitations are discussed, and further perspectives are tentatively given. This review provides new insights into the application of SERS as a reliable tool for pathogenic bacteria detection.
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Affiliation(s)
- Panxue Wang
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Yan Sun
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Xiang Li
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Li Wang
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Ying Xu
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Lili He
- Department of Food Science, University of Massachusetts Amherst, 102 Holdsworth Way, MA, 01003, USA
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China.
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25
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Kolm C, Cervenka I, Aschl UJ, Baumann N, Jakwerth S, Krska R, Mach RL, Sommer R, DeRosa MC, Kirschner AKT, Farnleitner AH, Reischer GH. DNA aptamers against bacterial cells can be efficiently selected by a SELEX process using state-of-the art qPCR and ultra-deep sequencing. Sci Rep 2020; 10:20917. [PMID: 33262379 PMCID: PMC7708460 DOI: 10.1038/s41598-020-77221-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
DNA aptamers generated by cell-SELEX against bacterial cells have gained increased interest as novel and cost-effective affinity reagents for cell labelling, imaging and biosensing. Here we describe the selection and identification of DNA aptamers for bacterial cells using a combined approach based on cell-SELEX, state-of-the-art applications of quantitative real-time PCR (qPCR), next-generation sequencing (NGS) and bioinformatic data analysis. This approach is demonstrated on Enterococcus faecalis (E. faecalis), which served as target in eleven rounds of cell-SELEX with multiple subtractive counter-selections against non-target species. During the selection, we applied qPCR-based analyses to evaluate the ssDNA pool size and remelting curve analysis of qPCR amplicons to monitor changes in pool diversity and sequence enrichment. Based on NGS-derived data, we identified 16 aptamer candidates. Among these, aptamer EF508 exhibited high binding affinity to E. faecalis cells (KD-value: 37 nM) and successfully discriminated E. faecalis from 20 different Enterococcus and non-Enterococcus spp. Our results demonstrate that this combined approach enabled the rapid and efficient identification of an aptamer with both high affinity and high specificity. Furthermore, the applied monitoring and assessment techniques provide insight into the selection process and can be highly useful to study and improve experimental cell-SELEX designs to increase selection efficiency.
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Affiliation(s)
- Claudia Kolm
- Molecular Diagnostics Group, Department IFA-Tulln, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Tulln, Austria.,ICC Interuniversity Cooperation Centre Water and Health, Vienna, Austria
| | - Isabella Cervenka
- Molecular Diagnostics Group, Department IFA-Tulln, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Tulln, Austria.,ICC Interuniversity Cooperation Centre Water and Health, Vienna, Austria
| | - Ulrich J Aschl
- Molecular Diagnostics Group, Department IFA-Tulln, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Tulln, Austria.,ICC Interuniversity Cooperation Centre Water and Health, Vienna, Austria
| | - Niklas Baumann
- Molecular Diagnostics Group, Department IFA-Tulln, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Tulln, Austria.,ICC Interuniversity Cooperation Centre Water and Health, Vienna, Austria
| | - Stefan Jakwerth
- ICC Interuniversity Cooperation Centre Water and Health, Vienna, Austria.,Institute for Hygiene and Applied Immunology, Medical University Vienna, Vienna, Austria
| | - Rudolf Krska
- Institute of Bioanalytics and Agro-Metabolomics, Department IFA-Tulln, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria.,School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Robert L Mach
- Research Group Synthetic Biology and Molecular Biotechnology (166-5-1), Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Regina Sommer
- ICC Interuniversity Cooperation Centre Water and Health, Vienna, Austria.,Institute for Hygiene and Applied Immunology, Medical University Vienna, Vienna, Austria
| | - Maria C DeRosa
- Department of Chemistry, Carleton University, Ottawa, Canada
| | - Alexander K T Kirschner
- ICC Interuniversity Cooperation Centre Water and Health, Vienna, Austria.,Institute for Hygiene and Applied Immunology, Medical University Vienna, Vienna, Austria.,Research Unit Water Quality and Health, Department Physiology, Pharmacology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Andreas H Farnleitner
- ICC Interuniversity Cooperation Centre Water and Health, Vienna, Austria.,Research Unit Water Quality and Health, Department Physiology, Pharmacology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria.,Research Group Environmental Microbiology and Molecular Diagnostics (166-5-3), Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Georg H Reischer
- Molecular Diagnostics Group, Department IFA-Tulln, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Tulln, Austria. .,ICC Interuniversity Cooperation Centre Water and Health, Vienna, Austria. .,Research Group Environmental Microbiology and Molecular Diagnostics (166-5-3), Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
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26
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Shen Y, Xu L, Li Y. Biosensors for rapid detection of Salmonella in food: A review. Compr Rev Food Sci Food Saf 2020; 20:149-197. [PMID: 33443806 DOI: 10.1111/1541-4337.12662] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 09/04/2020] [Accepted: 10/01/2020] [Indexed: 12/13/2022]
Abstract
Salmonella is one of the main causes of foodborne infectious diseases, posing a serious threat to public health. It can enter the food supply chain at various stages of production, processing, distribution, and marketing. High prevalence of Salmonella necessitates efficient and effective approaches for its identification, detection, and monitoring at an early stage. Because conventional methods based on plate counting and real-time polymerase chain reaction are time-consuming and laborious, novel rapid detection methods are urgently needed for in-field and on-line applications. Biosensors provide many advantages over conventional laboratory assays in terms of sensitivity, specificity, and accuracy, and show superiority in rapid response and potential portability. They are now recognized as promising alternative tools and one of the most on-site applicable and end user-accessible methods for rapid detection. In recent years, we have witnessed a flourishing of studies in the development of robust and elaborate biosensors for detection of Salmonella in food. This review aims to provide a comprehensive overview on Salmonella biosensors by highlighting different signal-transducing mechanisms (optical, electrochemical, piezoelectric, etc.) and critically analyzing its recent trends, particularly in combination with nanomaterials, microfluidics, portable instruments, and smartphones. Furthermore, current challenges are emphasized and future perspectives are discussed.
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Affiliation(s)
- Yafang Shen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China.,Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, Arkansas
| | - Lizhou Xu
- Department of Materials, Imperial College London, London, UK
| | - Yanbin Li
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, Arkansas
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27
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Trunzo NE, Hong KL. Recent Progress in the Identification of Aptamers Against Bacterial Origins and Their Diagnostic Applications. Int J Mol Sci 2020; 21:ijms21145074. [PMID: 32708376 PMCID: PMC7404326 DOI: 10.3390/ijms21145074] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 12/18/2022] Open
Abstract
Aptamers have gained an increasing role as the molecular recognition element (MRE) in diagnostic assay development, since their first conception thirty years ago. The process to screen for nucleic acid-based binding elements (aptamers) was first described in 1990 by the Gold Laboratory. In the last three decades, many aptamers have been identified for a wide array of targets. In particular, the number of reports on investigating single-stranded DNA (ssDNA) aptamer applications in biosensing and diagnostic platforms have increased significantly in recent years. This review article summarizes the recent (2015 to 2020) progress of ssDNA aptamer research on bacteria, proteins, and lipids of bacterial origins that have implications for human infections. The basic process of aptamer selection, the principles of aptamer-based biosensors, and future perspectives will also be discussed.
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28
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Schmitz FRW, Valério A, de Oliveira D, Hotza D. An overview and future prospects on aptamers for food safety. Appl Microbiol Biotechnol 2020; 104:6929-6939. [PMID: 32588103 PMCID: PMC7315907 DOI: 10.1007/s00253-020-10747-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023]
Abstract
Introduction Many bacteria are responsible for infections in humans and plants, being found in vegetables, water, and medical devices. Most bacterial detection methods are time-consuming and take days to give the result. Aptamers are a promising alternative for a quick and reliable measurement technique to detect bacteria present in food products. Selected aptamers are DNA or RNA oligonucleotides that can bind with bacteria or other molecules with affinity and specificity for the target cells by the SELEX or cell-SELEX technique. This method is based on some rounds to remove the non-ligand oligonucleotides, leaving the aptamers specific to bind to the selected bacteria. Compared with conventional methodologies, the detection approach using aptamers is a rapid, low-cost form of analysis. Objective This review summarizes obtention methods and applications of aptamers in the food industry and biotechnology. Besides, different techniques with aptamers are presented, which enable more effective target detection. Conclusion Applications of aptamers as biosensors, or the association of aptamers with nanomaterials, may be employed in analyses by colorimetric, fluorescence, or electrical devices. Additionally, more efficient ways of sample preparation are presented, which can support food safety to provide human health, with a low-cost method for contaminant detection.Key points • Aptamers are promising for detecting contaminants outbreaks. • Studies are needed to identify aptamers for different targets. |
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Affiliation(s)
- Fernanda Raquel Wust Schmitz
- Department of Chemical Engineering and Food Engineering (EQA), Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil
| | - Alexsandra Valério
- Department of Chemical Engineering and Food Engineering (EQA), Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil
| | - Débora de Oliveira
- Department of Chemical Engineering and Food Engineering (EQA), Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil.
| | - Dachamir Hotza
- Department of Chemical Engineering and Food Engineering (EQA), Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil
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29
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Luo F, Li Z, Dai G, Lu Y, He P, Wang Q. Simultaneous detection of different bacteria by microchip electrophoresis combined with universal primer-duplex polymerase chain reaction. J Chromatogr A 2020; 1615:460734. [DOI: 10.1016/j.chroma.2019.460734] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022]
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30
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Gutiérrez-Santana JC, Toscano-Garibay JD, López-López M, Coria-Jiménez VR. Aptamers coupled to nanoparticles in the diagnosis and treatment of microbial infections. Enferm Infecc Microbiol Clin 2020; 38:331-337. [PMID: 31948707 DOI: 10.1016/j.eimc.2019.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022]
Abstract
There are nanoparticles with remarkable antibacterial characteristics and aptamers able to recognize specific pathogenic bacteria with high affinity and specificity. The combination of both systems has been used to design rapid bacterial detection methods with excellent detection limits. Likewise, the synergism between aptamers and nanoparticles have allowed to optimize the antimicrobial activity of antibiotics and other nanostructures providing them with activity bacterium-specific, turning into attractive and promising tools to fight against bacteria resistant to multiple antimicrobials.
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Affiliation(s)
- Juan Carlos Gutiérrez-Santana
- Laboratorio de Bacteriología Experimental, Instituto Nacional de Pediatría, Ciudad de México, México; Universidad Autónoma Metropolitana, Unidad Xochimilco, Ciudad de México, México.
| | - Julia Dolores Toscano-Garibay
- Unidad de Investigación en Microbiología y Toxicología, Dirección de Investigación, Hospital Juárez de México, Ciudad de México, México
| | - Marisol López-López
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Unidad Xochimilco, Ciudad de México, México
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31
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Afrasiabi S, Pourhajibagher M, Raoofian R, Tabarzad M, Bahador A. Therapeutic applications of nucleic acid aptamers in microbial infections. J Biomed Sci 2020; 27:6. [PMID: 31900238 PMCID: PMC6941257 DOI: 10.1186/s12929-019-0611-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/19/2019] [Indexed: 02/07/2023] Open
Abstract
Today, the treatment of bacterial infections is a major challenge, due to growing rate of multidrug-resistant bacteria, complication of treatment and increased healthcare costs. Moreover, new treatments for bacterial infections are limited. Oligonucleotide aptamers are single stranded DNAs or RNAs with target-selective high-affinity feature, which considered as nucleic acid-based affinity ligands, replacing monoclonal antibodies. The aptamer-based systems have been found to be talented tools in the treatment of microbial infections, regarding their promising anti-biofilm and antimicrobial activities; they can reduce or inhibit the effects of bacterial toxins, and inhibit pathogen invasion to immune cell, as well as they can be used in drug delivery systems. The focus of this review is on the therapeutic applications of aptamers in infections. In this regard, an introduction of infections and related challenges were presented, first. Then, aptamer definition and selection, with a brief history of aptamers development against various pathogens and toxins were reviewed. Diverse strategies of aptamer application in drug delivery, as well as, the effect of aptamers on the immune system, as the main natural agents of human defense against pathogens, were also discussed. Finally, the future trends in clinical applications of this technology were discussed.
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Affiliation(s)
- Shima Afrasiabi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Pourhajibagher
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Raoofian
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Maryam Tabarzad
- Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Abbas Bahador
- Oral Microbiology Laboratory, Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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32
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Detection of Gram-negative bacterial outer membrane vesicles using DNA aptamers. Sci Rep 2019; 9:13167. [PMID: 31511614 PMCID: PMC6739373 DOI: 10.1038/s41598-019-49755-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 08/23/2019] [Indexed: 12/03/2022] Open
Abstract
Infection of various pathogenic bacteria causes severe illness to human beings. Despite the research advances, current identification tools still exhibit limitations in detecting Gram-negative bacteria with high accuracy. In this study, we isolated single-stranded DNA aptamers against multiple Gram-negative bacterial species using Toggle-cell-SELEX (systemic evolution of ligands by exponential enrichment) and constructed an aptamer-based detection tool towards bacterial secretory cargo released from outer membranes of Gram-negative bacteria. Three Gram-negative bacteria, Escherichia coli DH5α, E. coli K12, and Serratia marcescens, were sequentially incubated with the pool of random DNA sequences at each SELEX loop. Two aptamers selected, GN6 and GN12, were 4.2-times and 3.6-times higher binding to 108 cells of Gram-negative bacteria than to Gram-positive bacteria tested, respectively. Using GN6 aptamer, we constructed an Enzyme-linked aptamer assay (ELAA) to detect bacterial outer membrane vesicles (OMVs) of Gram-negative bacteria, which contain several outer membrane proteins with potent immunostimulatory effects. The GN6-ELAA showed high sensitivity to detect as low as 25 ng/mL bacterial OMVs. Aptamers developed in this study show a great potential to facilitate medical diagnosis and early detection of bacterial terrorism, based on the ability to detect bacterial OMVs of multiple Gram-negative bacteria.
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33
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Kaur SJ, Gilman V, Duong M, Asher DM, Gregori L. Rapid selection of single-stranded DNA aptamers binding Staphylococcus epidermidis in platelet concentrates. Biotechniques 2019; 65:331-338. [PMID: 30477331 DOI: 10.2144/btn-2018-0081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Staphylococcus epidermidis is the most common transfusion-associated pathogen contaminating platelet concentrates. Methods to reduce or eliminate contaminating bacteria from platelet units are critical for improving the safety of blood transfusions. We used rapid isolation of DNA aptamers (RIDA) to identify single-stranded (ss)DNA aptamers as ligands that specifically bind to S. epidermidis. Five target-specific ssDNA aptamers (76 mer) were obtained under stringent selection conditions. Aptamer SE43 demonstrated higher binding affinity compared with scrambled control. Furthermore, when binding assays were conducted in platelet concentrate, there was a twofold increase in binding affinity compared with the SE43 binding in buffer alone. Our data identified an aptamer that may be useful as a ligand to capture, detect or remove S. epidermidis contaminant from platelet concentrates.
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Affiliation(s)
- Simran J Kaur
- Division of Emerging & Transfusion-Transmitted Diseases, Laboratory of Bacterial & Transmissible Spongiform Encephalopathy Agents, Center for Biologics Evaluation & Research, Office of Blood Research & Review, US Food & Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.,Current Address: Department of Microbiology and Immunology, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201, USA
| | - Vladimir Gilman
- Engineering Center of Excellence, 267 Farley Road, Hollis, NH 03049, USA
| | - Minh Duong
- Engineering Center of Excellence, 267 Farley Road, Hollis, NH 03049, USA
| | - David M Asher
- Division of Emerging & Transfusion-Transmitted Diseases, Laboratory of Bacterial & Transmissible Spongiform Encephalopathy Agents, Center for Biologics Evaluation & Research, Office of Blood Research & Review, US Food & Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Luisa Gregori
- Division of Emerging & Transfusion-Transmitted Diseases, Laboratory of Bacterial & Transmissible Spongiform Encephalopathy Agents, Center for Biologics Evaluation & Research, Office of Blood Research & Review, US Food & Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
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Wang L, Wang R, Wei H, Li Y. Selection of aptamers against pathogenic bacteria and their diagnostics application. World J Microbiol Biotechnol 2018; 34:149. [PMID: 30220026 DOI: 10.1007/s11274-018-2528-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/31/2018] [Indexed: 10/28/2022]
Abstract
Aptamers are short nucleotide sequences which can specifically bind to a variety of targets with high affinity. They are identified and selected via systematic evolution of ligands by exponential enrichment (SELEX). Compared to antibodies, aptamers offer several advantages including easy labeling, high stability and lower cost. Those advantages make it possible to be a potential for use as a recognition probe to replace antibody in the diagnostic field. This article is intended to provide a comprehensive review, which is focused on systemizing recent advancements concerning SELEX procedures, with special emphasis on the key steps in SELEX procedures. The principles of various aptamer-based detections of pathogenic bacteria and their application are discussed in detail, including colorimetric detection, fluorescence detection, electrochemical detection, lateral flow strip test, mass sensitive detection and PCR-based aptasensor. By discussing recent research and future trends based on many excellent publications and reviews, we attempt to give the readers a comprehensive view in the field of aptamer selection against pathogenic bacteria and their diagnostics application. Authors hope that this review will promote lively and valuable discussions in order to generate new ideas and approaches towards the development of aptamer-based methods for application in pathogenic bacteria diagnosis.
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Affiliation(s)
- Lijun Wang
- School of Food and Bioengineering, Xihua University, Chengdu, 610039, 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
| | - 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, 203 Engineering Hall, Fayetteville, AR, 72701, USA.
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35
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Wei X, Zhou W, Sanjay ST, Zhang J, Jin Q, Xu F, Dominguez DC, Li X. Multiplexed Instrument-Free Bar-Chart SpinChip Integrated with Nanoparticle-Mediated Magnetic Aptasensors for Visual Quantitative Detection of Multiple Pathogens. Anal Chem 2018; 90:9888-9896. [PMID: 30028601 PMCID: PMC6157022 DOI: 10.1021/acs.analchem.8b02055] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A portable multiplexed bar-chart SpinChip (MB-SpinChip) integrated with nanoparticle-mediated magnetic aptasensors was developed for visual quantitative instrument-free detection of multiple pathogens. This versatile multiplexed SpinChip combines aptamer-specific recognition and nanoparticle-catalyzed pressure amplification to achieve a sample-to-answer output for sensitive point-of-care testing (POCT). This is the first report of pathogen detection using a volumetric bar-chart chip, and it is also the first bar-chart chip using a "spinning" mechanism to achieve multiplexed bar-chart detection. Additionally, the introduction of the spin unit not only enabled convenient sample introduction from one inlet to multiple separate channels in the multiplexed detection, but also elegantly solved the pressure cross-interference problem in the multiplexed volumetric bar-chart chip. This user-friendly MB-SpinChip allows visual quantitative detection of multiple pathogens simultaneously with high sensitivity but without utilizing any specialized instruments. Using this MB-SpinChip, three major foodborne pathogens including Salmonella enterica, Escherichia coli, and Listeria monocytogenes were specifically quantified in apple juice with limits of detection of about 10 CFU/mL. This MB-SpinChip with a bar-chart-based visual quantitative readout has great potential for the rapid simultaneous detection of various pathogens at the point of care and wide applications in food safety, environmental surveillance, and infectious disease diagnosis.
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Affiliation(s)
- Xiaofeng Wei
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Wan Zhou
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Sharma T. Sanjay
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Jie Zhang
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Qijie Jin
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
- College of Materials Science and Engineering, Nanjing Tech University, Nanjing, 210009, People’s Republic of China
| | - Feng Xu
- Bioinspired Engineering and Biomechanics Center, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
| | - Delfina C. Dominguez
- College of Health Sciences, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - XiuJun Li
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
- Biomedical Engineering, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
- Border Biomedical Research Center, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
- Environmental Science and Engineering, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
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36
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Srinivasan S, Ranganathan V, DeRosa MC, Murari BM. Label-free aptasensors based on fluorescent screening assays for the detection of Salmonella typhimurium. Anal Biochem 2018; 559:17-23. [PMID: 30081031 DOI: 10.1016/j.ab.2018.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/02/2018] [Accepted: 08/02/2018] [Indexed: 10/28/2022]
Abstract
We report two label-free fluorescent aptasensor methods for the detection of S. typhimurium. In the first method, we have used a ''turn off'' approach in which the aptamer is first intercalated with SYBR Green I (SG), leading to a greatly enhanced fluorescence signal. The addition of S. typhimurium (approximately 1530-96938 CFU/mL), which specifically binds with its aptamer and releases SG, leads to a linear decrease in fluorescence intensity. The lowest detection limit achieved with this approach was in the range of 733 CFU/mL. In the second method, a ''turn on'' approach was designed for S. typhimurium through the Förster resonance energy transfer (FRET) between Rhodamine B (RB) and gold nanoparticles (AuNPs). When the aptamer and AuNPs were mixed with RB, the fluorescence of RB was significantly quenched via FRET. The aptamer adsorbs to the AuNP surface to protect them from salt-induced aggregation, which leads to the fluorescence quenching of RB in presence of AuNPs. Upon the addition of S. typhimurium, S. typhimurium specifically binds with its aptamer and loses the capability to stabilize AuNPs. Thus, the salt easily induces the aggregation of AuNPs, resulting in the fluorescence recovery of the quenched RB. S. typhimurium concentrations ranging from 1530 to 96938 CFU/mL with the detection limit of 464 CFU/mL was achieved with this methodology. Given these data, some insights into the molecular interactions between the aptamer and the bacterial target are provided. These aptasensor methods also may be adapted for the detection of a wide variety of targets.
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Affiliation(s)
- Sathya Srinivasan
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore, 632 104, TN, India; Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.
| | - Velu Ranganathan
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.
| | - Maria C DeRosa
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.
| | - Bhaskar Mohan Murari
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore, 632 104, TN, India; Department of Sensor and Biomedical Technology, School of Electronics Engineering, VIT University, Vellore, 632 104, TN, India.
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Kaur H, Bruno JG, Kumar A, Sharma TK. Aptamers in the Therapeutics and Diagnostics Pipelines. Theranostics 2018; 8:4016-4032. [PMID: 30128033 PMCID: PMC6096388 DOI: 10.7150/thno.25958] [Citation(s) in RCA: 231] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/16/2018] [Indexed: 12/17/2022] Open
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides that can selectively bind to small molecular ligands or protein targets with high affinity and specificity, by acquiring unique three-dimensional structures. Aptamers have the advantage of being highly specific, relatively small in size, non-immunogenic and can be easily stabilized by chemical modifications, thus allowing expansion of their diagnostic and therapeutic potential. Since the invention of aptamers in the early 1990s, great efforts have been made to make them clinically relevant for diseases like macular degeneration, cancer, thrombosis and inflammatory diseases. Furthermore, owing to the aforementioned advantages and unique adaptability of aptamers to point-of-care platforms, aptamer technology has created a stable niche in the field of in vitro diagnostics by enhancing the speed and accuracy of diagnoses. The aim of this review is to give an overview on aptamers, highlight the inherent therapeutic and diagnostic opportunities and challenges associated with them and present various aptamers that have reached therapeutic clinical trials, diagnostic markets or that have immediate translational potential for therapeutics and diagnostics applications.
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Affiliation(s)
| | - John G. Bruno
- Operational Technologies Corporation, 4100 NW Loop 410, Suite 100, San Antonio, Texas 78229, USA
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Tarun Kumar Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute (THSTI), Faridabad-121001, Haryana, India
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Furst AL, Smith MJ, Francis MB. New Techniques for the Generation and Analysis of Tailored Microbial Systems on Surfaces. Biochemistry 2018; 57:3017-3026. [DOI: 10.1021/acs.biochem.8b00324] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ariel L. Furst
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
| | - Matthew J. Smith
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
| | - Matthew B. Francis
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720-1460, United States
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Pan Q, Luo F, Liu M, Zhang XL. Oligonucleotide aptamers: promising and powerful diagnostic and therapeutic tools for infectious diseases. J Infect 2018; 77:83-98. [PMID: 29746951 PMCID: PMC7112547 DOI: 10.1016/j.jinf.2018.04.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 01/02/2018] [Accepted: 04/08/2018] [Indexed: 12/21/2022]
Abstract
The entire human population is at risk of infectious diseases worldwide. Thus far, the diagnosis and treatment of human infectious diseases at the molecular and nanoscale levels have been extremely challenging tasks because of the lack of effective probes to identify and recognize biomarkers of pathogens. Oligonucleotide aptamers are a class of small nucleic acid ligands that are composed of single-stranded DNA (ssDNA) or RNA and act as affinity probes or molecular recognition elements for a variety of targets. These aptamers have an exciting potential for diagnose and/or treatment of specific diseases. In this review, we highlight areas where aptamers have been developed as diagnostic and therapeutic agents for both bacterial and viral infectious diseases as well as aptamer-based detection.
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Affiliation(s)
- Qin Pan
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Fengling Luo
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Min Liu
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China.
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40
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Park KS. Nucleic acid aptamer-based methods for diagnosis of infections. Biosens Bioelectron 2018; 102:179-188. [PMID: 29136589 PMCID: PMC7125563 DOI: 10.1016/j.bios.2017.11.028] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 02/07/2023]
Abstract
Infectious diseases are a serious global problem, which not only take an enormous human toll but also incur tremendous economic losses. In combating infectious diseases, rapid and accurate diagnostic tests are required for pathogen identification at the point of care (POC). In this review, investigations of diagnostic strategies for infectious diseases that are based on aptamers, especially nucleic acid aptamers, oligonucleotides that have high affinities and specificities toward their targets, are described. Owing to their unique features including low cost of production, easy chemical modification, high chemical stability, reproducibility, and low levels of immunogenicity and toxicity, aptamers have been widely utilized as bio-recognition elements (bio-receptors) for the development of infection diagnostic systems. We discuss nucleic acid aptamer-based methods that have been developed for diagnosis of infections using a format that organizes discussion according to the target pathogenic analytes including toxins or proteins, whole cells and nucleic acids. Also included is, a summary of recent advances made in the sensitive detection of pathogenic bacteria utilizing the isothermal nucleic acid amplification method. Lastly, a nucleic acid aptamer-based POC system is described and future directions of studies in this area are discussed.
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Affiliation(s)
- Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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41
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Mondal B, Ramlal S, Lavu PS, N B, Kingston J. Highly Sensitive Colorimetric Biosensor for Staphylococcal Enterotoxin B by a Label-Free Aptamer and Gold Nanoparticles. Front Microbiol 2018; 9:179. [PMID: 29487580 PMCID: PMC5816949 DOI: 10.3389/fmicb.2018.00179] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/25/2018] [Indexed: 11/20/2022] Open
Abstract
A simple, sensitive and selective colorimetric biosensor for the detection of Staphylococcal enterotoxin B (SEB) was developed using SEB-binding aptamer (SEB2) as recognition element and unmodified gold nanoparticles (AuNPs) as colorimetric probes. The assay is based on color change from red to purple due to conformational change of aptamer in the presence of SEB, and the phenomenon of salt-induced AuNPs aggregation which could be monitored by naked eye or UV–vis spectrometer. Results showed that the AuNPs can effectively differentiate the SEB induced conformational change of the aptamer in the presence of a given high salt concentration. A linear response in the range of 50 μg/mL to 0.5 ng/mL of SEB concentration was obtained. The assay was highly specific to SEB as compared to other related toxins. The limit of detection (LOD) of SEB achieved within few minutes was 50 ng/mL visually and spectrometric method improved it to 0.5 ng/mL. Robustness of the assay was tested in artificially spiked milk samples and cross-checked using in house developed sandwich ELISA (IgY as capturing and SEB specific monoclonal as revealing antibody) and PCR. This colorimetric assay could be a suitable alternative over existing methods during biological emergencies due to its simplicity, sensitive and cost effectiveness.
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Affiliation(s)
- Bhairab Mondal
- Microbiology Division, Defence Food Research Laboratory, Mysore, India
| | - Shylaja Ramlal
- Microbiology Division, Defence Food Research Laboratory, Mysore, India
| | - Padma S Lavu
- Microbiology Division, Defence Food Research Laboratory, Mysore, India
| | - Bhavanashri N
- Microbiology Division, Defence Food Research Laboratory, Mysore, India
| | - Joseph Kingston
- Microbiology Division, Defence Food Research Laboratory, Mysore, India
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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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43
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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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44
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Yüce M, Kurt H. How to make nanobiosensors: surface modification and characterisation of nanomaterials for biosensing applications. RSC Adv 2017. [DOI: 10.1039/c7ra10479k] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
This report aims to provide the audience with a guideline for construction and characterisation of nanobiosensors that are based on widely used affinity probes including antibodies and aptamers.
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Affiliation(s)
- Meral Yüce
- Sabanci University
- Nanotechnology Research and Application Centre
- Istanbul
- Turkey
| | - Hasan Kurt
- Istanbul Medipol University
- School of Engineering and Natural Sciences
- Istanbul
- Turkey
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45
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Pei Q, Wang Y, Liu S, Qin Y, Leng X, Cui X, Huang J. Exonuclease III-aided autonomous cascade signal amplification: a facile and universal DNA biosensing platform for ultrasensitive electrochemical detection of S. typhimurium. NEW J CHEM 2017. [DOI: 10.1039/c7nj01626c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A novel electrochemical biosensor based on exonuclease III-aided autonomous cascade signal amplification for the ultrasensitive and highly specific detection of S. typhimurium.
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Affiliation(s)
- Qianqian Pei
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- P. R. China
| | - Yu Wang
- School of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- P. R. China
| | - Su Liu
- School of Resources and Environment
- University of Jinan
- Jinan 250022
- P. R. China
| | - Yifei Qin
- School of Resources and Environment
- University of Jinan
- Jinan 250022
- P. R. China
| | - Xueqi Leng
- School of Resources and Environment
- University of Jinan
- Jinan 250022
- P. R. China
| | - Xuejun Cui
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- P. R. China
| | - Jiadong Huang
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- P. R. China
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Cordeiro M, Ferreira Carlos F, Pedrosa P, Lopez A, Baptista PV. Gold Nanoparticles for Diagnostics: Advances towards Points of Care. Diagnostics (Basel) 2016; 6:diagnostics6040043. [PMID: 27879660 PMCID: PMC5192518 DOI: 10.3390/diagnostics6040043] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/13/2016] [Accepted: 11/18/2016] [Indexed: 12/24/2022] Open
Abstract
The remarkable physicochemical properties of gold nanoparticles (AuNPs) have prompted developments in the exploration of biomolecular interactions with AuNP-containing systems, in particular for biomedical applications in diagnostics. These systems show great promise in improving sensitivity, ease of operation and portability. Despite this endeavor, most platforms have yet to reach maturity and make their way into clinics or points of care (POC). Here, we present an overview of emerging and available molecular diagnostics using AuNPs for biomedical sensing that are currently being translated to the clinical setting.
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Affiliation(s)
- Mílton Cordeiro
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal.
- Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal.
| | - Fábio Ferreira Carlos
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal.
| | - Pedro Pedrosa
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal.
| | - António Lopez
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal.
| | - Pedro Viana Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal.
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