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Liu X, Yuan W, Xiao H. Recent progress on DNAzyme-based biosensors for pathogen detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4917-4937. [PMID: 38984495 DOI: 10.1039/d4ay00934g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Pathogens endanger food safety, agricultural productivity, and human health. Those pathogens are spread through direct/indirect contact, airborne transmission and food/waterborne transmission, and some cause severe health consequences. As the population grows and global connections intensify, the transmission of infectious diseases expands. Traditional detection methods for pathogens still have some shortcomings, such as time-consuming procedures and high operational costs. To fulfil the demands for simple and effective detection, numerous biosensors have been developed. DNAzyme, a unique DNA structure with catalytic activity, is gradually being applied in the field of pathogen detection owing to its ease of preparation and use. In this review, we concentrated on the two main types of DNAzyme, hemin/G-quadruplex DNAzyme (HGD) and RNA-cleaving DNAzyme (RCD), explaining their research progress in pathogen detection. Furthermore, we introduced two additional novel DNAzymes, CLICK 17 DNAzyme and Supernova DNAzyme, which showed promising potential in pathogen detection. Finally, we summarize the strengths and weaknesses of these four DNAzymes and offer feasible recommendations for the development of biosensors.
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Affiliation(s)
- Xingxing Liu
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
- Department of Immunology and Microbiology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, P. R. China
| | - Wenxu Yuan
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
- Department of Immunology and Microbiology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, P. R. China
| | - Heng Xiao
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
- Department of Immunology and Microbiology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, P. R. China
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Liu Y, Wei C, Wan H, Sarengaowa, Liang X, Jiang T, Dong Y, Zhao X, Zhong T. Preliminary Study on Rapid and Simultaneous Detection of Viable Escherichia coli O157:H7, Staphylococcus aureus, and Salmonella by PMA-mPCR in Food. Molecules 2023; 28:5835. [PMID: 37570805 DOI: 10.3390/molecules28155835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Escherichia coli O157:H7, Staphylococcus aureus, and Salmonella are major foodborne pathogens that are widespread in nature and responsible for several outbreaks of food safety accidents. Thus, a rapid and practical technique (PMA-mPCR) was developed for the simultaneous detection of viable E. coli O157:H7, S. aureus, and Salmonella in pure culture and in a food matrix. To eliminate false positive results, propidium monoazide (PMA) was applied to selectively suppress the DNA amplification of dead cells. The results showed the optimum concentration of PMA is 5.0 µg/mL. The detection limit of this assay by mPCR was 103 CFU/mL in the culture broth, and by PMA-mPCR was 104 CFU/mL both in pure culture and a food matrix (milk and ground beef). In addition, the detection of mixed viable and dead cells was also explored in this study. The detection sensitivity ratio of viable and dead counts was less than 1:10. Therefore, the PMA-mPCR assay proposed here might provide an efficient detection tool for the simultaneous detection of viable E. coli O157:H7, S. aureus, and Salmonella and also have great potential for the detection and concentration assessment of VBNC cells.
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Affiliation(s)
- Yao Liu
- School of Pharmacy and Food Science, Zhuhai College of Science and Technology, Zhuhai 519041, China
| | - Caijiao Wei
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Hui Wan
- Nanchang Agricultural Technology Popularization Center, Nanchang 330299, China
| | - Sarengaowa
- School of Pharmacy and Food Science, Zhuhai College of Science and Technology, Zhuhai 519041, China
| | - Xiaoping Liang
- School of Pharmacy and Food Science, Zhuhai College of Science and Technology, Zhuhai 519041, China
| | - Tao Jiang
- School of Pharmacy and Food Science, Zhuhai College of Science and Technology, Zhuhai 519041, China
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao 999078, China
| | - Yuhe Dong
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao 999078, China
| | - Xihong Zhao
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Tian Zhong
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao 999078, China
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Cai Q, Shi H, Sun M, Ma N, Wang R, Yang W, Qiao Z. Sensitive Detection of Salmonella Based on CRISPR-Cas12a and the Tetrahedral DNA Nanostructure-Mediated Hyperbranched Hybridization Chain Reaction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:16382-16389. [PMID: 36512680 DOI: 10.1021/acs.jafc.2c05831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Salmonella severely threatens global human health and causes financial burden. The ability to sensitively detect Salmonella in food samples is highly valuable but remains a challenge. Herein, a sensitive detection method for Salmonella was developed by coupling immunomagnetic separation with the CRISPR-Cas12a system and the tetrahedral DNA nanostructure-mediated hyperbranched hybridization chain reaction (TDN-hHCR). In the detection system, the target Salmonella was immunomagnetically separated and labeled with bio-barcode DNA-modified gold nanoparticles (AuNPs), which could transfer and magnify the signal of a bacterial cell into numerous bio-barcode DNA molecules. Afterward, the bio-barcode DNA can trigger the trans-cleavage activity of CRISPR-Cas12a to inhibit the process of the TDN-hHCR to generate a fluorescence readout. Due to the high immunomagnetic separation efficiency and the effective signal amplification of CRISPR-Cas12a and the TDN-hHCR, Salmonella as low as 8 CFU/mL could be easily detected. Meanwhile, this has been applied for practical use and showed the capability to detect 17 and 25 CFU/mL in spiked milk and egg white, respectively, indicating its potential application in real samples.
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Affiliation(s)
- Qiqi Cai
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Hanxing Shi
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Mengni Sun
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Na Ma
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Rui Wang
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200438, China
| | - Wenge Yang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Zhaohui Qiao
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
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Lee JE, Kim SA, Park HJ, Mun H, Ha KS, Shim WB. Colorimetric detection of norovirus by helicase-dependent amplification method based on specific primers integrated with HRPzyme. Anal Bioanal Chem 2022; 414:6723-6733. [PMID: 35931785 DOI: 10.1007/s00216-022-04247-5] [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: 06/09/2022] [Revised: 07/11/2022] [Accepted: 07/21/2022] [Indexed: 11/28/2022]
Abstract
Noroviruses (NoVs) are the most common causes of epidemic gastroenteritis, responsible for at least 50% of all gastroenteritis outbreaks worldwide and significant causes of foodborne illness. In the USA, approximately 21 million illnesses attributable to NoVs have annually occurred. Therefore, there is a great demand to develop a rapid, low-cost, and accurate detection method for NoVs. This study first reported colorimetric helicase-dependent amplification (HDA) methods based on specific primers integrated with HRPzyme for the rapid and sensitive detection of NoV GI and GII. The colorimetric HDA methods exhibited a detection limit of 10 copies mL-1 of each NoV GI and GII and were confirmed to be specific to each NoV GI and GII. The period required to complete the HDA method was 2 h, including a step of RNA extraction and cDNA synthesis without expensive instruments such as a thermal cycler and detector. The cutoff value of the method for the oyster artificially inoculated with a known amount of NoV was all 102 copies g-1 for NoV GI and GII. Therefore, the HDA method developed in this study can be useful tool for the on-site detection of NoVs in food samples.
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Affiliation(s)
- Jeong-Eun Lee
- Institute of Smart Farm, Gyeongsang National University, Jinju, 52828, Gyeongnam, Korea
| | - Sol-A Kim
- Division of Applied Life Science, Graduate School, Gyeongsang National University, Jinju, 52828, Gyeongnam, Korea
| | - Hyun-Jin Park
- Division of Applied Life Science, Graduate School, Gyeongsang National University, Jinju, 52828, Gyeongnam, Korea
| | - Hyoyoung Mun
- Apteasy MJ Inc., 333 Cheomdangwagi-ro, Technopark, Gwangju, 61008, Korea
| | - Kwang-Soo Ha
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science, Tongyeong, 53085, Korea
| | - Won-Bo Shim
- Institute of Smart Farm, Gyeongsang National University, Jinju, 52828, Gyeongnam, Korea. .,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 52828, Gyeongnam, Korea. .,Department of Food Science and Technology, Gyeongsang National University, Jinju, 52828, Gyeongnam, Korea.
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Du R, Yang X, Jin P, Guo Y, Cheng Y, Yu H, Xie Y, Qian H, Yao W. G-quadruplex based biosensors for the detection of food contaminants. Crit Rev Food Sci Nutr 2022; 63:8808-8822. [PMID: 35389275 DOI: 10.1080/10408398.2022.2059753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
G-quadruplex (G4) is a very interesting DNA structure, commonly associated with cancer and its treatment. With flexible binding ability, G4 has been extended as a significant component in biosensors. On account of its simple operation, high sensitivity and low cost, G4-based biosensors have attracted considerable interest for the detection of food contaminants. In this review, research published in recent 5 years is collated from a principle perspective, that is target recognition and signal transduction. Contaminants with G4 binding capacity are illustrated, emerging G4-based biosensors including colorimetric, electrochemical and fluorescent sensors are also elaborated. The current review indicates that G4 has provided an efficient and effective solution for the rapid detection of food contaminants. A distinctive feature of G4 as recognition unit is the simple composition, but the selectivity is still unsatisfactory. As signal reporter, G4/hemin DNAzyme has not only achieved amplified signals, but also enabled visualized detection, which offers great potential for on-site measurement. With improved selectivity and visualized signal, the combination of aptamer and G4 seems to be an ideal strategy. This promising combination should be developed for the real-time monitor of multiple contaminants in food matrix.
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Affiliation(s)
- Rong Du
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiebingqing Yang
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Ping Jin
- Suzhou Product Quality Supervision and Inspection Institute, Suzhou, China
| | - Yahui Guo
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Engineering Research Center of Dairy Quality and Safety Control Technology (Ministry of Education), Inner Mongolia University, Inner Mongolia Autonomous Region, China
| | - Yuliang Cheng
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hang Yu
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yunfei Xie
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Engineering Research Center of Dairy Quality and Safety Control Technology (Ministry of Education), Inner Mongolia University, Inner Mongolia Autonomous Region, China
| | - He Qian
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
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Conventional and Emerging Techniques for Detection of Foodborne Pathogens in Horticulture Crops: a Leap to Food Safety. FOOD BIOPROCESS TECH 2022. [DOI: 10.1007/s11947-021-02730-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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Hitabatuma A, Wang P, Su X, Ma M. Metal-Organic Frameworks-Based Sensors for Food Safety. Foods 2022; 11:foods11030382. [PMID: 35159532 PMCID: PMC8833942 DOI: 10.3390/foods11030382] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/11/2022] [Accepted: 01/21/2022] [Indexed: 01/07/2023] Open
Abstract
Food contains a variety of poisonous and harmful substances that have an impact on human health. Therefore, food safety is a worldwide public concern. Food detection approaches must ensure the safety of food at every step of the food supply chain by monitoring and evaluating all hazards from every single step of food production. Therefore, early detection and determination of trace-level contaminants in food are one of the most crucial measures for ensuring food safety and safeguarding consumers’ health. In recent years, various methods have been introduced for food safety analysis, including classical methods and biomolecules-based sensing methods. However, most of these methods are laboratory-dependent, time-consuming, costly, and require well-trained technicians. To overcome such problems, developing rapid, simple, accurate, low-cost, and portable food sensing techniques is essential. Metal-organic frameworks (MOFs), a type of porous materials that present high porosity, abundant functional groups, and tunable physical and chemical properties, demonstrates promise in large-number applications. In this regard, MOF-based sensing techniques provide a novel approach in rapid and efficient sensing of pathogenic bacteria, heavy metals, food illegal additives, toxins, persistent organic pollutants (POPs), veterinary drugs, and pesticide residues. This review focused on the rapid screening of MOF-based sensors for food safety analysis. Challenges and future perspectives of MOF-based sensors were discussed. MOF-based sensing techniques would be useful tools for food safety evaluation owing to their portability, affordability, reliability, sensibility, and stability. The present review focused on research published up to 7 years ago. We believe that this work will help readers understand the effects of food hazard exposure, the effects on humans, and the use of MOFs in the detection and sensing of food hazards.
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Affiliation(s)
| | | | - Xiaoou Su
- Correspondence: ; Tel.: +86-82106577
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Hwang SH, Kim JH, Park J, Park KS. Fluorescence nucleobase analogue-based strategy with high signal-to-noise ratio for ultrasensitive detection of food poisoning bacteria. Analyst 2021; 145:6307-6312. [PMID: 32706347 DOI: 10.1039/d0an01026j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We developed a simple and ultrasensitive strategy for the identification of foodborne pathogens utilizing a fluorescent nucleobase analogue [2-aminopurine (2-AP)]-containing split G-quadruplex that binds blocker DNA. Compared to a previous strategy that did not use blocker DNA, this strategy showed a significant increase in the signal-to-noise ratio-by approximately 300%-owing to the displacement of the blocker DNA by the target DNA that induces the formation of an active G-quadruplex structure, thereby leading to a substantial increase in the 2-AP fluorescence signal. The proposed strategy was rationally combined with polymerase chain reaction, which resulted in the successful determination of genomic DNA (within the range of 10-106 copies) derived from the food poisoning bacterium Escherichia coli, with a limit of detection of 5.2 copies and high selectivity. In addition, the practical applicability of this method was demonstrated by analyzing E. coli-spiked lettuce samples.
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Affiliation(s)
- Sung Hyun Hwang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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9
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Ahmad M, Sharma P, Kamai A, Agrawal A, Faruq M, Kulshreshtha A. HRPZyme Assisted Recognition of SARS-CoV-2 infection by Optical Measurement (HARIOM). Biosens Bioelectron 2021; 187:113280. [PMID: 34020221 PMCID: PMC8088041 DOI: 10.1016/j.bios.2021.113280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/13/2021] [Accepted: 04/21/2021] [Indexed: 11/28/2022]
Abstract
In order to define public health policies, simple, inexpensive and robust detection methods for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are vital for mass-testing in resource limited settings. The current choice of molecular methods for identification of SARS-CoV-2 infection includes nucleic acid-based testing (NAT) for viral genetic material and antigen-based testing for viral protein identification. Host exposure is detected using antibody detection assays. While NATs require sophisticated instrument and trained manpower, antigen tests are plagued by their low sensitivity and specificity. Thus, a test offering sensitive detection for presence of infection as a colorimetric readout holds promise to enable mass testing in resource constrained environments by minimally trained personnel. Here we present a novel HRPZyme Assisted Recognition of Infection by Optical Measurement (HARIOM) assay which combines specificity of NATs with sensitivity of enzymatic assays resulting in enhanced signal to noise ratios in an easily interpretable colorimetric readout. Using this assay, we could detect up to 102 copies of synthetic viral RNA spiked in saliva as a detection matrix. Validating our assay on suspected human subjects, we found concordance with PCR based readouts with visible colorimetric distinction between positive and negative samples in less than an hour. We believe that this assay holds the potential to aid in mass screening to detect SARS-CoV-2 infection by facilitating colorimetric detection with minimal resources and less trained personnel.
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Affiliation(s)
- Mohd Ahmad
- Molecular Immunogenetics Laboratory, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Pooja Sharma
- Genomics and Other Omics Tools for Enabling Medical Decision (GOMED), CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
| | - Asangla Kamai
- Genomics and Other Omics Tools for Enabling Medical Decision (GOMED), CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
| | - Anurag Agrawal
- Molecular Immunogenetics Laboratory, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Mohammed Faruq
- Genomics and Other Omics Tools for Enabling Medical Decision (GOMED), CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
| | - Ankur Kulshreshtha
- Molecular Immunogenetics Laboratory, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
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Yang E, Liao W, Lin Q, An H, Li D, Wei F, Duan Y. Quantitative Analysis of Salmonella typhimurium Based on Elemental-Tags Laser-Induced Breakdown Spectroscopy. Anal Chem 2020; 92:8090-8096. [PMID: 32431153 DOI: 10.1021/acs.analchem.9b05608] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Current rapid bacterial detection methods are dedicated to the classification and identification of bacteria. However, there is still a lack of a method for specific quantitative analysis of certain bacteria. In this work, a method based on elemental-tags laser-induced breakdown spectroscopy (ETLIBS) was developed for the rapid and specific quantitative analysis of Salmonella typhimurium (S. ty). Elemental tags were first synthesized by assembling copper nanoparticles (CuNPs) with poly(thymine) (poly-T) template that linked with the aptamer sequence. Under the specific recognition of the aptamer, S. ty can be fully combined with the elemental tags within 30 min to achieve labeling. Afterward, the silicon nanowires (SiNWs) array modified with Au@Ag nanoparticles (SiNWs-Au@Ag) was employed to capture S. ty in 30 min. Attributed to the rapid analysis superiority of ETLIBS mapping, 100 spectra of SiNWs-Au@Ag/S. ty/CuNPs can be obtained in 5 min. It was found that the peak area of the Cu(I) atomic emission line at 324.75 nm fitted by the Voigt profile was linearly related to the bacterial concentration in the range of 102-106 CFU/mL(R2 = 0.978). Furthermore, ETLIBS mapping achieved a low limit of detection (LOD) of 61 CFU/mL and showed good selectivity to S. ty compared with other bacteria. Besides, the method exhibited preeminent detection performance in spiked samples with the recoveries of 87-113%. With the advantages of rapidity, high efficiency, and specificity, the proposed method is expected to be a powerful tool for bacterial detection.
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Affiliation(s)
- Enlai Yang
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Wenlong Liao
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, People's Republic of China
| | - Qingyu Lin
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Huifang An
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Dan Li
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Fujing Wei
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
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Huang J, Sun J, Warden AR, Ding X. Colorimetric and photographic detection of bacteria in drinking water by using 4-mercaptophenylboronic acid functionalized AuNPs. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106885] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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12
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Safdar S, Ven K, van Lent J, Pavie B, Rutten I, Dillen A, Munck S, Lammertyn J, Spasic D. DNA-only, microwell-based bioassay for multiplex nucleic acid detection with single base-pair resolution using MNAzymes. Biosens Bioelectron 2020; 152:112017. [PMID: 31941617 DOI: 10.1016/j.bios.2020.112017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/17/2022]
Abstract
In disease diagnostics, single- and multiplex nucleic acid (NA) detection, with the potential to discriminate mutated strands, is of paramount importance. Current techniques that rely on target amplification or protein-enzyme based signal amplification are highly relevant, yet still plagued by diverse drawbacks including erroneous target amplification, and the limited stability of protein enzymes. As a solution, we present a multicomponent nucleic acid enzymes (MNAzymes)-based system for singleplex and multiplex detection of NA targets in microwells down to femtomolar (fM) concentrations, without the need for any target amplification or protein enzymes, while operating at room temperature and with single base-pair resolution. After successful validation of the MNAzymes in solution, their performance was further verified on beads in bulk and in femtoliter-sized microwells. The latter is not only a highly simplified system compared to previous microwell-based bioassays but, with the detection limit of 180 fM, it is to-date the most sensitive NAzyme-mediated, bead-based approach, that does not rely on target amplification or any additional signal amplification strategies. Furthermore, we demonstrated, for the first time, multiplexed target detection in microwells, both from buffer and nasopharyngeal swab samples, and presented superior single base-pair resolution of this assay. Because of the design flexibility of MNAzymes and direct demonstration in swab samples, this system holds great promise for multiplexed detection in other clinically relevant matrices without the need for any additional NA or protein components. Moreover, these findings open up the potential for the development of next-generation, protein-free diagnostic tools, including digital assays with single-molecule resolution.
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Affiliation(s)
- Saba Safdar
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium
| | - Karen Ven
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium
| | - Julie van Lent
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium
| | - Benjamin Pavie
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, 3000, Leuven, Belgium
| | - Iene Rutten
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium
| | - Annelies Dillen
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium
| | - Sebastian Munck
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, 3000, Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium.
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium
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13
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Mei L, Wang Q. Advances in Using Nanotechnology Structuring Approaches for Improving Food Packaging. Annu Rev Food Sci Technol 2020; 11:339-364. [PMID: 31905018 DOI: 10.1146/annurev-food-032519-051804] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent advances in food packaging materials largely rely on nanotechnology structuring. Owing to several unique properties of nanostructures that are lacking in their bulk forms, the incorporation of nanostructures into packaging materials has greatly improved the performance and enriched the functionalities of these materials. This review focuses on the functions and applications of widely studied nanostructures for developing novel food packaging materials. Nanostructures that offer antimicrobial activity, enhance mechanical and barrier properties, and monitor food product freshness are discussed and compared. Furthermore, the safety and potential toxicity of nanostructures in food products are evaluated by summarizing the migration activity of nanostructures to different food systems and discussing the metabolism of nanostructures at the cellular level and in animal models.
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Affiliation(s)
- Lei Mei
- Department of Nutrition and Food Science, College of Agriculture and Natural Resources, University of Maryland, College Park, Maryland 20740, USA;
| | - Qin Wang
- Department of Nutrition and Food Science, College of Agriculture and Natural Resources, University of Maryland, College Park, Maryland 20740, USA;
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Kim K, Kim H, Jang H, Park J, Jung GY, Kim MG. Self-Powered Biosensors Using Various Light Sources in Daily Life Environments: Integration of p-n Heterojunction Photodetectors and Colorimetric Reactions for Biomolecule Detection. ACS APPLIED MATERIALS & INTERFACES 2018; 10:39487-39493. [PMID: 30375844 DOI: 10.1021/acsami.8b13457] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Electronic biosensors operating without power supply are high in demand owing to increasing interest in point-of-care (POC) coupled with portable and wearable electronic devices for smart healthcare services. Although self-powered electronic sensors have emerged with the promise of resolving the energy supply problems, achieving sufficient sensitivity to targets in real samples is highly challenging because of the matrix effect caused by electroactive species. In this study, we developed a self-powered biosensor platform by combining n-indium gallium zinc oxide (IGZO)/p-Si heterojunction photodetectors and physically separated colorimetric reactions. The self-powered biosensors were applied to glucose detection in real human samples using light sources from daily life environments such as fluorescent light and sunlight. The sensors showed high sensitivity and stability from 0.01 to 10 mg mL-1 of glucose in human saliva and urine without matrix effect from the electroactive species in real samples. In addition, a small change in glucose concentration in human serum was distinguishable with a resolution of 0.01 mg mL-1. Notably, these results were obtained using well-developed and widely used materials like Si and IGZO with simple deposition techniques. Moreover, this self-powered biosensing platform can be universally applied for the detection of all biomolecules being detected by colorimetric assays. To the best of our knowledge, this is the first report on such self-powered biosensors, which could be a promising candidate for future POC biosensors integrated with portable and wearable electronic devices.
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Re-engineering 10-23 core DNA- and MNAzymes for applications at standard room temperature. Anal Bioanal Chem 2018; 411:205-215. [PMID: 30341659 DOI: 10.1007/s00216-018-1429-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/02/2018] [Accepted: 10/10/2018] [Indexed: 12/15/2022]
Abstract
DNA- and MNAzymes are nucleic acid-based enzymes (NAzymes), which infiltrated the otherwise protein-rich field of enzymology three decades ago. The 10-23 core NAzymes are one of the most widely used and well-characterized NAzymes, but often require elevated working temperatures or additional complex modifications for implementation at standard room temperatures. Here, we present a generally applicable method, based on thermodynamic principles governing hybridization, to re-engineer the existing 10-23 core NAzymes for use at 23 °C. To establish this, we first assessed the activity of conventional NAzymes in the presence of cleavable and non-cleavable substrate at 23 °C as well as over a temperature gradient. These tests pointed towards a non-catalytic mechanism of signal generation at 23 °C, suggesting that conventional NAzymes are not suited for use at this temperature. Following this, several novel NAzyme-substrate complexes were re-engineered from the conventional ones and screened for their performance at 23 °C. The complex with substrate and substrate-binding arms of the NAzymes shortened by four nucleotides on each terminus demonstrated efficient catalytic activity at 23 °C. This has been further validated over a dilution of enzymes or enzyme components, revealing their superior performance at 23 °C compared to the conventional 10-23 core NAzymes at their standard operating temperature of 55 °C. Finally, the proposed approach was applied to successfully re-engineer three other new MNAzymes for activity at 23 °C. As such, these re-engineered NAzymes present a remarkable addition to the field by further widening the diverse repertoire of NAzyme applications.
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Ahn H, Batule BS, Seok Y, Kim MG. Single-Step Recombinase Polymerase Amplification Assay Based on a Paper Chip for Simultaneous Detection of Multiple Foodborne Pathogens. Anal Chem 2018; 90:10211-10216. [DOI: 10.1021/acs.analchem.8b01309] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Heeseop Ahn
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Cheomdan-gwagiro, Gwangju 500-712, Republic of Korea
| | - Bhagwan Sahebrao Batule
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Cheomdan-gwagiro, Gwangju 500-712, Republic of Korea
| | - Youngung Seok
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Cheomdan-gwagiro, Gwangju 500-712, Republic of Korea
| | - Min-Gon Kim
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Cheomdan-gwagiro, Gwangju 500-712, Republic of Korea
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Batule BS, Kim SU, Mun H, Choi C, Shim WB, Kim MG. Colorimetric Detection of Norovirus in Oyster Samples through DNAzyme as a Signaling Probe. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:3003-3008. [PMID: 29381353 DOI: 10.1021/acs.jafc.7b05289] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Worldwide, norovirus is one of the most associated causes of acute gastroenteritis, which leads to nearly 50 000 child deaths every year in developing countries. Therefore, there is great demand to develop a rapid, low-cost, and accurate detection assay for the foodborne norovirus infection to reduce mortality caused by norovirus. Considering the importance of norovirus, we have demonstrated a highly sensitive and specific colorimetric detection method for analysis of human norovirus genogroups I and II (HuNoV GI and GII) in oyster samples. This is the first report to employ colorimetric HRPzyme-integrated polymerase chain reaction (PCR) for direct norovirus detection from the real shellfish samples. We found that the HRPzyme-integrated PCR method is more sensitive than the gel electrophoresis approach and could detect the HuNoV GI and GII genome up to 1 copy/mL. The specificity of the proposed method was successfully demonstrated for HuNoV GI and GII. Further, we performed testing HuNoVs in the spiked oyster samples, and the HRPzyme-integrated PCR method proved to be an ultrasensitive and selective method for detecting HuNoVs in the real samples. By integration of the proposed method with the portable PCR machine, it would be more reliable to improve food safety by detecting HuNoVs in the different types of shellfish, such as oyster and mussel, at the production field.
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Affiliation(s)
| | | | | | - Changsun Choi
- Department of Food and Nutrition, College of Biotechnology and Natural Resources , Chung-Ang University , Anseong , Gyounggi 17546 , Republic of Korea
| | - Won-Bo Shim
- Department of Agricultural Chemistry and Food Science and Technology , Gyeongsang National University , 900 Gajwa-dong , Jinju , Gyeongnam 660-701 , Republic of Korea
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Kim SU, Batule BS, Mun H, Byun JY, Shim WB, Kim MG. Colorimetric molecular diagnosis of the HIV gag gene using DNAzyme and a complementary DNA-extended primer. Analyst 2018; 143:695-699. [PMID: 29299545 DOI: 10.1039/c7an01520h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have developed a novel strategy for the colorimetric detection of PCR products by utilizing a target-specific primer modified at the 5'-end with an anti-DNAzyme sequence. A single-stranded DNAzyme sequence folds into a G-quadruplex structure with hemin and shows strong peroxidase activity. When the complementary strand binds to the DNAzyme sequence, it blocks the formation of the G-quadraduplex structure and loses its peroxidase activity. In the presence of the target gene, PCR amplification proceeds, and anti-DNAzyme sequence modified primers present in the reaction mixture form a double strand through primer extension. Therefore, it does not block the DNAzyme sequence. Further, a colorimetric signal is generated by the addition of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) and H2O2 at the end of the reaction. We have successfully detected a single copy of the HIV type 1 gag gene in buffer and 10 copies in human serum. The strategy developed could be used to detect DNA and RNA in complex biological samples by simple primer designing that includes DNAzyme and a DNA extended primer.
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Affiliation(s)
- Seong U Kim
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea.
| | - Bhagwan S Batule
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea
| | - Hyoyoung Mun
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea
| | - Ju-Young Byun
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea
| | - Won-Bo Shim
- Department of Agricultural Chemistry and Food Science and Technology, Gyeongsang National University, 900 Gajwa-dong Jinju, Gyeongnam 660-701, Republic of Korea
| | - Min-Gon Kim
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea. and Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea
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