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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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Fang Y, Wang C, Wang Y, Hu J, Lai M, Liu P, Zhang H. Naked-eye detection of plant viral disease using polymerase chain reaction amplification and DNAzyme. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1003-1011. [PMID: 38269430 DOI: 10.1039/d3ay01367g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Plant viral diseases can seriously affect the yield and quality of crops. In this work, a convenient and highly sensitive biosensor for the visual detection of plant viral disease is proposed by the PCR-induced generation of DNAzyme. In the absence of nucleic acid for a target plant virus, the primers prohibited the production of G-quadruplex by forming a hairpin structure. However, PCR amplification occurred and generated a number of specific PCR products with free G-quadruplex sequences at both ends in the presence of the target cDNA. A catalytically active G-quadruplex DNAzyme was formed with the help of K+ and hemin, resulting in the formation of colored products visible to the naked eye and a strong absorbance by the addition of ABTS2- and H2O2. The absorbance and the logarithm of target cDNA concentrations showed a good linear relationship in the range of 10 fM-1.0 nM, with a linear regression equation of A = 0.1402 lg c + 0.3761 (c: fM) and a detection limit of 0.19 fM. This method was successfully applied to the analysis of emerging tobacco mosaic virus (TMV) infections in tobacco leaf samples collected in the field due to its flexibility and convenience, indicating a potential application for the early detection of plant viral disease.
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Affiliation(s)
- Yongwei Fang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Chuang Wang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Yuli Wang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Jiandong Hu
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou, Henan 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou, Henan 450002, China
| | - Miao Lai
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Pengfei Liu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Hong Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
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Han L, Chen M, Song Y, Yan Z, Zhou D, Pan L, Tu K. Development of a Dual Mode UCNPs-MB Biosensor in Combination with PCR for Sensitive Detection of Salmonella. BIOSENSORS 2023; 13:bios13040475. [PMID: 37185550 PMCID: PMC10136931 DOI: 10.3390/bios13040475] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023]
Abstract
In recent years, the high prevalence of Salmonella has emerged as a serious threat to public safety, prompting attempts to utilize accurate, rapid, and direct methods to ensure food safety. In this study, a multifunctional platform featuring dual-mode detection channels (colorimetric-fluorescence) combined with polymer chain reaction (PCR) was proposed for the sensitive and rapid detection of Salmonella. Additionally, the colorimetric measurements were achieved by color changes induced by methylene blue (MB) insertion into the double-stranded DNA, and the fluorescence measurements were performed by internal filter effect (IFE)-induced fluorescence quenching of upconversion nanoparticles (UCNPs) by MB. The results showed that the IFE and PCR amplification processes improved the sensitivity of the sensor towards Salmonella detection, with a limit of detection (LOD) of 21.8 CFU/mL. Moreover, this colorimetric-fluorescence dual-mode PCR biosensor was applied to determine Salmonella in food samples, such as chicken, egg, and fish, which produced satisfactory results. Overall, the present study results demonstrate the potential for combining PCR amplification with IFE to develop an efficient and reliable dual-mode analysis platform to safeguard food security.
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Affiliation(s)
- Lu Han
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Min Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yaqi Song
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongyu Yan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Dandan Zhou
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Leiqing Pan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Kang Tu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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Yin C, Yuan N, Zhang Y, Guo W, Liu J, Yang Q, Zhang W. Electrochemical Biosensor Based on Single Primer Isothermal Amplification (SPIA) for Sensitive Detection of Salmonella in Food. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02387-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Lu X, Li D, Luo Z, Duan Y. A dual-functional fluorescent biosensor based on enzyme-involved catalytic hairpin assembly for the detection of APE1 and miRNA-21. Analyst 2022; 147:2834-2842. [PMID: 35621039 DOI: 10.1039/d2an00108j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Both apurinic/apyrimidinic endonuclease 1 (APE1) and microRNA-21 (miRNA-21) have been reported to be related to tumors, enabling them to be the biomarkers of several cancers. This has led to the development of various biosensors to detect APE1 or miRNA-21. However, biosensors that focus on single target detection are subject to low accuracy. In this work, a fluorescent biosensor based on enzyme-involved catalytic hairpin assembly (CHA) for the detection of APE1 and miRNA-21 was developed, aimed at improving the accuracy of early-phase diagnosis of cancers. Two hairpin structured DNA probes (H1 and H2) were utilized to concatenate the enzyme-assisted circuit and CHA circuit in the system. The stem of H1 with a blunt end was modified with an AP site, while H2 was modified with 6-FAM at the 5' terminal and Dabcyl at the 3' terminal. In the presence of APE1, H1 was cleaved from the AP site to expose the toehold sequence. Then, miRNA-21 bound with the toehold sequence to initiate the CHA reaction between H1 and H2. The assembled product of CHA triggered the 6-FAM of H2 at a distance from Dabcyl, which recovered the fluorescence signal. It is worth noting that only under the co-stimulation of APE1 and miRNA-21 can the fluorescence signal be detected, indicating that the biosensor could work as an AND logic gate. The proposed dual-functional biosensor achieved a limit of detection (LOD) of 0.016 U mL-1 for APE1 and 0.25 nM for miRNA-21 and APE1, respectively, and also exhibits good selectivity and stability for the two biomarkers. Thus, the biosensor has great potential to be applied as a new platform for cancer diagnosis.
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Affiliation(s)
- Xiaoyong Lu
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P.R. China.
| | - Dan Li
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, Shaanxi, P.R. China.
| | - Zewei Luo
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, Shaanxi, P.R. China.
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P.R. China.
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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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Du M, Li J, Liu Q, Wang Y, Chen E, Kang F, Tu C. Rapid detection of trace Salmonella in milk using an effective pretreatment combined with droplet digital polymerase chain reaction. Microbiol Res 2021; 251:126838. [PMID: 34390956 DOI: 10.1016/j.micres.2021.126838] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 11/24/2022]
Abstract
Salmonella is one of the most dangerous food-borne pathogens around the world to cause a threat to humans and it is urgent to develop the rapid detection method of trace Salmonella in food. Although many advanced techniques have been widely applied to shorten the detection time, the pretreatment method usually used of traditional enrichment and plate culturing to separate Salmonella are complicated and time-consuming. Herein, we developed an effective pretreatment method based on in situ enrichment culture with an immunomagnetic separation step, combined with droplet digital polymerase chain reaction (ddPCR) technology to achieve rapid detection of trace Salmonella in milk, which allowed detecting as low as 10-1 CFU/mL level of Salmonella. It took 8 h to perform the entire testing process from pretreatment to ddPCR detection and analysis. The pretreatment method could be a suitable platform integrating with many detection techniques for the rapid detection of trace Salmonella.
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Affiliation(s)
- Meihong Du
- Beijing Engineering Research Center of Food Safety Analysis, Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical and Chemical Analysis, Beijing, 100089, China.
| | - Jingwen Li
- Beijing Engineering Research Center of Food Safety Analysis, Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical and Chemical Analysis, Beijing, 100089, China
| | - Qingjun Liu
- Beijing Engineering Research Center of Food Safety Analysis, Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical and Chemical Analysis, Beijing, 100089, China
| | - Yanfei Wang
- Solid Waste and Chemicals Management Center, MEE, Beijing, 100029, China
| | - Erning Chen
- Beijing Engineering Research Center of Food Safety Analysis, Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical and Chemical Analysis, Beijing, 100089, China
| | - Fuying Kang
- Beijing Engineering Research Center of Food Safety Analysis, Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical and Chemical Analysis, Beijing, 100089, China
| | - Chenxiao Tu
- Beijing Engineering Research Center of Food Safety Analysis, Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical and Chemical Analysis, Beijing, 100089, China
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Wang S. Construction of DNA Biosensors for Mercury (II) Ion Detection Based on Enzyme-Driven Signal Amplification Strategy. Biomolecules 2021; 11:biom11030399. [PMID: 33800447 PMCID: PMC8001444 DOI: 10.3390/biom11030399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 02/03/2023] Open
Abstract
Mercury ion (Hg2+) is a well-known toxic heavy metal ion. It is harmful for human health even at low concentrations in the environment. Therefore, it is very important to measure the level of Hg2+. Many methods, reviewed in several papers, have been established on DNA biosensors for detecting Hg2+. However, few reviews on the strategy of enzyme-driven signal amplification have been reported. In this paper, we reviewed this topic by dividing the enzymes into nucleases and DNAzymes according to their chemical nature. Initially, we introduce the nucleases including Exo III, Exo I, Nickase, DSN, and DNase I. In this section, the Exo III-driven signal amplification strategy was described in detail. Because Hg2+ can help ssDNA fold into dsDNA by T-Hg-T, and the substrate of Exo III is dsDNA, Exo III can be used to design Hg2+ biosensor very flexibly. Then, the DNAzyme-assisted signal amplification strategies were reviewed in three categories, including UO22+-specific DNAzymes, Cu2+-specific DNAzymes and Mg2+-specific DNAzymes. In this section, the Mg2+-specific DNAzyme was introduced in detail, because this DNAzyme has highly catalytic activity, and Mg2+ is very common ion which is not harmful to the environment. Finally, the challenges and future perspectives were discussed.
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Affiliation(s)
- Shuchang Wang
- School of Life Sciences, East China Normal University, Shanghai 200241, China
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