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Qian S, Chen Y, Wang X, Wang T, Che Y, Wu J, Ye Z, Xu J. CRISPR/Cas12a-Assisted Dual Visualized Detection of SARS-CoV-2 on Frozen Shrimps. BIOSENSORS 2023; 13:138. [PMID: 36671975 PMCID: PMC9855800 DOI: 10.3390/bios13010138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/27/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Given the possibility that food contaminated with SARS-CoV-2 might become an infection source, there is an urgent need for us to develop a rapid and accurate nucleic acid detection method for SARS-CoV-2 in food to ensure food safety. Here, we propose a sensitive, specific, and reliable molecular detection method for SARS-CoV-2. It has a mechanism to control amplicon contamination. Swabs from spiked frozen shrimps were used as detection samples, which were processed by heating at 95 °C for 30 s. These preprocessed samples served as the templates for subsequent amplification. A colorimetric LAMP reaction was carried out to amplify both the SARS-CoV-2 target and the MS2 phage simultaneously in one tube. MS2 phage was detected by colorimetric LAMP as the internal control, while SARS-CoV-2 was detected with a CRISPR/Cas12a system. The fluorescence results could be visually detected with an ultraviolet lamp. Meanwhile, uracil was incorporated during the LAMP reaction to provide an amplicon contamination proof mechanism. This test could detect as low as 20 copies of SARS-CoV-2 in one reaction. Additionally, the detection could be finished in 45 min. The test only needs a heating block and an ultraviolet lamp, which shows the potential for field detection.
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Affiliation(s)
- Siwenjie Qian
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Yanju Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Tingzhang Wang
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Yang Che
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of on Site Processing Equipment for Agricultural Products, Ministry of Agriculture, Hangzhou 310058, China
| | - Zhangying Ye
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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2
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Li Q, Li Y, Gao Q, Jiang C, Tian Q, Ma C, Shi C. Real-time monitoring of isothermal nucleic acid amplification on a smartphone by using a portable electrochemical device for home-testing of SARS-CoV-2. Anal Chim Acta 2022; 1229:340343. [PMID: 36156220 PMCID: PMC9449873 DOI: 10.1016/j.aca.2022.340343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 07/27/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022]
Abstract
Home-testing of SARS-CoV-2 is an ideal approach for controlling the pandemic of COVID-19 and alleviating the shortage of medical resource caused by this acute infectious disease. Herein, a portable device that enables real-time monitoring of isothermal nucleic acid amplification tests (INAATs) through the electrochemistry method was fabricated for home-testing of SARS-CoV-2. First, a disposable plug-and-play pH-sensitive potentiometric sensor that matches this electrochemical INAATs (E-INAATs) device was designed to allow the label-free pH sensing detection of nucleic acid. By applying Nafion film on the polyaniline-based working electrode, this sensor exhibited an excellent linear potentiometric response to pH value in the range of 6.0–8.5 with a slope of −37.45 ± 1.96 mV/pH unit. A Bluetooth module was integrated into this device to enable the users real-time monitoring INAATs on their smartphones at home. Moreover, by presetting criteria, the detection results could be automatically judged by the device to avoid human errors. Finally, the utility of this E-INAATs device was demonstrated by detecting the presence of SARS-CoV-2 nucleocapsid protein gene in artificial samples with a sensitivity of 2 × 102 copies/test within 25 min, which was comparable with fluorescence and colorimetric assay. This portable, easy-operated, sensitive, and affordable device is particularly desirable for the full integration of household SARS-CoV-2 detection products and will open a new prospect for the control of infectious diseases via electrochemical NAATs.
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Affiliation(s)
- Qi Li
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, PR China
| | - Yang Li
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, PR China
| | - Qian Gao
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, PR China
| | - Chao Jiang
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, PR China
| | - Qingwu Tian
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, PR China.
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Chao Shi
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, PR China.
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3
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Development of Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Detecting Feline Coronavirus. Animals (Basel) 2022; 12:ani12162075. [PMID: 36009664 PMCID: PMC9405184 DOI: 10.3390/ani12162075] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/30/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Feline coronavirus infecting domestic cats can cause feline infectious peritonitis (FIP), a fatal infectious disease. Several relevant clinical diagnoses and molecular methods are complicated and often ambiguous for veterinarians. In this work developed a rapid, sensitive, specific, and easy-to-visualize colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay with a novel LAMP primer set that has high specificity was developed using neutral red as an indicator dye. This proposed procedure could reliably detect FCoV RNA from effusion fluids comparable to the conventional PCR method. Considering these advantages, the RT-LAMP developed here has great potential on FIP-associated FCoV surveillance. Together with other sophisticated molecular diagnostic tools, this method can further be exploited in clinical laboratories to inspect suspected cats with effusive FIP. Abstract Feline infectious peritonitis (FIP) is a worldwide fatal disease caused by a mutant feline coronavirus (FCoV). Simple and efficient molecular detection methods are needed. Here, sensitive, specific, rapid, and reliable colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed to detect the ORF1a/1b gene of FCoV from cats with suspected FIP using neutral red as an indicator. Novel LAMP primers were specifically designed based on the gene of interest. The isothermal assay could visually detect FCoV at 58 °C for 50 min. The RT-LAMP assay was highly specific and had no cross-reactivity with other related feline viruses. The detection limit of FCoV detection by RT-LAMP was 20 fg/µL. A blind clinical test (n = 81) of the developed RT-LAMP procedure was in good agreement with the conventional PCR method. In the light of its performance specificity, sensitivity, and easy visualization, this neutral-red-based RT-LAMP approach would be a fruitful alternative molecular diagnostic tool for veterinary inspection of FCoV when combined with nucleotide sequencing or specific PCR to affirm the highly virulent FIP-associated FCoV.
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Zhang F, Gao C, Bai L, Chen Y, Liang S, Lv X, Sun J, Wang S. Dual-color blending based visual LAMP for food allergen detection: A strategy with enlarged color variation range and contrast. Food Chem X 2022; 13:100201. [PMID: 35498982 PMCID: PMC9039889 DOI: 10.1016/j.fochx.2021.100201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023] Open
Abstract
A near contrast color change was obtained by blending HNB and CR colorimetric LAMP detection process. The sensitivity of the dual-color blending method was comparable to the real-time LAMP. The ratio between the two visual dyes in the dual-color blending method is crucial. The reaction is conducted in one tube and no lid-opening was needed.
Food allergy has been a serious public health problem around the world. Its prevention relies heavily on the effective avoidance of any contaminated food, making clear and accurate detection very important. LAMP is one of the most potent methods for allergen rapid detection. However, its current colorimetric readouts usually have low color contrast and narrow color variation range. Thus, here we proposed a strategy based on color evolution to enlarge the variation range as well as the contrast to improve its suitability for naked-eye observation. By simply blending two commonly used color change processes during amplification, a wider color variation window, and a near contrast color change, purple-to-green with a hues difference of 10 were obtained. Three important allergens (walnuts, hazelnuts, and peanuts) were tested with a comparable sensitivity towards fluorescent real-time LAMP. Its feasibility for practical use has also been studied. This simple but effective strategy provides a new idea for the colorimetric detection of LAMP amplicons and can be applied to various fields.
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Affiliation(s)
- Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Chenshan Gao
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China.,Beijing Laboratory of Food Quality and Safety, Beijing Technology and Business University, Beijing 100048, China
| | - Linlin Bai
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Yiquan Chen
- Clinical Laboratory, Nanan Hospital, Nanan 362300, China
| | - Shuying Liang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Xucong Lv
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Jinyuan Sun
- Beijing Laboratory of Food Quality and Safety, Beijing Technology and Business University, Beijing 100048, China
| | - Shaoyun Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
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Padzil F, Mariatulqabtiah AR, Tan WS, Ho KL, Isa NM, Lau HY, Abu J, Chuang KP. Loop-Mediated Isothermal Amplification (LAMP) as a Promising Point-of-Care Diagnostic Strategy in Avian Virus Research. Animals (Basel) 2021; 12:ani12010076. [PMID: 35011181 PMCID: PMC8744981 DOI: 10.3390/ani12010076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/02/2021] [Accepted: 12/04/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Many of the existing screening methods of avian viruses depend on clinical symptoms and pathological gross examinations that still necessitate confirmatory microscopic testing. Confirmation of a virus is often conducted at centralized laboratories that are well-equipped with instruments for virus isolation, hemagglutinin inhibition, virus neutralization, ELISA, PCR and qPCR. These assays are known for their great accuracy and sensitivity, and hence are set as standard practices. Nevertheless, limitations arise due to the time, cost and on-site applicability. As the technology progresses, molecular diagnostics should be more accessible to isolated areas and even practicable for use by non-skilled personnel such as farmers and private breeders. One of the point-of-care diagnostic strategies to consider for such matters is loop-mediated isothermal amplification (LAMP). Abstract Over the years, development of molecular diagnostics has evolved significantly in the detection of pathogens within humans and their surroundings. Researchers have discovered new species and strains of viruses, while mitigating the viral infections that occur, owing to the accessibility of nucleic acid screening methods such as polymerase chain reaction (PCR), quantitative (real-time) polymerase chain reaction (qPCR) and reverse-transcription qPCR (RT-qPCR). While such molecular detection methods are widely utilized as the benchmark, the invention of isothermal amplifications has also emerged as a reliable tool to improvise on-field diagnosis without dependence on thermocyclers. Among the established isothermal amplification technologies are loop-mediated isothermal amplification (LAMP), recombinant polymerase amplification (RPA), strand displacement activity (SDA), nucleic acid sequence-based amplification (NASBA), helicase-dependent amplification (HDA) and rolling circle amplification (RCA). This review highlights the past research on and future prospects of LAMP, its principles and applications as a promising point-of-care diagnostic method against avian viruses.
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Affiliation(s)
- Faiz Padzil
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (F.P.); (W.S.T.); (N.M.I.)
- Institute for Medical Research, National Institute of Health, Setia Alam, Shah Alam 40170, Selangor, Malaysia
| | - Abdul Razak Mariatulqabtiah
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (F.P.); (W.S.T.); (N.M.I.)
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +60-297-691-938
| | - Wen Siang Tan
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (F.P.); (W.S.T.); (N.M.I.)
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Nurulfiza Mat Isa
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (F.P.); (W.S.T.); (N.M.I.)
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Han Yih Lau
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), Persiaran MARDI-UPM, Serdang 43400, Selangor, Malaysia;
| | - Jalila Abu
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Kuo-Pin Chuang
- International Degree Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung 912, Taiwan;
- Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- School of Dentistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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6
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Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing. Talanta 2021; 226:122146. [PMID: 33676697 DOI: 10.1016/j.talanta.2021.122146] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 01/19/2023]
Abstract
Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.
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Zhu H, Fohlerová Z, Pekárek J, Basova E, Neužil P. Recent advances in lab-on-a-chip technologies for viral diagnosis. Biosens Bioelectron 2020; 153:112041. [PMID: 31999560 PMCID: PMC7126858 DOI: 10.1016/j.bios.2020.112041] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022]
Abstract
The global risk of viral disease outbreaks emphasizes the need for rapid, accurate, and sensitive detection techniques to speed up diagnostics allowing early intervention. An emerging field of microfluidics also known as the lab-on-a-chip (LOC) or micro total analysis system includes a wide range of diagnostic devices. This review briefly covers both conventional and microfluidics-based techniques for rapid viral detection. We first describe conventional detection methods such as cell culturing, immunofluorescence or enzyme-linked immunosorbent assay (ELISA), or reverse transcription polymerase chain reaction (RT-PCR). These methods often have limited speed, sensitivity, or specificity and are performed with typically bulky equipment. Here, we discuss some of the LOC technologies that can overcome these demerits, highlighting the latest advances in LOC devices for viral disease diagnosis. We also discuss the fabrication of LOC systems to produce devices for performing either individual steps or virus detection in samples with the sample to answer method. The complete system consists of sample preparation, and ELISA and RT-PCR for viral-antibody and nucleic acid detection, respectively. Finally, we formulate our opinions on these areas for the future development of LOC systems for viral diagnostics.
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Affiliation(s)
- Hanliang Zhu
- Ministry of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Zdenka Fohlerová
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic
| | - Jan Pekárek
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic
| | - Evgenia Basova
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic
| | - Pavel Neužil
- Ministry of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China; Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic.
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8
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Zhang M, Ye J, He JS, Zhang F, Ping J, Qian C, Wu J. Visual detection for nucleic acid-based techniques as potential on-site detection methods. A review. Anal Chim Acta 2019; 1099:1-15. [PMID: 31986265 DOI: 10.1016/j.aca.2019.11.056] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/15/2022]
Abstract
Nucleic acid-based techniques could achieve highly sensitive detection by amplifying template molecules to millions of folds. It has been one of the most valued analytical methods and is applied in many detection fields, such as diagnosis of infectious diseases, food safety assurance and so on. Nucleic acid-based techniques consist of three steps: nucleic acid extraction, amplification, and product detection. Among them, the detection step plays a vital role because it shows the results directly. As the trend of detection is simple, rapid and instrument-free, it is of necessity to carry out visual detection, where the result read-out could be visible and distinguished by the naked eye. In this critical review, advanced visual detection methods are summarized and discussed in detail, aiming to promote the potential application in on-site detection.
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Affiliation(s)
- Mengyao Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jing Ye
- Zhijiangnan Think Tank, Zhejiang Institute of Science and Technology Information, Hangzhou, 310006, China
| | - Jin-Song He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Jianfeng Ping
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Cheng Qian
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of on Site Processing Equipment for Agricultural Products, Ministry of Agriculture, Hangzhou, 310058, China.
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Mason MG, Botella JR. A simple, robust and equipment-free DNA amplification readout in less than 30 seconds. RSC Adv 2019; 9:24440-24450. [PMID: 35527854 PMCID: PMC9069613 DOI: 10.1039/c9ra04725e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/29/2019] [Indexed: 11/21/2022] Open
Abstract
Molecular based diagnostic methods rely on the amplification of pathogen DNA but naked eye visualization of results is still challenging. We present here a simple and highly reliable DNA amplification readout system for naked eye detection of isothermally or PCR amplified DNA in less than 30 seconds. This system utilizes spermine to precipitate DNA amplicons and initiate bridging flocculation of a mix of charcoal and diatomaceous earth particles in suspension. In the absence of amplification, the charcoal particles remain suspended resulting in a black, non-transparent colloid solution while positive samples in which DNA amplification has occurred can be identified within seconds as the particles flocculate and settle leaving a transparent liquid phase. We have coupled this method with our rapid dipstick DNA purification method and isothermal DNA amplification to create a simple four-step diagnostic system that can be preassembled to reduce unnecessary manipulation in the field. The method's simplicity, low cost, minimal equipment and clear presence/absence readout makes it ideal for rapid diagnostic testing in the laboratory and in situations where users have limited technical training or resources including high school science classes and field-based research. A simple and highly reliable DNA amplification readout system for naked eye detection of amplified DNA in under 30 seconds.![]()
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Affiliation(s)
- Michael Glenn Mason
- Plant Genetic Engineering Laboratory
- School of Agriculture and Food Sciences
- The University of Queensland
- St. Lucia
- Australia
| | - José Ramón Botella
- Plant Genetic Engineering Laboratory
- School of Agriculture and Food Sciences
- The University of Queensland
- St. Lucia
- Australia
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10
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A Sensitive Potentiometric Sensor for Isothermal Amplification-Coupled Detection of Nucleic Acids. SENSORS 2018; 18:s18072277. [PMID: 30011898 PMCID: PMC6068556 DOI: 10.3390/s18072277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 12/27/2022]
Abstract
A disposable potentiometric sensor was newly developed for the amplification-coupled detection of nucleic acids. The hydrogen-ion is generally released during isothermal amplification of nucleic acids. The surface potential on the oxide-functionalized electrode of the extended gate was directly measured using full electrical circuits with the commercial metal-oxide semiconductor field-effect transistors (MOSFETs) and ring oscillator components, which resulted in cost-effective, portable and scalable real-time nucleic acid analysis. The current-starved ring oscillator changes surface potential to its frequency depending on the square of the variation in pH with a high signal-to-noise ratio during isothermal amplification. The device achieves a conversion rate of 20.5 kHz/mV and a detection resolution of 200 µV for the surface potential. It is demonstrated that the sensor successfully monitors in real-time isothermal amplification of the extracted nucleic acids from Salmonella pathogenic bacteria. The in situ variations in the frequency of the pH-sensitive sensor were compared with the results of both a conventional optical device and pH-meter during isothermal amplification.
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11
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Wang J, Song M, Hu C, Wu K. Portable, Self-Powered, and Light-Addressable Photoelectrochemical Sensing Platforms Using pH Meter Readouts for High-Throughput Screening of Thrombin Inhibitor Drugs. Anal Chem 2018; 90:9366-9373. [DOI: 10.1021/acs.analchem.8b01979] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Juan Wang
- Key Laboratory for Material Chemistry of Energy Conversion and Storage, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mengmeng Song
- Key Laboratory of Analytical Chemistry for Biology and Medicine, Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Chengguo Hu
- Key Laboratory of Analytical Chemistry for Biology and Medicine, Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Kangbing Wu
- Key Laboratory for Material Chemistry of Energy Conversion and Storage, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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12
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Zhao J, Gao J, Zheng T, Yang Z, Chai Y, Chen S, Yuan R, Xu W. Highly sensitive electrochemical assay for Nosema bombycis gene DNA PTP1 via conformational switch of DNA nanostructures regulated by H + from LAMP. Biosens Bioelectron 2018; 106:186-192. [PMID: 29427924 DOI: 10.1016/j.bios.2018.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/16/2018] [Accepted: 02/01/2018] [Indexed: 10/18/2022]
Abstract
The portable and rapid detection of biomolecules via pH meters to monitor the concentration of hydrogen ions (H+) from biological reactions (e.g. loop-mediated isothermal amplification, LAMP) has attracted research interest. However, this assay strategy suffered from inherent drawback of low sensitivity, resulting in great limitations in practical applications. Herein, a novel electrochemical biosensor was constructed for highly sensitive detection of Nosema bombycis gene DNA (PTP1) through transducing chemical stimuli H+ from PTP1-based LAMP into electrochemical output signal of electroactive ferrocene (Fc). With use of target PTP1 as the template, the H+ from LAMP induced the conformational switch of pH-responsive DNA nanostructures (DNA NSs, Fc-Sp@Ts) that was assembled by the hybridization of Fc-labeled signal probe (Fc-Sp) with DNA-based receptor (Ts). Due to the folding of Ts into stable triplex structure at decreased pH, the configuration change of Fc-Sp@Ts led to the releasing of Fc-Sp, which was subsequently immobilized in the electrode interface through the hybridization with the capture probe modified with -SH (SH-Cp), generating amplified electrochemical signal from Fc. The developed biosensor for PTP1 exhibited a reliable linear range of 1 fg µL-1 to 50 ng µL-1 with the limit of detection of 0.31 fg µL-1. Thus, by the regulation of H+ from LAMP reaction on DNA NSs allostery, this novel and simple transduction scheme would be interesting and promising to open up a novel analytical route for sensitive monitoring of different target DNAs in related disease diagnosis.
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Affiliation(s)
- Jianmin Zhao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jiaxi Gao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ting Zheng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Zhehan Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Shihong Chen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Wenju Xu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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13
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Converting pyrophosphate generated during loop mediated isothermal amplification to ATP: Application to electrochemical detection of Nosema bombycis genomic DNA PTP1. Biosens Bioelectron 2017; 102:518-524. [PMID: 29202437 DOI: 10.1016/j.bios.2017.11.066] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/21/2017] [Accepted: 11/24/2017] [Indexed: 02/08/2023]
Abstract
Traditionally, genomic DNA detection is relay on a rigorous DNA amplification process, which always accompanied with complicated gel electrophoresis or expensive fluorescence detection methods. In this work, we have translated genomic DNA detection into adenosine triphosphate (ATP) test based on a split aptamer-based electrochemical sandwich assay. The key characteristic of our method are list as follows: first, nucleic acid amplification of the target gene was performed by the use of a loop mediated isothermal amplification (LAMP) process. The pyrophosphate (PPi), which released as the byproduct during the LAMP reaction, were further converted into ATP in the presence of adenosine 5'-phosphosulfate (APS) and ATP sulfurylase. Thereafter, the converted ATP was detected by constructing an electrochemical sandwich aptasensor. With such design, the conversion from the difficult detecting target (genomic DNA) into a convenient measured object (ATP) has been achieved. This proposed strategy was highly sensitive for Nosema bombycis genomic DNA PTP1 detection with a detection limit as low as 0.47 fg/μL and a linear range from 0.001pg/μL to 50ng/μL. And we supposed that this novel target conversion electroanalytical strategy established a universal approach for quantitative analysis of any other kinds of nucleic acid in assistance of nucleic acid polymerization reaction.
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14
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Hu C, Kalsi S, Zeimpekis I, Sun K, Ashburn P, Turner C, Sutton JM, Morgan H. Ultra-fast electronic detection of antimicrobial resistance genes using isothermal amplification and Thin Film Transistor sensors. Biosens Bioelectron 2017; 96:281-287. [DOI: 10.1016/j.bios.2017.05.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/20/2017] [Accepted: 05/08/2017] [Indexed: 12/19/2022]
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15
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Ma W, Xu L, de Moura AF, Wu X, Kuang H, Xu C, Kotov NA. Chiral Inorganic Nanostructures. Chem Rev 2017; 117:8041-8093. [DOI: 10.1021/acs.chemrev.6b00755] [Citation(s) in RCA: 485] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | - André F. de Moura
- Department
of Chemistry, Federal University of São Carlos, CP 676, CEP 13.565-905, São Carlos, SP, Brazil
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16
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Safavieh M, Kanakasabapathy MK, Tarlan F, Ahmed MU, Zourob M, Asghar W, Shafiee H. Emerging Loop-Mediated Isothermal Amplification-Based Microchip and Microdevice Technologies for Nucleic Acid Detection. ACS Biomater Sci Eng 2016; 2:278-294. [PMID: 28503658 PMCID: PMC5425166 DOI: 10.1021/acsbiomaterials.5b00449] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rapid, sensitive, and selective pathogen detection is of paramount importance in infectious disease diagnosis and treatment monitoring. Currently available diagnostic assays based on polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) are time-consuming, complex, and relatively expensive, thus limiting their utility in resource-limited settings. Loop-mediated isothermal amplification (LAMP) technique has been used extensively in the development of rapid and sensitive diagnostic assays for pathogen detection and nucleic acid analysis and hold great promise for revolutionizing point-of-care molecular diagnostics. Here, we review novel LAMP-based lab-on-a-chip (LOC) diagnostic assays developed for pathogen detection over the past several years. We review various LOC platforms based on their design strategies for pathogen detection and discuss LAMP-based platforms still in development and already in the commercial pipeline. This review is intended as a guide to the use of LAMP techniques in LOC platforms for molecular diagnostics and genomic amplifications.
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Affiliation(s)
- Mohammadali Safavieh
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
| | - Manoj K. Kanakasabapathy
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
| | - Farhang Tarlan
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
| | - Minhaz U. Ahmed
- Biosensors and Biotechnology Laboratory, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, Negara Brunei Darussalam
| | - Mohammed Zourob
- Department of Chemistry, College of Science, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia
| | - Waseem Asghar
- Department of Computer Engineering & Electrical Engineering and Computer Science, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida 33431, United States
| | - Hadi Shafiee
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
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17
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Xie S, Yuan Y, Chai Y, Yuan R. Tracing Phosphate Ions Generated during Loop-Mediated Isothermal Amplification for Electrochemical Detection of Nosema bombycis Genomic DNA PTP1. Anal Chem 2015; 87:10268-74. [DOI: 10.1021/acs.analchem.5b01858] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Shunbi Xie
- State Key Laboratory of Silkworm
Genome Biology, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yali Yuan
- State Key Laboratory of Silkworm
Genome Biology, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yaqin Chai
- State Key Laboratory of Silkworm
Genome Biology, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ruo Yuan
- State Key Laboratory of Silkworm
Genome Biology, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
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18
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Xie S, Yuan Y, Song Y, Zhuo Y, Li T, Chai Y, Yuan R. Using the ubiquitous pH meter combined with a loop mediated isothermal amplification method for facile and sensitive detection of Nosema bombycis genomic DNA PTP1. Chem Commun (Camb) 2015; 50:15932-5. [PMID: 25381873 DOI: 10.1039/c4cc06449f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here we show an amplification-coupled detection method for directly measuring released hydrogen ions during the loop mediated isothermal amplification (LAMP) procedure by using a pH meter. The genomic DNA of Nosema bombycis (N. bombycis) was amplified and detected by employing this LAMP-pH meter platform for the first time.
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Affiliation(s)
- Shunbi Xie
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education (Southwest University), College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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19
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Aydemir N, McArdle H, Patel S, Whitford W, Evans CW, Travas-Sejdic J, Williams DE. A Label-Free, Sensitive, Real-Time, Semiquantitative Electrochemical Measurement Method for DNA Polymerase Amplification (ePCR). Anal Chem 2015; 87:5189-97. [PMID: 25946200 DOI: 10.1021/acs.analchem.5b00079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Oligonucleotide hybridization to a complementary sequence that is covalently attached to an electrochemically active conducting polymer (ECP) coating the working electrode of an electrochemical cell causes an increase in reaction impedance for the ferro-ferricyanide redox couple. We demonstrate the use of this effect to measure, in real time, the progress of DNA polymerase chain reaction (PCR) amplification of a minor component of a DNA extract. The forward primer is attached to the ECP. The solution contains other PCR components and the redox couple. Each cycle of amplification gives an easily measurable impedance increase. Target concentration can be estimated by cycle count to reach a threshold impedance. As proof of principle, we demonstrate an electrochemical real-time quantitative PCR (e-PCR) measurement in the total DNA extracted from chicken blood of an 844 base pair region of the mitochondrial Cytochrome c oxidase gene, present at ∼1 ppm of total DNA. We show that the detection and semiquantitation of as few as 2 copies/μL of target can be achieved within less than 10 PCR cycles.
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Affiliation(s)
| | | | - Selina Patel
- ∇School of Biological Sciences, University of Auckland, Auckland 1022, New Zealand
| | - Whitney Whitford
- ∇School of Biological Sciences, University of Auckland, Auckland 1022, New Zealand
| | - Clive W Evans
- ∇School of Biological Sciences, University of Auckland, Auckland 1022, New Zealand
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20
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Zhang F, Wang R, Wang L, Wu J, Ying Y. Tracing phosphate ions generated during DNA amplification and its simple use for visual detection of isothermal amplified products. Chem Commun (Camb) 2014; 50:14382-5. [DOI: 10.1039/c4cc06973k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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