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Chen L, Hu M, Zhou X. Trends in developing one-pot CRISPR diagnostics strategies. Trends Biotechnol 2024:S0167-7799(24)00185-9. [PMID: 39095257 DOI: 10.1016/j.tibtech.2024.07.007] [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: 04/27/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024]
Abstract
The integration of nucleic acid amplification (NAA) with the CRISPR detection system has led to significant advancements and opportunities for development in molecular diagnostics. Nevertheless, the incompatibility between CRISPR cleavage and NAA has significantly impeded the commercialization of this technology. Currently, several one-pot detection strategies based on CRISPR systems have been devised to address concerns regarding aerosol contamination risk and operational complexity associated with step-by-step detection as well as the sensitivity limitation of conventional one-pot methods. In this review, we provide a comprehensive introduction and outlook of the various solutions of the one-pot CRISPR assay for practitioners who are committed to developing better CRISPR nucleic acid detection technologies to promote the progress of molecular diagnostics.
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Affiliation(s)
- Lin Chen
- School of Life sciences, South China Normal University, Guangzhou 510631, P. R. China
| | - Menglu Hu
- School of Life sciences, South China Normal University, Guangzhou 510631, P. R. China.
| | - Xiaoming Zhou
- School of Life sciences, South China Normal University, Guangzhou 510631, P. R. China; MOE Key laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
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2
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Lin S, Zhang X, Tian A, Wang P, Li Y, Shi C, Ma C, Fan Y. Boron nitride nanoplate-based strand exchange amplification with enhanced sensitivity and rapidity for quantitative detection of Staphylococcus aureus in food samples. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:892-898. [PMID: 38247331 DOI: 10.1039/d3ay02076b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Staphylococcus aureus is one of the most common foodborne pathogens that can cause serious food poisoning and infectious diseases in humans. Standard identification approaches include nucleic acid amplification, but current amplification tools suffer from low amplification efficiency, resulting in the risk of low sensitivity and long detection time. Herein, boron nitride nanoplates (BNNPs) were chosen as an additive for enhancing the sensitivity and rapidity of strand exchange amplification (SEA), thereby successfully expanding the application of nucleic acid detection for detecting Staphylococcus aureus in food samples. As a result, SEA based on boron nitride nanoplates (BNNP-SEA) was employed for sensitive and rapid detection of foodborne pathogen Staphylococcus aureus. Compared with classical SEA, the BNNP-based SEA assay was more than 10-fold sensitive, and the detection time was reduced by 15 minutes. The optimized BNNP-based SEA shows a wide linear range from 40 pg to 50 ng in a diluted solution of the target DNA with a low detection limit of 40 pg. Moreover, the BNNP-based SEA achieves the quantitative detection of Staphylococcus aureus in different food samples (pork, beef, mutton, duck, milk and shrimp). In contrast to the classical SEA, the BNNP-based SEA method enabled sensitive and rapid detection of Staphylococcus aureus in the above food samples at concentrations as low as 5 × 103 CFU mL-1. The BNNP-based SEA assay is specific, sensitive and reliable, offering a valuable diagnostic technology for routine analysis in food safety research.
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Affiliation(s)
- Shuo Lin
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Xin Zhang
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Anning Tian
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Pengyu Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Yong Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, 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 the Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, China
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Yaofang Fan
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
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Zhao Y, Zhuang L, Tian P, Ma M, Wu G, Zhang Y. Rapid diagnosis of acute myocardial infarction based on reverse transcription-accelerated strand exchange amplification of miR-208a. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4442-4451. [PMID: 37610127 DOI: 10.1039/d3ay01116j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Acute myocardial infarction (AMI) is a prevalent cardiovascular disease associated with high morbidity and mortality, posing a significant threat to human health. Therefore, early diagnosis of AMI has become a focal point of research. MiR-208 is specifically expressed in the heart and is involved in the regulation of cardiomyocyte hypertrophy, cardiac fibrosis, and other myocardial gene expressions. It is expected to be applied in the clinical detection of AMI due to its release by damaged myocardial cells within 3 hours of AMI. In this study, we developed a denatured bubble-mediated reverse transcription-accelerated strand exchange amplification (RT-ASEA) method to detect the early biomarker miR-208a of AMI. The novel approach allowed rapid amplification of miR-208a in 15 minutes, with good performance in terms of repeatability (CV < 6%), determination limit (1 × 100 pmol L-1), and linearity (R2 = 0.9690). Based on the analysis of 42 clinical samples, a strong correlation was observed between the Ct value of miR-208a detected by the RT-ASEA method and the cTnI concentration, considered the gold standard for diagnosis of AMI. The research suggested that the RT-ASEA method could be applied to distinguish between AMI and healthy groups. The area under the receiver operating characteristic curve (AUC) was 0.9976, with a sensitivity of 96% and a specificity of 100%. Optimized RT-ASEA is a reliable and efficient method for miRNA detection. Furthermore, this study provides crucial data support for the development of miR-208a as an early biomarker for AMI, which is of great significance in life and health.
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Affiliation(s)
- Ying Zhao
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Linlin Zhuang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Peilong Tian
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Ming Ma
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, P. R. China.
| | - Yu Zhang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
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4
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Chen Q, Tu F, Chen X, Yu Y, Gu Y, Wang Y, Liu Z. Visual isothermal amplification detection of ASFV based on trimeric G-quadruplex cis-cleavage activity of Cas-12a. Anal Biochem 2023:115235. [PMID: 37422063 DOI: 10.1016/j.ab.2023.115235] [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: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023]
Abstract
African swine fever virus (ASFV) is a kind of DNA virus and can infect both domestic pigs and wild boars with fatality up to 100%. The contaminated meat products mainly led to the worldwide transmission of ASFV. The outbreak of ASF greatly affects the supply stability of meat products as well as the development of the global pig industry. In this study, a visual isothermal amplification detection assay for ASFV based on trimeric G-quadruplex cis-cleavage activity of Cas12a was developed. The introduction of Cas12a could discriminate the specific amplification from the non-specific amplification and improve the sensitivity. The detection limit was as low as 0.23 copies/μL. This assay had good potential in the detection of ASFV and would be helpful for the stability of meat production and supply.
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Affiliation(s)
- Qiming Chen
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Fangming Tu
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Xiaodi Chen
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Yang Yu
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Yimeng Gu
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Yikai Wang
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Zhanmin Liu
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
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5
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Jena S, Gaur D, Dubey NC, Tripathi BP. Advances in paper based isothermal nucleic acid amplification tests for water-related infectious diseases. Int J Biol Macromol 2023:125089. [PMID: 37245760 DOI: 10.1016/j.ijbiomac.2023.125089] [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: 02/11/2023] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 05/30/2023]
Abstract
Water-associated or water-related infectious disease outbreaks are caused by pathogens such as bacteria, viruses, and protozoa, which can be transmitted through contaminated water sources, poor sanitation practices, or insect vectors. Low- and middle-income countries bear the major burden of these infections due to inadequate hygiene and subpar laboratory facilities, making it challenging to monitor and detect infections in a timely manner. However, even developed countries are not immune to these diseases, as inadequate wastewater management and contaminated drinking water supplies can also contribute to disease outbreaks. Nucleic acid amplification tests have proven to be effective for early disease intervention and surveillance of both new and existing diseases. In recent years, paper-based diagnostic devices have made significant progress and become an essential tool in detecting and managing water-associated diseases. In this review, we highlight the importance of paper and its variants as a diagnostic tool and discuss the properties, design modifications, and various paper-based device formats developed and used for detecting water-associated pathogens.
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Affiliation(s)
- Saikrushna Jena
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Divya Gaur
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Nidhi C Dubey
- Department of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Bijay P Tripathi
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
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Zhang P, Li Y, Zhang D, Zhu X, Guo J, Ma C, Shi C. Real-time detection of SARS-CoV-2 in clinical samples via ultrafast ligation-dependent RNA transcription amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1915-1922. [PMID: 37000537 DOI: 10.1039/d3ay00093a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
RNA has been recognized as an important biomarker of many infectious pathogens; thus, sensitive, simple and rapid detection of RNA is urgently required for the control of epidemics. Herein, we report an ultrafast ligation-dependent RNA transcription amplification assay with high sensitivity and specificity for real-time detection of SARS-CoV-2 in real clinical samples, termed splint-based cascade transcription amplification (SCAN). Target RNA is first recognized by two DNA probes, which are then ligated together by SplintR, followed by the binding of the T7 promotor and T7 RNA polymerase to the ligated probe and the start of the transcription process. By introducing a vesicular stomatitis virus (VSV) terminator in the ligated probe, large amounts of RNA transcripts are rapidly produced within 10 min, which then directly hybridize with molecular beacons (MBs) and trigger the conformational switch of the MBs to generate a fluorescence signal that can be monitored in real time. The SCAN assay, which can be completed within 30-50 min, has a limit of detection of 104 copies per mL, while exhibiting high specificity to distinguish the target pathogen from those causing similar syndromes. More importantly, the results of SCAN for SARS-CoV-2 detection in clinical samples display great agreement with the most used qRT-PCR and qRT-LAMP, indicating great potential in the diagnosis of pathogens in clinical practice.
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Affiliation(s)
- Peng Zhang
- 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.
| | - Dongmei Zhang
- Qingdao Special Servicemen Recuperation Center of PLA Navy, Qingdao, 266071, PR China
| | - Xinghao Zhu
- 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.
| | - Jinling Guo
- 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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7
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Wang Y, Zhang L, Shen Y, Yu EYW, Ding X. Nested Phosphorothioated Hybrid Primer-Mediated Isothermal Amplification for Specific and Dye-Based Subattomolar Nucleic Acid Detection at Low Temperatures. ACS Sens 2023; 8:1261-1271. [PMID: 36867102 DOI: 10.1021/acssensors.2c02754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Developing dye-based isothermal nucleic acid amplification (INAA) at low temperatures such as 37 °C remains a technical challenge. Here, we describe a nested phosphorothioated (PS) hybrid primer-mediated isothermal amplification (NPSA) assay which only utilizes EvaGreen (a DNA-binding dye) to achieve specific and dye-based subattomolar nucleic acid detection at 37 °C. The success of low-temperature NPSA essentially depends on employing Bacillus smithii DNA polymerase, a strand-displacing DNA polymerase with wide range of activation temperature. However, the NPSA's high efficiency entails nested PS-modified hybrid primers and the additives of urea and T4 Gene 32 Protein. To address the inhibition of urea on reverse transcription (RT), one-tube two-stage recombinase-aided RT-NPSA (rRT-NPSA) is established. By targeting human Kirsten rat sarcoma viral (KRAS) oncogene, NPSA (rRT-NPSA) stably detects 0.2 aM of KRAS gene (mRNA) within 90 (60) min. In addition, rRT-NPSA possesses subattomolar sensitivity to detect human ribosomal protein L13 mRNA. The NPSA/rRT-NPSA assays are also validated to obtain consistent results with PCR/RT-PCR methods on qualitatively detecting DNA/mRNA targets extracted from cultured cells and clinical samples. As a dye-based, low-temperature INAA method, NPSA inherently facilitates the development of miniaturized diagnostic biosensors.
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Affiliation(s)
- Yaru Wang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
- Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China
| | - Lanxiang Zhang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
- Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China
| | - Yuqing Shen
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
- Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China
| | - Evan Yi-Wen Yu
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
- Department of Epidemiology & Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Xiong Ding
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
- Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China
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Gou H, Lin Q, Shen H, Jia K, Liang Y, Peng J, Zhang C, Qu X, Li Y, Lin J, Zhang J, Liao M. A novel linear displacement isothermal amplification with strand displacement probes (LDIA-SD) in a pocket-size device for point-of-care testing of infectious diseases. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 379:133244. [PMID: 36589905 PMCID: PMC9789534 DOI: 10.1016/j.snb.2022.133244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Nucleic acid amplification is crucial for disease diagnosis, especially lethal infectious diseases such as COVID-19. Compared with PCR, isothermal amplification methods are advantageous for point-of-care testing (POCT). However, complicated primer design limits their application in detecting some short targets or sequences with abnormal GC content. Herein, we developed a novel linear displacement isothermal amplification (LDIA) method using two pairs of conventional primers and Bacillus stearothermophilus (Bst) DNA polymerase, and reactions could be accelerated by adding an extra primer. Pseudorabies virus gE (high GC content) and Salmonella fimW (low GC content) genes were used to evaluate the LDIA assay. Using strand displacement (SD) probes, a LDIA-SD method was developed to realize probe-based specific detection. Additionally, we incorporated a nucleic acid-free extraction step and a pocket-sized device to realize POCT applications of the LDIA-SD method. The LDIA-SD method has advantages including facile primer design, high sensitivity and specificity, and applicability for POCT, especially for amplification of complex sequences and detection of infectious diseases.
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Affiliation(s)
- Hongchao Gou
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Qijie Lin
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Haiyan Shen
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Kaiyuan Jia
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yucen Liang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Junhao Peng
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Chunhong Zhang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Xiaoyun Qu
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yanbin Li
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jianhan Lin
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Jianmin Zhang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Ming Liao
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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9
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Chen Y, Sha L, Li W, Zhou L, Pei B, Bian X, Ji Y, Liu Y, Wang L, Yang H. Rapid quantitative detection of Klebsiella pneumoniae in infants with severe infection disease by point-of-care immunochromatographic technique based on nanofluorescent microspheres. Front Bioeng Biotechnol 2023; 11:1144463. [PMID: 36845192 PMCID: PMC9945336 DOI: 10.3389/fbioe.2023.1144463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
Background: Klebsiella pneumoniae (KP, K. pneumoniae) is one of the most important nosocomial pathogens that cause severe respiratory infections. As evolutionary high-toxic strains with drug resistance genes increase year by year, the infections caused by it are often accompanied by high mortality, which may be fatal to infants and can cause invasive infections in healthy adults. At present, the traditional clinical methods for detecting K. pneumoniae are cumbersome and time-consuming, and the accuracy and sensitivity are not high. In this study, nanofluorescent microsphere (nFM)-based immunochromatographic test strip (ICTS) quantitative testing platform were developed for point-of-care testing (POCT) method of K. pneumoniae. Methods: 19 clinical samples of infants were collected, the genus-specific gene of mdh was screened from K. pneumoniae. Polymerase chain reaction (PCR) combined with nFM-ICTS based on magnetic purification assay (PCR-ICTS) and strand exchange amplification (SEA) combined with nFM-ICTS based on magnetic purification assay (SEA-ICTS) were developed for the quantitative detection of K. pneumoniae. The sensitivity and specificity of SEA-ICTS and PCR-ICTS were demonstrated by the existing used classical microbiological methods, the real-time fluorescent quantitative PCR (RTFQ-PCR) and PCR assay based on agarose gel electrophoresis (PCR-GE). Results: Under optimum working conditions, the detection limits of PCR-GE, RTFQ-PCR, PCR-ICTS and SEA-ICTS are 7.7 × 10-3, 2.5 × 10-6, 7.7 × 10-6, 2.82 × 10-7 ng/μL, respectively. The SEA-ICTS and PCR-ICTS assays can quickly identify K. pneumoniae, and could specifically distinguish K. pneumoniae samples from non-K. pneumoniae samples. Experiments have shown a diagnostic agreement of 100% between immunochromatographic test strip methods and the traditional clinical methods on the detection of clinical samples. During the purification process, the Silicon coated magnetic nanoparticles (Si-MNPs) were used to removed false positive results effectively from the products, which showed of great screening ability. The SEA-ICTS method was developed based on PCR-ICTS, which is a more rapid (20 min), low-costed method compared with PCR-ICTS assay for the detection of K. pneumoniae in infants. Only need a cheap thermostatic water bath and takes a short detection time, this new method can potentially serve as an efficient point-of-care testing method for on-site detection of pathogens and disease outbreaks without fluorescent polymerase chain reaction instruments and professional technicians operation.
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Affiliation(s)
- Ying Chen
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Lulu Sha
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Wenqing Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Liuyan Zhou
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Bing Pei
- Department of Clinical Laboratory, Suqian First People’s Hospital, Suqian, China
| | - Xinyu Bian
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Yongxin Ji
- Nanjing Nanoeast Biotech Co., Ltd., Nanjing, China
| | - Yiping Liu
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Li Wang
- Department of Clinical Laboratory, Xuzhou First People’s Hospital, Xuzhou, China,*Correspondence: Li Wang, ; Huan Yang,
| | - Huan Yang
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China,*Correspondence: Li Wang, ; Huan Yang,
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10
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Duan Y, Zhang X, Li Y, Zhao X, Zhao X, Chen L, Shi C, Ma C, Wang X. Amino-modified silica membrane capable of DNA extraction and enrichment for facilitated isothermal amplification detection of Mycoplasma pneumoniae. J Pharm Biomed Anal 2023; 224:115190. [PMID: 36463769 DOI: 10.1016/j.jpba.2022.115190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 11/29/2022]
Abstract
Herein, we developed a facile integrated Mycoplasma pneumoniae diagnosis platform by combining amino-modified silica membrane (AMSM)-based nucleic acids fast extraction and enrichment with colorimetric isothermal amplification detection. AMSM demonstrates a strong ability to capture and enrich nucleic acids in complicated biological matrices, and the purified AMSM/nucleic acids composite could be directly used to perform isothermal amplification including denaturation bubble-mediated strand exchange amplification (SEA) and loop-mediated isothermal amplification (LAMP) reactions. Through comparing clinical specimens, excellent performance of AMSM-based SEA assay with 93.33% sensitivity and 100% specificity relative to real-time PCR was observed, and for AMSM-based LAMP was 96.67% and 100%, respectively. The diagnostic procedure could be completed within 55 min, and the colorimetric-based visual result further alleviates the use of sophisticated equipment. The proposed approach possesses great potential as a simple and time-saving alternative for point-of-care testing (POCT) of M. pneumoniae in resource-limited regions.
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Affiliation(s)
- Yake Duan
- 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
| | - Xin Zhang
- 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
| | - Yong Li
- 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
| | - Xiaoli Zhao
- 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
| | - Xiaowen Zhao
- Core Laboratory, The Affiliated Qingdao Central Hospital of Qingdao University, Qingdao 266042, PR China
| | - Lei Chen
- Department of Laboratory Medicine, The Second People's Hospital of Weifang, Weifang 261041, 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, and 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
| | - Xiujuan Wang
- 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.
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11
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Sun R, Chen J, Wang Y, Zhang Z, Li Y, Li F, Ma C, Han Q, Shi Y. Rapid, specific and sensitive detection of Vibrio parahaemolyticus in seafood by accelerated strand exchange amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:655-662. [PMID: 36655424 DOI: 10.1039/d2ay01889f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Vibrio parahaemolyticus infectious diseases caused by seafood contamination may be life-threatening to people with weak immunity. The detection of the Vibrio parahaemolyticus pathogen in aquatic foods is critical for reducing the outbreak of human Vibrio parahaemolyticus-associated diseases. In this study, a highly sensitive, specific, and time-saving real-time narrow thermal-cycling amplification detection method was developed based on accelerated strand exchange amplification (ASEA). It can detect cultured Vibrio parahaemolyticus at concentrations as low as 25 CFU mL-1. In addition, for artificially spiked scallop meat, the detection limit was 1.8 × 103 CFU g-1 without pre-culture and 18 CFU g-1 of initial inoculum after 3 h enrichment. The whole assay, starting from DNA extraction, can be completed within 20 min. The ASEA detection method established in this study is an effective tool for the rapid detection of Vibrio parahaemolyticus strains in a large number of seafood samples.
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Affiliation(s)
- Ritong Sun
- 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.
| | - Jiao Chen
- 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.
| | - Yingeng Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, PR China
| | - Zheng Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, PR China
| | - Yong Li
- 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.
| | - Fengmei Li
- 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.
| | - 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.
| | - Qingxia Han
- Bin Zhou Polytechnic, Qingdao, 256600, PR China
| | - Yanjing Shi
- 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.
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12
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Wang Y, Chen Q, Wang Y, Chen X, Tu F, Li J, Liu Z. A visual denaturation bubble-mediated strand exchange amplification and RGB visual analysis-based assay for quantitative detection of Helicobacter pylori in saliva. ANAL SCI 2023; 39:483-491. [PMID: 36729320 DOI: 10.1007/s44211-022-00251-y] [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: 10/14/2022] [Accepted: 12/14/2022] [Indexed: 02/03/2023]
Abstract
Helicobacter pylori (H. pylori) is a class I carcinogen causing gastric cancer. Almost 50% of people on earth have been infected and it is worse in developing countries. Early diagnosis of H. pylori infection is the most important strategy for preventing the spread and worse consequences. H. pylori can be isolated from human saliva, and the sampling of saliva is easy and convenient. Therefore, we developed a visual denaturation bubble-mediated strand exchange amplification and RGB visual analysis-based assay for quantitative detection of H. pylori in saliva in this study. Under the optimized reaction temperature and time, the SEA reaction could be finished in 30 min with a simple reaction system and low dependency on equipment. The detection results could be qualitatively identified by the naked eye and quantitatively analyzed by a developed RGB visual analysis method. The limit of detection (LOD) of RGB visual analysis was 10.8 CFU/mL. This assay had good specificity and anti-interference capacity. In the artificial contamination test, the recovery rate of our assay was between 99.3% and 111.5%, with RSD values ranging from 1.7% to 3.5%. These indicated our assay also had good reliability in the detection of saliva. We believe this assay showed good potential for better non-invasive diagnosis of H. pylori infection.
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Affiliation(s)
- Yingying Wang
- School of Life Sciences, Shanghai University, 381 Nanchen Rd, Shanghai, 200444, China
| | - Qiming Chen
- School of Life Sciences, Shanghai University, 381 Nanchen Rd, Shanghai, 200444, China
| | - Yilu Wang
- School of Life Sciences, Shanghai University, 381 Nanchen Rd, Shanghai, 200444, China
| | - Xiaodi Chen
- School of Life Sciences, Shanghai University, 381 Nanchen Rd, Shanghai, 200444, China
| | - Fangmin Tu
- School of Life Sciences, Shanghai University, 381 Nanchen Rd, Shanghai, 200444, China
| | - Junhai Li
- Department of Oncology, No. 215 Hospital of Shaanxi Nuclear Industry, Shaanxi Province, 35 West Weiyang Rd, Xianyang City, 712000, China.
| | - Zhanmin Liu
- School of Life Sciences, Shanghai University, 381 Nanchen Rd, Shanghai, 200444, China.
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13
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Zhuang L, Gong J, Shen Q, Yang J, Zhang D, Zhang P, Xie H, Hao P, Zhang Y, Zhu M. Graphene oxide-assisted optimized narrow-thermal-cycling amplification for accurate detection of Salmonella spp. ANAL SCI 2023; 39:191-202. [PMID: 36357755 DOI: 10.1007/s44211-022-00213-4] [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: 09/02/2022] [Accepted: 11/02/2022] [Indexed: 11/12/2022]
Abstract
Salmonella is a rod-shaped, Gram-negative zoonotic pathogen that poses a serious global socioeconomic and public health threat. Rapid and accurate detection of Salmonella spp. is critical for effective control of its infection. In this study, an accurate, sensitive and specific graphene oxide-assisted accelerated strand exchange amplification (GO-ASEA) method for rapid detection of Salmonella spp. was developed and validated. The detection limit of the GO-ASEA method was 8.6 × 101 fg μL-1 of Salmonella genomic DNA or 1 × 101 CFU g-1 of Salmonella in spiked chicken faeces free of pre-enrichment. And the GO-ASEA method could specifically detect Salmonella spp. without cross-reactivity with other enteric pathogens. In addition, the novel method achieved Salmonella detection within 30 min and was validated using 209 clinical samples, showing its good clinical applicability. Therefore, the GO-ASEA method is a new optional tool for the rapid detection of pathogenic microorganisms, which is ideal for food safety monitoring and high-throughput detection.
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Affiliation(s)
- Linlin Zhuang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, 212400, Jurong, People's Republic of China.,State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, 210096, Nanjing, People's Republic of China
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, 225125, Yangzhou, People's Republic of China
| | - Qiuping Shen
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, 212400, Jurong, People's Republic of China
| | - Jianbo Yang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, 212400, Jurong, People's Republic of China
| | - Di Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, 225125, Yangzhou, People's Republic of China
| | - Ping Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, 225125, Yangzhou, People's Republic of China
| | - Haiqiang Xie
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, 212400, Jurong, People's Republic of China
| | - Pan Hao
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, 212400, Jurong, People's Republic of China
| | - Yu Zhang
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, 210096, Nanjing, People's Republic of China.
| | - Mengling Zhu
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, 212400, Jurong, People's Republic of China.
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14
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Cao X, Chen C, Zhu Q. Biosensors based on functional nucleic acids and isothermal amplification techniques. Talanta 2023; 253:123977. [PMID: 36201957 DOI: 10.1016/j.talanta.2022.123977] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 12/13/2022]
Abstract
In the past few years, with the in-depth research of functional nucleic acids and isothermal amplification techniques, their applications in the field of biosensing have attracted great interest. Since functional nucleic acids have excellent flexibility and convenience in their structural design, they have significant advantages as recognition elements in biosensing. At the same time, isothermal amplification techniques have higher amplification efficiency, so the combination of functional nucleic acids and isothermal amplification techniques can greatly promote the widespread application of biosensors. For the purpose of further improving the performance of biosensors, this review introduces several widely used functional nucleic acids and isothermal amplification techniques, as well as their classification, basic principles, application characteristics, and summarizes their important applications in the field of biosensing. We hope to provide some references for the design and construction of new tactics to enhance the detection sensitivity and detection range of biosensing.
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Affiliation(s)
- Xiuen Cao
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
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15
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Li Y, Gao Y, Ling N, Shen Y, Zhang D, Ou D, Zhang X, Jiao R, Zhu C, Ye Y. Rapid and simple quantitative identification of Listeria monocytogenes in cheese by isothermal sequence exchange amplification based on surface-enhanced Raman spectroscopy. J Dairy Sci 2022; 105:9450-9462. [DOI: 10.3168/jds.2022-22181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022]
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16
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An all-in-one nucleic acid enrichment and isothermal amplification platform for rapid detection of Listeria monocytogenes. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109096] [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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17
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Botella JR. Point-of-Care DNA Amplification for Disease Diagnosis and Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:1-20. [PMID: 36027938 DOI: 10.1146/annurev-phyto-021621-115027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.
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Affiliation(s)
- José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia;
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18
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Qin P, Li Y, Yao B, Zhu Y, Xu J, Yao L, Chen W. Rational incorporating of loop-mediated isothermal amplification with fluorescence anisotropy for rapid, sensitive and on-site identification of pork adulteration. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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Zhuang L, Yang J, Song C, Sun L, Zhao B, Shen Q, Ren X, Shi H, Zhang Y, Zhu M. Accurate, rapid and highly sensitive detection of African swine fever virus via graphene oxide-based accelerated strand exchange amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:2072-2082. [PMID: 35546107 DOI: 10.1039/d2ay00610c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
African swine fever is an acute, severe and highly contagious infectious disease caused by African swine fever virus (ASFV), posing a huge threat to the global swine industry. Rapid and accurate diagnostic methods are of great significance for the effective prevention and control of ASFV transmission. In this work, we established and evaluated a graphene oxide-based accelerated strand exchange amplification (GO-ASEA) method for rapid, highly sensitive, and quantitative detection of ASFV. The use of GO provided a novel solution reference for improving the specificity of strand exchange amplification and solving the potential false positive problem caused by primer dimers. The detection limit of the GO-ASEA assay was 5.8 × 10-1 copies per μL of ASFV (equal to 2.9 copies per reaction) or 5.8 × 100 copies per μL of ASFV in spiked swine nasal swabs. The selectivity of the GO-ASEA assay was supported by the ASFV DNA reference material and another seven porcine-derived viruses with similar clinical symptoms. The GO-ASEA assay took only about 29 minutes and was validated with 6 inactivated specimens and 52 swine nasal swabs, showing excellent clinical applicability. The novel assay is an accurate and practical method for rapid, highly sensitive detection of ASFV, and can potentially serve as a robust tool in epidemic prevention and point-of-care diagnosis.
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Affiliation(s)
- Linlin Zhuang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Jianbo Yang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Chunlei Song
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Li Sun
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Bin Zhao
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Qiuping Shen
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Xiyan Ren
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Hongjing Shi
- Yangzhou Jianong Animal Husbandry Technology Co., Ltd, Yangzhou 225251, P. R. China
| | - Yu Zhang
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Mengling Zhu
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
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20
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Xia X, Yang H, Cao J, Zhang J, He Q, Deng R. Isothermal nucleic acid amplification for food safety analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116641] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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21
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Zhao X, Zhang J, Duan Y, Wan Q, Zhang X, Chen J, Shi C, Gao Y, Ma C. An ultra-fast, one-step RNA amplification method for the detection of Salmonella in seafood. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1111-1116. [PMID: 35212687 DOI: 10.1039/d1ay02056k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Salmonella is one of the most common pathogens associated with food-borne illness resulting from seafood consumption. Herein, an accelerated strand exchange amplification (ASEA) requiring only a pair of primers and one polymerase was first reported for ultra-fast, one-step RNA amplification detection of Salmonella in seafood. The ASEA method could detect Salmonella typhimurium DNA in dilutions as low as 10 copies per reaction and displayed good specificity for Salmonella under the interference of a variety of food-borne pathogens. In particular, ASEA could detect RNA in one step without additional reverse transcription. The detection limit for Salmonella in artificially contaminated oyster was 1 CFU mL-1 following 12 h of enrichment. Moreover, excellent performance of this assay was observed with 99.02% consistency relative to real-time PCR through actual sample detection. Combined with the rapid nucleic acid extraction method, the entire detection process could be completed within 20 min. Therefore, this assay opens up new prospects for the detection of food-borne pathogens in seafood with its rapidity, which would be very beneficial for food safety supervision and pathogen detection of high-throughput samples.
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Affiliation(s)
- Xiaoli Zhao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, College of Chemistry, Molecular Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Jian Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, College of Chemistry, Molecular Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Yake Duan
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, College of Chemistry, Molecular Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Qianyi Wan
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, College of Chemistry, Molecular Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Xin Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, College of Chemistry, Molecular Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Jiao Chen
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, College of Chemistry, Molecular Engineering, 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, The Clinical Laboratory Department of the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, PR China
| | - Yan Gao
- Marine Science Research Institute of Shandong Provice (National Oceanographic Center of Qingdao), Qingdao 266071, China
| | - Cuiping Ma
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, College of Chemistry, Molecular Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
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22
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Signal-enhanced visual strand exchange amplification detection of African swine fever virus by the introduction of multimeric G-quadruplex/hemin DNAzyme. ANAL SCI 2022; 38:675-682. [DOI: 10.1007/s44211-022-00087-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/11/2022] [Indexed: 01/11/2023]
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23
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Ye X, Wang N, Li Y, Fang X, Kong J. A high-specificity flap probe-based isothermal nucleic acid amplification method based on recombinant FEN1-Bst DNA polymerase. Biosens Bioelectron 2021; 192:113503. [PMID: 34303138 PMCID: PMC8280370 DOI: 10.1016/j.bios.2021.113503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/29/2021] [Accepted: 07/12/2021] [Indexed: 01/02/2023]
Abstract
The COVID-19 pandemic has unfortunately demonstrated how easily infectious diseases can spread and harm human life and society. As of writing, pandemic has now been on-going for more than one year. There is an urgent need for new nucleic acid-based methods that can be used to diagnose pathogens early, quickly, and accurately to effectively impede the spread of infections and gain control of epidemics. We developed a flap probe-based isothermal nucleic acid amplification method that is triggered by recombinant FEN1-Bst DNA polymerase, which-through enzymatic engineering-has both DNA synthesis, strand displacement and cleavage functions. This novel method offers a simpler and more specific probe-primer pair than those of other isothermal amplifications. We tested the method's ability to detect SARS-CoV-2 (both ORF1ab and N genes), rotavirus, and Chlamydia trachomatis. The limits of detection were 10 copies/μL for rotavirus, C. trachomatis, and SARS-CoV-2 N gene, and 100 copies/μL for SARS-CoV-2 ORF1ab gene. There were no cross-reactions among 11 other common pathogens with characteristics similar to those of the test target, and the method showed 100% sensitivity and 100% specificity in clinical comparisons with RT-PCR testing. In addition to real-time detection, the endpoint could be displayed under a transilluminator, which is a convenient reporting method for point-of-care test settings. Therefore, this novel nucleic acid senor has great potential for use in clinical diagnostics, epidemic prevention, and epidemic control.
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Affiliation(s)
- Xin Ye
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Ning Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yang Li
- Shanghai Suxin Biotechnology Co. Ltd., Shanghai, 201318, PR China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
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24
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Zhuang L, Gong J, Ma M, Ji Y, Tian P, Mei X, Gu N, Zhang Y. Tri-primer-enhanced strand exchange amplification combined with rapid lateral flow fluorescence immunoassay to detect SARS-CoV-2. Analyst 2021; 146:6650-6664. [PMID: 34610060 DOI: 10.1039/d1an00858g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The novel coronavirus disease 2019 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been surging rapidly around the world, which has exposed humanity to unprecedented economic, social and health impacts. To achieve efficient and accurate detection of SARS-CoV-2 on site, we developed and verified a rapid and sensitive fluorescence lateral flow immunoassay based on the innovative enhanced strand exchange amplification (ESEA-LFIA) in this study. With good amplification efficiency for short-sequence targets, ESEA is an ideal choice for the point-of-care testing of SARS-CoV-2 with a high mutation rate. ESEA reaction can be completed in one step and verified by restriction enzyme digestion. The design consisting of three working primers greatly improved the amplification efficiency. Amplification of the target sequences of the RdRP and N genes can be accomplished under the same reaction conditions, and does not require expensive instruments. The sensitivity of the ESEA-LFIA assay targeting the RdRP and N genes was 90 copies per μL and 70 copies per μL, respectively. Specificity tests showed that the novel assay can specifically detect SARS-CoV-2, and had no cross-reactivity with 9 closely-related human pathogenic coronaviruses and other common respiratory pathogens with similar clinical manifestations. The cutoff values of the RdRP and N gene assays are 11 and 12, respectively, and the assays can be completed within 1 h. The novel strategy proposed in this study is a sensitive and specific method for the rapid detection of SARS-CoV-2, and is suitable as an effective potential bioanalytical tool to respond to future regional or global outbreaks of emerging infectious pathogens with high mutation rates.
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Affiliation(s)
- Linlin Zhuang
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, P. R. China
| | - Ming Ma
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Yongxin Ji
- Nanjing Nanoeast Biotech Co., Ltd, Nanjing 211000, P. R. China
| | - Peilong Tian
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Xiuming Mei
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China. .,Nanjing Product Quality Supervision and Inspection Institute, Nanjing 210019, P. R. China
| | - Ning Gu
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Yu Zhang
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
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Shi Y, Ye P, Yang K, Meng J, Guo J, Pan Z, Zhao W, Guo J. Application of centrifugal microfluidics in immunoassay, biochemical analysis and molecular diagnosis. Analyst 2021; 146:5800-5821. [PMID: 34570846 DOI: 10.1039/d1an00629k] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Rapid diagnosis plays a vital role in daily life and is effective in reducing treatment costs and increasing curability, especially in remote areas with limited availability of resources. Among the various common methods of rapid diagnosis, centrifugal microfluidics has many unique advantages, such as less sample consumption, more precise valve control for sequential loading of samples, and accurately separated module design in a microfluidic network to minimize cross-contamination. Therefore, in recent years, centrifugal microfluidics has been extensively researched, and it has been found to play important roles in biology, chemistry, and medicine. Here, we review the latest developments in centrifugal microfluidic platforms in immunoassays, biochemical analyses, and molecular diagnosis, in recent years. In immunoassays, we focus on the application of enzyme-linked immunosorbent assay (ELISA); in biochemical analysis, we introduce the application of plasma and blood cell separation; and in molecular diagnosis, we highlight the application of nucleic acid amplification tests. Additionally, we discuss the characteristics of the methods under each platform as well as the enhancement of the corresponding performance parameters, such as the limit of detection, separation efficiency, etc. Finally, we discuss the limitations associated with the existing applications and potential breakthroughs that can be achieved in this field in the future.
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Affiliation(s)
- Yuxing Shi
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Peng Ye
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Kuojun Yang
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Jie Meng
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Jiuchuan Guo
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Zhixiang Pan
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Wenhao Zhao
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Jinhong Guo
- School of Information and Communication Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China.
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Gao Y, Ye Y, Xu J, Wu Q, Yao B, Chen W. Rapid and easy quantitative identification of Cronobacter spp. in infant formula milk powder by isothermal strand-exchange-amplification based molecular capturing lateral flow strip. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Yakushevich LV, Krasnobaeva LA. Ideas and methods of nonlinear mathematics and theoretical physics in DNA science: the McLaughlin-Scott equation and its application to study the DNA open state dynamics. Biophys Rev 2021; 13:315-338. [PMID: 34178171 PMCID: PMC8214655 DOI: 10.1007/s12551-021-00801-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/22/2021] [Indexed: 12/11/2022] Open
Abstract
The review is devoted to a new and rapidly developing area related to the application of ideas and methods of nonlinear mathematics and theoretical physics to study the internal dynamics of DNA and, in particular, the behavior of the open states of DNA. There are two main competing approaches to this research. The first approach is based on the molecular dynamics method, which takes into account the motions of all structural elements of the DNA molecule and all interactions between them. The second approach is based on prior selection of the main (dominant) motions and their mathematical description using a small number of model equations. This review describes the results of the study of the open states of DNA performed within the framework of the second approach using the McLaughlin-Scott equation. We present the results obtained both in the case of homogeneous sequences: poly (A), poly (T), poly (G) and poly (C), and in the inhomogeneous case when the McLaughlin-Scott equation has been used for studying the dynamics of open states activated in the promoters A1, A2 and A3 of the bacteriophage T7 genome, in the genes IFNA17, ADRB2, NOS1 and IL-5, in the pBR322 and pTTQ18 plasmids. Particular attention is paid to the results concerning the effect of various external fields on the behavior of open states. In the concluding part of the review, new possibilities and prospects for the development of the considered approach and especially of the McLaughlin-Scott equation are discussed. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12551-021-00801-0.
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Affiliation(s)
- Ludmila V. Yakushevich
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Larisa A. Krasnobaeva
- Siberian State Medical University, Tomsk, Russia
- Tomsk State University, Tomsk, Russia
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Zheng C, Wang K, Zheng W, Cheng Y, Li T, Cao B, Jin Q, Cui D. Rapid developments in lateral flow immunoassay for nucleic acid detection. Analyst 2021; 146:1514-1528. [PMID: 33595550 DOI: 10.1039/d0an02150d] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, lateral flow assay (LFA) for nucleic acid detection has drawn increasing attention in the point-of-care testing fields. Due to its rapidity, easy implementation, and low equipment requirement, it is well suited for use in rapid diagnosis, food authentication, and environmental monitoring under source-limited conditions. This review will discuss two main research directions of lateral flow nucleic acid tests. The first one is the incorporation of isothermal amplification methods with LFA, which ensures an ultra-high testing sensitivity under non-laboratory conditions. The two most commonly used methodologies will be discussed, namely Loop-mediated Isothermal Amplification (LAMP) and Recombinase Polymerase Amplification (RPA), and some novel methods with special properties will also be introduced. The second research direction is the development of novel labeling materials. It endeavors to increase the sensitivity and quantifiability of LFA testing, where signals can be read and analyzed by portable devices. These methods are compared in terms of limits of detection, detection times, and quantifiabilities. It is anticipated that future research on lateral flow nucleic acid tests will focus on the integration of the whole testing process into a microfluidic system and the combination with molecular diagnostic tools such as clustered regularly interspaced short palindromic repeats to facilitate a rapid and accurate test.
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Affiliation(s)
- Chujun Zheng
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai Engineering Research Center for Intelligent diagnosis and treatment instrument, Key Laboratory of Thin Film and Microfabrication Technology (Ministry of Education), Shanghai 200240, China.
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29
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Lan L, Huang J, Liu M, Yin Y, Wei C, Cai Q, Meng X. Polymerization and isomerization cyclic amplification for nucleic acid detection with attomolar sensitivity. Chem Sci 2021; 12:4509-4518. [PMID: 34163716 PMCID: PMC8179492 DOI: 10.1039/d0sc05457g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/11/2020] [Indexed: 12/25/2022] Open
Abstract
DNA amplification is one of the most valuable tools for the clinical diagnosis of nucleic acid-related diseases, but current techniques for DNA amplification are based on intermolecular polymerization reactions, resulting in the risk of errors in the intermolecular reaction pattern. In this article, we introduce the concept of intramolecular polymerization and isomerization cyclic amplification (PICA), which extends a short DNA strand to a long strand containing periodic repeats of a sequence through cyclic alternating polymerization and isomerization. To the best of our knowledge, this is the first time that a real ssDNA self-extension method without any additional auxiliary oligonucleotides has been reported. By interfacing PICA with external molecular elements, it can be programmed to respond to different targets. Herein, we designed two distinct types of amplified nucleic acid detection platforms that can be implemented with PICA, including cyclic reverse transcription (CRT) and cyclic replication (CR). We experimentally demonstrate the mechanisms of CRT-PICA and CR-PICA using mammalian miRNA and virus DNA. The results showed that this proposed detection platform has excellent sensitivity, selectivity, and reliability. The detection level could reach the aM level, that is, several copies of target molecules can be detected if a small volume is taken into account.
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Affiliation(s)
- Lin Lan
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Jin Huang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Mengtan Liu
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Yao Yin
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Can Wei
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Qinyun Cai
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Xiangxian Meng
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
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Wang H, Wang X, Zhao M, Shi C, Ma C. Ratiometric Electrochemical Biosensor for the Sensitive Determination of DNA by a Hairpin DNA Probe. ANAL LETT 2021. [DOI: 10.1080/00032719.2020.1871001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Haixia Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, 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, China
| | - Xuejiao Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, 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, China
| | - Mingyuan Zhao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, 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, 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, and Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Cuiping Ma
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, 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, China
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Hou J, Li Y, Ma C, Shi C. Accelerated denaturation bubble-mediated strand exchange amplification for rapid and accurate detection of canine parvovirus. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:5514-5522. [PMID: 33164005 DOI: 10.1039/d0ay01751e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Canine parvovirus (CPV), a strong infectious canine pathogen, has been recognized as a threat to canine health worldwide since the 1970s. Although convenient detection methods have been developed, such as the colloidal gold test strip, most of these methods are based on antibody detection, which is relatively ineffective for detecting pathogens during the incubation period. For institutions and businesses with many dogs, e.g., dog training centers and kennels, more sensitive detection methods are required to prevent the swift spread of CPV. Thus, we developed accelerated denaturation bubble-mediated strand exchange amplification (ASEA) for CPV detection, and it is a rapid, convenient, and cost-effective method. ASEA was able to distinguish CPV genomic DNA in a mixture that included canine genomic DNA as well as nucleic acids sourced from nine other common pathogens, with detection of target DNA as low as 8.0 × 10-18 M within 16.6 min. Coupled with the thermal lysis method modified by us that only requires 3 min to perform, the entire detection procedure can be completed within approximately 20 min and only requires a simple heating block and an ordinary fluorescence PCR instrument. Moreover, ASEA exhibited greater sensitivity than colloidal gold test strips in actual specimen detection. This technique is rapid, easy to perform, and highly sensitive, and therefore, this approach has the potential to rapidly detect CPV in institutions with large populations of dogs.
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Affiliation(s)
- Jie Hou
- 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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32
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A novel isothermal detection method for the universal element of genetically modified soybean. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00541-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Accurate, rapid and low-cost diagnosis of Mycoplasma pneumoniae via fast narrow-thermal-cycling denaturation bubble-mediated strand exchange amplification. Anal Bioanal Chem 2020; 412:8391-8399. [PMID: 33040157 PMCID: PMC7548028 DOI: 10.1007/s00216-020-02977-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/12/2022]
Abstract
Mycoplasma pneumoniae is a strong infectious pathogen that may cause severe respiratory infections. Since this pathogen may possess a latent period after infection, which sometimes leads to misdiagnosis by traditional diagnosis methods, the establishment of a rapid and sensitive diagnostic method is crucial for transmission prevention and timely treatment. Herein, a novel detection method was established for M. pneumoniae detection. The method, which improves upon a denaturation bubble-mediated strand exchange amplification (SEA) that we developed in 2016, is called accelerated SEA (ASEA). The established ASEA achieved detection of 1% M. pneumoniae genomic DNA in a DNA mixture from multiple pathogens, and the limit of detection (LOD) of ASEA was as low as 1.0 × 10-17 M (approximately 6.0 × 103 copies/mL). Considering that the threshold of an asymptomatic carriage is normally recommended as 1.0 × 104 copies/mL, this method was able to satisfy the requirement for practical diagnosis of M. pneumoniae. Moreover, the detection process was finished within 20.4 min, significantly shorter than real-time PCR and SEA. Furthermore, ASEA exhibited excellent performance in clinical specimen analysis, with sensitivity and specificity of 96.2% and 100%, respectively, compared with the "gold standard" real-time PCR. More importantly, similar to real-time PCR, ASEA requires only one pair of primers and ordinary commercial polymerase, and can be carried out using a conventional fluorescence real-time PCR instrument, which makes this method low-cost and easy to accomplish. Therefore, ASEA has the potential for wide use in the rapid detection of M. pneumoniae or other pathogens in large numbers of specimens. Graphical abstract.
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34
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Liu M, Li M, Ma C, Shi C. Detection of canine parvovirus and feline panleukopenia virus in fecal samples by strand exchange amplification. J Vet Diagn Invest 2020; 32:880-886. [PMID: 32996420 DOI: 10.1177/1040638720962067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Canine parvovirus 2 (CPV-2) and feline panleukopenia virus (FPLV) often cause acute enteric disease in their hosts. A simple, rapid, and effective method for the on-site detection of these viruses would be useful. We used a denaturation bubble-mediated strand exchange amplification (SEA) method to successfully detect CPV-2 and FPLV in fecal samples. SEA could detect as little as 3.6 pg/μL of CPV-2 and 6.6 pg/μL of FPLV genomic DNA following a 40-min incubation at an isothermal temperature of 61°C. Unlike PCR, SEA does not require complicated equipment, and positive samples produce a color change that can be visualized by the naked eye. Additionally, SEA is simpler than PCR because no extraction is needed, and heating of the fecal sample at 98°C can be performed with a heating block or water bath. This rapid and effective nucleic acid detection platform could be used as a point-of-care test for the detection of CPV-2 and FPLV.
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Affiliation(s)
- Mengmeng Liu
- Department of Pathogenic Biology, School of Basic Medicine, College of Life Sciences, Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, the Clinical Laboratory Department of the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, P.R. China
| | - Mengzhe Li
- Department of Pathogenic Biology, School of Basic Medicine, College of Life Sciences, Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, the Clinical Laboratory Department of the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, P.R. China
| | - Cuiping Ma
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Shandong, P.R. China
| | - Chao Shi
- Department of Pathogenic Biology, School of Basic Medicine, College of Life Sciences, Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, the Clinical Laboratory Department of the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, P.R. China
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35
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Zhao X, Wang X, Wang X, Liu S, Jing H, Wang H, Shi C, Ma C. A visual on‐site method for African swine fever virus detection in raw pig tissues. J Food Saf 2020. [DOI: 10.1111/jfs.12848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Xiaoli Zhao
- Key Laboratory of Optic‐electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, College of Chemistry and Molecular Engineering Qingdao University of Science and Technology Qingdao People's Republic of China
| | - Xiudan Wang
- Key Laboratory of Optic‐electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, College of Chemistry and Molecular Engineering Qingdao University of Science and Technology Qingdao People's Republic of China
| | - Xuejiao Wang
- Key Laboratory of Optic‐electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, College of Chemistry and Molecular Engineering Qingdao University of Science and Technology Qingdao People's Republic of China
| | - Sen Liu
- Navid Biotech Co., Ltd. Qingdao People's Republic of China
| | - Hao Jing
- Navid Biotech Co., Ltd. Qingdao People's Republic of China
| | - HaiXia Wang
- Key Laboratory of Optic‐electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, College of Chemistry and Molecular Engineering Qingdao University of Science and Technology Qingdao People's Republic of 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, and Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University Qingdao University Qingdao People's Republic of China
| | - Cuiping Ma
- Key Laboratory of Optic‐electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, College of Chemistry and Molecular Engineering Qingdao University of Science and Technology Qingdao People's Republic of China
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36
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Wang X, Wang X, Shi C, Ma C, Chen L. Highly sensitive visual detection of nucleic acid based on a universal strand exchange amplification coupled with lateral flow assay strip. Talanta 2020; 216:120978. [DOI: 10.1016/j.talanta.2020.120978] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 10/24/2022]
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Wang X, Yan C, Wang X, Zhao X, Shi C, Ma C. Integrated silica membrane–based nucleic acid purification, amplification, and visualization platform for low-cost, rapid detection of foodborne pathogens. Anal Bioanal Chem 2020; 412:6927-6938. [DOI: 10.1007/s00216-020-02823-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/09/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
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38
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Li M, Liu M, Ma C, Shi C. Rapid DNA detection and one-step RNA detection catalyzed by Bst DNA polymerase and narrow-thermal-cycling. Analyst 2020; 145:5118-5122. [PMID: 32648859 DOI: 10.1039/d0an00975j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We reported a novel detection method named accelerated strand exchange amplification by employing Bst DNA polymerase and narrow-thermal-cycling for the first time, achieving direct detection of 120 copies of DNA within 15 min and 1.2 × 105 copies of RNA within 20 min and sparking the revolution of the use of routine isothermal polymerases for diverse applications.
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Affiliation(s)
- Mengzhe Li
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, and Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, PR China.
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39
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Development of a direct and visual isothermal method for meat adulteration detection in low resource settings. Food Chem 2020; 319:126542. [DOI: 10.1016/j.foodchem.2020.126542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 07/31/2019] [Accepted: 03/01/2020] [Indexed: 12/30/2022]
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40
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Yin Y, Wu Z, Li G, Huang J, Guo Q, Meng X. A DNA molecular diagnostic technology with LAMP-like sensitivity based on one pair of hairpin primers-mediated isothermal polymerization amplification. Anal Chim Acta 2020; 1134:144-149. [PMID: 33059860 DOI: 10.1016/j.aca.2020.05.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/16/2020] [Accepted: 05/23/2020] [Indexed: 11/18/2022]
Abstract
With the rapid development of isothermal amplification technology, DNA molecular diagnosis has become an important reference for clinical treatment. In this work, we have designed a DNA molecular diagnostic technology with LAMP-like sensitivity for nucleic acid analysis and detection based on only one pair of hairpin primers. This DNA molecular diagnostic technology consists of Bst DNA polymerase and one pair of hairpin primers, which are designed easily by adding a stem-loop structure to a target binding domain. When the target is present, the polymerization reaction between the hairpin primers and the target generates a specific dumbbell DNA similar to LAMP, which triggers cyclic amplification reactions to extend a series of long dsDNA products with repeated sequences by inserting fluorescent dye Eva Green observed the increase in fluorescence signal. In our method, using the hairpin primers-mediated isothermal polymerization amplification, we can specifically monitor 3-5 copies of the target nucleic acid in the system without labeling and temperature cycling in the reaction. In addition, serum samples from 13 patients with suspected schistosomiasis were targeted; we further demonstrated the ability of the technology to detect complex clinic samples, and its potentially inestimable applicability in clinic early molecular diagnostic research.
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Affiliation(s)
- Yao Yin
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
| | - Zuoci Wu
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
| | - Guangping Li
- Hunan Province Institute of Schistosoma, Yueyang, 414000, China
| | - Jin Huang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
| | - Qiuping Guo
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China.
| | - Xiangxian Meng
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China.
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41
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Zou Y, Mason MG, Botella JR. Evaluation and improvement of isothermal amplification methods for point-of-need plant disease diagnostics. PLoS One 2020; 15:e0235216. [PMID: 32598374 PMCID: PMC7323990 DOI: 10.1371/journal.pone.0235216] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/10/2020] [Indexed: 01/01/2023] Open
Abstract
A number of isothermal DNA amplification technologies claim to be ideal for point-of-need (PON) applications as they enable reactions to be performed using a single-temperature heat source (e.g. water bath). Thus, we examined several isothermal amplification methods focusing on simplicity, cost, sensitivity and reproducibility to identify the most suitable method(s) for low resource PON applications. A number of methods were found unsuitable as they either involved multiple temperature incubations, were relatively expensive or required relatively large amounts target DNA for amplification. Among the methods examined, loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) were found to be the most suitable for PON applications as they are both single step methods that provide highly sensitive and reproducible amplifications. The speed of LAMP reactions was greatly enhanced, up to 76%, with the addition of loop primers while the presence of swarm primers and the sequestration of free magnesium ions with nucleotides also enhanced the amplification speed. In contrast, we were unable to enhance RPA's performance from the original published literature. While both RPA and LAMP have some drawbacks, either isothermal technology can reliably be used for on-site diagnostics with minimal equipment.
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Affiliation(s)
- Yiping Zou
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Michael Glenn Mason
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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42
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Li M, Ge A, Liu M, Ma B, Ma C, Shi C. A fully integrated hand-powered centrifugal microfluidic platform for ultra-simple and non-instrumental nucleic acid detection. Talanta 2020; 219:121221. [PMID: 32887122 DOI: 10.1016/j.talanta.2020.121221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 12/18/2022]
Abstract
Hand-powered centrifugal microfluidics combined with isothermal nucleic acid amplification testing (NAAT) have been one of the most promising rapid detection platforms in resource-limited settings. However, current hand-powered centrifuges still suffer from customized instrument-based operation and low rotation rate; and most isothermal NAAT were conducted with complicated reaction systems for DNA detection and required an additional step for RNA detection. Herein, we built a fully hand-powered centrifugal miniaturized NAAT platform inspired by buzzer toys, which embedded sample preparation, strand exchange amplification (SEA) and visual fluorescence detection together. The centrifugal disc was easily fabricated, and operated the mixing in 1 min by simply dragging the looped rope through it with a mean input force of 16.5 N, enabling its rotation rate reach 5000 rpm. In addition, SEA was an ultra-simple one-step DNA or RNA detection method initiated by Bst DNA polymerase and a pair of primers, and thus we took all its merits and integrate it into microfluidic systems firstly. Furthermore, taking Vibrio parahemolyticus as an example, the microfluidic platform achieved DNA or RNA detection within 1 h; and the detection limit of the microchip for artificially spiked oysters was 103 CFU/g without cumbersome sample preparation, and reached to 100 CFU/g after enrichment. Therefore, we provided an ultra-simple and non-instrumental microfluidic platform powered merely by hands, performing general potential in sample-to-answer NAAT for versatile pathogens in remote regions.
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Affiliation(s)
- Mengzhe Li
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, PR China
| | - Anle Ge
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, PR China
| | - Mengmeng Liu
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, PR China
| | - Bo Ma
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, PR China
| | - Cuiping Ma
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, 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, Qingdao University, Qingdao, 266071, PR China.
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43
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Wang X, Niu S, Wei M, Liu S, Liu R, Shi C, Ma C. Ultrasensitive electrochemical DNA biosensor based on a tetrahedral structure and proximity-dependent surface hybridization. Analyst 2020; 145:150-156. [PMID: 31720590 DOI: 10.1039/c9an01897b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The DNA tetrahedron has developed a broad spectrum of applications in biosensor construction thanks to its excellent mechanical rigidity and structural stability. However, how to construct a highly sensitive biosensor using a DNA tetrahedron is still a challenge. In this work, an ultrasensitive electrochemical biosensor based on a DNA tetrahedral nanostructure was developed with the help of synergy from proximity-dependent hybridization. To decrease the steric hindrance of DNA tetrahedra to proximity-dependent hybridization, the detection signal was set on the inclined side chain structure of a DNA tetrahedral sensing system. Additionally, when the target hybridized with the DNA probe, the ferrocene (Fc) labeled on the end of the DNA probe was driven close to the surface of the biosensor, providing a sensitive faradaic current. The experimental results exhibited a good linear relationship from 1 fM to 10 pM with a linear correlation coefficient of 0.9977, and a high sensitivity with a detection limit of 0.2 fM. Our DNA biosensor also showed good stability according to electrode characterization and target detection at different time scales and the anti-jamming capabilities in a complicated biological extraction environment were excellent. The electrochemical sensing system established here has greatly improved the detection sensitivity of a DNA biosensor based on a DNA tetrahedron, which will further promote its practical applications.
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Affiliation(s)
- Xuejiao Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China.
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44
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Zhuang L, Gong J, Ji Y, Tian P, Kong F, Bai H, Gu N, Zhang Y. Lateral flow fluorescent immunoassay based on isothermal amplification for rapid quantitative detection of Salmonella spp. Analyst 2020; 145:2367-2377. [PMID: 32031182 DOI: 10.1039/c9an02011j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Salmonella spp. are zoonotic pathogens of substantial public health concern. To enable detection in the field or under instrument-free conditions, we developed a rapid and robust lateral flow fluorescent immunoassay based on strand exchange amplification (SEA-LFIA) for the quantitative detection of Salmonella spp. As far as we know, this work is the first report regarding the use of Bst DNA polymerase-assisted SEA for fluorescence sensing to detect Salmonella spp. The SEA method was further confirmed by enzymatic digestion and Sanger dideoxy sequencing. The specificity of SEA-LFIA assay was verified by 89 Salmonella strains (18 Salmonella reference strains and 71 clinical isolates) and 15 non-Salmonella reference strains (different genera). The sensitivity of SEA-LFIA assay was 6 × 100 CFU mL-1 of Salmonella pure culture or 3 × 104 CFU 25 g-1 of artificially spiked raw chicken meat. Using this assay, it was found that 37 (16%) of the 236 samples collected were positive, which was consistent with the results of conventional PCR. The cutoff value is 15 and SEA-LFIA assay only takes ∼30 min without high equipment and reagent cost. In addition, the proposed strategy can be easily extended by redesigning the corresponding amplification primers to detect target analytes. In conclusion, the optimized SEA-LFIA assay is an efficient and specific method for the detection of Salmonella spp., and can potentially serve as a new on-site diagnostic tool in life sciences.
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Affiliation(s)
- Linlin Zhuang
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
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45
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Primer design strategy for denaturation bubble-mediated strand exchange amplification. Anal Biochem 2020; 593:113593. [PMID: 31978455 DOI: 10.1016/j.ab.2020.113593] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/18/2020] [Accepted: 01/18/2020] [Indexed: 02/07/2023]
Abstract
Denaturation bubble-mediated strand exchange amplification (SEA) is a novel, rapid isothermal nucleic acid amplification has been applied for point-of-care molecular diagnostic in food safety, meat adulteration, forest disease and animal disease. Nevertheless, the absence of specialized strategy for SEA primers design led to long-time of primer screening progress before SEA reaction execution, which would largely increase the time consuming when SEA is utilized for detecting other new targets. In this present work, we investigated the impact of the following primers' attributes on SEA efficiency, including Tm value, 3' end G/C content, self-complementary and 3' complementary, according to which we demonstrated that optimal Tm value and reaction temperature were all 61 °C, while 3'-terminal nucleotide should be G/C, as the SEA reaction induced by the primers possessing these attributes exhibited significantly lower threshold time (Tt) value. Moreover, self-complementary and 3' complementary of primers should be avoided. Besides, we also discussed the consideration priority order of these factors, which was self-complementary and 3' complementary, Tm value and 3' end G/C content in turn. Because the SEA primer design strategy is first presented, our work will greatly promote the application of SEA in point-of-care test.
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46
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Liu S, Wei M, Liu R, Kuang S, Shi C, Ma C. Lab in a Pasteur pipette: low-cost, rapid and visual detection of Bacillus cereu using denaturation bubble-mediated strand exchange amplification. Anal Chim Acta 2019; 1080:162-169. [DOI: 10.1016/j.aca.2019.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 06/04/2019] [Accepted: 07/05/2019] [Indexed: 12/16/2022]
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47
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Single enzyme-based stem-loop and linear primers co-mediated exponential amplification of short gene sequences. Anal Chim Acta 2019; 1081:193-199. [PMID: 31446958 DOI: 10.1016/j.aca.2019.07.055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/06/2019] [Accepted: 07/25/2019] [Indexed: 11/20/2022]
Abstract
Isothermal DNA amplification only using a Bacillus stearothermophilus (Bst) DNA polymerase such as loop-mediated isothermal amplification typically entails multiple target sites for primer design and is thereby not suited for the amplification of short gene sequences, for example, the sequences with size below 200 nucleotides (nt). Here we present SLIMP, a novel single enzyme-based isothermal amplification of short gene sequence mediated by both stem-loop and linear primers. In SLIMP, a pair of stem-loop primers and a pair of linear primers are specifically designed to recognize only two target sites. Linear primers in SLIMP are similar as conventional PCR primers, but stem-loop primers are the modified linear primers through attaching a stem-loop structure at their 5'-ends. Attributed to this unique primer design, three basic reaction modes including linear-priming, single stem-loop-priming, and double stem-loop-priming amplifications co-mediate the SLIMP process under the function of Bst DNA polymerase. As a proof-of-concept assay, a synthetic 80 nt sequence from hepatitis B virus S gene was used as the template to develop SLIMP. On performance, SLIMP detection possesses high sensitivity and specificity, good selectivity, and the potential for analysing real sample. Therefore, SLIMP is expected as a novel alternative to amplify short gene sequences using a single enzyme.
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48
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Ye X, Fang X, Li Y, Wang L, Li X, Kong J. Sequence-Specific Probe-Mediated Isothermal Amplification for the Single-Copy Sensitive Detection of Nucleic Acid. Anal Chem 2019; 91:6738-6745. [PMID: 31046251 DOI: 10.1021/acs.analchem.9b00812] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
There is currently the lack of a method for precisely monitoring the progress of isothermal amplification reactions by means of sequence-specific fluorescent probes like the TaqMan probe used in the PCR system. Here, we created a circular fluorescent probe-mediated isothermal amplification (CFPA) method. This novel method uses two circular fluorescent probes and Bst DNA polymerase to construct an overlapping structure that can be cut off by flap structure-specific endonuclease 1, separating the fluorescence and quenching groups on the probes. The results showed single-copy sensitivity, ultrahigh specificity, stability (C.V. < 0.1), and anti-interference ability in detecting nucleic acid samples. A clinical trial demonstrated the perfect effectiveness of this method in the diagnosis of rotavirus infection and consistency with the gold standard method used in the clinic ( p > 0.05). In summary, we present a new, reliable, and precise isothermal amplification approach for applications in biomedical research and the clinical accurate diagnosis of pathogen infections.
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Affiliation(s)
- Xin Ye
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , P. R. China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , P. R. China
| | - Yang Li
- Shanghai Suchuang Diagnostic Products Co., Ltd, Shanghai 201318 , P. R. China.,Shanghai Suxin Biotechnology Co. Ltd, Shanghai 201318 , P. R. China
| | - Lijuan Wang
- Shanghai Suchuang Diagnostic Products Co., Ltd, Shanghai 201318 , P. R. China.,Shanghai Suxin Biotechnology Co. Ltd, Shanghai 201318 , P. R. China
| | - Xinxin Li
- Shanghai Suchuang Diagnostic Products Co., Ltd, Shanghai 201318 , P. R. China.,Shanghai Suxin Biotechnology Co. Ltd, Shanghai 201318 , P. R. China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , P. R. China
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49
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A simple isothermal nucleic acid amplification method for the effective on-site identification for adulteration of pork source in mutton. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.11.040] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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50
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Liu C, Shi C, Li M, Wang M, Ma C, Wang Z. Rapid and Simple Detection of Viable Foodborne Pathogen Staphylococcus aureus. Front Chem 2019; 7:124. [PMID: 30931298 PMCID: PMC6424009 DOI: 10.3389/fchem.2019.00124] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/18/2019] [Indexed: 12/27/2022] Open
Abstract
Staphylococcus aureus (S. aureus) contamination in food safety has become a worldwide health problem. In this work, we utilized RNA one-step detection of denaturation bubble-mediated Strand Exchange Amplification (SEA) method to realize the detection of viable foodborne pathogen S. aureus. A pair of S. aureus specific primers were designed for the SEA reaction by targeting hypervariable V2 region of 16S rDNA and the amplification reaction was finished about 1 h. The results of amplification reaction could be observed by the naked eyes with a significant color change from light yellow to red to realize the colorimetric detection of S. aureus. Therefore, there only required an isothermal water bath, which was very popular for areas with limited resources. In real sample testing, although the SEA detection was so time-saving compared with the traditional plating method, the SEA method showed great consistency with the traditional plating method. In view of the above-described advantages, we provided a simple, rapid and equipment-free detection method, which had a great potential on ponit-of-care testing (POCT) application. Our method reported here will also provide a POCT detection platform for other food-borne pathogens in food, even pathogenic bacteria from other fields.
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Affiliation(s)
- Caiyan Liu
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, College of Chemistry and Chemical Engineering, College of Life Sciences, Qingdao University, Qingdao, China
| | - Chao Shi
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, College of Chemistry and Chemical Engineering, College of Life Sciences, Qingdao University, Qingdao, China
| | - Mengzhe Li
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, College of Chemistry and Chemical Engineering, College of Life Sciences, Qingdao University, Qingdao, China
| | - Mengyuan Wang
- The Affiliated Hospital of Qingdao University Medical College, Qingdao, China
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Zonghua Wang
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, College of Chemistry and Chemical Engineering, College of Life Sciences, Qingdao University, Qingdao, China
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