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Shi Y, Tan Q, Gong T, Li QY, Zhu Y, Duan X, Yang C, Ding JW, Li S, Xie H, Li Y, Chen L. Cascaded signal amplification strategy for ultra-specific, ultra-sensitive, and visual detection of Shigella flexneri. Mikrochim Acta 2024; 191:271. [PMID: 38632191 DOI: 10.1007/s00604-024-06309-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/03/2024] [Indexed: 04/19/2024]
Abstract
Pathogen infections including Shigella flexneri have posed a significant threat to human health for numerous years. Although culturing and qPCR were the gold standards for pathogen detection, time-consuming and instrument-dependent restrict their application in rapid diagnosis and economically less-developed regions. Thus, it is urgently needed to develop rapid, simple, sensitive, accurate, and low-cost detection methods for pathogen detection. In this study, an immunomagnetic beads-recombinase polymerase amplification-CRISPR/Cas12a (IMB-RPA-CRISPR/Cas12a) method was built based on a cascaded signal amplification strategy for ultra-specific, ultra-sensitive, and visual detection of S. flexneri in the laboratory. Firstly, S. flexneri was specifically captured and enriched by IMB (Shigella antibody-coated magnetic beads), and the genomic DNA was released and used as the template in the RPA reaction. Then, the RPA products were mixed with the pre-loaded CRISPR/Cas12a for fluorescence visualization. The results were observed by naked eyes under LED blue light, with a sensitivity of 5 CFU/mL in a time of 70 min. With no specialized equipment or complicated technical requirements, the IMB-RPA-CRISPR/Cas12a diagnostic method can be used for visual, rapid, and simple detection of S. flexneri and can be easily adapted to monitoring other pathogens.
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Affiliation(s)
- Yaoqiang Shi
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Qi Tan
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Tao Gong
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Qing-Yuan Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Ya Zhu
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Xiaoqiong Duan
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Chunhui Yang
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Jia-Wei Ding
- Clinical Laboratory Department, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, 650051, Yunnan, China
| | - Shilin Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - He Xie
- The Hospital of Xidian Group, Xi'an, 710077, China
| | - Yujia Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China.
| | - Limin Chen
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China.
- The Joint Laboratory On Transfusion-Transmitted Diseases (TTDs) Between Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Nanning Blood Center, Nanning Blood Center, Nanning, 530007, China.
- The Hospital of Xidian Group, Xi'an, 710077, China.
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Chen A, Zhuo Y, Chai Y, Yuan R. Bipedal DNA walker mediated enzyme-free exponential isothermal signal amplification for rapid detection of microRNA. Chem Commun (Camb) 2019; 55:13932-13935. [DOI: 10.1039/c9cc06214a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This work reported an electrochemiluminescence (ECL) biosensor based on a bipedal DNA walker mediated enzyme-free exponential isothermal DNA signal amplification, which achieved sensitive and rapid detection of microRNA (miRNA).
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Affiliation(s)
- Anyi Chen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ying Zhuo
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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Abstract
High-throughput profiling/sensing of nucleic acids has recently emerged as a highly promising strategy for the early diagnosis and improved prognosis of a broad range of pathologies, most notably cancer. Among the potential biomarker candidates, microRNAs (miRNAs), a class of non-coding RNAs of 19-25 nucleotides in length, are of particular interest due to their role in the post-transcriptional regulation of gene expression. Developing miRNA sensing technologies that are quantitative, ultrasensitive and highly specific has proven very challenging because of their small size, low natural abundance and the high degree of sequence similarity among family members. When compared to optical based methods, electrochemical sensors offer many advantages in terms of sensitivity and scalability. This non-comprehensive review aims to break-down and highlight some of the most promising strategies for electrochemical sensing of microRNA biomarkers.
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Affiliation(s)
- Philip Gillespie
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
| | - Danny O'Hare
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
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Arter WE, Charmet J, Kong J, Saar KL, Herling TW, Müller T, Keyser UF, Knowles TPJ. Combining Affinity Selection and Specific Ion Mobility for Microchip Protein Sensing. Anal Chem 2018; 90:10302-10310. [PMID: 30070105 DOI: 10.1021/acs.analchem.8b02051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The sensitive detection of proteins is a key objective in many areas of biomolecular science, ranging from biophysics to diagnostics. However, sensing in complex biological fluids is hindered by nonspecific interactions with off-target species. Here, we describe and demonstrate an assay that utilizes both the chemical and physical properties of the target species to achieve high selectivity in a manner not possible by chemical complementarity alone, in complex media. We achieve this objective through a combinatorial strategy, by simultaneously exploiting free-flow electrophoresis for target selection, on the basis of electrophoretic mobility, and conventional affinity-based selection. In addition, we demonstrate amplification of the resultant signal by a catalytic DNA nanocircuit. This approach brings together the inherent solution-phase advantages of microfluidic sample handling with isothermal, enzyme-free signal amplification. With this method, no surface immobilization or washing steps are required, and our assay is well suited to monoepitopic targets, presenting advantages over conventional ELISA techniques.
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Affiliation(s)
- William E Arter
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K.,Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Jérôme Charmet
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Institute of Digital Healthcare, International Digital Laboratory, WMG , University of Warwick , Coventry CV4 7AL , U.K
| | - Jinglin Kong
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K
| | - Kadi L Saar
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Therese W Herling
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | | | - Ulrich F Keyser
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K
| | - Tuomas P J Knowles
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K.,Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
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Shi C, Wang Y, Zhang M, Ma C. DNA Self-assembly Catalyzed by Artificial Agents. Sci Rep 2017; 7:6818. [PMID: 28754968 PMCID: PMC5533707 DOI: 10.1038/s41598-017-07210-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/27/2017] [Indexed: 11/08/2022] Open
Abstract
Nucleic acids have been shown to be versatile molecules and engineered to produce various nanostructures. However, the poor rate of these uncatalyzed nucleic acid reactions has restricted the development and applications. Herein, we reported a novel finding that DNA self-assembly could be nonenzymatically catalyzed by artificial agents with an increasing dissociation rate constant K2. The catalytic role of several artificial agents in DNA self-assembly was verified by real-time fluorescent detection or agarose gel electrophoresis. We found that 20% PEG 200 could significantly catalyze DNA self-assembly and increase the reaction efficiency, such as linear hybridization chain reaction (HCR) and exponential hairpin assembly (EHA). Therefore, we foresee that a fast and efficient DNA self-assembly in structural DNA nanotechnology will be desirable.
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Affiliation(s)
- Chao Shi
- College of Life Sciences, Qingdao University, Qingdao, 266071, P.R. China
| | - Yifan Wang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P.R. China
| | - Menghua Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P.R. China
| | - Cuiping Ma
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P.R. China.
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