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Tan P, Chen Y, Chang H, Liu T, Wang J, Lu Z, Sun M, Su G, Wang Y, Wang HD, Leung C, Rao H, Wu C. Deep learning assisted logic gates for real-time identification of natural tetracycline antibiotics. Food Chem 2024; 454:139705. [PMID: 38820637 DOI: 10.1016/j.foodchem.2024.139705] [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: 02/03/2024] [Revised: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 06/02/2024]
Abstract
The overuse and misuse of tetracycline (TCs) antibiotics, including tetracycline (TTC), oxytetracycline (OTC), doxycycline (DC), and chlortetracycline (CTC), pose a serious threat to human health. However, current rapid sensing platforms for tetracyclines can only quantify the total amount of TCs mixture, lacking real-time identification of individual components. To address this challenge, we integrated a deep learning strategy with fluorescence and colorimetry-based multi-mode logic gates in our self-designed smartphone-integrated toolbox for the real-time identification of natural TCs. Our ratiometric fluorescent probe (CD-Au NCs@ZIF-8) encapsulated carbon dots and Au NCs in ZIF-8 to prevent false negative or positive results. Additionally, our independently developed WeChat app enabled linear quantification of the four natural TCs using the fluorescence channels. The colorimetric channels were also utilized as outputs of logic gates to achieve real-time identification of the four individual natural tetracyclines. We anticipate this strategy could provide a new perspective for effective control of antibiotics.
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Affiliation(s)
- Ping Tan
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Yuhui Chen
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Hongrong Chang
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Tao Liu
- College of Information Engineering, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Jian Wang
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China.
| | - Zhiwei Lu
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Mengmeng Sun
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Gehong Su
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Yanying Wang
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Huimin David Wang
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Xingda Road, South District, Taichung 402, Taiwan, China
| | - Chunghang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa 999078, Macao
| | - Hanbing Rao
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China.
| | - Chun Wu
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China.
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Bai Y, Xu P, Li S, Wang D, Zhang K, Zheng D, Yue D, Zhang G, He S, Li Y, Zou H, Deng Y. Signal amplification strategy of DNA self-assembled biosensor and typical applications in pathogenic microorganism detection. Talanta 2024; 272:125759. [PMID: 38350248 DOI: 10.1016/j.talanta.2024.125759] [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: 11/05/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
Biosensors have emerged as ideal analytical devices for various bio-applications owing to their low cost, convenience, and portability, which offer great potential for improving global healthcare. DNA self-assembly techniques have been enriched with the development of innovative amplification strategies, such as dispersion-to-localization of catalytic hairpin assembly, and dumbbell hybridization chain reaction, which hold great significance for building biosensors capable of realizing sensitive, rapid and multiplexed detection of pathogenic microorganisms. Here, focusing primarily on the signal amplification strategies based on DNA self-assembly, we concisely summarized the strengths and weaknesses of diverse isothermal nucleic acid amplification techniques. Subsequently, both single-layer and cascade amplification strategies based on traditional catalytic hairpin assembly and hybridization chain reaction were critically explored. Furthermore, a comprehensive overview of the recent advances in DNA self-assembled biosensors for the detection of pathogenic microorganisms is presented to summarize methods for biorecognition and signal amplification. Finally, a brief discussion is provided about the current challenges and future directions of DNA self-assembled biosensors.
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Affiliation(s)
- Yuxin Bai
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Pingyao Xu
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Shi Li
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Dongsheng Wang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Kaijiong Zhang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Dongming Zheng
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Daifan Yue
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Guiji Zhang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Shuya He
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Yan Li
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China.
| | - Haimin Zou
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China.
| | - Yao Deng
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China.
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Wu C, Yue Y, Huang B, Ji H, Wu L, Huang H. CRISPR-powered microfluidic biosensor for preamplification-free detection of ochratoxin A. Talanta 2024; 269:125414. [PMID: 37992484 DOI: 10.1016/j.talanta.2023.125414] [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: 08/15/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
The CRISPR technology, which does not require complex instruments, expensive reagents or professional operators, has attracted a lot of attention. When utilizing the CRISPR-Cas system for detection, the pre-amplification step is often necessary to enhance sensitivity. However, this approach tends to introduce complexity and prolong the time required. To address this issue, we employed Pd@PCN-222 nanozyme to label single-stranded DNA, referred to as Pd@PCN-222 CRISPR nanozyme, which serves as the reporter of the CRISPR system. Pd@PCN-222 nanozyme possess exceptional catalytic activity for the reduction of H2O2. Compared with traditional electrochemical probe ferrocene and methylene blue without catalytic activity, there is a significant amplification of the electrochemical signal. So the need for pre-amplification was eliminated. In this study, we constructed a CRISPR-Cas system for ochratoxin A, utilizing the Pd@PCN-222 CRISPR nanozyme to amplified signal avoiding pre-amplification with outstanding detection of 1.21 pg/mL. Furthermore, we developed a microfluidic electrochemical chip for the on-site detection of ochratoxin A. This achievement holds significant promise in establishing a practical on-site detection platform for identifying food safety hazards.
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Affiliation(s)
- Chengyuan Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yuanyuan Yue
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | | | - Hanxu Ji
- Key Laboratory of Biotoxin Analysis & Assessment for State Market Regulation, Nanjing Institute of Product Quality Inspection & Testing, Nanjing, 210019, China
| | - Lina Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
| | - He Huang
- Food Laboratory of Zhongyuan, Luohe, 462300, Henan, China.
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Duan M, Zhao Y, Liu Y, He Y, Dai R, Chen J, Li X, Jia F. A low-background and wash-free signal amplification F-CRISPR biosensor for sensitive quantitative and visible qualitative detection of Salmonella Typhimurium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168905. [PMID: 38016549 DOI: 10.1016/j.scitotenv.2023.168905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023]
Abstract
In traditional CRISPR-based biosensors, the cleavage-induced signal generation is insufficient because only a signals is generated at a CRISPR-induced cleavage. Herein, we developed an improved CRISPR/Cas12a-based biosensor with an enlarged signal generation which integrated the hybridization chain reaction (HCR) and low-background Förster Resonance Energy Transfer (FRET) signal output mode. The HCR with nucleic acid self-assembly capability was used as a signal carrier to load more signaling molecules. To get the best signal amplification, three different fluorescence signal output modes (fluorescence recovery, FRET and low-background FRET) generated by two fluoresceins, FAM and Cy5, were fully investigated and compared. The results indicated that the low-background FRET signal output mode with the strictest signal generation conditions yielded the highest signal-to-noise ratio (S/N) (19.17) and the most obvious fluorescence color change (from red to yellow). In optimal conditions, the proposed biosensor was successfully applied for Salmonella Typhimurium (S. Typhimurium) detection with 6 h (including 4 h for sample pre-treatment) from the initial target processing to the final detection result. The qualitative sensitivity, reliant on color changes, was 103 CFU/mL. The quantitative sensitivity, calculated by the fluorescence value, were 1.62 × 101 CFU/mL, 3.72 × 102 CFU/mL, and 8.71 × 102 CFU/mL in buffer solution, S. Typhimurium-spiked milk samples, and S.Typhimurium-spiked chicken samples, respectively. The excellent detection performance of the proposed biosensor endowed its great application potential in food and environment safety monitoring.
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Affiliation(s)
- Miaolin Duan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yijie Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yana Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yawen He
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Ruitong Dai
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Xingmin Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Fei Jia
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA.
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Li R, Jing Z, Yang G, Yuan R, Hu FX, Chen S. Nickel Single-Atom Catalyst Boosts Electrochemiluminescence of Graphitic Carbon Nitride for Sensitive Detection of HBV DNA. Anal Chem 2023; 95:18207-18214. [PMID: 38010370 DOI: 10.1021/acs.analchem.3c03989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Owing to excellent catalytic activity, single-atom catalysts (SACs) have recently attracted considerable research interest in the electrochemiluminescence (ECL) field. However, the applications of SACs are mostly limited to conventional luminol ECL system. Hence, it is necessary to explore the application of SACs in more ECL systems. In this work, nickel single-atom catalysts (Ni SACs) were successfully applied in the graphitic carbon nitride (g-C3N4)-H2O2 ECL system to significantly enhance its cathodic emission. Notably, g-C3N4 acted not only as an ECL luminophore but also as a support to anchor Ni SACs. Ni SACs can significantly activate H2O2 to produce abundant OH• radicals for enhancing the cathodic ECL emission of g-C3N4. Ni SACs-anchored g-C3N4 (Ni SACs@g-C3N4) had a 10-fold enhanced ECL intensity as compared to g-C3N4. Finally, the Ni SACs@g-C3N4-H2O2 ECL system was developed to detect hepatitis B virus (HBV) DNA by incorporating an entropy-driven DNA walking machine-assisted CRISPR-Cas12a amplification strategy. The constructed biosensor exhibited excellent detection performance for HBV DNA with a limit of detection as low as 17 aM. This work puts forward a new idea for enhancing the cathodic ECL of g-C3N4-H2O2 and expands the application of SACs in the ECL system.
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Affiliation(s)
- Rongfang Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Zhiwei Jing
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Guomin Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Fang Xin Hu
- Institute of Materials Science & Devices, Suzhou University of Science and Technology, Suzhou 215009, People's Republic of China
| | - Shihong Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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