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Niu CB, Lv QY, Song X, Guo Q, Ling XQ, Chen J, Cui HF. DNA nanoassembly based turn-on amplification probe for sensitive colorimetric CRISPR/Cas12a-mediated detection of pathogen DNA. Talanta 2024; 277:126348. [PMID: 38852348 DOI: 10.1016/j.talanta.2024.126348] [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: 03/14/2024] [Revised: 05/21/2024] [Accepted: 05/31/2024] [Indexed: 06/11/2024]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) system has been explored as an efficient tool for nucleic acid diagnostics. However, it normally needs instrumentation or produces turn-off signals. Herein, a bulged Y-shape DNA (Y-DNA) nanoassembly was designed and synthesized as a novel turn-on probe. A CRISPR/Cas12a and Y-DNA probe mediated colorimetric assay (named as CYMCOA) strategy was developed for visual detection of pathogen DNA. Upon activating Cas12a with pathogen DNA, the Y-DNA bulge is catalytically trans-cleaved, releasing the G-quadruplex sequence embedded in the Y-DNA nanoassembly as a peroxidase-like DNAzyme. Visible signals with chromogen substrates are thus produced. The CYMCOA strategy was combined with recombinase polymerase amplification (RPA), an isothermal amplification technique, in detecting Helicobacter pylori (Hp) bacteria and SARS-CoV-2 N plasmids as two model pathogens. The bioassay has very excellent detection sensitivity and specificity, owing to the triple cascade amplification reactions and the very low mismatch tolerance. The lower limit of detection values were 0.16 cfu⋅mL-1, 1.5 copies⋅μL-1, and 0.17 copies⋅μL-1 for Hp bacteria, Hp plasmids, and SARS-CoV-2 N plasmids respectively. The detection is fast and accurate. The colorimetric bioassay strategy provides to be a simple, accurate, fast and instrumentation-free platform for nucleic acids detections in various settings, including crude and emergent situations.
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Affiliation(s)
- Chang-Bin Niu
- School of Life Sciences, Zhengzhou University, Science Avenue 100#, Zhengzhou, 450001, China
| | - Qi-Yan Lv
- School of Life Sciences, Zhengzhou University, Science Avenue 100#, Zhengzhou, 450001, China
| | - Xiaojie Song
- School of Life Sciences, Zhengzhou University, Science Avenue 100#, Zhengzhou, 450001, China
| | - Qian Guo
- School of Life Sciences, Zhengzhou University, Science Avenue 100#, Zhengzhou, 450001, China
| | - Xiao-Qing Ling
- School of Life Sciences, Zhengzhou University, Science Avenue 100#, Zhengzhou, 450001, China
| | - Junyang Chen
- School of Life Sciences, Zhengzhou University, Science Avenue 100#, Zhengzhou, 450001, China
| | - Hui-Fang Cui
- School of Life Sciences, Zhengzhou University, Science Avenue 100#, Zhengzhou, 450001, China.
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Zhang J, Tang L, Liu D, Zhang S, Ding X, Gao G, Deng X, Liu Z, Tian X, He W, Hu B, Huang Z. Reducing COVID-19 diagnostic errors with dNTPαSe supplementation. Analyst 2023; 148:1214-1220. [PMID: 36825426 DOI: 10.1039/d2an01698b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Timely and accurate diagnosis of COVID-19 is critical for controlling the pandemic. As the standard method to diagnose SARS-CoV-2, the real-time reverse transcription polymerase chain reaction (RT-qPCR) has good convenience. However, RT-qPCR still has a relatively high false-negative rate, particularly in the case of detecting low viral loads. In this study, using selenium-modified nucleoside triphosphates (dNTPαSe) in the RT-PCR reactions, we successfully increased the detection sensitivity and reduced the false-negative rate in COVID-19 diagnosis. By detecting positive controls, pseudovirus, and clinical samples with the commercial kits, we found that the dNTPαSe supplementation to these kits could generally offer smaller Ct values, permit the viral detection even in single-digit copies, and increase the detection specificity, sensitivity, and accuracy, thereby reducing the false-negative rate. Our experimental results demonstrated that dNTPαSe supplementation can make the commercial kits more specific, sensitive, and accurate, and this method is a convenient and efficient strategy for the disease detection and diagnosis.
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Affiliation(s)
- Jun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064. .,SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, China
| | - Ling Tang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Dan Liu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Shun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Xiaoling Ding
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Guolong Gao
- Sichuan International Travel Health Care Center (Chengdu Customs Port Clinic), China.
| | - Xiaodong Deng
- Sichuan International Travel Health Care Center (Chengdu Customs Port Clinic), China.
| | - Zhengying Liu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Xi Tian
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Wei He
- Sichuan International Travel Health Care Center (Chengdu Customs Port Clinic), China.
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064.
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China, 610064. .,SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, China
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Zhang S, Tang L, Zhang J, Sun W, Liu D, Chen J, Hu B, Huang Z. Single-Atom-Directed Inhibition of De Novo DNA Synthesis in Isothermal Amplifications. Anal Chem 2022; 94:15763-15771. [DOI: 10.1021/acs.analchem.2c03489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan 610095, China
| | - Ling Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Jun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Wen Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Dan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Jiuyi Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan 610095, China
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Bodulev OL, Sakharov IY. A Microtiter-Plate Chemiluminescence Method for the Determination of MicroRNA-141 Based on the Application of Catalytic Hairpin Assembly and a Streptavidin–Polyperoxidase Conjugate. JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1134/s1061934822040050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mao J, Tang S, Liang S, Pan W, Kang Y, Cheng J, Yu D, Chen J, Lou J, Zhao H, Zhou J. A new self-passivating template with the phosphorothioate strategy to effectively improve the detection limit and applicability of exponential amplification reaction. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:3947-3953. [PMID: 34528948 DOI: 10.1039/d1ay00520k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Exponential amplification reaction (EXPAR) has attracted much attention due to its simple primers and high amplification efficiency, but its applications are hindered by severe non-specificity amplification. Convenient exogenous chemical modification methods modified the entire template while inhibiting both non-specific and specific amplification. In this paper, we proposed a new self-passivating template with the phosphorothioate strategy to effectively improve the detection limit and applicability of EXPAR. We phosphorothioated several bases where the sequence was prone to form transient intermolecular 3'-end hybridization, thereby inhibiting the non-specific interactions and preventing the extension of templates by DNA polymerase. The melting temperature (Tm) curve and density functional theory (DFT) proved that the stability of hydrogen bonds between phosphorothioated bases did decrease. Benefitting from this strategy, the detection limit had been improved by 3 orders of magnitude. Moreover, due to the antioxidation property of phosphorothioate, this strategy showed good stability in serum, reflecting its excellent prospects in clinical sampling and detection.
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Affiliation(s)
- Jikai Mao
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Shiyi Tang
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Sijia Liang
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
| | - Wufan Pan
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Yanlei Kang
- Zhejiang Province Key Laboratory of Smart Management & Application of Modern Agricultural Resources, School of Information Engineering, Huzhou University, Huzhou, 313000, Zhejiang Province, China
| | - Jianbo Cheng
- Yantai Univ, Sch Chem & Chem Engn, Lab Theoret & Computat Chem, Yantai 264005, China
| | - Dongdong Yu
- Hospital of Zhejiang University, Zhejiang University, Hangzhou 310000, China
| | - Jie Chen
- Department of Gastroenterology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, 310052, China
| | - Jingan Lou
- Department of Gastroenterology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, 310052, China
| | - Hong Zhao
- Department of Gastroenterology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, 310052, China
| | - Jianguang Zhou
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
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