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Ma T, Zhang Q, Zhang S, Yue D, Wang F, Ren Y, Zhang H, Wang Y, Wu Y, Liu LE, Yu F. Research progress of human key DNA and RNA methylation-related enzymes assay. Talanta 2024; 273:125872. [PMID: 38471421 DOI: 10.1016/j.talanta.2024.125872] [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: 12/26/2023] [Revised: 02/18/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024]
Abstract
Gene methylation-related enzymes (GMREs) are disfunction and aberrantly expressed in a variety of cancers, such as lung, gastric, and pancreatic cancers and have important implications for human health. Therefore,it is critical for early diagnosis and therapy of tumor to develop strategies that allow rapid and sensitive quantitative and qualitative detection of GMREs. With the development of modern analytical techniques and the application of various biosensors, there are numerous methods have been developed for analysis of GMREs. Therefore, this paper provides a systematic review of the strategies for level and activity assay of various GMREs including methyltransferases and demethylase. The detection methods mainly involve immunohistochemistry, colorimetry, fluorescence, chemiluminescence, electrochemistry, etc. Then, this review also addresses the coordinated role of various detection probes, novel nanomaterials, and signal amplification methods. The aim is to highlight potential challenges in the present field, to expand the analytical application of GMREs detection strategies, and to meet the urgent need for future disease diagnosis and intervention.
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Affiliation(s)
- Tiantian Ma
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Qiongwen Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuying Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Dan Yue
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fanting Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yujie Ren
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Hengmiao Zhang
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Yinuo Wang
- Zhengzhou Foreign Language School, Zhengzhou 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Li-E Liu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fei Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
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2
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Wang H, Tang H, Qiu X, Li Y. Solid-State Glass Nanopipettes: Functionalization and Applications. Chemistry 2024; 30:e202400281. [PMID: 38507278 DOI: 10.1002/chem.202400281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/28/2024] [Accepted: 03/19/2024] [Indexed: 03/22/2024]
Abstract
Solid-state glass nanopipettes provide a promising confined space that offers several advantages such as controllable size, simple preparation, low cost, good mechanical stability, and good thermal stability. These advantages make them an ideal choice for various applications such as biosensors, DNA sequencing, and drug delivery. In this review, we first delve into the functionalized nanopipettes for sensing various analytes and the methods used to develop detection means with them. Next, we provide an in-depth overview of the advanced functionalization methodologies of nanopipettes based on diversified chemical kinetics. After that, we present the latest state-of-the-art achievements and potential applications in detecting a wide range of targets, including ions, molecules, biological macromolecules, and single cells. We examine the various challenges that arise when working with these targets, as well as the innovative solutions developed to overcome them. The final section offers an in-depth overview of the current development status, newest trends, and application prospects of sensors. Overall, this review provides a comprehensive and detailed analysis of the current state-of-the-art functionalized nanopipette perception sensing and development of detection means and offers valuable insights into the prospects for this exciting field.
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Affiliation(s)
- Hao Wang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education, School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, 235000, Anhui, P.R. China
| | - Haoran Tang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education, School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, 235000, Anhui, P.R. China
| | - Xia Qiu
- Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, P.R. China
| | - Yongxin Li
- Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, P.R. China
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3
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Ahmed SA, Liu Y, Xiong T, Zhao Y, Xie B, Pan C, Ma W, Yu P. Iontronic Sensing Based on Confined Ion Transport. Anal Chem 2024; 96:8056-8077. [PMID: 38663001 DOI: 10.1021/acs.analchem.4c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Affiliation(s)
- Saud Asif Ahmed
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ying Liu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Tianyi Xiong
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yueru Zhao
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Boyang Xie
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Cong Pan
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Wenjie Ma
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
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4
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Huang Y, Zhao Z, Yi G, Zhang M. Importance of DNA nanotechnology for DNA methyltransferases in biosensing assays. J Mater Chem B 2024; 12:4063-4079. [PMID: 38572575 DOI: 10.1039/d3tb02947f] [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: 04/05/2024]
Abstract
DNA methylation is the process by which specific bases on a DNA sequence acquire methyl groups under the catalytic action of DNA methyltransferases (DNMT). Abnormal changes in the function of DNMT are important markers for cancers and other diseases; therefore, the detection of DNMT and the selection of its inhibitors are critical to biomedical research and clinical practice. DNA molecules can undergo intermolecular assembly to produce functional aggregates because of their inherently stable physical and chemical properties and unique structures. Conventional DNMT detection methods are cumbersome and complicated processes; therefore, it is necessary to develop biosensing technology based on the assembly of DNA nanostructures to achieve rapid analysis, simple operation, and high sensitivity. The design of the relevant program has been employed in life science, anticancer drug screening, and clinical diagnostics. In this review, we explore how DNA assembly, including 2D techniques like hybridization chain reaction (HCR), rolling circle amplification (RCA), catalytic hairpin assembly (CHA), and exponential isothermal amplified strand displacement reaction (EXPAR), as well as 3D structures such as DNA tetrahedra, G-quadruplexes, DNA hydrogels, and DNA origami, enhances DNMT detection. We highlight the benefits of these DNA nanostructure-based biosensing technologies for clinical use and critically examine the challenges of standardizing these methods. We aim to provide reference values for the application of these techniques in DNMT analysis and early cancer diagnosis and treatment, and to alert researchers to challenges in clinical application.
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Affiliation(s)
- Yuqi Huang
- Clinical Laboratory, Chongqing Jiulongpo District People's Hospital, Chongqing 400050, China.
| | - Zixin Zhao
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China.
| | - Gang Yi
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China.
| | - Mingjun Zhang
- Clinical Laboratory, Chongqing Jiulongpo District People's Hospital, Chongqing 400050, China.
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5
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Zhang X, Wu ZQ, Zheng YW, Song J, Zhao WW, Xu JJ. Bridging Ionic Current Rectification and Resistive-Pulse Sensing for Reliable Wide-Linearity Detection. Anal Chem 2024; 96:6444-6449. [PMID: 38597812 DOI: 10.1021/acs.analchem.4c00629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
As two mainstream ionic detection techniques, ionic current rectification (ICR) suffers from large fluctuations in trace level detection, while resistive-pulse sensing (RPS) encounters easy clogs in high-concentration detection. By rationally matching the nanopore size with the DNA tetrahedron (TDN), this work bridges the two techniques to achieve reliable detection with wide linearity. As a representative analyte, miRNA-10b could specifically combine with and release TDN from the interior wall, which thus induced the simultaneous generation of distinct ICR and RPS signals. The ICR signals could be attributed to the balance between the effective orifice and surface charge density of the inner wall, while the RPS signals were induced by the complex of miRNA-10b and TDN passing through the nanopore. Such an operation contributed to a wide detection range of 1 fM-1 nM with a good linearity. The feasibility of this method is also validated in single-cell and real plasma detection.
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Affiliation(s)
- Xian Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zeng-Qiang Wu
- School of Public Health, Institute of Analytical Chemistry for Life Science, Nantong University, Nantong 226019, China
| | - You-Wei Zheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Juan Song
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, China
| | - Wei-Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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Zhao T, Pang X, Wang C, Wang L, Yang Y, Wang J, Jia J, Liu X, Xu S, Luo X. Plasmonic Gold Nanostar-Based Probes with Distance-Dependent Plasmon-Enhanced Fluorescence for Ultrasensitive DNA Methyltransferase Assay. Anal Chem 2024; 96:4402-4409. [PMID: 38457775 DOI: 10.1021/acs.analchem.3c04122] [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: 03/10/2024]
Abstract
The ultrasensitive DNA methyltransferase (Dam MTase) assay is of high significance for biomedical research and clinical diagnosis because of its profound effect on gene regulation. However, detection sensitivity is still limited by shortcomings, including photobleaching and weak signal intensities of conventional fluorophores at low concentrations. Plasmonic nanostructures with ultrastrong electromagnetic fields and fluorescence enhancement capability that can overcome these intrinsic defects hold great potential for ultrasensitive bioanalysis. Herein, a silica-coated gold nanostars (Au NSTs@SiO2)-based plasmon-enhanced fluorescence (PEF) probe with 20 "hot spots" was developed for ultrasensitive detection of Dam MTase. Here, the Dam Mtase assay was achieved by detecting the byproduct PPi of the rolling circle amplification reaction. It is worth noting that, benefiting from the excellent fluorescence enhancement capability of Au NSTs originating from their 20 "hot spots", the detection limit of Dam Mtase was reduced by nearly 105 times. Moreover, the proposed Au NST-based PEF probe enabled versatile evaluation of Dam MTase inhibitors as well as endogenous Dam MTase detection in GW5100 and JM110 Escherichia coli cell lysates, demonstrating its potential in biomedical analysis.
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Affiliation(s)
- Tingting Zhao
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Xiaozhe Pang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Congkai Wang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Lei Wang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Yifan Yang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Junqi Wang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Jiangfei Jia
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Xinxue Liu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Shenghao Xu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
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7
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Cai H, Huang Y, Lin Y, Luo F, Chen L, Guo L, Lin C, Wang J, Qiu B, Lin Z. Portable Sensor for Aflatoxin B1 Based on the Regulation of Resistance of a Microchannel Using a Multimeter as Readout. ACS Sens 2024; 9:494-501. [PMID: 38215311 DOI: 10.1021/acssensors.3c02486] [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] [Indexed: 01/14/2024]
Abstract
Changes in the charge density on the inner surface of the microchannel can modulate the ion concentration at the tip, thus causing changes in the resistance of the system. In this study, this property is adopted to construct a portable sensor using a multimeter and aflatoxin B1 (AFB1) is used as the model target. Initially, the cDNA/aptamer complex is modified in the microchannel. The inner microchannel surface's charge density is then altered by the recognition of the target, leading to a change in the system's resistance, which can be conveniently monitored using a multimeter. Critical parameters influencing the performance of the system are optimized. Under optimum conditions, the resistance is linearly related to the logarithm of AFB1 concentration in the range of 100 fM-10 nM and the detection limit is 46 fM (S/N = 3). The resistive measurement is separated from the recognition reaction of the target, reducing the matrix interference during the detection process. This sensor boasts high sensitivity and specificity coupled with commendable reproducibility and stability. It is applied to assay the AFB1 content successfully in an actual sample of corn. Moreover, this approach is cost-effective, user-friendly, and highly accurate.
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Affiliation(s)
- Huabin Cai
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Yanling Huang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Yue Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Fang Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Lifen Chen
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing, Zhejiang 314001, China
| | - Longhua Guo
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing, Zhejiang 314001, China
| | - Cuiying Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Jian Wang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
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Stuber A, Schlotter T, Hengsteler J, Nakatsuka N. Solid-State Nanopores for Biomolecular Analysis and Detection. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:283-316. [PMID: 38273209 DOI: 10.1007/10_2023_240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.
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Affiliation(s)
- Annina Stuber
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Tilman Schlotter
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Julian Hengsteler
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland.
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Zhang X, Dou H, Chen X, Lin M, Dai Y, Xia F. Solid-State Nanopore Sensors with Enhanced Sensitivity through Nucleic Acid Amplification. Anal Chem 2023; 95:17153-17161. [PMID: 37966312 DOI: 10.1021/acs.analchem.3c03806] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Solid-state nanopores have wide applications in DNA sequencing, energy conversion and storage, seawater desalination, sensors, and reactors due to their high stability, controllable geometry, and a variety of pore-forming materials. Solid-state nanopore sensors can be used for qualitative and quantitative analyses of ions, small molecules, proteins, and nucleic acids. The combination of nucleic acid amplification and solid-state nanopores to achieve trace detection of analytes is gradually attracting attention. This review outlines nucleic acid amplification strategies for enhancing the sensitivity of solid-state nanopore sensors by summarizing the articles published in the past 10 years. The future development prospects and challenges of nucleic acid amplification in solid-state nanopore sensors are discussed. This review helps readers better understand the field of solid-state nanopore sensors. We believe that solid-state nanopore sensors will break through the bottleneck of traditional detection and become a powerful single-molecule detection platform.
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Affiliation(s)
- Xiaojin Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Huimin Dou
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xiaorui Chen
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Yu Dai
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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Zhang S, Shao H, Li KB, Shi W, Han DM. Nanofluidic sensing platform for PNK assay using nonlinear hybridization chain reaction and its application in DNA logic circuit. Biosens Bioelectron 2023; 240:115632. [PMID: 37647684 DOI: 10.1016/j.bios.2023.115632] [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: 05/07/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
In this study, a polyethyleneimine (PEI)/Zr4+-functionalized nanofluidic sensing platform based on nonlinear hybridization chain reaction (NHCR) was developed for PNK activity assay. With the existence of PNK, the hairpin HPNK was cleaved by λ exonuclease, liberating the initiator T-DNA. Then T-DNA triggered the nonlinear HCR in solution and the reaction products were absorbed onto the nanopore, which changed the surface charge of nanofluidic device and could be detected by current-voltage characteristic curves. Compared to traditional linear HCR, the nonlinear HCR exhibits a higher sensitivity and order of growth kinetics, making it a powerful signal amplifier in bioanalysis. Due to the powerful amplification efficiency of nonlinear HCR, high sensitivity of the nanopore and specific recognition site of PNK/λ-Exo, an ultrasensitive and selective PNK sensing approach had been developed and applied to precisely quantitate the PNK activity with a LOD of 0.0001 U/mL. Moreover, utilizing this nanofluidic system as a foundation, we constructed a logic circuit that utilized PNK, adenosine diphosphate (ADP), and (NH4)2SO4 as input elements. ADP and (NH4)2SO4 had a crucial function in facilitating the PNK to regulate the DNA logic gate. By modifying the target and inhibitors, the nanofluidic device could detect a variety of stimuli and execute more advanced logical operations.
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Affiliation(s)
- Siqi Zhang
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China
| | - Huahao Shao
- Zhijiang College of Zhejiang University of Technology, Shaoxing, Zhejiang, 312000, China
| | - Kai-Bin Li
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China.
| | - Wei Shi
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China
| | - De-Man Han
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China.
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11
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Fangyu Zhou, Chen H, Fan T, Guo Z, Liu F. Fluorescence turn-off strategy for sensitive detection of DNA methyltransferase activity based on DNA-templated gold nanoclusters. Heliyon 2023; 9:e17724. [PMID: 37449164 PMCID: PMC10336507 DOI: 10.1016/j.heliyon.2023.e17724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 06/07/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
DNA methylation results in a variety of human diseases and the DNA methylation process is mediated by DNA methyltransferases, which have therefore become potential targets for disease treatment. In this study, a turn-off nanogold biological probe system was successfully created for determining the activity of DNA methyltransferases (M.SssI MTase). A dumbbell-shaped DNA probe with a site-recognizable region of M. SssI MTase and a fluorescent signal probe based on a DNA-templated gold nanocluster (DNA-AuNC) probe combined for the quantitative detection of M. SssI MTase. This dumbbell-shaped DNA probe was methylated by M. SssI MTase, and the dumbbell-shaped DNA probe with a methyl group was recognized by an endonuclease (GlaI) and cleaved into hairpin DNA. The dGTP was added to the 3'-OH terminus of hairpin DNA fragments in the presence of terminal deoxynucleotidyl transferase (TdT), and the hairpin DNA was extended with a G-rich sequence that can be used as an inactivation probe. When the inactivation probe was combined with the signal probe, the fluorescent signal disappeared due to the photoinduced electron transfer effect. Methyltransferase activity was then detected based on the turn-off principle of the fluorescence signal from the DNA-AuNCs. The bioprobe enabled sensitive detection of M. SssI MTase with a detection limit of 0.178 U mL-1 and good specificity. The bioprobe demonstrated good detection efficiency in both human serum and cell lysates, and its unique fluorescence turn-off mechanism provided good resistance to interference, thus increasing its potential application in complex biological samples. Moreover, it is suitable for screening and assessing the inhibitory activity of M. SssI MTase inhibitors, and therefore has significant potential for disease diagnosis and drug discovery.
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Affiliation(s)
- Fangyu Zhou
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Hui Chen
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Tingting Fan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Zixia Guo
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Feng Liu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
- National & Local United Engineering Lab for Personalized Anti-Tumor Drugs, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, PR China
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12
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Chen X, Zhou S, Wang Y, Zheng L, Guan S, Wang D, Wang L, Guan X. Nanopore Single-molecule Analysis of Biomarkers: Providing Possible Clues to Disease Diagnosis. Trends Analyt Chem 2023; 162:117060. [PMID: 38106545 PMCID: PMC10722900 DOI: 10.1016/j.trac.2023.117060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Biomarker detection has attracted increasing interest in recent years due to the minimally or non-invasive sampling process. Single entity analysis of biomarkers is expected to provide real-time and accurate biological information for early disease diagnosis and prognosis, which is critical to the effective disease treatment and is also important in personalized medicine. As an innovative single entity analysis method, nanopore sensing is a pioneering single-molecule detection technique that is widely used in analytical bioanalytical fields. In this review, we overview the recent progress of nanopore biomarker detection as new approaches to disease diagnosis. In highlighted studies, nanopore was focusing on detecting biomarkers of different categories of communicable and noncommunicable diseases, such as pandemic Covid-19, AIDS, cancers, neurologic diseases, etc. Various sensitive and selective nanopore detecting strategies for different types of biomarkers are summarized. In addition, the challenges, opportunities, and direction for future development of nanopore-based biomarker sensors are also discussed.
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Affiliation(s)
- Xiaohan Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Shuo Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Ling Zheng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Sarah Guan
- Hinsdale Central High School, Hinsdale, IL 60521, USA
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
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13
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Zhang S, Shao H, Li KB, Shi W, Wang Y, Han DM, Mo J. Ultrasensitive fluorescence detection of multiple DNA methyltransferases based on DNA walkers and hyperbranched rolling circle amplification. Anal Chim Acta 2023; 1252:341057. [PMID: 36935155 DOI: 10.1016/j.aca.2023.341057] [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: 01/27/2023] [Revised: 03/03/2023] [Accepted: 03/05/2023] [Indexed: 03/11/2023]
Abstract
The accurate and ultrasensitive detection of multiple methyltransferases was in great request for clinical diagnosis and epigenetic therapy. Here, a novel fluorescence assay was proposed for ultrasensitive CpG methyltransferase (M.SssI) and DNA adenine methyltransferase (Dam) activity detection based on hyperbranched rolling circle amplification (HRCA) and DNA walkers. The biosensor showed an extremely high sensitivity due to the dual-amplification strategy of HRCA and DNA walker. The LOD of the biosensor for M.SssI and Dam methyltransferase was estimated at 0.0004 U/mL and 0.001 U/mL, respectively. Without the presence of M.SssI methyltransferase, the corresponding recognition site of hairpin HM was cleaved by HpaII endonuclease, generating a DNA fragment (T-DNA) and inducing the DNA walker-HRCA reaction. Since the HRCA products contained numerous double-strand DNA (dsDNA), SYBR Green I could be embedded in the dsDNA, leading to a high fluorescent signal. In the presence of M.SssI methyltransferase, the corresponding recognition site of hairpin HM was methylated and the HpaII endonuclease-catalyzed stem of hairpin HM dissociation was hindered, leading to no DNA fragment (T-DNA) present. Hence, the DNA walker-HRCA reaction was not initiated and the fluorescent signal of SYBR Green I remained at a low level. Similarly, DNA adenine methyltransferase (Dam) and its inhibitors could also be detected by redesigning hairpin HD with the Dam recognition sequences. Furthermore, the sensing system was applied to analyze the endogenic Dam methyltransferase in the real samples such as E. coli cell lysate.
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Affiliation(s)
- Siqi Zhang
- Department of Hepatobiliary Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Jiaojiang, Zhejiang, 318000, China; School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China
| | - Huahao Shao
- Zhijiang College of Zhejiang University of Technology, Shaoxing, Zhejiang, 312000, China
| | - Kai-Bin Li
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China
| | - Wei Shi
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China
| | - Yichao Wang
- Department of Hepatobiliary Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Jiaojiang, Zhejiang, 318000, China.
| | - De-Man Han
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China.
| | - Jinggang Mo
- Department of Hepatobiliary Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Jiaojiang, Zhejiang, 318000, China.
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14
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Yi W, Zhang C, Zhang Q, Zhang C, Lu Y, Yi L, Wang X. Solid-State Nanopore/Nanochannel Sensing of Single Entities. Top Curr Chem (Cham) 2023; 381:13. [PMID: 37103594 DOI: 10.1007/s41061-023-00425-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/07/2023] [Indexed: 04/28/2023]
Abstract
Solid-state nanopores/nanochannels, with their high stability, tunable geometry, and controllable surface chemistry, have recently become an important tool for constructing biosensors. Compared with traditional biosensors, biosensors constructed with solid-state nanopores/nanochannels exhibit significant advantages of high sensitivity, high specificity, and high spatiotemporal resolution in the detection single entities (such as single molecules, single particles, and single cells) due to their unique nanoconfined space-induced target enrichment effect. Generally, the solid-state nanopore/nanochannel modification method is the inner wall modification, and the detection principles are the resistive pulse method and the steady-state ion current method. During the detection process, solid-state nanopore/nanochannel is easily blocked by single entities, and interfering substances easily enter the solid-state nanopore/nanochannel to generate interference signals, resulting in inaccurate measurement results. In addition, the problem of low flux in the detection process of solid-state nanopore/nanochannel, these defects limit the application of solid-state nanopore/nanochannel. In this review, we introduce the preparation and functionalization of solid-state nanopore/nanochannel, the research progress in the field of single entities sensing, and the novel sensing strategies on solving the above problems in solid-state nanopore/nanochannel single-entity sensing. At the same time, the challenges and prospects of solid-state nanopore/nanochannel for single-entity electrochemical sensing are also discussed.
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Affiliation(s)
- Wei Yi
- School of Biology and Chemistry, Minzu Normal University of Xingyi, Xingyi, 562400, People's Republic of China
| | - Chuanping Zhang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Qianchun Zhang
- School of Biology and Chemistry, Minzu Normal University of Xingyi, Xingyi, 562400, People's Republic of China
| | - Changbo Zhang
- School of Biology and Chemistry, Minzu Normal University of Xingyi, Xingyi, 562400, People's Republic of China
| | - Yebo Lu
- College of Information Science and Engineering, Jiaxing University, Jiaxing, 314001, People's Republic of China.
| | - Lanhua Yi
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, School of Chemistry, Xiangtan University, Xiangtan, 411105, People's Republic of China.
| | - Xingzhu Wang
- School of Electrical Engineering, University of South China, Hengyang, 421001, People's Republic of China.
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15
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Recent advance in nucleic acid amplification-integrated methods for DNA methyltransferase assay. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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16
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Ma W, Xie W, Tian R, Zeng X, Liang L, Hou C, Huo D, Wang D. An ultrasensitive aptasensor of SARS-CoV-2 N protein based on ion current rectification with nanopipettes. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 377:133075. [PMID: 36467330 PMCID: PMC9700395 DOI: 10.1016/j.snb.2022.133075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/09/2022] [Accepted: 11/25/2022] [Indexed: 05/27/2023]
Abstract
Since the outbreak of COVID-19 in the world, it has spread rapidly all over the world. Rapid and effective detection methods have been a focus of research. The SARS-CoV-2 N protein (NP) detection methods currently in use focus on specific recognition of antibodies, but the reagents are expensive and difficult to be produced. Here, aptamer-functionalized nanopipettes utilize the unique ion current rectification (ICR) of nanopipette to achieve rapid and highly sensitive detection of trace NP, and can significantly reduce the cost of NP detection. In the presence of NP, the surface charge at the tip of the nanopipette changes, which affects ion transport and changes the degree of rectification. Quantitative detection of NP is achieved through quantitative analysis. Relying on the high sensitivity of nanopipettes to charge fluctuations, this sensor platform achieves excellent sensing performance. The sensor platform exhibited a dynamic working range from 102-106 pg/mL with a detection limit of 73.204 pg/mL, which showed great potential as a tool for rapidly detecting SARS-CoV-2. As parallel and serial testing are widely used in the clinic to avoid missed diagnosis or misdiagnosis, we hope this platform can play a role in controlling the spread and prevention of COVID-19.
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Affiliation(s)
- Wenhao Ma
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Wanyi Xie
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Rong Tian
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Xiaoqing Zeng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Liyuan Liang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, PR China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
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17
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A sensing strategy combining T7 promoter-contained DNA probe with CRISPR/Cas13a for detection of bacteria and human methyltransferase. Anal Chim Acta 2022; 1227:340266. [DOI: 10.1016/j.aca.2022.340266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/03/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022]
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