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Liu Y, Shi Y, Wang S, Liu S, Shang M, Zhao B, Liu H, Yang C, Wang F, Kwok CK, Wang H. Hook-Like DNAzyme-Activated Autocatalytic Biosensor for the Universal Detection of Pathogenic Bacteria. Anal Chem 2024. [PMID: 38990770 DOI: 10.1021/acs.analchem.4c01757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
DNAzyme-based assays have found extensive utility in pathogenic bacteria detection but often suffer from limited sensitivity and specificity. The integration of a signal amplification strategy could address this challenge, while the existing combination methods require extensive modification to accommodate various DNAzymes, limiting the wide-spectrum bacteria detection. We introduced a novel hook-like DNAzyme-activated autocatalytic nucleic acid circuit for universal pathogenic bacteria detection. The hook-like connector DNA was employed to seamlessly integrate the recognition element DNAzyme with the isothermal enzyme-free autocatalytic hybridization chain reaction and catalytic hairpin assembly for robust exponential signal amplification. This innovative autocatalytic circuit substantially amplifies the output signals from the DNAzyme recognition module, effectively overcoming DNAzyme's inherent sensitivity constraints in pathogen identification. The biosensor exhibits a strong linear response within a range of 1.5 × 103 to 3.7 × 107 CFU/mL, achieving a detection limit of 1.3 × 103 CFU/mL. Noted that the sensor's adaptability as a universal detection platform is established by simply modifying the hook-like connector module, enabling the detection of various pathogenic bacteria of considerable public health importance reported by the World Health Organization, including Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, and Salmonella typhimurium. Additionally, the specificity of DNAzyme in bacterial detection is markedly improved due to the signal amplification process of the autocatalytic circuit. This hook-like DNAzyme-activated autocatalytic platform presents a versatile, sensitive, and specific approach for pathogenic bacteria detection, promising to significantly expand the applications of DNAzyme in bacteria detection.
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Affiliation(s)
- Yaqi Liu
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Yulong Shi
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Siyuan Wang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Sijia Liu
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Min Shang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Bingyue Zhao
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Hanghang Liu
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Changying Yang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430000, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong ,Hong Kong SAR 999077, China
| | - Huimin Wang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
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2
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Chang W, Zheng Z, Ma Y, Du Y, Shi X, Wang C. An electrochemical aptasensor for methylamphetamine rapid detection by single-on mode based on competition with complementary DNA. Sci Rep 2024; 14:9279. [PMID: 38654039 DOI: 10.1038/s41598-024-59505-6] [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: 09/17/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
A simple and rapid electrochemical sensing method with high sensitivity and specificity of aptamers was developed for the detection of methylamphetamine (MAMP). A short anti-MAMP thiolated aptamer (Apt) with a methylene blue (MB) probe at 3'-end was immobilized on the surface of a gold electrode (MB-Apt-S/GE). The electrochemical signal appeared when MAMP presenting in the sample solution competed with cDNA for binding with MB-Apt-S. Under optimized conditions, the liner range of this signal-on electrochemical aptasensor for the detection of MAMP achieved from 1.0 to 10.0 nmol/L and 10.0-400 nmol/L. LOD 0.88 nmol/L were obtained. Satisfactory spiked recoveries of saliva and urine were also obtained. In this method, only 5 min were needed to incubate before the square wave voltammetry (SWV) analysis, which was much more rapid than other electrochemical sensors, leading to a bright and broad prospect for the detection of MAMP in biological sample. This method can be used for on-site rapid detection on special occasions, such as drug driving scenes, entertainment venues suspected of drug use, etc.
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Affiliation(s)
- Wenzhuo Chang
- Key Laboratory of Evidence Science Techniques Research and Application of Gansu Province, Gansu University of Political Science and Law, Lanzhou, 730070, China
- College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, China
| | - Zhixiang Zheng
- Key Laboratory of Evidence Science Techniques Research and Application of Gansu Province, Gansu University of Political Science and Law, Lanzhou, 730070, China.
| | - Yongjun Ma
- College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, China.
| | - Yongling Du
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Xuezhao Shi
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Chunming Wang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
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3
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Sun Z, Ren Y, Zhu W, Xiao Y, Wu H. DNA nanotechnology-based nucleic acid delivery systems for bioimaging and disease treatment. Analyst 2024; 149:599-613. [PMID: 38221846 DOI: 10.1039/d3an01871g] [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: 01/16/2024]
Abstract
Nucleic acids, including DNA and RNA, have been considered as powerful and functional biomaterials owing to their programmable structure, good biocompatibility, and ease of synthesis. However, traditional nucleic acid-based probes have always suffered from inherent limitations, including restricted cell internalization efficiency and structural instability. In recent years, DNA nanotechnology has shown great promise for the applications of bioimaging and drug delivery. The attractive superiorities of DNA nanostructures, such as precise geometries, spatial addressability, and improved biostability, have enabled them to be a novel category of nucleic acid delivery systems for biomedical applications. In this review, we introduce the development of DNA nanotechnology, and highlight recent advances of DNA nanostructure-based delivery systems for cellular imaging and therapeutic applications. Finally, we propose the challenges as well as opportunities for the future development of DNA nanotechnology in biomedical research.
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Affiliation(s)
- Zhaorong Sun
- Department of Pharmacy, The Second Affiliated Hospital of Shandong First Medical University, Tai'an, Shandong, 271000, China
| | - Yingjie Ren
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Wenjun Zhu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Yuliang Xiao
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Han Wu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
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4
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Chai H, Chen X, Shi R, Miao P. Irregular DNA Triangular Prism/Triplex Assembly for Duplicate MiRNA Analysis with Nicking Endonuclease-Mediated Amplification. Anal Chem 2023; 95:4564-4569. [PMID: 36812460 DOI: 10.1021/acs.analchem.3c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Highly sensitive and selective detection of microRNA (miRNA) is becoming more and more important in the discovery, diagnosis, and prognosis of various diseases. Herein, we develop a three-dimensional DNA nanostructure based electrochemical platform for duplicate detection of miRNA amplified by nicking endonuclease. Target miRNA first helps construction of three-way junction structures on the surfaces of gold nanoparticles. After nicking endonuclease-powered cleavage reactions, single-stranded DNAs labeled with electrochemical species are released. These strands can be facilely immobilized at four edges of the irregular triangular prism DNA (iTPDNA) nanostructure via triplex assembly. By evaluating the electrochemical response, target miRNA levels can be determined. In addition, the triplexes can be disassociated by simply changing pH conditions, and the iTPDNA biointerface can be regenerated for duplicate analyses. The developed electrochemical method not only exhibits an excellent prospect in the detection of miRNA but also may inspire the engineering of recyclable biointerfaces for biosensing platforms.
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Affiliation(s)
- Hua Chai
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Xifeng Chen
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.,Jinan Guoke Medical Technology Development Co., Ltd., Jinan 250103, China
| | - Ruiju Shi
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.,Jinan Guoke Medical Technology Development Co., Ltd., Jinan 250103, China
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5
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He H, Zhou Y, Chen B, Zhang Y, Zhong X, Xu L, Guo B, Yin C, Zhou X, Li Q, Huang Z, Luo G, Guo X. Nucleic acid amplification with specific signal filtration and magnification for ultrasensitive colorimetric detection. Talanta 2023; 253:123978. [PMID: 36209643 DOI: 10.1016/j.talanta.2022.123978] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022]
Abstract
Recently, sensitive, fast and low cost nucleic acid isothermal amplification technologies (such as loop-mediated isothermal amplification, LAMP) have attracted great attention in the urgent needs of point-of-care testing (POCT) and regular epidemic prevention and control. However, unlike PCR which usually employs TaqMan probe to report specific signals, specific-signal-output strategies in isothermal amplification are immature and visual detection even rare, which limits their popularity in POCT. We hypothesize to address this issue by designing a visual-signal-report system to both filtrate and magnify the target information in isothermal amplification. In this work, we developed a specific signal filtration and magnification colorimetric isothermal sensing platform (SFMC for short) for ultrasensitive detection of DNA and RNA. SFMC consists of two processes: an isothermal amplification with specific signal filtration and a self-replication catalyzed hairpin assembly (SRCHA) for rapid target-specific signal magnification and outputting. With these unique properties, this biosensing platform could detect target DNA as low as 5 copies per reaction and target RNA as low as 10 copies per reaction by naked eyes. Benefited from the excellent colorimetric detection performance, this biosensing platform has been successfully used for African swine fever virus (ASFV) and SARS-CoV-2 detection.
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Affiliation(s)
- Hongfei He
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Yan Zhou
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China; School of Pharmacy & School of Preclinical Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Bin Chen
- Sichuan Provincial Center for Animal Disease Control and Prevention, Chengdu, 610041, PR China
| | - Yi Zhang
- Sichuan Provincial Center for Animal Disease Control and Prevention, Chengdu, 610041, PR China
| | - Xiaowu Zhong
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Lei Xu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Bin Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Chong Yin
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Xi Zhou
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Qingrong Li
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, PR China.
| | - Guangcheng Luo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China.
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China.
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6
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Tian Z, Zhou C, Zhang C, Wu M, Duan Y, Li Y. Recent advances of catalytic hairpin assembly and its application in bioimaging and biomedicine. J Mater Chem B 2022; 10:5303-5322. [PMID: 35766024 DOI: 10.1039/d2tb00815g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic hairpin assembly (CHA) appears to be a particularly appealing nucleic acid circuit because of its powerful amplification capability, simple protocols, and enzyme-free and isothermal conditions, and can combine with various signal output modes for the biosensing of various analytes. Especially in the last five years, vast CHA related studies have sprung up. With the deep exploration of the CHA mechanism, some novel and excellent CHA strategies have been proposed; meanwhile the CHA cascade strategies with various amplification techniques further improve the analysis performance. Furthermore, diverse CHA based biosensors have been tactfully engineered and extensively employed in imaging applications in living cells and in vivo ascribed to its gentle reaction, efficient amplification and universality. Hence, we present a comprehensive and systematic summary of the progress in CHA and its application in bioimaging and biomedicine to date. At first, we introduced the mechanism and diversification of CHA in detail, including the newly developed CHA and its ingenious combination with a variety of other technologies. Concurrently, we summarized the latest application progress of different CHA strategies in bioimaging and biomedicine, highlighting the merits and drawbacks of representative approaches. Finally, we put forward some views on the challenges and prospects of CHA in bioimaging and biomedicine in the future.
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Affiliation(s)
- Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Chen Zhou
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Chuyan Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Mengfan Wu
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China.
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China.
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
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7
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Liu Y, Kong L, Li H, Yuan R, Chai Y. Electrochemical Aptamer Biosensor Based on ATP-Induced 2D DNA Structure Switching for Rapid and Ultrasensitive Detection of ATP. Anal Chem 2022; 94:6819-6826. [PMID: 35471959 DOI: 10.1021/acs.analchem.2c00613] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, a two-dimensional (2D) DNA structure with multiple ATP aptamers was elegantly designed to establish an electrochemical biosensor for rapid and sensitive detection of ATP based on ATP-induced structure switching. Concretely, the prepared 2D DNA structure containing numerous ATP aptamers as ATP-specific toehold switches could not only immobilize a large number of methylene blue (MB) for generating a remarkable electrochemical signal, but also greatly increase the local concentration of ATP aptamers to obviously enhance the capture efficiency of ATP. Once the target ATP interacted with the toehold switches, the 2D DNA structure could be sharply collapsed to trigger the burst release of MB from the electrode surface, ultimately resulting in a significantly decreased electrochemical signal for ultrasensitive detection of target ATP over a short period of time. Impressively, by dexterously adjusting the length of the ATP-specific toehold switches to 15-base, optimization of the binding affinity between ATP and the toehold switches was achieved for cutting down the detection time to 30 min and achieving a low detection limit of 0.3 pM, which addressed the shortcoming of time-consuming and poor sensitivity in the previous sensors with a small quantity of ATP aptamers and deficient binding affinity to ATP. Consequently, this strategy opened a promising avenue for ultrasensitive and rapid detection of various biomolecules in biomedical application and disease diagnosis.
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Affiliation(s)
- Ying Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Lingqi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Hao Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of 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, People's Republic of China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
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8
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Catalytic hairpin assembly as cascade nucleic acid circuits for fluorescent biosensor: design, evolution and application. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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9
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Li H, Kou B, Yuan Y, Chai Y, Yuan R. Porous Fe 3O 4@COF-Immobilized gold nanoparticles with excellent catalytic performance for sensitive electrochemical detection of ATP. Biosens Bioelectron 2022; 197:113758. [PMID: 34798499 DOI: 10.1016/j.bios.2021.113758] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/20/2022]
Abstract
In this work, a "signal-off" electrochemical biosensor was established for sensitive detection of adenosine triphosphate (ATP) based on Fe3O4@covalent organic framework-immobilized gold nanoparticles (Fe3O4@COF-Au NPs) porous composite material as a nanocarrier. The proposed Fe3O4@COF-Au NPs could effectively confine Au NPs in the uniform channels of the Fe3O4@COF, which successfully avoided Au NPs aggregation to a certain extent and provided a comparatively independent and stable micro-environment via its hydrophobic porous nanochannels, thereby owning excellent electro-catalytic performance for the reduction of 4-nitrophenol. Moreover, the Fe3O4@COF-Au NPs nanomaterials were served as functional platform for immobilizing DNA substrate (S0), which was used to bind with the conversion product (S1) of the target ATP for subsequent branched hybridization chain reaction (b-HCR) to form dendritic DNA strands to hinder electron transfer between Fe3O4@COF-Au NPs and 4-nitrophenol, finally achieving sensitive detection of ATP with a wide linear range of 5 pM-50 μM and a low detection limit of 1.6 pM. Such strategy provides a multifunctional immobilized platform for the sensitive detection of ATP and a versatile strategy for monitoring other biomolecules.
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Affiliation(s)
- Hao 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
| | - Beibei Kou
- 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
| | - Yali 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
| | - Yaqin Chai
- 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.
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10
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Gao M, Hu J, Wang J, Liu M, Zhu X, Saeed S, Hu C, Song Z, Xu H, Wang Z. Self-Assembly of DNA molecules in magnetic Fields. NANOTECHNOLOGY 2021; 33:065603. [PMID: 34087806 DOI: 10.1088/1361-6528/ac084f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/03/2021] [Indexed: 06/12/2023]
Abstract
In this work, a rich variety of self-assembled DNA patterns were obtained in the magnetic field. Herein, atomic force microscopy (AFM) was utilized to investigate the effects of the concentration of DNA solution, intensity and direction of magnetic field and modification of mica surface by different cations on the self-assembly of DNA molecules. It was found that owning to the change of the DNA concentration, even under the same magnetic field, the DNA self-assembly results were different. Thein situtest results showed that the DNA self-assembly in an magnetic field was more likely to occur in liquid phase than in gas phase. In addition, whether in a horizontal or vertical magnetic field, a single stretched dsDNA was obtained in a certain DNA concentration and magnetic field intensity. Besides, the modification of cations on the mica surface significantly increased the force between the DNA molecules and mica surface, and further changed the self-assembly of DNA molecules under the action of magnetic field.
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Affiliation(s)
- Mingyan Gao
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Jing Hu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Jianfei Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Mengnan Liu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Xiaona Zhu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Sadaf Saeed
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Cuihua Hu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Zhengxun Song
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Hongmei Xu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- JR3CN & IRAC, University of Bedfordshire, Luton LU1 3JU, United Kingdom
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11
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Song X, Ding Q, Zhang J, Sun R, Yin L, Wei W, Pu Y, Liu S. Smart Catalyzed Hairpin Assembly-Induced DNAzyme Nanosystem for Intracellular UDG Imaging. Anal Chem 2021; 93:13687-13693. [PMID: 34583508 DOI: 10.1021/acs.analchem.1c03332] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Uracil DNA glycosylase (UDG) is one of the key initiators for the base excision repair pathway. Since abnormal UDG expression is associated with various diseases, sensitive detection of UDG activity is critical for early clinical diagnosis. Here, a smart catalyzed hairpin assembly (CHA)-DNAzyme nanosystem is developed for intracellular UDG imaging by incorporating CHA and DNAzyme onto MnO2 nanosheets. In this strategy, the biodegradable MnO2 nanosheets are employed as nanocarriers for efficiently adsorbing and delivering five DNA probes into cells by endocytosis. Then, the MnO2 nanosheets are degraded by cellular glutathione to release the DNA modules at the same intracellular position. Liberated Mn2+, an indispensable DNAzyme cofactor, was used to promote catalytic cleavage for facilitating the cascade process in cells. Based on the uracil site-recognition and -excision operation of the target UDG, the activated CHA-DNAzyme nanosystem generates lots of DNAzyme-assisted CHA products, turning on the fluorescence resonance energy transfer response. This autocatalytic CHA-DNAzyme nanosystem provides a detectable minimum UDG concentration of 0.23 mU/mL, which is comparable to some reported UDG detection approaches. As a multiple signal amplification strategy, the CHA-DNAzyme nanosystem realizes the UDG imaging in living cells with enhanced sensitivity, indicating great promise in the prediction and diagnosis of early-stage cancer.
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Affiliation(s)
- Xiaolei Song
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, PR China
| | - Qin Ding
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, PR China
| | - Juan Zhang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, PR China
| | - Rongli Sun
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, PR China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, PR China
| | - Wei Wei
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, PR China.,Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210009, PR China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, PR China
| | - Songqin Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210009, PR China
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12
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Catalytic hairpin DNA assembly-based chemiluminescent assay for the detection of short SARS-CoV-2 target cDNA. Talanta 2021; 233:122505. [PMID: 34215120 PMCID: PMC8124025 DOI: 10.1016/j.talanta.2021.122505] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 12/16/2022]
Abstract
Colorimetric sensors are recognized as a promising means for target molecule detection as they provide rapid, cost-effective, and facile sensing visible to the naked eye. Challenges remain though in terms of their detection sensitivity and specificity for short-length target genes. Herein, we demonstrate the successful combination of the catalytic hairpin DNA assembly (CHA) approach with enzyme-linked immunosorbent assay (ELISA)-mimicking techniques for a simple, sensitive, and sequence-specific colorimetric assay to detect short SARS-CoV-2 target cDNA. In the developed CHA-based chemiluminescent assay, a low concentration of target cDNA is continuously recycled to amplify dimeric DNA probes from two biotinylated hairpin DNA until the hairpin DNA is completely consumed. The dimeric DNA probes are effectively immobilized in a neutravidin-coated microplate well and then capture neutravidin-conjugated horseradish peroxidase via biotin-neutravidin interactions, resulting in a sensitive and selective colorless-to-blue color change. The developed sensing system exhibits a high sensitivity with a detection limit of ~1 nM for target cDNA as well as the ability to precisely distinguish a single-base mismatched mutant gene within 2 h. As the proposed system does not require complex protocols or expensive equipment to amplify target cDNA, it has the potential to be utilized as a powerful tool to improve the detection sensitivity of target genes for clinical diagnostics with colorimetric detection.
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13
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He H, Luo G, Zhang J, Tang L, Zhou Y, Hu B, Dai J, Huang Z. Signal Extraction, Transformation, and Magnification for Ultrasensitive and Specific Detection of Nucleic Acids. Anal Chem 2021; 93:10611-10618. [PMID: 34297543 DOI: 10.1021/acs.analchem.1c01812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleic acid noises caused by the background and nonspecificity amplifications can jeopardize accurate polymerization and detection of nucleic acids, especially when they are analyzed in low copies. We hypothesize to reduce the noises by designing a system for specific signal extraction, transformation, and magnification to improve the specificity and sensitivity. Herein, by developing an extractor-trigger complex (ET-Combo) for the system, we have established isothermal and hybridizing combined amplifications: a one-pot detection system with two-step amplification coupled by ET-Combo. To our surprise, the signal extraction is only successful when ET-Combo is included in the first amplification. Our signal extracting, filtering, and relaying system with ET-Combo is rapid and specific, removing the noises generated during the isothermal amplification under elevated temperatures. To match the first amplification, we have designed and established a hybridizing chain reaction at high temperature. This one-pot system can resist disruption of background noises and allow detection of DNA up to five copies (single digit). With the high sensitivity, specificity, and noise resistance, our system has been successfully used to diagnose clinical samples of human papillomavirus (HPV) with the genotyping specificity.
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Affiliation(s)
- Hongfei He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Guangcheng Luo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan, P. R. China
| | - Jun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Ling Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Yan Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Jianyuan Dai
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.,SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu 610000, Sichuan, China
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14
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Xiong Y, Dai J, Zhang Y, Zhou C, Yuan H, Xiao D. A label-free fluorescent biosensor based on a catalyzed hairpin assembly for HIV DNA and lead detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2391-2395. [PMID: 33972958 DOI: 10.1039/d1ay00410g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Herein, a label-free fluorescent signal amplification system based on a catalyzed hairpin assembly (CHA) is reported. In this system, two hairpin probes, H1 and H2, were well-designed in which G-quadruplex sequences were integrated into H2. The CHA reaction was triggered by target/trigger DNA and G-quadruplex sequences were released, which can bind the fluorescent amyloid dye thioflavin T (ThT) to provide fluorescence signals. At the same time, target/trigger DNA was released from the product of the CHA reaction (H1-H2), which continued to initiate the next CHA cycle, and the signal was eventually amplified. This signal amplification approach has been successfully used to develop a label-free fluorescent sensing platform for sensitive detection of human immunodeficiency virus (HIV) DNA and Pb2+.
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Affiliation(s)
- Yu Xiong
- College of Chemical Engineering, Sichuan University, Chengdu 610065, China.
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15
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Zhao L, Mao J, Hu L, Zhang S, Yang X. Self-replicating catalyzed hairpin assembly for rapid aflatoxin B1 detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:222-226. [PMID: 33346755 DOI: 10.1039/d0ay01827a] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Herein, a rapid signal amplified aflatoxin B1 (AFB1) detection system based on self-replicating catalyzed hairpin assembly (SRCHA) has been constructed. In this SRCHA system, trigger DNA was initially blocked and two split trigger DNA sequences were integrated into two hairpin auxiliary probes, H1 and H2, respectively. In the presence of AFB1, the aptamer sequence was recognized by AFB1 and trigger DNA was released, which can initiate a CHA reaction and lead to the formation of a helix DNA H1-H2 complex. Then this complex can dissociate double-stranded probe DNA (F-Q) and the fluorescence signal was recovered. Meanwhile, the two split trigger DNA sequences came into close-enough proximity and a trigger DNA replica was formed. Then the obtained replicas can trigger an additional CHA reaction, leading to the rapid and significant enhancement of the fluorescence signal, and AFB1 can be detected within 15 min with a detection limit of 0.13 ng mL-1. This AFB1 detection system exhibits potential application in the on-site rapid detection of AFB1.
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Affiliation(s)
- Lijun Zhao
- Laboratory of Quality and Safety Risk Assessment for Livestock and Poultry Products(Chengdu), Ministry of Agriculture and Rural Affairs, Chengdu 610041, China and College of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Jianfei Mao
- Analysis and Testing Center of Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Li Hu
- Analysis and Testing Center of Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Shu Zhang
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu 610066, China
| | - Xiaofeng Yang
- Analysis and Testing Center of Sichuan Academy of Agricultural Science, Chengdu 610066, China.
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16
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Arrabito G, Aleeva Y, Ferrara V, Prestopino G, Chiappara C, Pignataro B. On the Interaction between 1D Materials and Living Cells. J Funct Biomater 2020; 11:E40. [PMID: 32531950 PMCID: PMC7353490 DOI: 10.3390/jfb11020040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 01/08/2023] Open
Abstract
One-dimensional (1D) materials allow for cutting-edge applications in biology, such as single-cell bioelectronics investigations, stimulation of the cellular membrane or the cytosol, cellular capture, tissue regeneration, antibacterial action, traction force investigation, and cellular lysis among others. The extraordinary development of this research field in the last ten years has been promoted by the possibility to engineer new classes of biointerfaces that integrate 1D materials as tools to trigger reconfigurable stimuli/probes at the sub-cellular resolution, mimicking the in vivo protein fibres organization of the extracellular matrix. After a brief overview of the theoretical models relevant for a quantitative description of the 1D material/cell interface, this work offers an unprecedented review of 1D nano- and microscale materials (inorganic, organic, biomolecular) explored so far in this vibrant research field, highlighting their emerging biological applications. The correlation between each 1D material chemistry and the resulting biological response is investigated, allowing to emphasize the advantages and the issues that each class presents. Finally, current challenges and future perspectives are discussed.
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Affiliation(s)
- Giuseppe Arrabito
- Dipartimento di Fisica e Chimica—Emilio Segrè, University of Palermo, Viale delle Scienze, Ed.17, 90128 Palermo, Italy;
| | - Yana Aleeva
- INSTM UdR Palermo, Viale delle Scienze, Ed.17, 90128 Palermo, Italy; (Y.A.); (C.C.)
| | - Vittorio Ferrara
- Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy;
| | - Giuseppe Prestopino
- Dipartimento di Ingegneria Industriale, Università di Roma “Tor Vergata”, Via del Politecnico 1, I-00133 Roma, Italy;
| | - Clara Chiappara
- INSTM UdR Palermo, Viale delle Scienze, Ed.17, 90128 Palermo, Italy; (Y.A.); (C.C.)
| | - Bruno Pignataro
- Dipartimento di Fisica e Chimica—Emilio Segrè, University of Palermo, Viale delle Scienze, Ed.17, 90128 Palermo, Italy;
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17
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Shi H, Dai J, Wang F, Xia Y, Xiao D, Zhou C. Rapid and colorimetric detection of nucleic acids based on entropy-driven circuit and DNAzyme-mediated autocatalytic reactions. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:2779-2784. [PMID: 32930309 DOI: 10.1039/d0ay00341g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this work, a novel, rapid and enzyme-free colorimetric biosensor for the detection of nucleic acids has been developed based on entropy-driven (EDC) circuit and DNAzyme-mediated autocatalytic reactions. On sensing the target DNA, the EDC reaction could be initiated and the intact Mg2+-dependent DNAzyme was formed in the reaction product; then, a "mimic target" DNA was generated during the cleavage process of DNAzyme, which in turn catalyzed the EDC reaction corresponding to an autocatalytic process. Meanwhile, numerous G-quadruplex structures were released and further interacted with hemin to form peroxidase-mimicking DNAzyme, inducing a remarkably amplified colorimetric signal. This autocatalytic EDC (AEDC) sensing system exhibited a linear relationship in the range from 20 pM to 10 nM with a detection limit of 10.2 pM. More importantly, benefitting from the Mg2+-dependent DNAzyme-mediated autocatalytic reaction, the detection time (20 min) was significantly reduced compared to that for the reported EDC strategies. In addition, this sensing system has been applied for the detection of target DNA in human serum samples, indicating that it is promising for the on-site and real-time detection of nucleic acids in biomedical research and disease diagnosis.
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Affiliation(s)
- Hongli Shi
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Jianyuan Dai
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Fang Wang
- College of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yushun Xia
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Dan Xiao
- College of Chemistry, Sichuan University, Chengdu 610064, China.
- College of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Cuisong Zhou
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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