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Wang H, Zou H, Wang F. Construction of Multiply Guaranteed DNA Sensors for Biological Sensing and Bioimaging Applications. Chembiochem 2024; 25:e202400266. [PMID: 38801028 DOI: 10.1002/cbic.202400266] [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: 03/21/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
Nucleic acids exhibit exceptional functionalities for both molecular recognition and catalysis, along with the capability of predictable assembly through strand displacement reactions. The inherent programmability and addressability of DNA probes enable their precise, on-demand assembly and accurate execution of hybridization, significantly enhancing target detection capabilities. Decades of research in DNA nanotechnology have led to advances in the structural design of functional DNA probes, resulting in increasingly sensitive and robust DNA sensors. Moreover, increasing attention has been devoted to enhancing the accuracy and sensitivity of DNA-based biosensors by integrating multiple sensing procedures. In this review, we summarize various strategies aimed at enhancing the accuracy of DNA sensors. These strategies involve multiple guarantee procedures, utilizing dual signal output mechanisms, and implementing sequential regulation methods. Our goal is to provide new insights into the development of more accurate DNA sensors, ultimately facilitating their widespread application in clinical diagnostics and assessment.
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Affiliation(s)
- Hong Wang
- Biological Products Laboratory, Chongqing Institute for Food and Drug Control, Chongqing, 430072, P. R. China
| | - Hanyan Zou
- Biological Products Laboratory, Chongqing Institute for Food and Drug Control, Chongqing, 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
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2
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Detection of average methylation level of specific genes by binary-probe hybridization. Talanta 2021; 234:122630. [PMID: 34364439 DOI: 10.1016/j.talanta.2021.122630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/24/2021] [Accepted: 06/17/2021] [Indexed: 01/13/2023]
Abstract
We developed a simple and highly-selective method for 5-methylcytosine detection of specific gene sequence based on binary-probe DNA hybridization. The sequence complementary to the target was designed into two probes, and each fragment of binary probes bound to a relatively short sequence of the target, which made it sensitive to the base mismatches introduced by bisulfite treatment. The advantages of a low detection limit of methylation abundance of 0.1% for the fully methylated target and high sensitivity of 10 pM have been proved by the successful design of binary-probe hybridization. The successful design of the binary probes makes it possible to quantify the average methylation levels of five CpG sites. Thirty-two DNA strands containing 5, 4, 3, 2, 1 and 0 CpG sites were successfully analyzed with the same pair of binary probes. The higher the average methylation level of the target was, the higher the degree of the hybridization reaction. Based on the simple construction of the binary-probe hybridization, the developed biosensor exhibited signals proportional to the average methylation level of the vimentin gene and could evaluate the average methylation level of artificial mixtures. Furthermore, the method has been used to detect vimentin methylation in a genomic context with good specificity, which indicated its potential in the pre-diagnosis of methylation related disease.
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Dong XY, Zhang RZ, Zhang TK, Liu FY. Novel Designing of Chemically Modified Electrode (CME) of the Bio‐MOF‐1 for the Detection of Dopamine Based on Inhibition of [Ru(bpy)
3
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2+
/DBAE System. ELECTROANAL 2021. [DOI: 10.1002/elan.201900758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- X. Y. Dong
- Department of Chemistry School of Chemical Engineering Dalian University of Technology Dalian 110624 PR China
| | - R. Z. Zhang
- Department of Chemistry School of Chemical Engineering Dalian University of Technology Dalian 110624 PR China
| | - T. K. Zhang
- Department of Chemistry School of Chemical Engineering Dalian University of Technology Dalian 110624 PR China
| | - F. Y. Liu
- Department of Chemistry School of Chemical Engineering Dalian University of Technology Dalian 110624 PR China
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4
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Wang Y, Shi H, Zhang L, Ge S, Meiling X, Wang X, Yu J. Two-dimensional black phosphorus nanoflakes: A coreactant-free electrochemiluminescence luminophors for selective Pb 2+ detection based on resonance energy transfer. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123601. [PMID: 32768863 DOI: 10.1016/j.jhazmat.2020.123601] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/25/2020] [Accepted: 07/25/2020] [Indexed: 06/11/2023]
Abstract
As a nondegradable environmental pollutant, lead ion (Pb2+) has been proven to be deleterious for environmental and health. Conveniently, quickly and accurately on-site detection of Pb2+ is of paramount importance. Herein, an electrochemiluminescence (ECL) assay protocol using two-dimensional black phosphorus (2D BP) nanoflakes as new ECL emitter for highly sensitive and selective trace Pb2+ was designed on the basis of Pb2+ induced ECL resonance energy transfer (ECL-RET) between 2D BP nanoflakes and Ag/AgCl nanocubes. Anodic green ECL emission of BP nanoflakes without any coreactants was achieved. It is noteworthy that the possible ECL mechanism and the influence of coreactants on the ECL behaviour of BP nanoflakes were further investigated. Benefitting from the well match between the ECL emission spectrum of BP nanoflakes (∼510 nm) and the absorption spectrum of Ag/AgCl nanocubes (200-300 nm and 400-700 nm), effective energy transfer yielded. The introduction of Pb2+ would lead to the detachment of Ag/AgCl nanocubes then result in an enhanced ECL emission. Based on this, the proposed method could accurately quantify the Pb2+ in the range from 0.5 pM to 5 nM, which exhibited comparative performance to previous work. Furthermore, this study presents the example of employing 2D BP nanoflakes as ECL emitters and constructing a coreactant-free ECL sensing platform, which might open up a promising route for the potential design and implement in clinical analysis.
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Affiliation(s)
- Yanhu Wang
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), 19 Keyuan Street, Jinan 250014, PR China; School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Huihui Shi
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Lina Zhang
- Shandong Provincial Key Laboratory of Preparation and Measurement of Building Materials, University of Jinan, Jinan 250022, PR China
| | - Shenguang Ge
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research, University of Jinan, Jinan 250022, PR China.
| | - Xu Meiling
- Shandong Provincial Key Laboratory of Preparation and Measurement of Building Materials, University of Jinan, Jinan 250022, PR China
| | - Xiao Wang
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), 19 Keyuan Street, Jinan 250014, PR China.
| | - Jinghua Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
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5
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Zhou Y, Yin H, Zhao WW, Ai S. Electrochemical, electrochemiluminescent and photoelectrochemical bioanalysis of epigenetic modifiers: A comprehensive review. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213519] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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6
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Zhang S, Huang J, Lu J, Liu M, Chen X, Su S, Mo F, Zheng J. Electrochemical and Optical Biosensing Strategies for DNA Methylation Analysis. Curr Med Chem 2020; 27:6159-6187. [DOI: 10.2174/0929867326666190903161750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/24/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022]
Abstract
DNA methylation is considered as a crucial part of epigenetic modifications and a popular
research topic in recent decades. It usually occurs with a methyl group adding to the fifth carbon
atom of cytosine while the base sequence of DNA remains unchanged. DNA methylation has significant
influences on maintaining cell functions, genetic imprinting, embryonic development and
tumorigenesis procedures and hence the analysis of DNA methylation is of great medical significance.
With the development of analytical techniques and further research on DNA methylation,
numerous DNA methylation detection strategies based on biosensing technology have been developed
to fulfill various study requirements. This article reviewed the development of electrochemistry
and optical biosensing analysis of DNA methylation in recent years; in addition, we also reviewed
some recent advances in the detection of DNA methylation using new techniques, such as
nanopore biosensors, and highlighted the key technical and biological challenges involved in these
methods. We hope this paper will provide useful information for the selection and establishment of
analysis of DNA methylation.
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Affiliation(s)
- Shu Zhang
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Jian Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Jingrun Lu
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Min Liu
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Xi Chen
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Shasha Su
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Fei Mo
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
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Li ZM, Pi T, Yan XL, Tang XM, Deng RH, Zheng XJ. Label-free and enzyme-free one-step rapid colorimetric detection of DNA methylation based on unmodified gold nanoparticles. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 238:118375. [PMID: 32438293 DOI: 10.1016/j.saa.2020.118375] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/22/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation has been identified as one of the important causes of tumorigenesis, so it is important to develop some advanced methods for detecting and quantifying DNA methylation. In this study, a label-free and enzyme-free one-step rapid colorimetric detection of DNA methylation based on unmodified Au nanoparticles(Au NPs)has been proposed. This method can quickly, efficiently, economically and easily colorimetric detect methylated DNA only by the color change of unmodified Au NPs solution without the covalent modification of Au NPs in advance or complicated instruments for implementation with practical limitations or expensive biological enzymes or traditional organic dyes during the reaction. The strategy employed the difference in electrostatic attraction of single-stranded DNA and double-stranded DNA against salt-induced aggregation of Au NPs. The method has a DNA methylated detection limit of 8.47 nM and it is distinctly visible to detect methylated DNA with the naked eye as low as 20 nM. Furthermore, the strategy has an ability to detect methylated DNA in the presence of abundant unmethylated DNA with the detection limit of 0.13% and as low as 1% methylated DNA can be distinguished in heterogeneous samples with the naked eye. Also, the stratagem provides a convenient and rapid platform for methylated DNA detection of human serum samples in one step, which displays a huge potential for clinical diagnosis and treatment of oncological diseases.
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Affiliation(s)
- Zhi-Mei Li
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China
| | - Ting Pi
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China
| | - Xi-Luan Yan
- College of resources, environment and chemical engineering, Nanchang university, Nanchang 330031, PR China
| | - Xiao-Meng Tang
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China
| | - Rui-Hong Deng
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China
| | - Xiang-Juan Zheng
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China.
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8
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Zhang Y, Li CC, Zhang X, Xu Q, Zhang CY. Development of Oxidation Damage Base-Based Fluorescent Probe for Direct Detection of DNA Methylation. Anal Chem 2020; 92:10223-10227. [PMID: 32664718 DOI: 10.1021/acs.analchem.0c01880] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA methylation has become a promising epigenetic biomarker for cancer diagnosis, prognosis, and therapy monitoring. Herein, we demonstrate for the first time the development of a new oxidation damage base (8-oxo-7,8-dihydroguanine (8-oxoG))-modified fluorescent probe for direct detection of DNA methylation. This fluorescent probe is labeled with carboxy-X-rhodamine (ROX) and black hole quencher 2 (BHQ2) at the 5' and 3' termini, respectively, with one 8-oxoG base modification in the middle position, and it can discriminate the methylated cytosine from the unmethylated cytosine. The presence of target methylated DNA may induce the recycle cleavage of fluorescent probes with the assistance of human 8-oxoG DNA glycosylase 1 (hOGG1) enzyme, resulting in an enhanced fluorescence signal. In comparison with the reported bisulfite treatment-based indirect approaches, this fluorescent probe can be used for direct detection of DNA methylation under isothermal conditions without the requirement of a stringent primer/template design, any thermal cycling, and ligation procedures, greatly simplifying the experimental processes. Moreover, this fluorescent probe exhibits good specificity and high sensitivity, and it can distinguish a 0.01% methylation level even in the presence of excess unmethylated DNA. Furthermore, this fluorescent probe can be used to detect DNA methylation in genomic DNA extracted from human colon cancer cells, holding great potential in epigenetic study and early clinical diagnosis.
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Affiliation(s)
- Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xuechong Zhang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, P. R. China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, P. R. China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
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9
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Wang H, Wang H, Sun Y, Liu X, Liu Y, Wang C, Zhang P, Li Z. A general strategy for highly sensitive analysis of genetic biomarkers at single-base resolution with ligase-based isothermally exponential amplification. Talanta 2020; 212:120754. [DOI: 10.1016/j.talanta.2020.120754] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 01/17/2023]
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10
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Lu HJ, Xu JJ, Zhou H, Chen HY. Recent advances in electrochemiluminescence resonance energy transfer for bioanalysis: Fundamentals and applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115746] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Pallares RM, Thanh NTK, Su X. Sensing of circulating cancer biomarkers with metal nanoparticles. NANOSCALE 2019; 11:22152-22171. [PMID: 31555790 DOI: 10.1039/c9nr03040a] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The analysis of circulating cancer biomarkers, including cell-free and circulating tumor DNA, circulating tumor cells, microRNA and exosomes, holds promise in revolutionizing cancer diagnosis and prognosis using body fluid analysis, also known as liquid biopsy. To enable clinical application of these biomarkers, new analytical tools capable of detecting them in very low concentrations in complex sample matrixes are needed. Metal nanoparticles have emerged as extraordinary analytical scaffolds because of their unique optoelectronic properties and ease of functionalization. Hence, multiple analytical techniques have been developed based on these nanoparticles and their plasmonic properties. The aim of this review is to summarize and discuss the present development on the use of metal nanoparticles for the analysis of circulating cancer biomarkers. We examine how metal nanoparticles can be used as (1) analytical transducers in various sensing principles, such as aggregation induced colorimetric assays, plasmon resonance energy transfer, surface enhanced Raman spectroscopy, and refractive index sensing, and (2) signal amplification elements in surface plasmon resonance spectroscopy and electrochemical detection. We critically discuss the clinical relevance of each category of circulating biomarkers, followed by a thorough analysis of how these nanoparticle-based designs have overcome some of the main challenges that gold standard analytical techniques currently face, and what new directions the field may take in the future.
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Affiliation(s)
- Roger M Pallares
- Biophysics Group, Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
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12
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Feng Q, Wang M, Qin L, Wang P. Dual-Signal Readout of DNA Methylation Status Based on the Assembly of a Supersandwich Electrochemical Biosensor without Enzymatic Reaction. ACS Sens 2019; 4:2615-2622. [PMID: 31507174 DOI: 10.1021/acssensors.9b00720] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A highly sensitive and selective biosensing system was designed to analyze DNA methylation using a dual-signal readout technique in combination with the signal amplification of supersandwich DNA structure. Through the ingenious design of target-triggered cascade of hybridization chain reaction, one target DNA could initiate the formation of supersandwich structure with multiple signal probes. As a result, one-to-multiple amplification effect was achieved, which conferred high sensitivity to target molecular recognition. Based on probe 1 labeled with ferrocene and probe 2 modified with methylene blue, the target DNA was clearly recognized by two electrochemical signals at independent potentials, which was helpful for the acquisition of more accurate detection results. Taking advantage of bisulfite conversion, the methylation status of cytosine (C) was changed to nucleic acid sequence status, which facilitated the hybridization-based detection without enzymatic reaction. Consequently, the methylated DNA was detected at the femtomolar level with satisfactory analytical parameters. The proposed system was effectively used to assess methylated DNA in human blood serum samples, illuminating the possibility of the sensing platform for applications in disease diagnosis and biochemistry research.
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Affiliation(s)
- Qiumei Feng
- Department of Chemistry, Jiangsu Normal University, Xuzhou 221116, China
| | - Mengying Wang
- Department of Chemistry, Jiangsu Normal University, Xuzhou 221116, China
| | - Li Qin
- Department of Chemistry, Jiangsu Normal University, Xuzhou 221116, China
| | - Po Wang
- Department of Chemistry, Jiangsu Normal University, Xuzhou 221116, China
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13
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Liu H, Luo J, Li Y, Zhu Q, Fang L, Huang H, Deng J, Zhang S, Huang J, Liang W, Zheng J. A novel photoelectrochemical strategy based on quenching effect of CdS quantum dots on PTB7 as photoelectroactive material for methylated DNA detection. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2019.113220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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14
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Kurinomaru T, Kojima N, Kurita R. Immobilization of DNA on Biosensing Devices with Nitrogen Mustard-Modified Linkers. ACTA ACUST UNITED AC 2019; 77:e85. [PMID: 31038292 DOI: 10.1002/cpnc.85] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Immobilization of DNA is an important step in relation to DNA-based biosensors and bioassays with multiple applications. This unit describes synthesis and applications of novel bifunctional linker molecules containing nitrogen mustard and one of two types of functional groups: cyclic disulfide or biotin. Two ways of immobilizing DNA on a surface are described. With the first method, a bifunctional alkylating linker molecule is first reacted with the target DNA to form alkylated DNA and then immobilized on a specific surface. With the second method, the bifunctional alkylating linker molecule is first attached to the surface, and then the target DNA is immobilized through an alkylating reaction with a nitrogen mustard moiety. We have also achieved immunochemical detection and quantification of 5-methylcytosine in a target DNA immobilized by the above methods. The methods for immobilization of intact DNA using novel bifunctional linker molecules are applicable to a wide range of biological analysis techniques. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Takaaki Kurinomaru
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan
| | - Naoshi Kojima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB/DAICENTER, Tsukuba, Japan
| | - Ryoji Kurita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB/DAICENTER, Tsukuba, Japan
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Zhang H, Wang LJ, Wang L, Chen H, Chen X, Zhang CY. Development of a cascade isothermal amplification approach for the sensitive detection of DNA methyltransferase. J Mater Chem B 2018; 7:157-162. [PMID: 32254960 DOI: 10.1039/c8tb02096e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methyltransferase (MTase) is an important epigenetic modification enzyme responsible for DNA methylation, and the dysregulation of DNA MTase activity is associated with various diseases in humans. Herein, we take advantage of the DNA lesion repair mechanism in vivo to develop a new fluorescence approach for the specific and sensitive detection of DNA methyltransferase (DNA MTase) on the basis of the DNA lesion repair-directed cascade isothermal amplification. Due to the high amplification efficiency of the uracil repair-mediated exponential isothermal amplification reaction (EXPAR), the efficient cleavage of endonuclease IV (Endo IV)-induced cyclic catalysis, and the low background signal caused by single uracil repair-mediated inhibition of nonspecific amplification, this approach exhibits high sensitivity with a detection limit of 0.014 U mL-1 for pure Dam MTase and 0.61 × 10-6 mg mL-1 for Dam MTase in E. coli cells and it can be further applied for the screening of DNA MTase inhibitors. More importantly, this approach can be applied to detect other DNA MTases by designing appropriate substrates, showing great potential in biomedical research and clinical diagnosis.
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Affiliation(s)
- Huige Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
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16
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Zhang K, Wang K, Huang Y, Zhu X, Xie M, Wang J. Sensitive detection of cytokine in complex biological samples by using MB track mediated DNA walker and nicking enzyme assisted signal amplification method combined biosensor. Talanta 2018; 189:122-128. [DOI: 10.1016/j.talanta.2018.06.074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 06/11/2018] [Accepted: 06/24/2018] [Indexed: 01/29/2023]
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17
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Gai QQ, Wang DM, Huang RF, Liang XX, Wu HL, Tao XY. Distance-dependent quenching and enhancing of electrochemiluminescence from tris(2, 2′-bipyridine) ruthenium (II)/tripropylamine system by gold nanoparticles and its sensing applications. Biosens Bioelectron 2018; 118:80-87. [DOI: 10.1016/j.bios.2018.07.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 10/28/2022]
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18
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Enzyme-free homogeneous electrochemical biosensor for DNA assay using toehold-triggered strand displacement reaction coupled with host-guest recognition of Fe 3O 4@SiO 2@β-CD nanocomposites. Biosens Bioelectron 2018; 114:37-43. [PMID: 29775857 DOI: 10.1016/j.bios.2018.04.035] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/04/2018] [Accepted: 04/16/2018] [Indexed: 12/31/2022]
Abstract
Taking advantages of the toehold-triggered strand displacement reaction (TSDR) and host-guest interaction of β-cyclodextrin (β-CD), a facile enzyme-free and homogeneous electrochemical sensing strategy was designed for the sensitive assay of target DNA using Fe3O4@SiO2@β-CD nanocomposites and ferrocene-labeled hairpin DNA (H-1) as the capture and electrochemical probes, respectively. Upon addition of target molecule, the initiated TSDR process induced the conformational change of H-1, and subsequently stimulated the dynamic assembly of assist probes (A-1 and A-2) to generate H-1:A-1:A-2 duplex along with the release of target sequence. The released target could drive the next TSDR recycling and finally result in the formation of numerous DNA duplex. After the molecular recognition of Fe3O4@SiO2@β-CD nanocomposites, a large number of duplex were easily separated from the supernatant solution under an external magnetic field, which led to a decreased H-1 concentration in residual solution, concomitant with a remarkable reduction of peak current. Under the optimized conditions, wide linear range (1-5000 pM), low detection limit (0.3 pM), desirable reproducibility, good selectivity, and satisfactory practical analysis were obtained by the combination of the superior recognition capability of β-CD, TSDR-induced signal amplification, and homogeneous electroanalytical method. The proposed detection strategy could offer a universal approach for the monitoring of various biological analytes via the rational design of probe sequences.
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19
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Kurinomaru T, Kojima N, Kurita R. An alkylating immobilization linker for immunochemical epigenetic assessment. Chem Commun (Camb) 2018; 53:8308-8311. [PMID: 28686257 DOI: 10.1039/c7cc02883k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A bifunctional linker molecule containing nitrogen mustard and a cyclic disulfide group has been developed for the covalent immobilization of intact DNA, which allows quantitative analysis of epigenomic modification in immobilized DNA using SPR-based immune sensing.
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Affiliation(s)
- Takaaki Kurinomaru
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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20
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Commercial glucometer as signal transducer for simple evaluation of DNA methyltransferase activity and inhibitors screening. Anal Chim Acta 2018; 1001:18-23. [DOI: 10.1016/j.aca.2017.11.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/31/2017] [Accepted: 11/14/2017] [Indexed: 12/20/2022]
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Yang Y, Yang G, Chen H, Zhang H, Feng JJ, Cai C. Electrochemical signal-amplified detection of 5-methylcytosine and 5-hydroxymethylcytosine in DNA using glucose modification coupled with restriction endonucleases. Analyst 2018; 143:2051-2056. [DOI: 10.1039/c7an02049j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A sensitive electrochemical assay based on glucose modification coupled with restriction endonucleases was fabricated for the detection of 5-methylcytosine and 5-hydroxymethylcytosine in DNA.
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Affiliation(s)
- Yin Yang
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| | - Guoqing Yang
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| | - Hongfei Chen
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| | - Hui Zhang
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| | - Jiu-Ju Feng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials
- College of Chemistry and Life Sciences
- Zhejiang Normal University
- Jinhua 321004
- China
| | - Chenxin Cai
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
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22
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Guo Z, Qiao B, Guo Q, Zhang H, Cai C, Feng JJ. Dual-signal ratiometric electrochemiluminescence assay for detecting the activity of human methyltransferase. Analyst 2018; 143:3353-3359. [DOI: 10.1039/c8an00611c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A ratiometric electrochemiluminescence assay using CdS:Eu NCs and luminol as signal emitters was fabricated for detecting the human methyltransferase activity.
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Affiliation(s)
- Zhihui Guo
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| | - Bin Qiao
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| | - Qunqun Guo
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| | - Hui Zhang
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| | - Chenxin Cai
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| | - Jiu-Ju Feng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials
- College of Chemistry and Life Sciences
- Zhejiang NormalUniversity
- Jinhua 321004
- China
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23
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Ouyang L, Hu Y, Zhu L, Cheng GJ, Irudayaraj J. A reusable laser wrapped graphene-Ag array based SERS sensor for trace detection of genomic DNA methylation. Biosens Bioelectron 2017; 92:755-762. [DOI: 10.1016/j.bios.2016.09.072] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/01/2016] [Accepted: 09/21/2016] [Indexed: 10/21/2022]
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24
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Zhang H, Guo Z, Dong H, Chen H, Cai C. An electrochemiluminescence assay for sensitive detection of methyltransferase activity in different cancer cells by hybridization chain reaction coupled with a G-quadruplex/hemin DNAzyme biosensing strategy. Analyst 2017; 142:2013-2019. [DOI: 10.1039/c7an00486a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A sensitive electrochemiluminescence assay coupled HCR with a G-quadruplex/hemin DNAzyme was fabricated for the detection of DNMT1 activity in cancer cells.
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Affiliation(s)
- Hui Zhang
- Jiangsu Key Laboratory of New Power Batteries
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of Biomedical Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
| | - Zhihui Guo
- Jiangsu Key Laboratory of New Power Batteries
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of Biomedical Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
| | - Huilei Dong
- Jiangsu Key Laboratory of New Power Batteries
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of Biomedical Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
| | - Hongfei Chen
- Jiangsu Key Laboratory of New Power Batteries
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of Biomedical Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of Biomedical Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
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25
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Electrochemical DNA sensor-based strategy for sensitive detection of DNA demethylation and DNA demethylase activity. Anal Chim Acta 2016; 934:66-71. [DOI: 10.1016/j.aca.2016.06.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 06/11/2016] [Accepted: 06/21/2016] [Indexed: 11/19/2022]
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26
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Wang L, Yu F, Wang F, Chen Z. Electrochemical detection of DNA methylation using a glassy carbon electrode modified with a composite made from carbon nanotubes and β-cyclodextrin. J Solid State Electrochem 2016. [DOI: 10.1007/s10008-016-3122-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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27
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Poh WJ, Wee CPP, Gao Z. DNA Methyltransferase Activity Assays: Advances and Challenges. Am J Cancer Res 2016; 6:369-91. [PMID: 26909112 PMCID: PMC4737724 DOI: 10.7150/thno.13438] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/12/2015] [Indexed: 12/28/2022] Open
Abstract
DNA methyltransferases (MTases), a family of enzymes that catalyse the methylation of DNA, have a profound effect on gene regulation. A large body of evidence has indicated that DNA MTase is potentially a predictive biomarker closely associated with genetic disorders and genetic diseases like cancer. Given the attention bestowed onto DNA MTases in molecular biology and medicine, highly sensitive detection of DNA MTase activity is essential in determining gene regulation, epigenetic modification, clinical diagnosis and therapeutics. Conventional techniques such as isotope labelling are effective, but they often require laborious sample preparation, isotope labelling, sophisticated equipment and large amounts of DNA, rendering them unsuitable for uses at point-of-care. Simple, portable, highly sensitive and low-cost assays are urgently needed for DNA MTase activity screening. In most recent technological advances, many alternative DNA MTase activity assays such as fluorescent, electrochemical, colorimetric and chemiluminescent assays have been proposed. In addition, many of them are coupled with nanomaterials and/or enzymes to significantly enhance their sensitivity. Herein we review the progress in the development of DNA MTase activity assays with an emphasis on assay mechanism and performance with some discussion on challenges and perspectives. It is hoped that this article will provide a broad coverage of DNA MTase activity assays and their latest developments and open new perspectives toward the development of DNA MTase activity assays with much improved performance for uses in molecular biology and clinical practice.
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28
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Nucleic acid tool enzymes-aided signal amplification strategy for biochemical analysis: status and challenges. Anal Bioanal Chem 2015; 408:2793-811. [DOI: 10.1007/s00216-015-9240-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/13/2015] [Accepted: 12/01/2015] [Indexed: 11/27/2022]
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29
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Su F, Wang L, Sun Y, Liu C, Duan X, Li Z. Highly sensitive detection of CpG methylation in genomic DNA by AuNP-based colorimetric assay with ligase chain reaction. Chem Commun (Camb) 2015; 51:3371-4. [PMID: 25621431 DOI: 10.1039/c4cc07688e] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a new ligase chain reaction-based colorimetric assay for detection of DNA methylation with ultrahigh sensitivity and selectivity. Using the proposed assay, as low as 0.01 fM methylated DNA can be detected by visualization of color changes of gold nanoparticles with the naked eye.
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Affiliation(s)
- Fengxia Su
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, Hebei Province, P. R. China.
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30
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Label-free electrochemical detection of methyltransferase activity and inhibitor screening based on endonuclease HpaII and the deposition of polyaniline. Biosens Bioelectron 2015; 73:188-194. [DOI: 10.1016/j.bios.2015.05.066] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/22/2015] [Accepted: 05/29/2015] [Indexed: 11/22/2022]
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31
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Chen H, Li W, Zhao P, Nie Z, Yao S. A CdTe/CdS quantum dots amplified graphene quantum dots anodic electrochemiluminescence platform and the application for ascorbic acid detection in fruits. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.08.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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32
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G-quadruplex DNAzyme-based electrochemiluminescence biosensing strategy for VEGF165 detection: Combination of aptamer-target recognition and T7 exonuclease-assisted cycling signal amplification. Biosens Bioelectron 2015; 74:98-103. [PMID: 26120816 DOI: 10.1016/j.bios.2015.05.069] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/19/2015] [Accepted: 05/29/2015] [Indexed: 01/05/2023]
Abstract
The expression profile of vascular endothelial growth factor (VEGF) is highly correlated with the occurrence and development of cancer. This work reports an electrochemiluminescence (ECL) approach for highly sensitive detection of VEGF165. This approach comprises aptamer-target recognition, T7 exonuclease (T7 Exo)-assisted cycling signal amplification and efficient quenching of ECL of CdS:Eu nanocrystals (NCs) by using DNAzyme. In this assay, CdS:Eu NCs were used as the ECL substrate, A guanine (G)-rich single-stranded DNA (ssDNA) sequence and VEGF165 aptamer were co-immobilized on the surface of the CdS:Eu NCs modified glassy carbon electrode. After recognition and binding to VEGF165, the aptamer moved away from the electrode surface and induced the proposed cyclic cleavage of the target DNA with T7 Exo. A large amount of G-rich ssDNA was released on the CdS:Eu film and folded into G-quadruplex/hemin DNAzyme in the presence of hemin and K(+), consequently decreasing the ECL intensity of CdS:Eu. A good linearity was obtained for VEGF165 detection within the range of 1 pM to 20 nM with a detection limit of 0.2 pM. This assay could be a universal and promising protocol for detection of various biomarkers for early clinical diagnosis.
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33
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Xi Q, Chen Y, Liu Z, Wang J. Development of a Novel Jet Detection Cell for Electrochemiluminescence Analysis. ANAL LETT 2015. [DOI: 10.1080/00032719.2015.1010119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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34
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Fluorescence quenching of graphene oxide combined with the site-specific cleavage of restriction endonuclease for deoxyribonucleic acid demethylase activity assay. Anal Chim Acta 2015; 869:74-80. [DOI: 10.1016/j.aca.2015.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/04/2015] [Accepted: 02/10/2015] [Indexed: 11/21/2022]
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35
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Shen Q, Han L, Fan G, Abdel-Halim E, Jiang L, Zhu JJ. Highly sensitive photoelectrochemical assay for DNA methyltransferase activity and inhibitor screening by exciton energy transfer coupled with enzyme cleavage biosensing strategy. Biosens Bioelectron 2015; 64:449-55. [DOI: 10.1016/j.bios.2014.09.044] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/15/2014] [Accepted: 09/19/2014] [Indexed: 01/29/2023]
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36
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Lou J, Liu S, Tu W, Dai Z. Graphene quantums dots combined with endonuclease cleavage and bidentate chelation for highly sensitive electrochemiluminescent DNA biosensing. Anal Chem 2015; 87:1145-51. [PMID: 25523862 DOI: 10.1021/ac5037318] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A novel strategy for highly sensitive electrochemiluminescence (ECL) detection of DNA was proposed based on site-specific cleavage of BamHI endonuclease combined with the excellent ECL activity of graphene quantum dots (GQDs) and bidentate chelation of the dithiocarbamate DNA (DTC-DNA) probe assembly. The difference between photoluminescence and ECL spectral peaks suggested that a negligible defect existed on the GQDs surface for generation of an ECL signal. The formed DTC-DNA was directly attached to the gold surface by bidentate anchoring (S-Au-S bonds), which conferred a strong affinity between the ligands and the gold surface, increasing the robustness of DNA immobilization on the gold surface. BamHI endonuclease site-specifically recognized and cleaved the duplex symmetrical sequence, which made the double-stranded DNA fragments and GQDs break off from the electrode surface, inducing a decrease of the ECL signal. Using hepatitis C virus-1b genotype complementary DNA (HCV-1b cDNA) as a model, a novel signal-off ECL DNA biosensor was developed based on variation of the ECL intensity before and after digestion of the DNA hybrid. Electrochemical impedance spectroscopy confirmed the successful fabrication of the ECL DNA biosensor. This ECL biosensor for HCV-1b cDNA determination exhibited a linear range from 5 fM to 100 pM with a detection limit of 0.45 fM at a signal-to-noise ratio of 3 and showed satisfactory selectivity and good stability, which validated the feasibility of the designed strategy. The proposed strategy may be conveniently combined with other specific biological recognition events for expansion of the biosensing application, especially in clinical diagnoses.
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Affiliation(s)
- Jing Lou
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, College of Chemistry and Materials Science, Nanjing Normal University , Nanjing, 210023, P. R. China
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37
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Lou J, Wang Z, Wang X, Bao J, Tu W, Dai Z. Highly sensitive “signal-on” electrochemiluminescent biosensor for the detection of DNA based on dual quenching and strand displacement reaction. Chem Commun (Camb) 2015; 51:14578-81. [DOI: 10.1039/c5cc06156c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A “signal-on” electrochemiluminescent DNA biosensing platform was proposed based on dual quenching and the strand displacement reaction.
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Affiliation(s)
- Jing Lou
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing
- P. R. China
| | - Zhaoyin Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing
- P. R. China
| | - Xiao Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing
- P. R. China
| | - Jianchun Bao
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing
- P. R. China
| | - Wenwen Tu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing
- P. R. China
| | - Zhihui Dai
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing
- P. R. China
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38
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Xue Q, Zhang Y, Xu S, Li H, Wang L, Li R, Zhang Y, Yue Q, Gu X, Zhang S, Liu J, Wang H. Magnetic nanoparticles-cooperated fluorescence sensor for sensitive and accurate detection of DNA methyltransferase activity coupled with exonuclease III-assisted target recycling. Analyst 2015; 140:7637-44. [DOI: 10.1039/c5an01546d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A magnetic nanoparticles-cooperated fluorescence sensor for DNA methyltransferase activity was developed by coupling with exonuclease III-assisted target recycling.
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39
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Xue Q, Wang L, Jiang W. Label-free molecular beacon-based quadratic isothermal exponential amplification: a simple and sensitive one-pot method to detect DNA methyltransferase activity. Chem Commun (Camb) 2015. [DOI: 10.1039/c5cc05410a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An illustration of the label-free molecular beacon-mediated quadratic isothermal exponential amplification strategy (LFMB-QIEA) for target Dam MTase detection.
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Affiliation(s)
- Qingwang Xue
- School of Pharmacy
- Shandong University
- Jinan 250012
- P. R. China
- Department of Chemistry
| | - Lei Wang
- School of Pharmacy
- Shandong University
- Jinan 250012
- P. R. China
| | - Wei Jiang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan 250100
- P. R. China
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40
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Wei W, Gao C, Xiong Y, Zhang Y, Liu S, Pu Y. A fluorescence method for detection of DNA and DNA methylation based on graphene oxide and restriction endonuclease HpaII. Talanta 2015; 131:342-7. [DOI: 10.1016/j.talanta.2014.07.094] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 07/25/2014] [Accepted: 07/30/2014] [Indexed: 01/07/2023]
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41
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Su F, Wang L, Sun Y, Liu C, Duan X, Li Z. Highly sensitive and multiplexed analysis of CpG methylation at single-base resolution with ligation-based exponential amplification. Chem Sci 2014; 6:1866-1872. [PMID: 28706642 PMCID: PMC5494546 DOI: 10.1039/c4sc03135k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/10/2014] [Indexed: 01/16/2023] Open
Abstract
DNA methylation is a primary epigenetic mechanism for transcriptional regulation during normal development and the occurrence of diseases, including cancers. DNA methylation has been increasingly utilized as a biomarker for cancer detection and differential diagnosis. Generally, one type of cancer is associated with several CpG methylation sites and detection of multiplexed CpG methylation can greatly improve the accuracy of cancer diagnosis. In this paper, we have developed a novel ligase chain reaction (LCR)-based method for multiplexed detection of CpG methylation in genomic DNA at single-base resolution. By rationally designing the two pairs of DNA probes for LCR, the bisulfite-treated methylated DNA target can be exponentially amplified by thermal cycling of the ligation reaction, in which one-base mismatch can be discriminated against, and thus high sensitivity and specificity for the detection of DNA methylation can be achieved. The LCR-based method can accurately determine as low as 10 aM methylated DNA fragment and 10 ng methylated genomic DNA. 0.1% methylated DNA can be detected in the presence of a large excess of unmethylated DNA. Moreover, by simply encoding one of the DNA probes in the LCR with a different length of poly(A) for detection of methylation at different CpG sites, the CpG methylation at different sites can produce LCR products with different lengths, and thus, can be simultaneously detected with one-tube LCR amplification and separation by capillary electrophoresis.
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Affiliation(s)
- Fengxia Su
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis , Ministry of Education , College of Chemistry and Environmental Science , Hebei University , Baoding 071002 , Hebei Province , P. R. China . ; ; Tel: +86 29 81530859
| | - Limei Wang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis , Ministry of Education , College of Chemistry and Environmental Science , Hebei University , Baoding 071002 , Hebei Province , P. R. China . ; ; Tel: +86 29 81530859
| | - Yueying Sun
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis , Ministry of Education , College of Chemistry and Environmental Science , Hebei University , Baoding 071002 , Hebei Province , P. R. China . ; ; Tel: +86 29 81530859
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China
| | - Xinrui Duan
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China
| | - Zhengping Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis , Ministry of Education , College of Chemistry and Environmental Science , Hebei University , Baoding 071002 , Hebei Province , P. R. China . ; ; Tel: +86 29 81530859.,Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China
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42
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Xue Q, Lv Y, Xu S, Zhang Y, Wang L, Li R, Yue Q, Li H, Gu X, Zhang S, Liu J. Highly sensitive fluorescence assay of DNA methyltransferase activity by methylation-sensitive cleavage-based primer generation exponential isothermal amplification-induced G-quadruplex formation. Biosens Bioelectron 2014; 66:547-53. [PMID: 25506903 DOI: 10.1016/j.bios.2014.12.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 12/31/2022]
Abstract
Site-specific identification of DNA methylation and assay of MTase activity are imperative for determining specific cancer types, provide insights into the mechanism of gene repression, and develop novel drugs to treat methylation-related diseases. Herein, we developed a highly sensitive fluorescence assay of DNA methyltransferase by methylation-sensitive cleavage-based primer generation exponential isothermal amplification (PG-EXPA) coupled with supramolecular fluorescent Zinc(II)-protoporphyrin IX (ZnPPIX)/G-quadruplex. In the presence of DNA adenine methylation (Dam) MTase, the methylation-responsive sequence of hairpin probe is methylated and cleaved by the methylation-sensitive restriction endonuclease Dpn I. The cleaved hairpin probe then functions as a signal primer to initiate the exponential isothermal amplification reaction (EXPAR) by hybridizing with a unimolecular DNA containing three functional domains as the amplification template, producing a large number of G-quadruplex nanostructures by utilizing polymerases and nicking enzymes as mechanical activators. The G-quadruplex nanostructures act as host for ZnPPIX that lead to supramolecular complexes ZnPPIX/G-quadruplex, which provides optical labels for amplified fluorescence detection of Dam MTase. While in the absence of Dam MTase, neither methylation/cleavage nor PG-EXPA reaction can be initiated and no fluorescence signal is observed. The proposed method exhibits a wide dynamic range from 0.0002 to 20U/mL and an extremely low detection limit of 8.6×10(-5)U/mL, which is superior to most conventional approaches for the MTase assay. Owing to the specific site recognition of MTase toward its substrate, the proposed sensing system was able to readily discriminate Dam MTase from other MTase such as M.SssI and even detect the target in a complex biological matrix. Furthermore, the application of the proposed sensing strategy for screening Dam MTase inhibitors was also demonstrated with satisfactory results. This novel method not only provides a promising platform for monitoring activity and inhibition of DNA MTases, but also shows great potentials in biological process researches, drugs discovery and clinical diagnostics.
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Affiliation(s)
- Qingwang Xue
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, China.
| | - Yanqin Lv
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, China
| | - Shuling Xu
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, China
| | - Yuanfu Zhang
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, China
| | - Lei Wang
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, China
| | - Rui Li
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, China
| | - Qiaoli Yue
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, China
| | - Haibo Li
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, China
| | - Xiaohong Gu
- Shandong Provincial Key Lab of Test Technology on Food Quality and Safety, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Shuqiu Zhang
- Shandong Provincial Key Lab of Test Technology on Food Quality and Safety, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jifeng Liu
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, China; Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China.
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Yan Z, Li Y, Zheng J, Zhou M. Electrogenerated chemiluminescence biosensing method for methyltransferase activity using tris(1, 10-phenanthroline) ruthenium-assembled graphene oxide. J Electroanal Chem (Lausanne) 2014. [DOI: 10.1016/j.jelechem.2014.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Sina AAI, Carrascosa LG, Palanisamy R, Rauf S, Shiddiky MJA, Trau M. Methylsorb: A Simple Method for Quantifying DNA Methylation Using DNA–Gold Affinity Interactions. Anal Chem 2014; 86:10179-85. [DOI: 10.1021/ac502214z] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Abu Ali Ibn Sina
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Laura G. Carrascosa
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Ramkumar Palanisamy
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Sakandar Rauf
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Muhammad J. A. Shiddiky
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Matt Trau
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
- School
of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland QLD
4072, Australia
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Ji L, Cai Z, Qian Y, Wu P, Zhang H, Cai C. Highly sensitive methyltransferase activity assay and inhibitor screening based on fluorescence quenching of graphene oxide integrated with the site-specific cleavage of restriction endonuclease. Chem Commun (Camb) 2014; 50:10691-4. [DOI: 10.1039/c4cc04428b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A sensitive and selective approach for the DNA methyltransferase activity assay and MTase inhibitor screening is reported.
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Affiliation(s)
- Lijuan Ji
- Jiangsu Key Laboratory of New Power Batteries
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210097, China
| | - Zhewei Cai
- Jiangsu Key Laboratory of New Power Batteries
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210097, China
| | - Yingdan Qian
- Jiangsu Key Laboratory of New Power Batteries
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210097, China
| | - Ping Wu
- Jiangsu Key Laboratory of New Power Batteries
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210097, China
| | - Hui Zhang
- Jiangsu Key Laboratory of New Power Batteries
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210097, China
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210097, China
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