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Li Y, Cai M, Zhang W, Liu Y, Yuan X, Han N, Li J, Jin S, Ding C. Cas12a-based direct visualization of nanoparticle-stabilized fluorescence signal for multiplex detection of DNA methylation biomarkers. Biosens Bioelectron 2024; 244:115810. [PMID: 37924654 DOI: 10.1016/j.bios.2023.115810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
The CRISPR-Cas12a RNA-guided complexes hold immense promise for nucleic acid detection. However, limitations arise from their specificity in detecting off-targets and the stability of the signal molecules. Here, we have developed a platform that integrates multiplex amplification and nanomolecular-reporting signals, allowing us to detect various clinically relevant nucleic acid targets with enhanced stability, sensitivity, and visual interpretation. Through the electrostatic co-assembly of the Oligo reporter with oppositely charged nanoparticles, we observed a significant enhancement in its stability in low-pollution environments, reaching up to a threefold increase compared to the original version. Additionally, the fluorescence efficiency was expanded by three orders of magnitude, broadening the detection range considerably. Utilizing a multiplex strategy, this assay can accomplish simultaneous detection of multiple targets and single-point indication detection of nine specific targets. This significant advancement heightened the sensitivity of disease screening and improved the accuracy of diagnosing disease-related changes. We tested this assay in a colorectal cancer model, demonstrating that it can identify DNA methylation features at the aM-level within 40-60 min. Validation using clinical samples yielded consistent results with qPCR and bisulfite sequencing, affirming the assay's reliability and potential for clinical applications.
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Affiliation(s)
- Yu Li
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Miaomiao Cai
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Wenwen Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Ying Liu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xiaoqing Yuan
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Na Han
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jing Li
- Yinchuan Hospital of Traditional Chinese Medicine, Ningxia, 750001, China
| | - Shengnan Jin
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Chunming Ding
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
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2
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Liu S, Su J, Xie X, Huang R, Li H, Luo R, Li J, Liu X, He J, Huang Y, Wu P. Detection of methyltransferase activity and inhibitor screening based on rGO-mediated silver enhancement signal amplification strategy. Anal Biochem 2023:115207. [PMID: 37290576 DOI: 10.1016/j.ab.2023.115207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/20/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
DNA methylation refers to the chemical modification process of obtaining a methyl group by the covalent bonding of a specific base in DNA sequence with S-adenosyl methionine (SAM) as a methyl donor under the catalysis of methyltransferase (MTase), which is related to the occurrence of multiple diseases. Therefore, the detection of MTase activity is of great significance for disease diagnosis and drug screening. Because reduced graphene oxide (rGO) has a unique planar structure and remarkable catalytic performance, it is not clear whether rGO can rapidly catalyze silver deposition as an effective way of signal amplification. However, in this study, we were pleasantly surprised to find that using H2O2 as a reducing agent, rGO can rapidly catalyze silver deposition, and its catalytic efficiency of silver deposition is significantly better than that of GO. Therefore, based on further verifying the mechanism of catalytic properties of rGO, we constructed a novel electrochemical biosensor (rGO/silver biosensor) for the detection of dam MTase activity, which has high selectivity and sensitivity to MTase in the range of 0.1 U/mL to 10.0 U/mL, and the detection limit is as low as 0.07 U/mL. Besides, this study also used Gentamicin and 5-Fluorouracil as inhibitor models, confirming that the biosensor has a good application prospect in the high-throughput screening of dam MTase inhibitors.
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Affiliation(s)
- Shuyan Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410008, China; State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Jing Su
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China; College of Chemistry & Chemical Engineering, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Xixiang Xie
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Rongping Huang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Haiping Li
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Ruiyu Luo
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Jinghua Li
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Xiyu Liu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Jian He
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China.
| | - Yong Huang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China.
| | - Pan Wu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China.
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3
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Recent advance in nucleic acid amplification-integrated methods for DNA methyltransferase assay. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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4
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Recent Progress and Challenges on the Microfluidic Assay of Pathogenic Bacteria Using Biosensor Technology. Biomimetics (Basel) 2022; 7:biomimetics7040175. [PMID: 36412703 PMCID: PMC9680295 DOI: 10.3390/biomimetics7040175] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/16/2022] [Accepted: 10/24/2022] [Indexed: 12/14/2022] Open
Abstract
Microfluidic technology is one of the new technologies that has been able to take advantage of the specific properties of micro and nanoliters, and by reducing the costs and duration of tests, it has been widely used in research and treatment in biology and medicine. Different materials are often processed into miniaturized chips containing channels and chambers within the microscale range. This review (containing 117 references) demonstrates the significance and application of nanofluidic biosensing of various pathogenic bacteria. The microfluidic application devices integrated with bioreceptors and advanced nanomaterials, including hyperbranched nano-polymers, carbon-based nanomaterials, hydrogels, and noble metal, was also investigated. In the present review, microfluid methods for the sensitive and selective recognition of photogenic bacteria in various biological matrices are surveyed. Further, the advantages and limitations of recognition methods on the performance and efficiency of microfluidic-based biosensing of photogenic bacteria are critically investigated. Finally, the future perspectives, research opportunities, potential, and prospects on the diagnosis of disease related to pathogenic bacteria based on microfluidic analysis of photogenic bacteria are provided.
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Han Y, Wang C, Zou X, Zhang Y, Xu Q, Zhang CY. Construction of an APE1-Mediated Cascade Signal Amplification Platform for Homogeneously Sensitive and Rapid Measurement of DNA Methyltransferase in Escherichia coli Cells. Anal Chem 2022; 94:5980-5986. [PMID: 35394287 DOI: 10.1021/acs.analchem.2c00439] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA methylation is an essential genomic epigenetic behavior in both eukaryotes and prokaryotes. Deregulation of DNA methyltransferase (Dam MTase) can change the DNA methylation level and cause various diseases. Herein, we develop an apurinic/apyrimidinic endonuclease 1 (APE1)-mediated cascade signal amplification platform for homogeneously sensitive and rapid measurement of Dam MTase in Escherichia coli cells. This assay involves a partial double-stranded DNA (dsDNA) substrate and two hairpin signal probes (HP1 and HP2) that are modified with Cy5 and BHQ2 at two ends, respectively. When Dam MTase is present, it methylates the dsDNA substrate, and subsequently, endonuclease DpnI cleaves the methylated substrate, yielding trigger probe 1. Hybridization of trigger probe 1 with HP1 forms a partial dsDNA containing an apurinic/apyrimidinic (AP) site, which is cleaved by APE1 to induce the cyclic cleavage of HP1 and the production of abundant trigger probe 2. Subsequent hybridization of trigger probe 2 with HP2 forms a partial dsDNA with an AP site, inducing the cyclic cleavage of HP2 by APE1. Consequently, cyclic cleavage of HP1 and HP2 induces the generation of abundant Cy5 molecules, which are easily measured by single-molecule imaging. This assay can be performed homogeneously and rapidly within 2 h, which is the shortest among the reported amplification-based assays. Moreover, it exhibits good selectivity and high sensitivity, and it can discriminate Dam MTase from other enzymes and screen inhibitors. Importantly, it can accurately measure the Dam MTase activity in serum and E. coli cells, with promising applications in clinical diagnosis and drug discovery.
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Affiliation(s)
- Yun Han
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chen Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,College of Chemistry and Chemical Engineering, Qilu Normal University, Jinan 250200, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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Adampourezare M, Hasanzadeh M, Seidi F. Optical bio-sensing of DNA methylation analysis: an overview of recent progress and future prospects. RSC Adv 2022; 12:25786-25806. [PMID: 36199327 PMCID: PMC9460980 DOI: 10.1039/d2ra03630d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/03/2022] [Indexed: 12/02/2022] Open
Abstract
DNA methylation as one of the most important epigenetic modifications has a critical role in regulating gene expression and drug resistance in treating diseases such as cancer. Therefore, the detection of DNA methylation in the early stages of cancer plays an essential role in disease diagnosis. The majority of routine methods to detect DNA methylation are very tedious and costly. Therefore, designing easy and sensitive methods to detect DNA methylation directly and without the need for molecular methods is a hot topic issue in bioscience. Here we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation. In addition, various types of labeled and label-free reactions along with the application of molecular methods and optical biosensors have been surveyed. Also, the effect of nanomaterials on the sensitivity of detection methods is discussed. Furthermore, a comprehensive overview of the advantages and disadvantages of each method are provided. Finally, the use of microfluidic devices in the evaluation of DNA methylation and DNA damage analysis based on smartphone detection has been discussed. Here, we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation.![]()
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Affiliation(s)
- Mina Adampourezare
- Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Nutrition Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzad Seidi
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
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Ge S, Ran M, Mao Y, Sun Y, Zhou X, Li L, Cao X. A novel DNA biosensor for the ultrasensitive detection of DNA methyltransferase activity based on a high-density "hot spot" SERS substrate and rolling circle amplification strategy. Analyst 2021; 146:5326-5336. [PMID: 34319337 DOI: 10.1039/d1an01034d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Herein, we proposed a novel biosensor based on a high-density "hot spot" Au@SiO2 array substrate and rolling circle amplification (RCA) strategy for the ultrasensitive detection of CpG methyltransferase (M.SssI) activity. In the presence of M.SssI, the RCA process can be triggered, causing the augmentation of the single-stranded DNA (ssDNA) at the tail of the double-stranded DNA (dsDNA), and the ssDNA can be hybridized with numerous DNA probes labeled with Raman reporters in the next steps. Afterwards, the resultant ssDNA can be modified to the Au@SiO2 array substrate with the SERS enhancement factor of 7.49 × 106. The substrate was synthesized by using a monolayer SiO2 array to pick up the Au nanoparticle (AuNP) array and finite-difference time-domain (FDTD) simulation showed its excellent SERS effect. Particularly, the developed biosensor displayed a significant sensitivity with a broad detection range covering from 0.005 to 50 U mL-1, and the limits of detection (LODs) in PBS buffer and human serum were 2.37 × 10-4 U mL-1 and 2.51 × 10-4 U mL-1, respectively. Finally, in order to verify the feasibility of its clinical application, the serum samples of healthy subjects and breast cancer, prostate cancer, gastric cancer and cervical cancer patients were analyzed, and the reliability of the results was also confirmed by western blot (WB) experiments. Taking advantage of these merits, the proposed biosensor can be a very promising alternative tool for the detection of M.SssI activity, which is of vital importance in the early detection and prevention of tumors.
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Affiliation(s)
- Shengjie Ge
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China.
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8
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DNA-functionalized biosensor for amplifying signal detection of DNA methyltransferase activity. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Wu J, Hu Q, Chen Q, Dai J, Wu X, Wang S, Lou X, Xia F. Modular DNA-Incorporated Aggregation-Induced Emission Probe for Sensitive Detection and Imaging of DNA Methyltransferase. ACS APPLIED BIO MATERIALS 2020; 3:9002-9011. [DOI: 10.1021/acsabm.0c01249] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jun Wu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Qinyu Hu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Qing Chen
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Jun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xia Wu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaoding Lou
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
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Araiza-Olivera D, Gutierrez-Aguilar M, Espinosa-García AM, García-García JA, Tapia-Orozco N, Sánchez-Pérez C, Palacios-Reyes C, Escárcega D, Villalón-López DN, García-Arrazola R. From bench to bedside: Biosensing strategies to evaluate endocrine disrupting compounds based on epigenetic events and their potential use in medicine. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2020; 80:103450. [PMID: 32622887 DOI: 10.1016/j.etap.2020.103450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 06/12/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
The relationship between endocrine system disorders and health risks due to chemical environmental compounds has become a growing concern in recent years. Involuntary exposure to endocrine disruptors (EDCs) is associated with the worldwide increase of diseases such as cancer, obesity, diabetes, and neurocortical disorders. EDCs are compounds that target the nuclear hormonereceptors (NHR) leading to epigenetic changes. Consequently, the use of biosensing strategies based on epigenetic events have a great potential to provide outstanding information about the exposition of EDCs and their evaluation in human health. This review addresses the novel trends in biosensing EDCs evaluation based on DNA methylation assays associated with different human diseases.
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Affiliation(s)
- D Araiza-Olivera
- Department of Chemistry and Biomolecules, Institute of Chemistry, UNAM, Mexico.
| | | | - A M Espinosa-García
- Unidad de Medicina Genómica, Hospital General de México, Dr. Balmis 148, Mexico City, Mexico.
| | - J A García-García
- Department of Education, Hospital General de México, Dr. Balmis 148, Mexico City, Mexico.
| | - N Tapia-Orozco
- Departmentof Food Science and Biotechnology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
| | - C Sánchez-Pérez
- Institute of Applied Sciences and Technology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
| | - C Palacios-Reyes
- Laboratory of Genetics and Molecular Diagnostics, Juarez Hospital of Mexico, Mexico City, Mexico.
| | - D Escárcega
- Instituto Tecnológico y de Estudios Superiores de Monterrey, Campus Ciudad de México, calle del Puente 222, Ejidos de Huipulco, Tlalpan 14380, Mexico City, Mexico.
| | - Demelza N Villalón-López
- Instituto Politénico Nacional-Escuela Nacional de Ciencias Biológicas, Departamento de Química Orgánica, Prolongación de Carpio y Plande Ayala, colonia Casco de Santo Tomás. Del, Miguel Hidalgo, 11350, Mexico.
| | - R García-Arrazola
- Departmentof Food Science and Biotechnology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
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Wang LJ, Han X, Qiu JG, Jiang B, Zhang CY. Cytosine-5 methylation-directed construction of a Au nanoparticle-based nanosensor for simultaneous detection of multiple DNA methyltransferases at the single-molecule level. Chem Sci 2020; 11:9675-9684. [PMID: 34094232 PMCID: PMC8161687 DOI: 10.1039/d0sc03240a] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/25/2020] [Indexed: 12/28/2022] Open
Abstract
DNA methylation at cytosine/guanine dinucleotide islands (CpGIs) is the most prominent epigenetic modification in prokaryotic and eukaryotic genomes. DNA methyltransferases (MTases) are responsible for genomic methylation, and their aberrant activities are closely associated with various diseases including cancers. However, the specific and sensitive detection of multiple DNA MTases has remained a great challenge due to the specificity of the methylase substrate and the rareness of methylation-sensitive restriction endonuclease species. Here, we demonstrate for the first time the cytosine-5 methylation-directed construction of a Au nanoparticle (AuNP)-based nanosensor for simultaneous detection of multiple DNA MTases at the single-molecule level. We used the methyl-directed endonuclease GlaI to cleave the site-specific 5-methylcytosine (5-mC). In the presence of CpG and GpC MTases (i.e., M.SssI and M.CviPI), their hairpin substrates are methylated at cytosine-5 to form the catalytic substrates for GlaI, respectively, followed by simultaneous cleavage by GlaI to yield two capture probes. These two capture probes can hybridize with the Cy5/Cy3-signal probes which are assembled on the AuNPs, respectively, to form the double-stranded DNAs (dsDNAs). Each dsDNA with a guanine ribonucleotide can act as the catalytic substrate for ribonuclease (RNase HII), inducing recycling cleavage of signal probes to liberate large numbers of Cy5 and Cy3 molecules from the AuNPs. The released Cy5 and Cy3 molecules can be simply quantified by total internal reflection fluorescence (TIRF)-based single-molecule imaging for simultaneous measurement of M.SssI and M.CviPI MTase activities. This method exhibits good specificity and high sensitivity with a detection limit of 2.01 × 10-3 U mL-1 for M.SssI MTase and 3.39 × 10-3 U mL-1 for M.CviPI MTase, and it can be further applied for discriminating different kinds of DNA MTases, screening potential inhibitors, and measuring DNA MTase activities in human serum and cell lysate samples, holding great potential in biomedical research, clinical diagnosis, drug discovery and cancer therapeutics.
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Affiliation(s)
- Li-Juan Wang
- 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 250014 China
| | - Xiao Han
- 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 250014 China
| | - Jian-Ge Qiu
- Academy of Medical Sciences, Zhengzhou University Zhengzhou 450000 China
| | - BingHua Jiang
- Academy of Medical Sciences, Zhengzhou University Zhengzhou 450000 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 250014 China
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12
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Chen L, Zhang Y, Xia Q, Luo F, Guo L, Qiu B, Lin Z. Fluorescence biosensor for DNA methyltransferase activity and related inhibitor detection based on methylation-sensitive cleavage primer triggered hyperbranched rolling circle amplification. Anal Chim Acta 2020; 1122:1-8. [PMID: 32503739 DOI: 10.1016/j.aca.2020.04.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/20/2020] [Accepted: 04/25/2020] [Indexed: 11/29/2022]
Abstract
Highly sensitive and selective detection of DNA adenine methylation methyltransferase (Dam MTase) activity is essential for clinical diagnosis and treatment as Dam MTase can catalyze DNA methylation and has a profound effect on gene regulation. In this study, a fluorescence biosensor has been developed for label-free detection of Dam MTase activity via methylation-sensitive cleavage primers triggered hyperbranched rolling circle amplification (HRCA). A hairpin DNA probe (HP) with a Dam MTase specific recognition sequence on the stem acting as a substrate has been designed. This substrate probe can be methylated by the target in the system and subsequently cleaved by DpnI, which results in the release of the primer release probe (RP) and hence in turn triggers the subsequent HRCA reaction. As the HRCA products contain many double-strand DNA (dsDNA) with different lengths, and the SYBR Green I can be embedded in the dsDNA to produce a strong fluorescence signal. However, in the absence of the target, the presence of the probe HP in the form of a hairpin cannot induce the HRCA reaction, and only weak fluorescence intensity can be detected. Under the optimized conditions, the fluorescence of the system has a linear relationship with the logarithm of the concentration of Dam MTase in the range of 2.5-70 U/mL with a detection limit of 1.8 U/mL. The Dam MTase can be well distinguished from other MTase analogs. The developed sensor was applied to detect target in serum and E. coli cell lysate, and the standard recovery rates were in the range of 96%-105%. The results showed that this method has great potential for assessing Dam MTase activity in complex biological samples. In addition, the method has been applied to detect the related inhibitors with high efficiency.
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Affiliation(s)
- Liping Chen
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Ying Zhang
- Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350005, China
| | - Qian Xia
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Fang Luo
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Longhua Guo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China.
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Dadmehr M, Karimi MA, Korouzhdehi B. A signal-on fluorescence based biosensing platform for highly sensitive detection of DNA methyltransferase enzyme activity and inhibition. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117731. [PMID: 31753656 DOI: 10.1016/j.saa.2019.117731] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
DNA methylation mediated by DNA methyltransferase (MTase) enzyme is internal cell mechanism which regulate the expression or suppression of crucial genes involve in cancer early diagnosis. Herein, highly sensitive fluorescence biosensing platform was developed for monitoring of DNA Dam MTase enzyme activity and inhibition based on fluorescence signal on mechanism. The specific Au NP functionalized oligonucleotide probe with overhang end as a template for the synthesis of fluorescent silver nanoclusters (Ag NCs) was designed to provide the FRET occurrence. Following, methylation and cleavage processes by Dam MTAse and DpnI enzymes respectively at specific probe recognition site could resulted to release of AgNCs synthesizer DNA fragment and returned the platform to fluorescence signal-on state through interrupting in FRET. Subsequently, amplified fluorescence emission signals of Ag NCs showed increasing linear relationship with amount of Dam MTase enzyme at the range of 0.1-20 U/mL and the detection limit was estimated at 0.05 U/mL. Superior selectivity of experiment was illustrated among other tested MTase and restriction enzymes due to the specific recognition of MTase toward its substrate. Furthermore, the inhibition effect of applied Dam MTase drug inhibitors screened and evaluated with satisfactory results which would be helpful for discovery of antimicrobial drugs. The real sample assay also showed the applicability of proposed method in human serum condition. This novel strategy presented an efficient and cost effective platform for sensitive monitoring of DNA MTase activity and inhibition which illustrated its great potential for further application in medical diagnosis and drug discovery.
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Affiliation(s)
- Mehdi Dadmehr
- Department of Biology, Payame Noor University, Tehran, Iran.
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14
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Li Y, Sun S, Tian X, Qiu JG, Jiang B, Zhang CY. A dumbbell probe-based dual signal amplification strategy for sensitive detection of multiple DNA methyltransferases. Chem Commun (Camb) 2020; 56:13627-13630. [DOI: 10.1039/d0cc05991a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Integration of a dumbbell probe with dual signal amplification enables simultaneously sensitive detection of multiple DNA methyltransferases.
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Affiliation(s)
- Yueying 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
| | - Shuli Sun
- 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
| | - Xiaorui Tian
- 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
| | - Jian-Ge Qiu
- Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou 450000
- China
| | - BingHua Jiang
- Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou 450000
- 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
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15
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Zhang S, Huang J, Lu J, Liu M, Li Y, Fang L, Huang H, Huang J, Mo F, Zheng J. A novel fluorescent biosensor based on dendritic DNA nanostructure in combination with ligase reaction for ultrasensitive detection of DNA methylation. J Nanobiotechnology 2019; 17:121. [PMID: 31812164 PMCID: PMC6898925 DOI: 10.1186/s12951-019-0552-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/25/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND DNA methylation detection is indispensable for the diagnosis and prognosis of various diseases including malignancies. Hence, it is crucial to develop a simple, sensitive, and specific detection strategy. METHODS A novel fluorescent biosensor was developed based on a simple dual signal amplification strategy using functional dendritic DNA nanostructure and signal-enriching polystyrene microbeads in combination with ligase detection reaction (LDR). Dendritic DNA self-assembled from Y-DNA and X-DNA through enzyme-free DNA catalysis of a hairpin structure, which was prevented from unwinding at high temperature by adding psoralen. Then dendritic DNA polymer labeled with fluorescent dye Cy5 was ligated with reporter probe into a conjugate. Avidin-labeled polystyrene microbeads were specifically bound to biotin-labeled capture probe, and hybridized with target sequence and dendritic DNA. LDR was triggered by adding Taq ligase. When methylated cytosine existed, the capture probe and reporter probe labeled with fluorescent dye perfectly matched the target sequence, forming a stable duplex to generate a fluorescence signal. However, after bisulfite treatment, unmethylated cytosine was converted into uracil, resulting in a single base mismatch. No fluorescence signal was detected due to the absence of duplex. RESULTS The obtained dendritic DNA polymer had a large volume. This method was time-saving and low-cost. Under the optimal experimental conditions using avidin-labeled polystyrene microbeads, the fluorescence signal was amplified more obviously, and DNA methylation was quantified ultrasensitively and selectively. The detection range of this sensor was 10-15 to 10-7 M, and the limit of detection reached as low as 0.4 fM. The constructed biosensor was also successfully used to analyze actual samples. CONCLUSION This strategy has ultrasensitivity and high specificity for DNA methylation quantification, without requiring complex processes such as PCR and enzymatic digestion, which is thus of great value in tumor diagnosis and biomedical research.
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Affiliation(s)
- Shu Zhang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.,Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China.,Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jian Huang
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jingrun Lu
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Min Liu
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Lichao Fang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Hui Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Jianjun Huang
- Department of Breast Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Fei Mo
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China. .,Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.
| | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.
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16
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Li Y, Wang L, Ding C, Luo X. Highly selective ratiometric electrogenerated chemiluminescence assay of DNA methyltransferase activity via polyaniline and anti-fouling peptide modified electrode. Biosens Bioelectron 2019; 142:111553. [DOI: 10.1016/j.bios.2019.111553] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/25/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
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17
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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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18
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Zhang J, Chai X, He XP, Kim HJ, Yoon J, Tian H. Fluorogenic probes for disease-relevant enzymes. Chem Soc Rev 2019; 48:683-722. [PMID: 30520895 DOI: 10.1039/c7cs00907k] [Citation(s) in RCA: 371] [Impact Index Per Article: 74.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Traditional biochemical methods for enzyme detection are mainly based on antibody-based immunoassays, which lack the ability to monitor the spatiotemporal distribution and, in particular, the in situ activity of enzymes in live cells and in vivo. In this review, we comprehensively summarize recent progress that has been made in the development of small-molecule as well as material-based fluorogenic probes for sensitive detection of the activities of enzymes that are related to a number of human diseases. The principles utilized to design these probes as well as their applications are reviewed. Specific attention is given to fluorogenic probes that have been developed for analysis of the activities of enzymes including oxidases and reductases, those that act on biomacromolecules including DNAs, proteins/peptides/amino acids, carbohydrates and lipids, and those that are responsible for translational modifications. We envision that this review will serve as an ideal reference for practitioners as well as beginners in relevant research fields.
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Affiliation(s)
- Junji Zhang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd., Shanghai 200237, P. R. China.
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19
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Xue H, Chen K, Zhou Q, Pan D, Zhang Y, Shen Y. Antimony selenide/graphene oxide composite for sensitive photoelectrochemical detection of DNA methyltransferase activity. J Mater Chem B 2019; 7:6789-6795. [DOI: 10.1039/c9tb01541h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
An Sb2Se3/graphene oxide composite was applied as both the photoelectrochemical probe and substrate for biomolecule conjugation for the construction of a “signal-off” sandwich-type biosensor for DNA methyltransferase activity detection.
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Affiliation(s)
- Huaijia Xue
- Medical School, School of Chemistry and Chemical Engineering, Southeast University
- Nanjing 210009
- China
| | - Kaiyang Chen
- Medical School, School of Chemistry and Chemical Engineering, Southeast University
- Nanjing 210009
- China
| | - Qing Zhou
- Medical School, School of Chemistry and Chemical Engineering, Southeast University
- Nanjing 210009
- China
| | - Deng Pan
- Medical School, School of Chemistry and Chemical Engineering, Southeast University
- Nanjing 210009
- China
| | - Yuanjian Zhang
- Medical School, School of Chemistry and Chemical Engineering, Southeast University
- Nanjing 210009
- China
| | - Yanfei Shen
- Medical School, School of Chemistry and Chemical Engineering, Southeast University
- Nanjing 210009
- China
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20
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Zhao H, Ma C, Yan Y, Chen M. A sensitive cyclic signal amplification fluorescence strategy for determination of methyltransferase activity based on graphene oxide and RNase H. J Mater Chem B 2019. [DOI: 10.1039/c9tb00743a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A sensitive fluorometric method for DNA methyltransferase activity detection based on graphene oxide and RNase H-assisted signal amplification.
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Affiliation(s)
- Han Zhao
- School of Life Sciences
- Central South University
- Changsha 410013
- China
| | - Changbei Ma
- School of Life Sciences
- Central South University
- Changsha 410013
- China
| | - Ying Yan
- School of Life Sciences
- Central South University
- Changsha 410013
- China
| | - Mingjian Chen
- School of Life Sciences
- Central South University
- Changsha 410013
- China
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21
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Mittal S, Thakur S, Mantha AK, Kaur H. Bio-analytical applications of nicking endonucleases assisted signal-amplification strategies for detection of cancer biomarkers -DNA methyl transferase and microRNA. Biosens Bioelectron 2019; 124-125:233-243. [DOI: 10.1016/j.bios.2018.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 12/31/2022]
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22
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Park C, Park H, Lee HJ, Lee HS, Park KH, Choi CH, Na S. Double amplified colorimetric detection of DNA using gold nanoparticles, enzymes and a catalytic hairpin assembly. Mikrochim Acta 2018; 186:34. [PMID: 30564970 DOI: 10.1007/s00604-018-3154-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/07/2018] [Indexed: 02/07/2023]
Abstract
The authors describe an isothermal and ultrasensitive colorimetric DNA assay that consists of two amplification stages using enzymes and a catalytic hairpin assembly (CHA). The first step consists in the selective amplification of DNA using Klenow fragment and nicking enzyme. The second step consists in the amplification of the optical signal by using a catalytic hairpin assembly. After two amplification steps, the DNA reaction induces the aggregation of the red gold nanoparticles to give a blue color shift. The degree of aggregation can be quantified by measurement of the ratio of the UV-vis absorbances of the solutions at 620 and 524 nm which are the wavelengths of the aggregated gold nanoparticles and bare gold nanoparticles. The detection limit is as low as 3.1 fM. Due to the use of a specific enzyme, only the desired DNAs will be detected. The method can be applied to the determination of DNA of various lengths. Despite the presence of large amounts of wildtype DNA, it can readily detect a target DNA. Conceivably, the technique has a large potential because of its high sensitivity and selectivity. Graphical abstract Schematic presentation of DNA detection using gold nanoparticles (AuNP), enzymes and catalytic hairpin assembly (CHA). Effective DNA detection is achieved through the aggregation of AuNPs which is caused by DNA amplification using enzymes and signal amplification using CHA.
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Affiliation(s)
- Chanho Park
- Department of Mechanical Engineering, Korea University, Seoul, 136-701, Republic of Korea
| | - Hyunjun Park
- Department of Mechanical Engineering, Korea University, Seoul, 136-701, Republic of Korea
| | - Hye Jin Lee
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University, Seoul, 136-701, South Korea
| | - Hye Sun Lee
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University, Seoul, 136-701, South Korea
| | - Kyong Hwa Park
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University, Seoul, 136-701, South Korea
| | - Chang-Hwan Choi
- Department of Mechanical Engineering, Stevens Institute of Technology, Hoboken, NJ, 07030, USA
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul, 136-701, Republic of Korea.
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23
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Bhattacharjee R, Moriam S, Umer M, Nguyen NT, Shiddiky MJA. DNA methylation detection: recent developments in bisulfite free electrochemical and optical approaches. Analyst 2018; 143:4802-4818. [PMID: 30226502 DOI: 10.1039/c8an01348a] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is one of the significant epigenetic modifications involved in mammalian development as well as in the initiation and progression of various diseases like cancer. Over the past few decades, an enormous amount of research has been carried out for the quantification of DNA methylation in the mammalian genome. Earlier, most of these methodologies used bisulfite treatment. However, the low conversion, false reading, longer assay time and complex chemical reaction are the common limitations of this method that hinder their application in routine clinical screening. Thus, as an alternative to bisulfite conversion-based DNA methylation detection, numerous bisulfite-free methods have been proposed. In this regard, electrochemical biosensors have gained much attention in recent years for being highly sensitive yet cost-effective, portable, and simple to operate. On the other hand, biosensors with optical readouts enable direct real time detection of biological molecules and are easily adaptable to multiplexing. Incorporation of electrochemical and optical readouts into bisulfite free DNA methylation analysis is paving the way for the translation of this important biomarker into standard patient care. In this review, we provide a critical overview of recent advances in the development of electrochemical and optical readout based bisulfite free DNA methylation assays.
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Affiliation(s)
- Ripon Bhattacharjee
- School of Environment and Science, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia.
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24
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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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25
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Xu X, Wang L, Li X, Cui W, Jiang W. Multiple sealed primers-mediated rolling circle amplification strategy for sensitive and specific detection of DNA methyltransferase activity. Talanta 2018; 194:282-288. [PMID: 30609532 DOI: 10.1016/j.talanta.2018.09.113] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/20/2018] [Accepted: 09/30/2018] [Indexed: 01/19/2023]
Abstract
DNA methyltransferase (MTase) aberrant expression has a close relationship to tumorigenesis. DNA MTase activity detection is of great importance to its biomedical research and theranostics study. Here, multiple sealed primers-mediated rolling circle amplification (RCA) strategy is developed for sensitively and specifically detecting DNA MTase activity. The DNA probe has a folded, double-loop structure that seals multiple primers. First, in the presence of DNA MTase, the DNA probe is methylated, which then gets cleaved by the restriction endonuclease and breaks into multiple DNA oligonucleotide fragments. Second, each DNA oligonucleotide fragment acts as an independent primer for triggering RCA reaction respectively, producing long DNA strands that contain several interval G-quadruplexes. Finally, copious of G-quadruplexes are obtained, which bind N-methylmesoporphyrin IX (NMM) to generate significantly enhanced fluorescence. When DNA MTase is absent or inactive, the DNA probe is stable and cannot release the primers for RCA reaction. In the proposed strategy, the action of DNA MTase on one DNA probe is converted to the multiple amplifications triggered by multiple released primers. The detection limit for Dam MTase is down to 0.0085 U/mL, and the target MTase can be well discriminated from its MTases analogues. The method is utilized in screening of Dam MTase inhibitors and analyzing of spiked Dam MTase in biological samples. The results suggest that the strategy may provide a promising tool for DNA MTase activity detection in biomedical research and cancer theranostics.
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Affiliation(s)
- Xiaowen Xu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, PR China
| | - Lei Wang
- School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China
| | - Xia Li
- Department of Chemistry, Liaocheng University, Liaocheng 252059, PR China
| | - Wanling Cui
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, PR China
| | - Wei Jiang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, PR China.
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26
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Photoelectrochemical determination of the activity of M.SssI methyltransferase, and a method for inhibitor screening. Mikrochim Acta 2018; 185:498. [DOI: 10.1007/s00604-018-3033-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/28/2018] [Indexed: 02/07/2023]
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27
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Wang LJ, Han X, Li CC, Zhang CY. Single-ribonucleotide repair-mediated ligation-dependent cycling signal amplification for sensitive and specific detection of DNA methyltransferase. Chem Sci 2018; 9:6053-6061. [PMID: 30079218 PMCID: PMC6053742 DOI: 10.1039/c8sc02215a] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/17/2018] [Indexed: 01/09/2023] Open
Abstract
Specific and sensitive detection of DNA MTase activity can be achieved by a single-ribonucleotide repair-mediated ligation-dependent cycling signal amplification approach.
DNA methylation is a predominant epigenetic modification that plays crucial roles in various cellular processes. DNA methyltransferase (MTase) is responsible for DNA methylation, and its dysregulation may induce aberrant methylation patterns that are closely related to cancers. Conventional methods for DNA MTase assay are usually cumbersome and laborious with poor sensitivity. Alternatively, some signal amplification strategies are employed to improve the sensitivity, but they suffer from poor specificity and consequently limited sensitivity due to the nonspecific amplification. Herein, we develop for the first time a new fluorescence method to specifically and sensitively detect DNA MTase activity on the basis of single-ribonucleotide repair-mediated ligation-dependent cycling signal amplification. In the presence of DNA MTase, the hairpin substrate is methylated and cleaved by endonuclease Dpn I, releasing a 24-nt cleavage product. The 24-nt cleavage product may function as a primer and adjacently hybridize with the ligation probes (LP1 and LP2) to form the template (LP1–LP2) for strand displacement amplification (SDA), initiating the single-ribonucleotide repair-mediated cyclic ligation-dependent SDA to produce a large number of reporter probes. The reporter probe can subsequently hybridize with the signal probe that is modified with FAM and BHQ1 to form a stable double-stranded DNA (dsDNA) duplex with a ribonucleotide mismatch. Ribonuclease HII (RNase HII) can excise the single ribonucleotide, resulting in the cyclic cleavage of signal probes and the generation of an enhanced fluorescence signal. Taking advantage of the high specificity of RNase HII-catalyzed single-ribonucleotide excision and the high amplification efficiency of cyclic ligation-dependent SDA, this assay exhibits the highest sensitivity reported so far with a detection limit of 4.8 × 10–6 U mL–1 and a large dynamic range of 5 orders of magnitude. Moreover, this method can be used for the discrimination of Dam MTase from other DNA MTases, the accurate quantification of Dam MTase activity in E. coli cells, and the screening of Dam MTase inhibitors, providing a new paradigm for biomedical research and clinical diagnosis.
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Affiliation(s)
- Li-Juan Wang
- 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 250014 , China . ; ; Tel: +86 531 86186033
| | - Xiao Han
- 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 250014 , China . ; ; Tel: +86 531 86186033
| | - 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 250014 , China . ; ; Tel: +86 531 86186033
| | - 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 250014 , China . ; ; Tel: +86 531 86186033
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28
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Hu GB, Xiong CY, Liang WB, Zeng XS, Xu HL, Yang Y, Yao LY, Yuan R, Xiao DR. Highly Stable Mesoporous Luminescence-Functionalized MOF with Excellent Electrochemiluminescence Property for Ultrasensitive Immunosensor Construction. ACS APPLIED MATERIALS & INTERFACES 2018; 10:15913-15919. [PMID: 29676561 DOI: 10.1021/acsami.8b05038] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In this work, a novel mesoporous luminescence-functionalized metal-organic framework (Ru-PCN-777) with high stability and excellent electrochemiluminescence (ECL) performance was synthesized by immobilizing Ru(bpy)2(mcpbpy)2+ on the Zr6 cluster of PCN-777 via a strong coordination bond between Zr4+ and -COO-. Consequently, the Ru(bpy)2(mcpbpy)2+ could not only cover the surface of PCN-777 but also graft into the interior of PCN-777, which greatly increased the loading amount of Ru(bpy)2(mcpbpy)2+ and effectively prevented the leaching of the Ru(bpy)2(mcpbpy)2+ resulting in a stable and high ECL response. Considering the above merits, we utilized the mesoporous Ru-PCN-777 to construct an ECL immunosensor to detect mucin 1 (MUC1) based on proximity-induced intramolecular DNA strand displacement (PiDSD). The ECL signal was further enhanced by the enzyme-assisted DNA recycling amplification strategy. As expected, the immunosensor had excellent sensitivity, specificity, and responded wide linearly to the concentration of MUC1 from 100 fg/mL to 100 ng/mL with a low detection limit of 33.3 fg/mL (S/N = 3). It is the first time that mesoporous Zr-MOF was introduced into ECL system to assay biomolecules, which might expand the application of mesoporous metal-organic frameworks (MOFs) in bioanalysis. This work indicates that the use of highly stable mesoporous luminescence-functionalized MOFs to enhance the ECL intensity and stability is a feasible strategy for designing and constructing high-performance ECL materials, and therefore may shed light on new ways to develop highly sensitive and selective ECL sensors.
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Affiliation(s)
- Gui-Bing Hu
- College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Cheng-Yi Xiong
- College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Wen-Bin Liang
- College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Xiao-Shan Zeng
- College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Hui-Ling Xu
- College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Yang Yang
- College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Li-Ying Yao
- College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Ruo Yuan
- College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Dong-Rong Xiao
- College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
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29
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Chen W, Fang X, Ye X, Li H, Cao H, Kong J. DNA nanomachine-assisted magnetic bead based target recycling and isothermal amplification for sensitive fluorescence determination of interferon-γ. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2511-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Zhang Y, Wang XY, Zhang Q, Zhang CY. Label-Free Sensitive Detection of DNA Methyltransferase by Target-Induced Hyperbranched Amplification with Zero Background Signal. Anal Chem 2017; 89:12408-12415. [PMID: 29083155 DOI: 10.1021/acs.analchem.7b03490] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
DNA methyltransferases (MTases) may specifically recognize the short palindromic sequences and transfer a methyl group from S-adenosyl-l-methionine to target cytosine/adenine. The aberrant DNA methylation is linked to the abnormal DNA MTase activity, and some DNA MTases have become promising targets of anticancer/antimicrobial drugs. However, the reported DNA MTase assays often involve laborious operation, expensive instruments, and radio-labeled substrates. Here, we develop a simple and label-free fluorescent method to sensitively detect DNA adenine methyltransferase (Dam) on the basis of terminal deoxynucleotidyl transferase (TdT)-activated Endonuclease IV (Endo IV)-assisted hyperbranched amplification. We design a hairpin probe with a palindromic sequence in the stem as the substrate and a NH2-modified 3' end for the prevention of nonspecific amplification. The substrate may be methylated by Dam and subsequently cleaved by DpnI, producing three single-stranded DNAs, two of which with 3'-OH termini may be amplified by hyperbranched amplification to generate a distinct fluorescence signal. Because high exactitude of TdT enables the amplification only in the presence of free 3'-OH termini and Endo IV only hydrolyzes the intact apurinic/apyrimidinic sites in double-stranded DNAs, zero background signal can be achieved. This method exhibits excellent selectivity and high sensitivity with a limit of detection of 0.003 U/mL for pure Dam and 9.61 × 10-6 mg/mL for Dam in E. coli cells. Moreover, it can be used to screen the Dam inhibitors, holding great potentials in disease diagnosis and drug development.
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Affiliation(s)
- Yan Zhang
- 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, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University , Jinan 250014, China
| | - Xin-Yan Wang
- 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, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University , Jinan 250014, China
| | - Qianyi Zhang
- Nantou High School Shenzhen , Shenzhen, 518052, China
| | - Chun-Yang Zhang
- 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, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University , Jinan 250014, China
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31
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A label-free electrochemical biosensor for methyltransferase activity detection and inhibitor screening based on graphene quantum dot and enzyme-catalyzed reaction. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2017.06.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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32
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Dudová Z, Bartošík M, Fojta M. Magnetic bead-based electrochemical assay for determination of DNA methyltransferase activity. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.02.104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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33
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Xu J, Zheng T, Le J, Jia L. Long-stem shaped multifunctional molecular beacon for highly sensitive nucleic acids determination via intramolecular and intermolecular interactions based strand displacement amplification. Analyst 2017; 142:4438-4445. [DOI: 10.1039/c7an01205e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
LS-MMB based intra-SDA and inter-SDA for amplified gene signaling.
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Affiliation(s)
- Jianguo Xu
- School of Food Science and Engineering
- Hefei University of Technology
- Hefei 230009
- China
- Cancer Metastasis Alert and Prevention Center
| | - Tingting Zheng
- Cancer Metastasis Alert and Prevention Center
- and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy
- Fuzhou University
| | - Jingqing Le
- Cancer Metastasis Alert and Prevention Center
- and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy
- Fuzhou University
| | - Lee Jia
- Cancer Metastasis Alert and Prevention Center
- and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy
- Fuzhou University
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34
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Magnetic bead-liposome hybrids enable sensitive and portable detection of DNA methyltransferase activity using personal glucose meter. Biosens Bioelectron 2017; 87:537-544. [DOI: 10.1016/j.bios.2016.08.103] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/20/2016] [Accepted: 08/29/2016] [Indexed: 11/18/2022]
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35
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Zhou J, Zhang X, Xiong E, Yu P, Li X, Chen J. SDR-recycling signal amplification for highly sensitive methyltransferase activity assay. J Electroanal Chem (Lausanne) 2016. [DOI: 10.1016/j.jelechem.2016.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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36
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Abstract
In the field of genetics, epigenetics is the study of changes in gene expression without any change in DNA sequences. Chemical base modification in DNA by DNA methyltransferase, and specifically methylation, has been well studied as the main mechanism of epigenetics. Therefore, the determination of DNA methylation of, for example, 5'-methylcytosine in the CpG sequence in mammals has attracted attention because it should prove valuable in a wide range of research fields including diagnosis, drug discovery, and therapy. Methylated DNA bases and DNA methyltransferase activity are analyzed using conventional methods; however, these methods are time-consuming and require complex multiple operations. Therefore, new methods and devices for DNA methylation analysis are now being actively developed. Furthermore, microfluidic technology has also been applied to DNA methylation analysis because the microfluidic platform offers the promising advantage of making it possible to perform thousands of DNA methylation reactions in small reaction volumes, resulting in a high-throughput analysis with high sensitivity. This review discusses epigenetics and the microfluidic platforms developed for DNA methylation analysis.
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Affiliation(s)
- Ryoji Kurita
- 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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37
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Quencher-free fluorescence strategy for detection of DNA methyltransferase activity based on exonuclease III-assisted signal amplification. Anal Bioanal Chem 2016; 408:8111-8116. [DOI: 10.1007/s00216-016-9914-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/13/2016] [Accepted: 08/29/2016] [Indexed: 12/25/2022]
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38
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Li X, Meng M, Zheng L, Xu Z, Song P, Yin Y, Eremin SA, Xi R. Chemiluminescence Immunoassay for S-Adenosylhomocysteine Detection and Its Application in DNA Methyltransferase Activity Evaluation and Inhibitors Screening. Anal Chem 2016; 88:8556-61. [DOI: 10.1021/acs.analchem.6b01579] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Xiaogang Li
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Meng Meng
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Lei Zheng
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Zhihuan Xu
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Pei Song
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Yongmei Yin
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
| | - Sergei A. Eremin
- Faculty
of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Rimo Xi
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People’s Republic of China
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39
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DNA–gold nanoparticles network based electrochemical biosensors for DNA MTase activity. Talanta 2016; 152:228-35. [DOI: 10.1016/j.talanta.2016.01.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 11/23/2022]
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40
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Cui W, Wang L, Jiang W. A dual amplification fluorescent strategy for sensitive detection of DNA methyltransferase activity based on strand displacement amplification and DNAzyme amplification. Biosens Bioelectron 2016; 77:650-5. [DOI: 10.1016/j.bios.2015.10.040] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/29/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
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41
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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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42
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Zhang W, Zu X, Song Y, Zhu Z, Yang CJ. Detection of DNA methyltransferase activity using allosteric molecular beacons. Analyst 2016; 141:579-84. [DOI: 10.1039/c5an01763g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Abnormal DNA methylation patterns caused by altered DNA methyltransferase (MTase) activity are closely associated with cancer. Herein, using DNA adenine methylation methyltransferase (Dam MTase) as a model analyte, we designed an allosteric molecular beacon (aMB) for sensitive detection of Dam MTase activity.
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Affiliation(s)
- Weiting Zhang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Collaborative Innovation Center of Chemistry for Energy Materials
- Key Laboratory for Chemical Biology of Fujian Province
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
| | - Xiaolong Zu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Collaborative Innovation Center of Chemistry for Energy Materials
- Key Laboratory for Chemical Biology of Fujian Province
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
| | - Yanling Song
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Collaborative Innovation Center of Chemistry for Energy Materials
- Key Laboratory for Chemical Biology of Fujian Province
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
| | - Zhi Zhu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Collaborative Innovation Center of Chemistry for Energy Materials
- Key Laboratory for Chemical Biology of Fujian Province
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
| | - Chaoyong James Yang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Collaborative Innovation Center of Chemistry for Energy Materials
- Key Laboratory for Chemical Biology of Fujian Province
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
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43
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Cao JX, Wang YS, Xue JH, Huang YQ, Li MH, Chen SH, Zhou B, Tang X, Wang XF, Zhu YF. Exonuclease III-assisted substrate fragment recycling amplification strategy for ultrasensitive detection of uranyl by a multipurpose DNAzyme. RSC Adv 2016. [DOI: 10.1039/c6ra20625e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Substrate fragment cleaved by UO22+ hybridizes with SSP6 to form dsDNA, triggering substrate fragment recycling amplification by Exo III.
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Affiliation(s)
- Jin-Xiu Cao
- College of Public Health
- University of South China
- Hengyang 421001
- PR China
- The Fifth Affiliated Hospital
| | - Yong-Sheng Wang
- College of Public Health
- University of South China
- Hengyang 421001
- PR China
| | - Jin-Hua Xue
- College of Public Health
- University of South China
- Hengyang 421001
- PR China
| | - Yan-Qin Huang
- College of Public Health
- University of South China
- Hengyang 421001
- PR China
| | - Ming-Hui Li
- College of Public Health
- University of South China
- Hengyang 421001
- PR China
| | - Si-Han Chen
- College of Public Health
- University of South China
- Hengyang 421001
- PR China
| | - Bin Zhou
- College of Public Health
- University of South China
- Hengyang 421001
- PR China
| | - Xian Tang
- College of Public Health
- University of South China
- Hengyang 421001
- PR China
| | - Xiao-Feng Wang
- College of Public Health
- University of South China
- Hengyang 421001
- PR China
| | - Yu-Feng Zhu
- College of Public Health
- University of South China
- Hengyang 421001
- PR China
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44
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Lai QQ, Liu MD, Gu CC, Nie HG, Xu XJ, Li ZH, Yang Z, Huang SM. A novel label-free fluorescence strategy for methyltransferase activity assay based on dsDNA-templated copper nanoparticles coupled with an endonuclease-assisted signal transduction system. Analyst 2016; 141:1383-9. [DOI: 10.1039/c5an02123e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A novel label-free fluorescence method by coupling dsDNA-templated CuNPs with endonuclease-assisted signal transduction has been developed for methyltransferase activity assay.
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Affiliation(s)
- Q. Q. Lai
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
| | - M. D. Liu
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
| | - C. C. Gu
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
| | - H. G. Nie
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
| | - X. J. Xu
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
| | - Z. H. Li
- The Institute of Molecular Medicine
- School of Optometry and Ophthalmology and Eye Hospital
- Wenzhou Medical University
- Wenzhou
- P. R. China
| | - Z. Yang
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
| | - S. M. Huang
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
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45
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Li F, Zhou YY, Peng T, Xu H, Zhang RB, Zhao H, Wang ZY, Lv JX, Wu ZS, Shen ZF. Highly sensitive detection of cancer-related genes based on complete fluorescence restoration of a molecular beacon with a functional overhang. Analyst 2016; 141:4417-23. [DOI: 10.1039/c6an00898d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A overhang-contained molecular beacon-based sensing system was developed for cancer gene diagnosisviaexecuting cyclical nucleic acid strand-displacement polymerization and complete restoration of the quenched fluorescence.
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46
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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47
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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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48
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Gang J. Simple and Sensitive Fluorescence Assay of Restriction Endonuclease on Graphene Oxide. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jongback Gang
- Department of Nano Chemistry; Gachon University; Gyeonggi-do 461-701 South Korea
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49
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Proximity-based electrochemical biosensor for highly sensitive determination of methyltransferase activity using gold nanoparticle-based cooperative signal amplification. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1564-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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50
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Li W, Liu X, Hou T, Li H, Li F. Ultrasensitive homogeneous electrochemical strategy for DNA methyltransferase activity assay based on autonomous exonuclease III-assisted isothermal cycling signal amplification. Biosens Bioelectron 2015; 70:304-9. [DOI: 10.1016/j.bios.2015.03.060] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 12/13/2022]
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