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Chen X, Dai Q, Qiu X, Luo X, Li Y. New nanosensor fabricated on single nanopore electrode filled with prussian blue and graphene quantum dots coated by polypyrrole for hydrogen peroxide sensing. Talanta 2024; 274:126043. [PMID: 38581852 DOI: 10.1016/j.talanta.2024.126043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 03/06/2024] [Accepted: 04/02/2024] [Indexed: 04/08/2024]
Abstract
Hydrogen peroxide (H2O2) is a common oxidant that plays an important role in many biological processes and is also an important medium analysis in various fields. In this work, a new electrochemical nanosensor capable of detecting and quantifying hydrogen peroxide was introduced. This nanosensor was fabricated by electrodepositing prussian blue (PB)/graphene quantum dots (GQDs)/polypyrrole (PPy) on single nanopore electrode etched from single gold nanoelectrode. This prepapred nanosensor exhibits good electrochemical response to hydrogen peroxide with high sensitivity and stability, with a linear response in the 2.0 and 80 μM by using amperometric method and differential pulse voltammetry (DPV) method. The limit of detections are 0.33 μM (S/N = 3) for amperometric method and 0.67 μM (S/N = 3) for differential pulse voltammetry (DPV) method, respectively. This nanosensor can be used for the determination of hydrogen peroxide in human urine, and can serve as a new electrochemical platform to monitor H2O2 release from single living cells due to its small overal dimension and high sensitivity.
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Affiliation(s)
- Xiaohu Chen
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Key Laboratory of Functional Molecular Solids, Ministry of Education, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Qingshan Dai
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Key Laboratory of Functional Molecular Solids, Ministry of Education, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Xia Qiu
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Key Laboratory of Functional Molecular Solids, Ministry of Education, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Xianzhun Luo
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Key Laboratory of Functional Molecular Solids, Ministry of Education, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Yongxin Li
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Key Laboratory of Functional Molecular Solids, Ministry of Education, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China.
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2
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Thonghlueng J, Ngernpimai S, Chuaephon A, Phanchai W, Wiwasuku T, Wanna Y, Wiratchawa K, Intharah T, Thanan R, Sakonsinsiri C, Puangmali T. Dual-Responsive Carbon Quantum Dots for the Simultaneous Detection of Cytosine and 5-Methylcytosine Interpreted by a Machine Learning-Assisted Smartphone. ACS APPLIED MATERIALS & INTERFACES 2023; 15:40141-40152. [PMID: 37585565 DOI: 10.1021/acsami.3c00785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
DNA methylation is an epigenetic alteration that results in 5-methylcytosine (5-mC) through the addition of a methyl group to the fifth carbon of a cytosine (C) residue. The methylation level, the ratio of 5-mC to C, in urine might be related to the whole-body epigenetic status and the occurrence of common cancers. To date, never before have any nanomaterials been developed to simultaneously determine C and 5-mC in urine samples. Herein, a dual-responsive fluorescent sensor for the urinary detection of C and 5-mC has been developed. This assay relied on changes in the optical properties of nitrogen-doped carbon quantum dots (CQDs) prepared by microwave-assisted pyrolysis. In the presence of C, the blue-shifted fluorescence intensity of the CQDs increased. However, fluorescence quenching was observed upon the addition of 5-mC. This was primarily due to photoinduced electron transfer as confirmed by the density functional theory calculation. In urine samples, our sensitive fluorescent sensor had detection limits for C and 5-mC of 43.4 and 74.4 μM, respectively, and achieved satisfactory recoveries ranging from 103.5 to 115.8%. The simultaneous detection of C and 5-mC leads to effective methylation level detection, achieving recoveries in the range of 104.6-109.5%. Besides, a machine learning-enabled smartphone was also developed, which can be effectively applied to the determination of methylation levels (0-100%). These results demonstrate a simple but very effective approach for detecting the methylation level in urine, which could have significant implications for predicting the clinical prognosis.
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Affiliation(s)
- Janpen Thonghlueng
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sawinee Ngernpimai
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Adulvit Chuaephon
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Witthawat Phanchai
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Theanchai Wiwasuku
- Functional Materials and Nanotechnology Center of Excellence, School of Science, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Yupaporn Wanna
- Department of Statistics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Kannika Wiratchawa
- Department of Statistics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Thanapong Intharah
- Department of Statistics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chadamas Sakonsinsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Theerapong Puangmali
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
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3
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Mendes CH, Silva MW, Oliveira SCB. Voltammetric determination of 5-methylcytosine at glassy carbon electrode. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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4
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Wei J, Hu Q, Gao Y, Hao N, Qian J, Wang K. A Multiplexed Self-Powered Dual-Photoelectrode Biosensor for Detecting Dual Analytes Based on an Electron-Transfer-Regulated Conversion Strategy. Anal Chem 2021; 93:6214-6222. [PMID: 33829776 DOI: 10.1021/acs.analchem.1c00503] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Due to the inherent mechanism limitation of photocatalytic fuel cell based self-powered biosensors (PFC-SPBs), it was difficult to distinguish the power density of various photoactive materials or recognition events in one detection process, which made it lack multitarget quantitative capacity. In order to solve this problem, we proposed an electron-transfer-regulated conversion strategy for the construction of multiplexed PFC-SPBs. Herein, the n-type CdS/Fe2O3 nanorod array (NR) heterojunction and p-type CuBr semiconductor were used as photoactive materials to prepare the photoanode and photocathode. Based on the appropriate Fermi level differentiation between these two photoelectrodes, a self-powered sensing platform driven by visible light without external energy supply was achieved. In this design, two kinds of common and easily coexisting mycotoxins OTA and AFB1 acted as model analytes. The coupling of "signal off" and "signal on" was realized by controlling the electronic transmission on the interface between the photoanode and photocathode, so as to achieve the simultaneous detection of two mycotoxins. This work established a proof-of-concept for the integration of a dual-photoelectrode with dual-assay that could provide the innovative inspiration for the formation of a general multiplexed self-powered sensing platform.
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Affiliation(s)
- Jie Wei
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Qinqin Hu
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Yun Gao
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Nan Hao
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Jing Qian
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Kun Wang
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China
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Chen J, Zhou B, Li Y, Zheng L, Guo H, Yang F. A “turn-on” fluorescent sensor for cytosine in aqueous media based on diamino-bridged biphenyl acrylonitrile. NEW J CHEM 2021. [DOI: 10.1039/d0nj05098a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A “turn-on” fluorescent sensor for cytosine in aqueous media was prepared.
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Affiliation(s)
- Jiaojiao Chen
- College of Chemistry and Materials
- Fujian Normal University
- Fuzhou 350007
- P. R. China
- Fujian Key Laboratory of Polymer Materials
| | - Bangyi Zhou
- College of Chemistry and Materials
- Fujian Normal University
- Fuzhou 350007
- P. R. China
- Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering
| | - Yongsheng Li
- College of Chemistry and Materials
- Fujian Normal University
- Fuzhou 350007
- P. R. China
| | - Linlu Zheng
- Fujian Provincial Key Laboratory of Featured Biochemical and Chemical Materials
- Ningde Normal University
- Ningde 352106
- P. R. China
| | - Hongyu Guo
- College of Chemistry and Materials
- Fujian Normal University
- Fuzhou 350007
- P. R. China
- Fujian Key Laboratory of Polymer Materials
| | - Fafu Yang
- College of Chemistry and Materials
- Fujian Normal University
- Fuzhou 350007
- P. R. China
- Fujian Key Laboratory of Polymer Materials
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Zhou Y, Yin H, Zhao WW, Ai S. Electrochemical, electrochemiluminescent and photoelectrochemical bioanalysis of epigenetic modifiers: A comprehensive review. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213519] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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7
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Zhang S, Huang J, Lu J, Liu M, Chen X, Su S, Mo F, Zheng J. Electrochemical and Optical Biosensing Strategies for DNA Methylation Analysis. Curr Med Chem 2020; 27:6159-6187. [DOI: 10.2174/0929867326666190903161750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/24/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022]
Abstract
DNA methylation is considered as a crucial part of epigenetic modifications and a popular
research topic in recent decades. It usually occurs with a methyl group adding to the fifth carbon
atom of cytosine while the base sequence of DNA remains unchanged. DNA methylation has significant
influences on maintaining cell functions, genetic imprinting, embryonic development and
tumorigenesis procedures and hence the analysis of DNA methylation is of great medical significance.
With the development of analytical techniques and further research on DNA methylation,
numerous DNA methylation detection strategies based on biosensing technology have been developed
to fulfill various study requirements. This article reviewed the development of electrochemistry
and optical biosensing analysis of DNA methylation in recent years; in addition, we also reviewed
some recent advances in the detection of DNA methylation using new techniques, such as
nanopore biosensors, and highlighted the key technical and biological challenges involved in these
methods. We hope this paper will provide useful information for the selection and establishment of
analysis of DNA methylation.
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Affiliation(s)
- Shu Zhang
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Jian Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Jingrun Lu
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Min Liu
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Xi Chen
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Shasha Su
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Fei Mo
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
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8
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Kim DM, Yoo SM. DNA-modifying enzyme reaction-based biosensors for disease diagnostics: recent biotechnological advances and future perspectives. Crit Rev Biotechnol 2020; 40:787-803. [DOI: 10.1080/07388551.2020.1764485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Dong Min Kim
- Center for Applied Life Science, Hanbat National University, Daejeon, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
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9
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Feng Q, Wang M, Han X, Chen Q, Dou B, Wang P. Construction of an Electrochemical Biosensing Platform Based on Hierarchical Mesoporous NiO@N-Doped C Microspheres Coupled with Catalytic Hairpin Assembly. ACS APPLIED BIO MATERIALS 2020; 3:1276-1282. [DOI: 10.1021/acsabm.9b01145] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Qiumei Feng
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Mengying Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Xiguang Han
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Qian Chen
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Baoting Dou
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Po Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
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10
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Feng Q, Qin L, Wang M, Wang P. Signal-on electrochemical detection of DNA methylation based on the target-induced conformational change of a DNA probe and exonuclease III-assisted target recycling. Biosens Bioelectron 2019; 149:111847. [PMID: 31733487 DOI: 10.1016/j.bios.2019.111847] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/29/2019] [Accepted: 11/02/2019] [Indexed: 11/16/2022]
Abstract
A promising electrochemical system was explored for DNA methylation detection according to the construction of a signal-on biosensor. Based on the ingenious design of probe DNA and auxiliary DNA, methylated target DNA triggered the exonuclease III (Exo III) digestion of auxiliary DNA from 3'-terminus, resulting in the conformational change of probe DNA with an electroactive methylene blue (MB) tag at 5'-terminus. Consequently, the MB tag in the probe DNA was close to the electrode surface for electron transfer, generating an increased current signal. Because of the target recycling of methylated DNA, significant signal amplification was obtained. Moreover, bisulfite conversion conferred an efficient approach for the universal analysis of any CpG sites without the restriction of specific DNA sequence. As a result, the target DNA with different methylation statuses were clearly recognized, and the fully methylated DNA was quantified in a wide range from 10 fM to 100 pM, with a detection limit of 4 fM. The present work realized the assay of methylated target DNA in serum samples with satisfactory results, illustrating the application performance of the system in complex sample matrix.
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Affiliation(s)
- Qiumei Feng
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Li Qin
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Mengying Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Po Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China.
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11
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Feng Q, Wang M, Qin L, Wang P. Dual-Signal Readout of DNA Methylation Status Based on the Assembly of a Supersandwich Electrochemical Biosensor without Enzymatic Reaction. ACS Sens 2019; 4:2615-2622. [PMID: 31507174 DOI: 10.1021/acssensors.9b00720] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A highly sensitive and selective biosensing system was designed to analyze DNA methylation using a dual-signal readout technique in combination with the signal amplification of supersandwich DNA structure. Through the ingenious design of target-triggered cascade of hybridization chain reaction, one target DNA could initiate the formation of supersandwich structure with multiple signal probes. As a result, one-to-multiple amplification effect was achieved, which conferred high sensitivity to target molecular recognition. Based on probe 1 labeled with ferrocene and probe 2 modified with methylene blue, the target DNA was clearly recognized by two electrochemical signals at independent potentials, which was helpful for the acquisition of more accurate detection results. Taking advantage of bisulfite conversion, the methylation status of cytosine (C) was changed to nucleic acid sequence status, which facilitated the hybridization-based detection without enzymatic reaction. Consequently, the methylated DNA was detected at the femtomolar level with satisfactory analytical parameters. The proposed system was effectively used to assess methylated DNA in human blood serum samples, illuminating the possibility of the sensing platform for applications in disease diagnosis and biochemistry research.
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Affiliation(s)
- Qiumei Feng
- Department of Chemistry, Jiangsu Normal University, Xuzhou 221116, China
| | - Mengying Wang
- Department of Chemistry, Jiangsu Normal University, Xuzhou 221116, China
| | - Li Qin
- Department of Chemistry, Jiangsu Normal University, Xuzhou 221116, China
| | - Po Wang
- Department of Chemistry, Jiangsu Normal University, Xuzhou 221116, China
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12
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Sato S, Nishi Y, Takenaka S. Electrochemical Aberrant Methylation Detection Based on Ferrocenyl Naphthalene Diimide Carrying β‐Cyclodextrin, FNC. ELECTROANAL 2019. [DOI: 10.1002/elan.201900282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Shinobu Sato
- Department of Applied ChemistryKyushu Institute of Technology Fukuoka 804-8550 Japan
- Research Center for Bio-microsensing TechnologyKyushu Institute of Technology Fukuoka 804-8550 Japan
| | - Yukiko Nishi
- Department of Applied ChemistryKyushu Institute of Technology Fukuoka 804-8550 Japan
| | - Shigeori Takenaka
- Department of Applied ChemistryKyushu Institute of Technology Fukuoka 804-8550 Japan
- Research Center for Bio-microsensing TechnologyKyushu Institute of Technology Fukuoka 804-8550 Japan
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13
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Amperometric sensing of hydrazine by using single gold nanopore electrodes filled with Prussian Blue and coated with polypyrrole and carbon dots. Mikrochim Acta 2019; 186:350. [PMID: 31093761 DOI: 10.1007/s00604-019-3486-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/05/2019] [Indexed: 01/26/2023]
Abstract
A nanoprobe for hydrazine sensing is described that is making use of a single gold nanopore electrode (SAuNPEs) that was modified by electro-deposition of Prussian Blue (PB) and then coated with a thin membrane of polypyrrole and carbon dots in order to enhance stability and catalytic activity. Best operated at a low potential of 0.3 V vs. Ag/AgCl, the nanosensor display good electrocatalytic activity towards the oxidation of hydrazine, with a linear response in the 0.5-80 μM hydrazine concentration range and a 0.18 μM detection limit (at S/N = 3). The method was applied to the determination of hydrazine in human urine. Graphical abstract Schematic presentation of the electrocatalytic oxidation of hydrazine using a single gold nanopore electrode that was modified by electro-deposition of Prussian Blue and then coated with a thin membrane of polypyrrole and carbon dots.
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14
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Voltammetric immunosensor for E-cadherin promoter DNA methylation using a Fe3O4-citric acid nanocomposite and a screen-printed carbon electrode modified with poly(vinyl alcohol) and reduced graphene oxide. Mikrochim Acta 2019; 186:170. [DOI: 10.1007/s00604-019-3234-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/04/2019] [Indexed: 12/12/2022]
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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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17
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Nunes FB, Bettega MHF, Sanchez SD. Substituents' effect in electron attachment to epigenetic modifications of cytosine. J Chem Phys 2018; 146:244314. [PMID: 28668047 DOI: 10.1063/1.4990439] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epigenetic modifications of cytosine have been found to influence differently in many processes in biological systems. In order to investigate the differences in electron attachment to different epigenetic modifications of cytosine, we reported the A″ component of the integral cross section of electron scattering by cytosine (C) and its epigenetic modifications 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Our results were obtained with the Schwinger multichannel method with pseudopotentials in the static-exchange (SE) and static-exchange plus polarization (SEP) approximations. In addition to the scattering results, we present electron attachment energies obtained through an empirical scaling relation for the five molecules. We observed three π* resonances for C, 5mC, and 5hmC and four for 5fC and 5caC, in both SE and SEP approximations. The cross sections show that the π* resonances of 5mC and 5hmC are located at higher energies than the resonances of C, while the resonances of 5fC and 5caC are located at lower energies. In order to investigate this shift in the resonances' positions, we analyzed the π* lowest-lying orbitals and the electronic density over the molecules. Using the inductive and mesomeric effects, we were able to analyze the influence of each substituent over the molecule and on the resonances' positions.
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Affiliation(s)
- Fernanda B Nunes
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-990 Curitiba, Paraná, Brazil
| | - Márcio H F Bettega
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-990 Curitiba, Paraná, Brazil
| | - Sergio d'Almeida Sanchez
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-990 Curitiba, Paraná, Brazil
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Povedano E, Vargas E, Montiel VRV, Torrente-Rodríguez RM, Pedrero M, Barderas R, Segundo-Acosta PS, Peláez-García A, Mendiola M, Hardisson D, Campuzano S, Pingarrón JM. Electrochemical affinity biosensors for fast detection of gene-specific methylations with no need for bisulfite and amplification treatments. Sci Rep 2018; 8:6418. [PMID: 29686400 PMCID: PMC5913137 DOI: 10.1038/s41598-018-24902-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/11/2018] [Indexed: 12/11/2022] Open
Abstract
This paper describes two different electrochemical affinity biosensing approaches for the simple, fast and bisulfite and PCR-free quantification of 5-methylated cytosines (5-mC) in DNA using the anti-5-mC antibody as biorecognition element. One of the biosensing approaches used the anti-5-mC as capture bioreceptor and a sandwich type immunoassay, while the other one involved the use of a specific DNA probe and the anti-5-mC as a detector bioreceptor of the captured methylated DNA. Both strategies, named for simplicity in the text as immunosensor and DNA sensor, respectively, were implemented on the surface of magnetic microparticles and the transduction was accomplished by amperometry at screen-printed carbon electrodes by means of the hydrogen peroxide/hydroquinone system. The resulting amperometric biosensors demonstrated reproducibility throughout the entire protocol, sensitive determination with no need for using amplification strategies, and competitiveness with the conventional enzyme-linked immunosorbent assay methodology and the few electrochemical biosensors reported so far in terms of simplicity, sensitivity and assay time. The DNA sensor exhibited higher sensitivity and allowed the detection of the gene-specific methylations conversely to the immunosensor, which detected global DNA methylation. In addition, the DNA sensor demonstrated successful applicability for 1 h-analysis of specific methylation in two relevant tumor suppressor genes in spiked biological fluids and in genomic DNA extracted from human glioblastoma cells.
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Affiliation(s)
- Eloy Povedano
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - Eva Vargas
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | | | - Rebeca M Torrente-Rodríguez
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - María Pedrero
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - Rodrigo Barderas
- Unidad Funcional de Investigación de Enfermedades Crónicas, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Pablo San Segundo-Acosta
- Unidad Funcional de Investigación de Enfermedades Crónicas, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Alberto Peláez-García
- Department of Pathology, Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz IdiPAZ, Madrid, Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets Group and Molecular Pathology Section, INGEMM, Hospital Universitario La Paz IdiPAZ, Madrid, Spain
| | - David Hardisson
- Department of Pathology, Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz IdiPAZ, Madrid, Spain.,Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain
| | - Susana Campuzano
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain.
| | - José M Pingarrón
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain.
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19
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Feng Q, Zhao X, Guo Y, Liu M, Wang P. Stochastic DNA walker for electrochemical biosensing sensitized with gold nanocages@graphene nanoribbons. Biosens Bioelectron 2018. [PMID: 29522905 DOI: 10.1016/j.bios.2018.02.050] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A target-driven stochastic DNA walking electrochemical biosensor sensitized with gold nanocages@graphene nanoribbons (Au NCs@GNRs) was explored for sensitive detection of target DNA. Benefited from the large surface area and excellent conductivity of Au NCs and GNRs, the proposed sensing platform not only improved the electron transfer kinetics involved in electrochemical reactions, but also enhanced the loading capability for stem-loop structural DNA segment (H). Upon the addition of target DNA, the hairpin structure of H was opened and H:target DNA duplex was formed based on toehold-mediated DNA strand displacement. In the presence of exonuclease III (Exo III), the H:target DNA duplex was digested. As a result, target DNA spontaneously dissociated from H:target DNA duplex and then hybridized with another H strand. Therefore, the continuous locomotion of target DNA unceasingly triggered new digestion process from near to far along the electrode surface, resulting in great signal amplification. The proposed strategy exhibited excellent detection performances for DNA analysis in complex matrix such as human serum, which illuminated the practical application field of the sensing platform.
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Affiliation(s)
- Qiumei Feng
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, P. R. China
| | - Xiaolei Zhao
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, P. R. China
| | - Yuehua Guo
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong 226001, P. R. China
| | - Mingkai Liu
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, P. R. China.
| | - Po Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, P. R. China.
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20
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Campuzano S, Pingarrón JM. Electrochemical Sensing of Cancer-related Global and Locus-specific DNA Methylation Events. ELECTROANAL 2018. [DOI: 10.1002/elan.201800004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Susana Campuzano
- Departamento de Química Analítica, Facultad de CC. Químicas; Universidad Complutense de Madrid; E-28040 Madrid Spain
| | - José M. Pingarrón
- Departamento de Química Analítica, Facultad de CC. Químicas; Universidad Complutense de Madrid; E-28040 Madrid Spain
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21
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Yoshida W, Baba Y, Banzawa K, Karube I. A quantitative homogeneous assay for global DNA methylation levels using CpG-binding domain- and methyl-CpG-binding domain-fused luciferase. Anal Chim Acta 2017; 990:168-173. [PMID: 29029740 DOI: 10.1016/j.aca.2017.07.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/14/2017] [Accepted: 07/21/2017] [Indexed: 02/01/2023]
Abstract
Global DNA methylation levels have been considered as biomarkers for cancer diagnostics because transposable elements that constitute approximately 45% of the human genome are hypomethylated in cancer cells. We have previously reported a homogeneous assay for measuring methylated CpG content of genomic DNA based on bioluminescence resonance energy transfer (BRET) using methyl-CpG-binding domain (MBD)-fused luciferase (MBD-luciferase). In this study, a homogeneous assay for measuring unmethylated CpG content of genomic DNA in the same platform was developed using CXXC domain-fused luciferase (CXXC-luciferase) that specifically recognizes unmethylated CpG. In this assay, CXXC-luciferase recognizes unmethylated CpG on genomic DNA, whereby BRET between luciferase and the fluorescent DNA intercalating dye is detected. We demonstrated that the BRET signal depended on the genomic DNA concentration (R2 = 0.99) and unmethylated CpG content determined by the bisulfite method (R2 = 0.97). There was a significant negative correlation between the BRET signal of the CXXC-luciferase-based assay and that of the MBD-luciferase-based assay (R2 = 0.92). Moreover, we demonstrated that the global DNA methylation level determined using the bisulfite method was dependent on the ratio of the BRET signal in the MBD-luciferase-based assay to the total BRET signal in the MBD-luciferase- and CXXC-luciferase-based assays (R2 = 0.99, relative standard deviation < 2.2%, and analysis speed < 35 min). These results demonstrated that global DNA methylation levels can be quantified by calculating the BRET signal ratio without any calibration curve.
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Affiliation(s)
- Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo 192-0982, Japan.
| | - Yuji Baba
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo 192-0982, Japan.
| | - Kyoko Banzawa
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo 192-0982, Japan.
| | - Isao Karube
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo 192-0982, Japan.
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22
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Kurita R, Yanagisawa H, Kamata T, Kato D, Niwa O. On-Chip Evaluation of DNA Methylation with Electrochemical Combined Bisulfite Restriction Analysis Utilizing a Carbon Film Containing a Nanocrystalline Structure. Anal Chem 2017; 89:5976-5982. [DOI: 10.1021/acs.analchem.7b00533] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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, Japan 305-8566
| | - Hiroyuki Yanagisawa
- Biomedical Research Institute,
National
Institute of Advanced Industrial Science and Technology (AIST) and
DAILAB, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan 305-8566
| | - Tomoyuki Kamata
- Biomedical Research Institute,
National
Institute of Advanced Industrial Science and Technology (AIST) and
DAILAB, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan 305-8566
| | - Dai Kato
- Biomedical Research Institute,
National
Institute of Advanced Industrial Science and Technology (AIST) and
DAILAB, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan 305-8566
| | - Osamu Niwa
- Biomedical Research Institute,
National
Institute of Advanced Industrial Science and Technology (AIST) and
DAILAB, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan 305-8566
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23
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Hossain T, Mahmudunnabi G, Masud MK, Islam MN, Ooi L, Konstantinov K, Hossain MSA, Martinac B, Alici G, Nguyen NT, Shiddiky MJA. Electrochemical biosensing strategies for DNA methylation analysis. Biosens Bioelectron 2017; 94:63-73. [PMID: 28259051 DOI: 10.1016/j.bios.2017.02.026] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 12/31/2022]
Abstract
DNA methylation is one of the key epigenetic modifications of DNA that results from the enzymatic addition of a methyl group at the fifth carbon of the cytosine base. It plays a crucial role in cellular development, genomic stability and gene expression. Aberrant DNA methylation is responsible for the pathogenesis of many diseases including cancers. Over the past several decades, many methodologies have been developed to detect DNA methylation. These methodologies range from classical molecular biology and optical approaches, such as bisulfite sequencing, microarrays, quantitative real-time PCR, colorimetry, Raman spectroscopy to the more recent electrochemical approaches. Among these, electrochemical approaches offer sensitive, simple, specific, rapid, and cost-effective analysis of DNA methylation. Additionally, electrochemical methods are highly amenable to miniaturization and possess the potential to be multiplexed. In recent years, several reviews have provided information on the detection strategies of DNA methylation. However, to date, there is no comprehensive evaluation of electrochemical DNA methylation detection strategies. Herein, we address the recent developments of electrochemical DNA methylation detection approaches. Furthermore, we highlight the major technical and biological challenges involved in these strategies and provide suggestions for the future direction of this important field.
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Affiliation(s)
- Tanvir Hossain
- Department of Biochemistry & Molecular Biology, Shahjalal University of Science & Technology, Sylhet 3114, Bangladesh
| | - Golam Mahmudunnabi
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science & Technology, Sylhet 3114, Bangladesh
| | - Mostafa Kamal Masud
- Department of Biochemistry & Molecular Biology, Shahjalal University of Science & Technology, Sylhet 3114, Bangladesh; Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia; Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia
| | - Md Nazmul Islam
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia; School of Natural Sciences, Griffith University (Nathan Campus), Nathan, QLD 4111, Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute, School of Biological Sciences, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Konstantin Konstantinov
- Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia
| | - Md Shahriar Al Hossain
- Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia
| | - Boris Martinac
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Gursel Alici
- ARC Centre of Excellence for Electromaterials Science, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia; School of Natural Sciences, Griffith University (Nathan Campus), Nathan, QLD 4111, Australia.
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24
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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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