1
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Goto A, Yoshida W. Hybridization-based CpG methylation level detection using methyl-CpG-binding domain-fused luciferase. Anal Bioanal Chem 2023; 415:2329-2337. [PMID: 36961575 DOI: 10.1007/s00216-023-04657-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/02/2023] [Accepted: 03/16/2023] [Indexed: 03/25/2023]
Abstract
Hypermethylation of tumor-suppressor genes and global hypomethylation, which is related to methylation level at the retroelement, have been recognized as features of the cancer genome. In this study, we developed a hybridization-based CpG methylation level detection method using methyl-CpG-binding domain-fused firefly luciferase (MBD-Fluc). In this method, methylated probe oligonucleotides were used to capture target oligonucleotides. Fully methylated and hemimethylated double-stranded DNA (dsDNA) was formed by hybridization of the methylated captured oligonucleotides with methylated or unmethylated target oligonucleotides, respectively. MBD-Fluc specifically binds to fully methylated dsDNA but not to hemimethylated dsDNA; therefore, methylated target oligonucleotides can be detected by measuring the luciferase activity of the bound MBD-Fluc. Using the corresponding methylated probe oligonucleotides, the CpG methylation levels of SEPT9, BRCA1, and long interspersed nuclear element-1 (LINE-1) oligonucleotides were quantified. Moreover, we demonstrated that the emission detection signal was not affected by the methylation state of the overhang region of the target oligonucleotide, which was not hybridized to the probe oligonucleotide, indicating that methylated CpG of the target region could be accurately detected. Unmethylated-CpG-binding domain-fused luciferases and 5-hydroxymethyl-CpG-binding domain-fused luciferases have been constructed, suggesting that other modified bases can be detected by the same platform.
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Affiliation(s)
- Ayano Goto
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Wataru Yoshida
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.
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2
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Liu S, Morihiro K, Takeuchi F, Li Y, Okamoto A. Interstrand crosslinking oligonucleotides elucidate the effect of metal ions on the methylation status of repetitive DNA elements. Front Chem 2023; 11:1122474. [PMID: 36711237 PMCID: PMC9881727 DOI: 10.3389/fchem.2023.1122474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
DNA methylation plays an important physiological function in cells, and environmental changes result in fluctuations in DNA methylation levels. Metal ions have become both environmental and health concerns, as they have the potential to disrupt the genomic DNA methylation status, even on specific sequences. In the current research, the methylation status of two typical repetitive DNA elements, i.e., long-interspersed nuclear element-1 (LINE-1) and alpha satellite (α-sat), was imaged and assessed using methylation-specific fluorescence in situ hybridization (MeFISH). This technique elucidated the effect of several metal ions on the methylation levels of repetitive DNA sequences. The upregulation and downregulation of the methylation levels of repetitive DNA elements by various metal ions were confirmed and depended on their concentration. This is the first example to investigate the effects of metal ions on DNA methylation in a sequence-specific manner.
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Affiliation(s)
- Shan Liu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kunihiko Morihiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Fumika Takeuchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Yufeng Li
- The Key Laboratory of Molecular Oncology of Hebei Province, Tangshan People’s Hospital, Tangshan, Hebei, China
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan,*Correspondence: Akimitsu Okamoto,
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3
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Helm M, Schmidt-Dengler MC, Weber M, Motorin Y. General Principles for the Detection of Modified Nucleotides in RNA by Specific Reagents. Adv Biol (Weinh) 2021; 5:e2100866. [PMID: 34535986 DOI: 10.1002/adbi.202100866] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/09/2021] [Indexed: 12/16/2022]
Abstract
Epitranscriptomics heavily rely on chemical reagents for the detection, quantification, and localization of modified nucleotides in transcriptomes. Recent years have seen a surge in mapping methods that use innovative and rediscovered organic chemistry in high throughput approaches. While this has brought about a leap of progress in this young field, it has also become clear that the different chemistries feature variegated specificity and selectivity. The associated error rates, e.g., in terms of false positives and false negatives, are in large part inherent to the chemistry employed. This means that even assuming technically perfect execution, the interpretation of mapping results issuing from the application of such chemistries are limited by intrinsic features of chemical reactivity. An important but often ignored fact is that the huge stochiometric excess of unmodified over-modified nucleotides is not inert to any of the reagents employed. Consequently, any reaction aimed at chemical discrimination of modified versus unmodified nucleotides has optimal conditions for selectivity that are ultimately anchored in relative reaction rates, whose ratio imposes intrinsic limits to selectivity. Here chemical reactivities of canonical and modified ribonucleosides are revisited as a basis for an understanding of the limits of selectivity achievable with chemical methods.
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Affiliation(s)
- Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Martina C Schmidt-Dengler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core facility, Nancy, F-54000, France.,Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, F-54000, France
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4
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Current Advances in DNA Methylation Analysis Methods. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8827516. [PMID: 33824878 PMCID: PMC8007345 DOI: 10.1155/2021/8827516] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/04/2021] [Accepted: 03/01/2021] [Indexed: 12/18/2022]
Abstract
DNA methylation is one of the epigenetic changes, which plays a major role in regulating gene expression and, thus, many biological processes and diseases. There are several methods for determining the methylation of DNA samples. However, selecting the most appropriate method for answering biological questions appears to be a challenging task. The primary methods in DNA methylation focused on identifying the state of methylation of the examined genes and determining the total amount of 5-methyl cytosine. The study of DNA methylation at a large scale of genomic levels became possible following the use of microarray hybridization technology. The new generation of sequencing platforms now allows the preparation of genomic maps of DNA methylation at the single-open level. This review includes the majority of methods available to date, introducing the most widely used methods, the bisulfite treatment, biological identification, and chemical cutting along with their advantages and disadvantages. The techniques are then scrutinized according to their robustness, high throughput capabilities, and cost.
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5
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Zhou Y, Yin H, Zhao WW, Ai S. Electrochemical, electrochemiluminescent and photoelectrochemical bioanalysis of epigenetic modifiers: A comprehensive review. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213519] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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6
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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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7
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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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8
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Havranová-Vidláková P, Krömer M, Sýkorová V, Trefulka M, Fojta M, Havran L, Hocek M. Vicinal Diol-Tethered Nucleobases as Targets for DNA Redox Labeling with Osmate Complexes. Chembiochem 2019; 21:171-180. [PMID: 31206939 DOI: 10.1002/cbic.201900388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Indexed: 12/19/2022]
Abstract
Six-valent osmium (osmate) complexes with nitrogenous ligands have previously been used for the modification and redox labeling of biomolecules involving vicinal diol moieties (typically, saccharides or RNA). In this work, aliphatic (3,4-dihydroxybutyl and 3,4-dihydroxybut-1-ynyl) or cyclic (6-oxo-6-(cis-3,4-dihydroxypyrrolidin-1-yl)hex-2-yn-1-yl, PDI) vicinal diols are attached to nucleobases to functionalize DNA for subsequent redox labeling with osmium(VI) complexes. The diol-linked 2'-deoxyribonucleoside triphosphates were used for the polymerase synthesis of diol-linked DNA, which, upon treatment with K2 OsO3 and bidentate nitrogen ligands, gave the desired Os-labeled DNA, which were characterized by means of the gel-shift assay and ESI-MS. Through ex situ square-wave voltammetry at a basal plane pyrolytic graphite electrode, the efficiency of modification/labeling of individual diols was evaluated. The results show that the cyclic cis-diol (PDI) was a better target for osmylation than that of the flexible aliphatic ones (alkyl- or alkynyl-linked). The osmate adduct-specific voltammetric signal obtained for OsVI -treated DNA decorated with PDI showed good proportionality to the number of PDI per DNA molecule. The OsVI reagents (unlike OsO4 ) do not attack nucleobases; thus offering specificity of modification on the introduced glycol targets.
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Affiliation(s)
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2, 12843, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Mojmír Trefulka
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská 135, 612 65, Brno, Czech Republic
| | - Miroslav Fojta
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská 135, 612 65, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Luděk Havran
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská 135, 612 65, Brno, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2, 12843, Czech Republic
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9
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Zeng H, He B, Yi C. Compilation of Modern Technologies To Map Genome-Wide Cytosine Modifications in DNA. Chembiochem 2019; 20:1898-1905. [PMID: 30809902 DOI: 10.1002/cbic.201900035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Indexed: 12/19/2022]
Abstract
Over the past few decades, various DNA modification detection methods have been developed; many of the high-resolution methods are based on bisulfite treatment, which leads to DNA degradation, to a degree. Thus, novel bisulfite-free approaches have been developed in recent years and shown to be useful for epigenome analysis in otherwise difficult-to-handle, but important, DNA samples, such as hmC-seal and hmC-CATCH. Herein, an overview of advances in the development of epigenome sequencing methods for these important DNA modifications is provided.
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Affiliation(s)
- Hu Zeng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Bo He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
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10
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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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11
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12
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Debnath TK, Okamoto A. Osmium Tag for Post-transcriptionally Modified RNA. Chembiochem 2018; 19:1653-1656. [PMID: 29799158 DOI: 10.1002/cbic.201800274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Indexed: 12/19/2022]
Abstract
5-Methylcytidine (m5 C) and 5-methyluridine (m5 U) are highly abundant post-transcriptionally modified nucleotides that are observed in various natural RNAs. Such nucleotides were labeled through a chemical approach, as both underwent oxidation at the C5=C6 double bond, leading to the formation of osmium-bipyridine complexes, which could be identified by mass spectrometry. This osmium tag made it possible to distinguished m5 C and m5 U from their isomers, 2'-O-methylcytidine and 2'-O-methyluridine, respectively. Queuosine and 2-methylthio-N6 -isopentenyladenosine in tRNA were also tagged through complex formation.
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Affiliation(s)
- Turja Kanti Debnath
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Akimitsu Okamoto
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
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13
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Chen Y, Hong T, Wang S, Mo J, Tian T, Zhou X. Epigenetic modification of nucleic acids: from basic studies to medical applications. Chem Soc Rev 2018; 46:2844-2872. [PMID: 28352906 DOI: 10.1039/c6cs00599c] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The epigenetic modification of nucleic acids represents one of the most significant areas of study in the field of nucleic acids because it makes gene regulation more complex and heredity more complicated, thus indicating its profound impact on aspects of heredity, growth, and diseases. The recent characterization of epigenetic modifications of DNA and RNA using chemical labelling strategies has promoted the discovery of these modifications, and the newly developed single-base or single-cell resolution mapping strategies have enabled large-scale epigenetic studies in eukaryotes. Due to these technological breakthroughs, several new epigenetic marks have been discovered that have greatly extended the scope and impact of epigenetic modifications in nucleic acids over the past few years. Because epigenetics is reversible and susceptible to environmental factors, it could potentially be a promising direction for clinical medicine research. In this review, we have comprehensively discussed how these epigenetic marks are involved in disease, including the pathogenesis, prevention, diagnosis and treatment of disease. These findings have revealed that the epigenetic modification of nucleic acids has considerable significance in various areas from methodology to clinical medicine and even in biomedical applications.
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Affiliation(s)
- Yuqi Chen
- College of Chemistry and Molecular Sciences, Institute of Advanced Studies, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Hubei, Wuhan 430072, P. R. China.
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14
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Zeng D, Wang Z, Meng Z, Wang P, San L, Wang W, Aldalbahi A, Li L, Shen J, Mi X. DNA Tetrahedral Nanostructure-Based Electrochemical miRNA Biosensor for Simultaneous Detection of Multiple miRNAs in Pancreatic Carcinoma. ACS APPLIED MATERIALS & INTERFACES 2017; 9:24118-24125. [PMID: 28660759 DOI: 10.1021/acsami.7b05981] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Specific and sensitive biomarker detection is essential to early cancer diagnosis. In this study, we demonstrate an ultrasensitive electrochemical biosensor with the ability to detect multiple pancreatic carcinoma (PC)-related microRNA biomarkers. By employing DNA tetrahedral nanostructure capture probes to enhance the detection sensitivity as well as a disposable 16-channel screen-printed gold electrode (SPGE) detection platform to enhance the detection efficiency, we were able to simultaneously detect four PC-related miRNAs: miRNA21, miRNA155, miRNA196a, and miRNA210. The detection sensitivity reached to as low as 10 fM. We then profiled the serum levels of the four miRNAs for PC patients and healthy individuals with our multiplexing electrochemical biosensor. Through the combined analyses of the four miRNAs, our results showed that PC patients could be discriminated from healthy controls with fairly high sensitivity. This multiplexing PCR-free miRNA detection sensor shows promising applications in early diagnosis of PC disease.
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Affiliation(s)
- Dongdong Zeng
- Shanghai Advanced Research Institute , Chinese Academy of Sciences, Shanghai 201210, China
- Shanghai University of Medicine & Health Sciences , Shanghai 201318, China
| | - Zehua Wang
- Shanghai Advanced Research Institute , Chinese Academy of Sciences, Shanghai 201210, China
| | - Zhiqiang Meng
- Fudan University Shanghai Cancer Center , Shanghai 200032, China
| | - Peng Wang
- Fudan University Shanghai Cancer Center , Shanghai 200032, China
| | - Lili San
- Shanghai Advanced Research Institute , Chinese Academy of Sciences, Shanghai 201210, China
| | - Wei Wang
- Shanghai Pudong New District Zhoupu Hospital , Shanghai 201211, China
| | - Ali Aldalbahi
- Chemistry Department, King Saud University , P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Li Li
- School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200241, China
| | - Juwen Shen
- School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200241, China
| | - Xianqiang Mi
- Shanghai Advanced Research Institute , Chinese Academy of Sciences, Shanghai 201210, China
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15
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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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16
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Wang Y, Zhang Y, Guo Y, Kang XF. Fast and precise detection of DNA methylation with tetramethylammonium-filled nanopore. Sci Rep 2017; 7:183. [PMID: 28298646 PMCID: PMC5428259 DOI: 10.1038/s41598-017-00317-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/21/2017] [Indexed: 11/22/2022] Open
Abstract
The tremendous demand for detecting methylated DNA has stimulated intensive studies on developing fast single-molecule techniques with excellent sensitivity, reliability, and selectivity. However, most of these methods cannot directly detect DNA methylation at single-molecule level, which need either special recognizing elements or chemical modification of DNA. Here, we report a tetramethylammonium-based nanopore (termed TMA-NP) sensor that can quickly and accurately detect locus-specific DNA methylation, without bisulfite conversion, chemical modification or enzyme amplification. In the TMA-NP sensor, TMA-Cl is utilized as a nanopore-filling electrolyte to record the ion current change in a single nanopore triggered by methylated DNA translocation through the pore. Because of its methyl-philic nature, TMA can insert into the methylcytosine-guanine (mC-G) bond and then effectively unfasten and reduce the mC-G strength by 2.24 times. Simultaneously, TMA can increase the stability of A-T to the same level as C-G. The abilities of TMA (removing the base pair composition dependence of DNA strands, yet highly sensing for methylated base sites) endow the TMA-NP sensor with high selectivity and high precision. Using nanopore to detect dsDNA stability, the methylated and unmethylated bases are easily distinguished. This simple single-molecule technique should be applicable to the rapid analysis in epigenetic research.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, P. R. China
| | - Yani Zhang
- College of Life Sciences, Northwest University, Xi'an, 710069, P. R. China
| | - Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, P. R. China
| | - Xiao-Feng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, P. R. China.
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17
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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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18
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Kejík Z, Kaplánek R, Havlík M, Bříza T, Jakubek M, Králová J, Mikula I, Martásek P, Král V. Optical probes and sensors as perspective tools in epigenetics. Bioorg Med Chem 2017; 25:2295-2306. [PMID: 28285925 DOI: 10.1016/j.bmc.2017.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/13/2016] [Accepted: 01/11/2017] [Indexed: 12/23/2022]
Abstract
Modifications of DNA cytosine bases and histone posttranslational modifications play key roles in the control of gene expression and specification of cell states. Such modifications affect many important biological processes and changes to these important regulation mechanisms can initiate or significantly contribute to the development of many serious pathological states. Therefore, recognition and determination of chromatin modifications is an important goal in basic and clinical research. Two of the most promising tools for this purpose are optical probes and sensors, especially colourimetric and fluorescence devices. The use of optical probes and sensors is simple, without highly expensive instrumentation, and with excellent sensitivity and specificity for target structural motifs. Accordingly, the application of various probes and sensors in the recognition and determination of cytosine modifications and structure of histones and histone posttranslational modifications, are discussed in detail in this review.
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Affiliation(s)
- Zdeněk Kejík
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Robert Kaplánek
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Martin Havlík
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Tomáš Bříza
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Milan Jakubek
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Jarmila Králová
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Ivan Mikula
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Pavel Martásek
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Vladimír Král
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic.
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19
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Xu Y, Gao X, Zhang L, Chen D, Dai Z, Zou X. Simultaneous detection of double gene-specific methylation loci based on hairpin probes tagged with electrochemical quantum dots barcodes. J Electroanal Chem (Lausanne) 2016. [DOI: 10.1016/j.jelechem.2016.06.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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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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21
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Labib M, Sargent EH, Kelley SO. Electrochemical Methods for the Analysis of Clinically Relevant Biomolecules. Chem Rev 2016; 116:9001-90. [DOI: 10.1021/acs.chemrev.6b00220] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Mahmoud Labib
- Department
of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | | | - Shana O. Kelley
- Department
of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada
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22
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Yoshida W, Yoshioka H, Bay DH, Iida K, Ikebukuro K, Nagasawa K, Karube I. Detection of DNA Methylation of G-Quadruplex and i-Motif-Forming Sequences by Measuring the Initial Elongation Efficiency of Polymerase Chain Reaction. Anal Chem 2016; 88:7101-7. [PMID: 27351368 DOI: 10.1021/acs.analchem.6b00982] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA methylation has been proposed as one of the promising biomarkers for cancer diagnosis. In this study, we developed a DNA methylation detection system utilizing G-quadruplex and i-motif-forming sequences that requires neither sodium bisulfite treatment nor methylated DNA ligands. We hypothesized that G-quadruplex and i-motif structures would be stabilized by DNA methylation and arrest DNA polymerase activity during quantitative polymerase chain reaction (qPCR). The PCR products from VEGF, RET G-quadruplex, and i-motif-forming sequences were used as templates and analyzed by qPCR. Our results indicated that the initial elongation efficiency of PCR decreased with increasing DNA methylation levels in the G-quadruplex and i-motif-forming sequences. Moreover, we demonstrated that the initial elongation efficiency of PCR decreased with increased DNA methylation of the VEGF region on genomic DNA. These results indicated that DNA methylation of the G-quadruplex and i-motif-forming sequences on genomic DNA can be detected by qPCR.
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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
| | - Hitomi Yoshioka
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Daniyah Habiballah Bay
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.,Biology Department, Umm Al-Qura University , P.O. Box 715, Makkah, 21955, Kingdom of Saudi Arabia
| | - Keisuke Iida
- Graduate School of Science and Engineering, Saitama University , Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Isao Karube
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
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23
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Wang Y, Liu C, Wang T, Hong T, Su H, Yu S, Song H, Liu S, Zhou X, Mao W, Zhou X. Highly Selective Detection of 5-Methylcytosine in Genomic DNA Based on Asymmetric PCR and Specific DNA Damaging Reagents. Anal Chem 2016; 88:3348-53. [DOI: 10.1021/acs.analchem.5b04939] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Yafen Wang
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Chaoxing Liu
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Tianlu Wang
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Tingting Hong
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Haomiao Su
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Shuyi Yu
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Hongwei Song
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Songmei Liu
- Zhongnan
Hospital, Wuhan University, Wuhan, Hubei 430071, P. R. China
| | - Xin Zhou
- Zhongnan
Hospital, Wuhan University, Wuhan, Hubei 430071, P. R. China
| | - Wuxiang Mao
- School
of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, Hubei 430073, P. R. China
| | - Xiang Zhou
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies, Wuhan University, Wuhan, Hubei 430072, P. R. China
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24
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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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25
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Okamoto A. Nucleic Acid Reaction Chemistry to Clarify the Fluctuating Quality and Quantity of Nucleic Acids. J SYN ORG CHEM JPN 2016. [DOI: 10.5059/yukigoseikyokaishi.74.474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Akimitsu Okamoto
- Research Center for Advanced Science and Technology, The University of Tokyo
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26
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Direct potential resolution and simultaneous detection of cytosine and 5-methylcytosine based on the construction of polypyrrole functionalized graphene nanowall interface. Electrochem commun 2015. [DOI: 10.1016/j.elecom.2015.09.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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27
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Kurita R, Yanagisawa H, Yoshioka K, Niwa O. On-Chip Sequence-Specific Immunochemical Epigenomic Analysis Utilizing Outward-Turned Cytosine in a DNA Bulge with Handheld Surface Plasmon Resonance Equipment. Anal Chem 2015; 87:11581-6. [DOI: 10.1021/acs.analchem.5b03520] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ryoji Kurita
- National Institute of Advanced Industrial Science and Technology, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan 305-8566
| | - Hiroyuki Yanagisawa
- National Institute of Advanced Industrial Science and Technology, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan 305-8566
| | - Kyoko Yoshioka
- National Institute of Advanced Industrial Science and Technology, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan 305-8566
| | - Osamu Niwa
- National Institute of Advanced Industrial Science and Technology, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan 305-8566
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28
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Kurita R, Yanagisawa H, Yoshioka K, Niwa O. Site-specific immunochemical methylation assessment from genome DNA utilizing a conformational difference between looped-out target and stacked-in nontarget methylcytosines. Biosens Bioelectron 2015; 70:366-71. [DOI: 10.1016/j.bios.2015.03.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 02/06/2023]
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29
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Zeng T, Liu L, Li T, Li Y, Gao J, Zhao Y, Wu HC. Detection of 5-methylcytosine and 5-hydroxymethylcytosine in DNA via host-guest interactions inside α-hemolysin nanopores. Chem Sci 2015; 6:5628-5634. [PMID: 28757950 PMCID: PMC5510575 DOI: 10.1039/c5sc01436k] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/24/2015] [Indexed: 01/17/2023] Open
Abstract
After selective modification with a host–guest complex, 5-methylcytosine and 5-hydroxymethylcytosine in ssDNA can be unambiguously detected by the generation of characteristic current events during the translocation of the modified DNA through α-hemolysin nanopores.
Cytosine methylation and hydroxymethylation are both important epigenetic modifications of DNA in mammalian cells. Therefore, profiling DNA (hydroxy)methylation across the genome is vital for understanding their roles in gene regulation. Here, we report a nanopore-based approach for quick and reliable detection of 5-methylcytosine and 5-hydroxymethylcytosine in DNA at the single-molecule level. The single-stranded DNA containing 5-methylcytosine or 5-hydroxymethylcytosine was first selectively modified on the epigenetic base to attach a host–guest complex. Threading of the modified DNA molecules through α-hemolysin nanopores causes unbinding of the host–guest complex and generates highly characteristic current signatures. Statistical analysis of the signature events affords quantitative information about 5-methylcytosine and 5-hydroxymethylcytosine in DNA. Our results suggest that other DNA modifications could also be detected with the developed method. Furthermore, we anticipate our nanopore sensing strategy to be generally useful in biochemical analysis and to find applications in the early diagnosis of diseases.
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Affiliation(s)
- Tao Zeng
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745.,National Center for Nanoscience and Technology of China , Beijing 100190 , China .
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745
| | - Ting Li
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745
| | - Yuru Li
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745
| | - Juan Gao
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745
| | - Yuliang Zhao
- National Center for Nanoscience and Technology of China , Beijing 100190 , China .
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745
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30
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Saheb A, Patterson S, Josowicz M. Probing for DNA methylation with a voltammetric DNA detector. Analyst 2014; 139:786-92. [PMID: 24358460 DOI: 10.1039/c3an02154h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A label-free electrochemical detection of DNA hybridization is used for probing synthetic methylated ssDNA 27-mer or 33-mer targets from the GSTP1-gene. The method is based on electrostatic modulation of the anion-exchange kinetics of a polypyrrole bilayer film deposited on platinum-microelectrodes to which a synthetic single-stranded 15-mer GSTP-1 promoter probe DNA has been attached (DNA detector). The effect of the contact of this DNA-detector with non-methylated and methylated complementary DNA sequences in Tris-buffer is compared using cyclic voltammetry (CV). The DNA-hybridization taking place at the electrode surface leads to a significant decrease of the CV area recorded after exposure to complementary target DNA in comparison to the CV change recorded for non-complementary DNA target. The performance of this miniaturized DNA detector was optimized with respect to hybridization time, temperature, and concentration of the target. It was also evaluated with respect to selectivity, sensitivity, and reproducibility. These results are significant for their possible use as a screening test for hypermethylated DNA sequences.
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Affiliation(s)
- Amir Saheb
- Albany State University, Department of Natural Sciences, Albany, GA, USA.
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31
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Okamoto A. DNA-Osmium Complexes: Recent Developments in the Operative Chemical Analysis of DNA Epigenetic Modifications. ChemMedChem 2014; 9:1958-65. [DOI: 10.1002/cmdc.201402114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Indexed: 12/26/2022]
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32
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Microdevices for detecting locus-specific DNA methylation at CpG resolution. Biosens Bioelectron 2014; 56:278-85. [DOI: 10.1016/j.bios.2014.01.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/13/2014] [Accepted: 01/17/2014] [Indexed: 12/15/2022]
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33
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Kubik G, Schmidt MJ, Penner JE, Summerer D. Programmierbare und hochaufgelöste In-vitro-Detektion von genomischem 5-Methylcytosin durch TALEs. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Kubik G, Schmidt MJ, Penner JE, Summerer D. Programmable and highly resolved in vitro detection of 5-methylcytosine by TALEs. Angew Chem Int Ed Engl 2014; 53:6002-6. [PMID: 24801054 DOI: 10.1002/anie.201400436] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/25/2014] [Indexed: 01/20/2023]
Abstract
Gene expression is extensively regulated by specific patterns of genomic 5-methylcytosine (mC), but the ability to directly detect this modification at user-defined genomic loci is limited. One reason is the lack of molecules that discriminate between mC and cytosine (C) and at the same time provide inherent, programmable sequence-selectivity. Programmable transcription-activator-like effectors (TALEs) have been observed to exhibit mC-sensitivity in vivo, but to only a limited extent in vitro. We report an mC-detection assay based on TALE control of DNA replication that displays unexpectedly strong mC-discrimination ability in vitro. The status and level of mC modification at single positions in oligonucleotides can be determined unambiguously by this assay, independently of the overall target sequence. Moreover, discrimination is reliably observed for positions bound by N-terminal and central regions of TALEs. This indicates the wide scope and robustness of the approach for highly resolved mC detection and enabled the detection of a single mC in a large, eukaryotic genome.
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Affiliation(s)
- Grzegorz Kubik
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz (Germany)
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35
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Chemiluminescence resonance energy transfer biosensing platform for site-specific determination of DNA methylation and assay of DNA methyltransferase activity using exonuclease III-assisted target recycling amplification. Biosens Bioelectron 2014; 54:48-54. [DOI: 10.1016/j.bios.2013.10.050] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/30/2013] [Accepted: 10/22/2013] [Indexed: 01/06/2023]
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36
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Detection of real sample DNA at a cadmium sulfide--chitosan/gelatin modified electrode. Colloids Surf B Biointerfaces 2013; 113:85-91. [PMID: 24060932 DOI: 10.1016/j.colsurfb.2013.08.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 08/18/2013] [Accepted: 08/20/2013] [Indexed: 11/22/2022]
Abstract
Cadmium sulfide (CdS) was combined with chitosan (Chi) and gelatin (Gel) to prepare a CdS-Chi/Gel modified electrode. Chi exhibits a large positive charge density and was to provide a uniform of CdS surface. Gel exhibits high mechanical strength and low toxicity toward mammalian cells, and is non-antigenic biopolymer. CdS-Chi exhibits a lower contact angle than that of bare CdS, indicating that the hydrophilicity of the sample surface had increased. Electrochemical impedance spectroscopy (EIS) was used to determine diffusion coefficients and to characterize the electron transfer kinetics during the redox reactions. The surface morphologies of CdS-Chi and Gel were characterized using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Differential pulse voltammetry (DPV) was used to detect the analytes. DPV not only increased the linear range of the electrocatalytic current, but also lowered the overpotential for oxidation interference in the measurements. The CdS electrode exhibited a enhanced electrocatalytic activity toward the analytes evaluated in this study. The presence of Gel enhanced the loading and stability of the electrode. The fabricated electrode was successfully used for the simultaneous electrochemical oxidation of guanine (G) and adenine (A).
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37
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Wang P, Chen H, Tian J, Dai Z, Zou X. Electrochemical evaluation of DNA methylation level based on the stoichiometric relationship between purine and pyrimidine bases. Biosens Bioelectron 2013; 45:34-9. [DOI: 10.1016/j.bios.2013.01.057] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 01/17/2013] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
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38
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Wu Y, Zhang B, Guo LH. Label-Free and Selective Photoelectrochemical Detection of Chemical DNA Methylation Damage Using DNA Repair Enzymes. Anal Chem 2013; 85:6908-14. [DOI: 10.1021/ac401346x] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Yiping Wu
- State Key Laboratory of Environmental Chemistry and
Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Bintian Zhang
- State Key Laboratory of Environmental Chemistry and
Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Liang-Hong Guo
- State Key Laboratory of Environmental Chemistry and
Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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39
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Zheng X, Wang L. Direct Electrocatalytic Oxidation and Simultaneous Determination of 5-Methylcytosine and Cytosine at Electrochemically Reduced Graphene Modified Glassy Carbon Electrode. ELECTROANAL 2013. [DOI: 10.1002/elan.201300040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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40
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Direct determination of 5-methylcytosine based on electrochemical activation of surfactant functionalized graphene modified pyrolytic graphite electrode. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2013.02.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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41
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Hu J, Xing X, Xu X, Wu F, Guo P, Yan S, Xu Z, Xu J, Weng X, Zhou X. Selective chemical labelling of 5-formylcytosine in DNA by fluorescent dyes. Chemistry 2013; 19:5836-40. [PMID: 23512548 DOI: 10.1002/chem.201300082] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Indexed: 12/27/2022]
Abstract
Direct labelling: 5-Formylcytosine in DNA can be selectively labelled by fluorescent dyes containing an active amino group. The labelled DNA shows strong fluorescence and can be detected by polyacrylamide gel electrophoresis (PAGE) and fluorescence measurements (see scheme). This method can distinguish 5-formylcytosine from other methylation forms of cytosine in DNA.
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Affiliation(s)
- Jianlin Hu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, PR China
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42
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Dai Z, Cai T, Zhu W, Gao X, Zou X. Simultaneous profiling of multiple gene-methylation loci by electrochemical methylation-specific ligase detection reaction. Chem Commun (Camb) 2013; 49:1939-41. [PMID: 23364409 DOI: 10.1039/c3cc38942a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel method of electrochemical methylation-specific ligation detection reaction is first presented for simultaneous evaluation of multiple gene-methylation loci in a single-tube experiment without PCR amplification or restriction enzyme reaction.
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Affiliation(s)
- Zong Dai
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
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43
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Wang T, Hong T, Tang T, Zhai Q, Xing X, Mao W, Zheng X, Xu L, Wu J, Weng X, Wang S, Tian T, Yuan B, Huang B, Zhuang L, Zhou X. Application of N-halogeno-N-sodiobenzenesulfonamide reagents to the selective detection of 5-methylcytosine in DNA sequences. J Am Chem Soc 2013; 135:1240-3. [PMID: 23301810 DOI: 10.1021/ja311229n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
To surmount the challenges of the locus determination and accurate quantification of 5-methyl-2'-deoxycytidine ((5Me)dC) in DNA fragments that contain multiple (5Me)dC residues, we designed and synthesized two N-halogeno-N-sodiobenzenesulfonamide reagents that provide a new chemical method for probing (5Me)dC in DNA sequences. When the strategy we provided was combined with β-glucosyltransferase, (5Me)dC could be distinguished from 5-hydroxymethyl-2'-deoxycytidine ((5hm)dC) and deoxycytidine (dC) through the introduction of a glucose moiety to the hydroxyl group of (5hm)dC.
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Affiliation(s)
- Tianlu Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of the Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
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44
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45
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Kanavarioti A, Greenman KL, Hamalainen M, Jain A, Johns AM, Melville CR, Kemmish K, Andregg W. Capillary electrophoretic separation-based approach to determine the labeling kinetics of oligodeoxynucleotides. Electrophoresis 2012; 33:3529-43. [PMID: 23147698 PMCID: PMC3939315 DOI: 10.1002/elps.201200214] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 06/01/2012] [Accepted: 06/14/2012] [Indexed: 12/19/2022]
Abstract
With the recent advances in electron microscopy (EM), computation, and nanofabrication, the original idea of reading DNA sequence directly from an image can now be tested. One approach is to develop heavy atom labels that can provide the contrast required for EM imaging. While evaluating tentative labels for the respective nucleobases in synthetic oligodeoxynucleotides (oligos), we developed a streamlined CE protocol to assess the label stability, reactivity, and selectivity. We report our protocol using osmium tetroxide 2,2'-bipyridine (Osbipy) as a thymidine (T) specific label. The observed rates show that the labeling process is kinetically independent of both the oligo length, and the base composition. The conditions, i.e. temperature, optimal Osbipy concentration, and molar ratio of reagents, to promote 100% conversion of the starting oligo to labeled product were established. Hence, the optimized conditions developed with the oligos could be leveraged to allow osmylation of effectively all Ts in ssDNA, while achieving minimal mislabeling. In addition, the approach and methods employed here may be adapted to the evaluation of other prospective contrasting agents/labels to facilitate next-generation DNA sequencing by EM.
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46
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Shanmuganathan R, Basheer NB, Amirthalingam L, Muthukumar H, Kaliaperumal R, Shanmugam K. Conventional and nanotechniques for DNA methylation profiling. J Mol Diagn 2012; 15:17-26. [PMID: 23127612 DOI: 10.1016/j.jmoldx.2012.06.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 06/13/2012] [Accepted: 06/28/2012] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is critical for gene silencing and is associated with the incidence of many diseases, including cancer. Underlying molecular mechanisms of human diseases and tissue-specific gene expression have been elucidated based on DNA methylation studies. This review highlights the advantages and drawbacks of various methylation screening techniques: blotting, genomic sequencing, bisulfite sequencing, methylation-specific PCR, methylated DNA immunoprecipitation, microarray analysis, matrix-assisted laser desorption ionization time-of-flight mass spectroscopy, nanowire transistor detection procedure, quantum dot-based nanoassay, single-molecule real-time detection, fluorimetric assay, electrochemical detection, and atomic force spectroscopy. The review provides insight for selecting a method or a combination of methods for DNA methylation analysis. Convergence of conventional and contemporary nanotechniques to enumerate methylation at specific CpG sites of oncogene would fill the gap in diagnosis of cancer.
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47
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Wang M, Xu Z, Chen L, Yin H, Ai S. Electrochemical Immunosensing Platform for DNA Methyltransferase Activity Analysis and Inhibitor Screening. Anal Chem 2012; 84:9072-8. [DOI: 10.1021/ac301620m] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mo Wang
- College of
Chemistry and Material Science, Shandong Agricultural University, Taian, 271018, PR
China
| | - Zhenning Xu
- College of
Chemistry and Material Science, Shandong Agricultural University, Taian, 271018, PR
China
| | - Lijian Chen
- College of
Chemistry and Material Science, Shandong Agricultural University, Taian, 271018, PR
China
| | - Huanshun Yin
- College of
Chemistry and Material Science, Shandong Agricultural University, Taian, 271018, PR
China
| | - Shiyun Ai
- College of
Chemistry and Material Science, Shandong Agricultural University, Taian, 271018, PR
China
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48
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Ligand-Incorporation Site in 5-Methylcytosine-Detection Probe Modulating the Site of Osmium Complexation with the Target DNA. Chem Biodivers 2012; 9:2000-7. [DOI: 10.1002/cbdv.201100425] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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49
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Bartošík M, Fojta M, Paleček E. Electrochemical detection of 5-methylcytosine in bisulfite-treated DNA. Electrochim Acta 2012. [DOI: 10.1016/j.electacta.2012.05.115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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50
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Kurita R, Niwa O. DNA methylation analysis triggered by bulge specific immuno-recognition. Anal Chem 2012; 84:7533-8. [PMID: 22880797 DOI: 10.1021/ac301702y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We report the sequence-selective discrimination of the cytosine methylation status in DNA with anti methylcytosine antibody for the first time. This was realized by employing an affinity measurement involving the target methylcytosine in a bulge region and anti methylcytosine antibody, following hybridization with a bulge-inducing DNA to ensure that only the target methylcytosine is located in the bulge. The affinity of the antibody for methylcytosine in the bulge was 79% of that in a single strand of DNA; however, the affinity for nontarget methylcytosine in a double strand of DNA decreased greatly. This is because the antibody cannot bind with an inwardly turned methylcytosine in the duplex region owing to the large antibody size. In contrast, the methylcytosine in the bulge is recognized by the antibody because it is available to rotate freely owing to the single bond between deoxyribose and phosphate in a DNA chain. By employing the difference between the affinity in the bulge and that in the duplex, we could determine selectively whether or not the target cytosine was methylated in an O(6)-methylguanine DNA methyltransferase (MGMT) promoter sequence with a single base level. The proposed bulge-specific assay technique can be combined with a widely used absorbance measurement method that employs the color change in tetramethyl benzidine induced by horseradish peroxidase-labeled secondary antibody. The sequence-selective discrimination of the methylation status could also be obtained with various types of interfering genomic DNA contamination without any conventional bisulfite treatment, polymerase chain reaction, (PCR) or electrophoresis.
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Affiliation(s)
- Ryoji Kurita
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, Tsukuba, Ibaraki, Japan.
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