|
1
|
Kaneyoshi S, Eguchi N, Fujimoto K, Fujii S, Sato S, Takenaka S. Cyclic ferrocenylnaphthalene diimides as a probe for electrochemical telomerase assay. J Inorg Biochem 2022; 230:111746. [DOI: 10.1016/j.jinorgbio.2022.111746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 11/29/2022]
|
|
2
|
|
|
3
|
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.
Collapse
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
| |
Collapse
|
|
4
|
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
| |
Collapse
|
|
5
|
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
| |
Collapse
|
|
6
|
Haque MH, Gopalan V, Islam MN, Masud MK, Bhattacharjee R, Hossain MSA, Nguyen NT, Lam AK, Shiddiky MJA. Quantification of gene-specific DNA methylation in oesophageal cancer via electrochemistry. Anal Chim Acta 2017; 976:84-93. [PMID: 28576321 DOI: 10.1016/j.aca.2017.04.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/10/2017] [Accepted: 04/10/2017] [Indexed: 02/07/2023]
Abstract
Development of simple and inexpensive method for the analysis of gene-specific DNA methylation is important for the diagnosis and prognosis of patients with cancer. Herein, we report a relatively simple and inexpensive electrochemical method for the sensitive and selective detection of gene-specific DNA methylation in oesophageal cancer. The underlying principle of the method relies on the affinity interaction between DNA bases and unmodified gold electrode. Since the affinity trend of DNA bases towards the gold surface follows as adenine (A) > cytosine (C) > guanine (G)> thymine (T), a relatively larger amount of bisulfite-treated adenine-enriched unmethylated DNA adsorbs on the screen-printed gold electrodes (SPE-Au) in comparison to the guanine-enriched methylated sample. The methylation levels were (i.e., different level of surface attached DNA molecules due to the base dependent differential adsorption pattern) quantified by measuring saturated amount of charge-compensating [Ru(NH3)6]3+ molecules in the surface-attached DNAs by chronocoulometry as redox charge of the [Ru(NH3)6]3+ molecules quantitatively reflects the amount of the adsorbed DNA confined at the electrode surface. The assay could successfully distinguish methylated and unmethylated DNA sequences at single CpG resolution and as low as 10% differences in DNA methylation. In addition, the assay showed fairly good reproducibility (% RSD= <5%) with better sensitivity and specificity by analysing various levels of methylation in two cell lines and eight fresh tissues samples from patients with oesophageal squamous cell carcinoma. Finally, the method was validated with methylation specific-high resolution melting curve analysis and Sanger sequencing methods.
Collapse
Affiliation(s)
- Md Hakimul Haque
- Cancer Molecular Pathology Laboratory in Menzies Health Institute Queensland, Griffith University and School of Medicine, Gold Coast, QLD 4222, Australia; School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology Laboratory in Menzies Health Institute Queensland, Griffith University and School of Medicine, Gold Coast, QLD 4222, Australia.
| | - Md Nazmul Islam
- School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Mostafa Kamal Masud
- School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials, University of Wollongong, NSW 2519, Australia
| | - Ripon Bhattacharjee
- School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Md Shahriar Al Hossain
- Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials, University of Wollongong, NSW 2519, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Alfred K Lam
- Cancer Molecular Pathology Laboratory in Menzies Health Institute Queensland, Griffith University and School of Medicine, Gold Coast, QLD 4222, Australia.
| | - Muhammad J A Shiddiky
- School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia.
| |
Collapse
|
|
7
|
Haraguchi K, Sato S, Habu M, Yada N, Hayakawa M, Takahashi O, Yoshioka I, Matsuo K, Tominaga K, Takenaka S. Oral Cancer Screening Based on Methylation Frequency Detection inhTERTGene Using Electrochemical Hybridization Assay via a Multi-electrode Chip Coupled with Ferrocenylnaphthalene Diimide. ELECTROANAL 2017. [DOI: 10.1002/elan.201700028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Kazuya Haraguchi
- Department of Science of Physical Functions; Division of Oral and Maxillofacial Surgery; Kyushu Dental University; 2-6-1 Manazuru, Kokurakitaku, Kitakyushu Fukuoka 803-8580 Japan
| | - Shinobu Sato
- Department of Applied Chemistry and Research Center for Bio-microsensing Technology; Kyushu Institute of Technology; 1-1 Sensui, Tobataku, Kitakyushu Fukuoka 804-8550 Japan
| | - Manabu Habu
- Department of Science of Physical Functions; Division of Oral and Maxillofacial Surgery; Kyushu Dental University; 2-6-1 Manazuru, Kokurakitaku, Kitakyushu Fukuoka 803-8580 Japan
| | - Naomi Yada
- Department of Health Promotion, Division of Oral Pathology; Kyushu Dental University; 2-6-1 Manazuru, Kokurakitaku, Kitakyushu Fukuoka 803-8580 Japan
| | - Mana Hayakawa
- Department of Science of Physical Functions; Division of Oral and Maxillofacial Surgery; Kyushu Dental University; 2-6-1 Manazuru, Kokurakitaku, Kitakyushu Fukuoka 803-8580 Japan
| | - Osamu Takahashi
- Department of Science of Physical Functions; Division of Oral and Maxillofacial Surgery; Kyushu Dental University; 2-6-1 Manazuru, Kokurakitaku, Kitakyushu Fukuoka 803-8580 Japan
| | - Izumi Yoshioka
- Department of Science of Physical Functions, Division of Oral Medicine; Kyushu Dental University; 2-6-1 Manazuru, Kokurakitaku, Kitakyushu Fukuoka 803-8580 Japan
| | - Kou Matsuo
- Department of Health Promotion, Division of Oral Pathology; Kyushu Dental University; 2-6-1 Manazuru, Kokurakitaku, Kitakyushu Fukuoka 803-8580 Japan
| | - Kazuhiro Tominaga
- Department of Science of Physical Functions; Division of Oral and Maxillofacial Surgery; Kyushu Dental University; 2-6-1 Manazuru, Kokurakitaku, Kitakyushu Fukuoka 803-8580 Japan
| | - Shigeori Takenaka
- Department of Applied Chemistry and Research Center for Bio-microsensing Technology; Kyushu Institute of Technology; 1-1 Sensui, Tobataku, Kitakyushu Fukuoka 804-8550 Japan
| |
Collapse
|
|
8
|
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: 49] [Impact Index Per Article: 7.0] [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.
Collapse
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.
| |
Collapse
|
|
9
|
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
|
|
10
|
Yin H, Yang Z, Li B, Zhou Y, Ai S. Electrochemical biosensor for DNA demethylase detection based on demethylation triggered endonuclease BstUI and Exonuclease III digestion. Biosens Bioelectron 2014; 66:266-70. [PMID: 25437362 DOI: 10.1016/j.bios.2014.11.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 11/06/2014] [Accepted: 11/17/2014] [Indexed: 12/13/2022]
Abstract
Herein, an electrochemical biosensor was fabricated for DNA demethylase detection based on DNA demethylation triggered endonuclease BstUI and Exonuclease III digestion. After the double-strand DNA was demethylated, it can be further digested by BstUI and formed a blunt end at the electrode surface. Then, the remained fragment of DNA-DNA duplex was further cleaved by exonuclease III and led to increased electrochemical signal. Based on this detection strategy, the biosensor showed high sensitivity with low detection limit of 0.15ng/mL. Moreover, the developed method also presented high selectivity and acceptable reproducibility. This work provides a novel detection platform for DNA demethylase detection.
Collapse
Affiliation(s)
- Huanshun Yin
- College of Chemistry and Material Science, Shandong Agricultural University, 271018 Taian, Shandong, PR China
| | - Zhiqing Yang
- College of Chemistry and Material Science, Shandong Agricultural University, 271018 Taian, Shandong, PR China
| | - Bingchen Li
- College of Chemistry and Material Science, Shandong Agricultural University, 271018 Taian, Shandong, PR China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Shandong Agricultural University, 271018 Taian, Shandong, PR China.
| | - Shiyun Ai
- College of Chemistry and Material Science, Shandong Agricultural University, 271018 Taian, Shandong, PR China.
| |
Collapse
|
|
11
|
Sato S, Saeki T, Tanaka T, Kanezaki Y, Hayakawa M, Haraguchi K, Kodama M, Nishihara T, Tominaga K, Takenaka S. Ferrocenylnaphthalene Diimide-Based Electrochemical Detection of Aberrant Methylation in hTERT Gene. Appl Biochem Biotechnol 2014; 174:869-79. [DOI: 10.1007/s12010-014-1030-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/19/2014] [Indexed: 12/19/2022]
|
|
12
|
Sun R, Wang L, Yu H, Abdin ZU, Chen Y, Huang J, Tong R. Molecular Recognition and Sensing Based on Ferrocene Derivatives and Ferrocene-Based Polymers. Organometallics 2014. [DOI: 10.1021/om5000453] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ruoli Sun
- State
Key Laboratory of Chemical Engineering, Department of Chemical and
Biological Engineering, Zhejiang University, Hangzhou 310027, People’s Republic of China
| | - Li Wang
- State
Key Laboratory of Chemical Engineering, Department of Chemical and
Biological Engineering, Zhejiang University, Hangzhou 310027, People’s Republic of China
| | - Haojie Yu
- State
Key Laboratory of Chemical Engineering, Department of Chemical and
Biological Engineering, Zhejiang University, Hangzhou 310027, People’s Republic of China
| | - Zain-ul- Abdin
- State
Key Laboratory of Chemical Engineering, Department of Chemical and
Biological Engineering, Zhejiang University, Hangzhou 310027, People’s Republic of China
| | - Yongsheng Chen
- State
Key Laboratory of Chemical Engineering, Department of Chemical and
Biological Engineering, Zhejiang University, Hangzhou 310027, People’s Republic of China
| | - Jin Huang
- State
Key Laboratory of Chemical Engineering, Department of Chemical and
Biological Engineering, Zhejiang University, Hangzhou 310027, People’s Republic of China
| | - Rongbai Tong
- State
Key Laboratory of Chemical Engineering, Department of Chemical and
Biological Engineering, Zhejiang University, Hangzhou 310027, People’s Republic of China
| |
Collapse
|
|
13
|
Naphthalene Diimide Carrying Two Cysteine Termini at Both Imide Linkers as a Molecular Staple. ELECTROANAL 2013. [DOI: 10.1002/elan.201300209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
|
14
|
An electrochemical biosensor for assay of DNA methyltransferase activity and screening of inhibitor. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2012.11.093] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
|
15
|
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]
|