A microchip electrophoretic assay for DNA methyltransferase activity based on methylation‐sensitive endonuclease DpnⅡ

Zhang, Yating; Zhang, Yan; Zhu, Ling; He, Pingang; Wang, Qingjiang

doi:10.1002/elps.201800236

Cited by 8 publications

(2 citation statements)

References 33 publications

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“…DNA methylation, as a most widely epigenetic modification, plays a critical part in the gene expression regulation, cell proliferation and senescence, and chromatin structure maintenance. − The aberrant DNA methylation has been considered to be associated with various cancers, such as cervix, prostate, and colorectal cancers. , The DNA methylation patterns are primarily regulated by DNA MTase . Therefore, sensitive determination of DNA MTase activity contributes to the early clinical diagnosis and has potential influence in the research of the carcinogenesis mechanism and anticancer drugs. − The golden standard for detection of DNA MTase activity is radioactive labeling of the methyl donor .…”

Section: Resultsmentioning

confidence: 99%

Cyclometalated Iridium(III) Complex-Sensitized NiO-Based-Cathodic Photoelectrochemical Platform for DNA Methyltransferase Assay

Cai

Zhang

Wang

et al. 2021

ACS Appl. Bio Mater.

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This work reports an efficient [(C6) 2 Ir(dppz)] + PF 6 − (C6 = coumarin 6 and dppz = dipyridophenazine)-sensitized NiO photocathode and its application in photoelectrochemical (PEC) bioanalysis field for the first time. This dye-sensitized NiO photocathode was found to exhibit a markedly enhanced cathodic photocurrent. A sensitive cathodic PEC platform was proposed integrating the as-prepared photocathode with enzyme-free cascaded amplification strategies of the catalytic hairpin assembly (CHA) and the hybridization chain reaction (HCR) for DNA methyltransferase (MTase) assay. A hairpin DNA(H Dam ) with specific recognition site of Dam MTase in its stem was designed. The site of H Dam was methylated in the presence of Dam MTase and then cut by endonuclease DpnI. The released loop fragment, as an initiator, triggered the CHA circuit and the follow-up HCR circuit, resulting in long dsDNA concatemers on the ITO electrode. Numerous [(C6) 2 Ir(dppz)] + PF 6− were intercalated into dsDNA, and highly efficient signal amplification was realized. Benefiting from the superior iridium(III) complex-sensitized NiO photocathode and effective amplification strategy, a detection limit of 0.0028 U/mL for the determination of Dam MTase was achieved. Moreover, this work further demonstrated that these proposed tactics could be applied to screen Dam MTase activity inhibitors.

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Section: Resultsmentioning

confidence: 99%

Cyclometalated Iridium(III) Complex-Sensitized NiO-Based-Cathodic Photoelectrochemical Platform for DNA Methyltransferase Assay

Cai

Zhang

Wang

et al. 2021

ACS Appl. Bio Mater.

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“…One of the current problems in modern bioinformatics is the processing of the gene expression data obtained in DNA microchip experiments [1] or the more modern method of mRNA molecule sequencing [2]. The peculiarities of experimental data include a large number of genes that determine the state of the corresponding biological organism.…”

Section: Introductionmentioning

confidence: 99%

A Hybrid Model of Cancer Diseases Diagnosis Based on Gene Expression Data with Joint Use of Data Mining Methods and Machine Learning Techniques

2023

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One of the current focuses of modern bioinformatics is the development of hybrid models to process gene expression data, in order to create diagnostic systems for various diseases. In this study, we propose a solution to this problem that combines an inductive spectral clustering algorithm, random forest classifier, convolutional neural network, and alternative voting method for making the final decision about patient condition. In the first stage, we apply the spectral clustering algorithm to gene expression profiles using inductive methods of objective clustering, with the calculation of internal, external, and balance clustering quality criteria. This results in clusters of mutually correlated and differently expressed gene expression profiles. In the second stage, we apply the random forest classifier and convolutional neural network to identify the examined objects, containing as attributes the gene expression values in the allocated clusters. The presented research solves both binary- and multi-classification tasks. The final decision about the patient’s condition is made using the alternative voting method, considering the classification results based on the gene expression data in various clusters. The simulation results showed that the proposed technique was highly effective, achieving a high accuracy in object identification when both classifiers were used. However, the convolutional neural network had a significantly higher data processing efficiency than the random forest algorithm, due to its substantially shorter processing time.

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Microchip-Based Devices for Bioanalytical Applications

Pinheiro

Baldo

Bressan

et al. 2021

Tools and Trends in Bioanalytical Chemistry

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A microchip electrophoretic assay for DNA methyltransferase activity based on methylation‐sensitive endonuclease DpnⅡ

Cited by 8 publications

References 33 publications

Cyclometalated Iridium(III) Complex-Sensitized NiO-Based-Cathodic Photoelectrochemical Platform for DNA Methyltransferase Assay

Cyclometalated Iridium(III) Complex-Sensitized NiO-Based-Cathodic Photoelectrochemical Platform for DNA Methyltransferase Assay

A Hybrid Model of Cancer Diseases Diagnosis Based on Gene Expression Data with Joint Use of Data Mining Methods and Machine Learning Techniques

Microchip-Based Devices for Bioanalytical Applications

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