Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay

Methylcytosines in mammalian genomes are the main epigenetic molecular codes that switch off the repertoire of genes in cell-type and cell-stage dependent manners. DNA methyltransferases (DMT) are dedicated to managing the status of cytosine methylation. DNA methylation is not only critical in norma...

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Autores principales:	Sook Ho Kim, Hae Jun Jung, Seok-Cheol Hong
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	Z-DNA DNA methylation nuclease-free single-molecule FRET methylcytosine sensitive natural DNA methyltransferase inhibitors Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/336da33dc9c1470fa98fc7120e7531db
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spelling	oai:doaj.org-article:336da33dc9c1470fa98fc7120e7531db2021-11-11T17:24:41ZZ-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay10.3390/ijms2221119901422-00671661-6596https://doaj.org/article/336da33dc9c1470fa98fc7120e7531db2021-11-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/21/11990https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067Methylcytosines in mammalian genomes are the main epigenetic molecular codes that switch off the repertoire of genes in cell-type and cell-stage dependent manners. DNA methyltransferases (DMT) are dedicated to managing the status of cytosine methylation. DNA methylation is not only critical in normal development, but it is also implicated in cancers, degeneration, and senescence. Thus, the chemicals to control DMT have been suggested as anticancer drugs by reprogramming the gene expression profile in malignant cells. Here, we report a new optical technique to characterize the activity of DMT and the effect of inhibitors, utilizing the methylation-sensitive B-Z transition of DNA without bisulfite conversion, methylation-sensing proteins, and polymerase chain reaction amplification. With the high sensitivity of single-molecule FRET, this method detects the event of DNA methylation in a single DNA molecule and circumvents the need for amplification steps, permitting direct interpretation. This method also responds to hemi-methylated DNA. Dispensing with methylation-sensitive nucleases, this method preserves the molecular integrity and methylation state of target molecules. Sparing methylation-sensing nucleases and antibodies helps to avoid errors introduced by the antibody’s incomplete specificity or variable activity of nucleases. With this new method, we demonstrated the inhibitory effect of several natural bio-active compounds on DMT. All taken together, our method offers quantitative assays for DMT and DMT-related anticancer drugs.Sook Ho KimHae Jun JungSeok-Cheol HongMDPI AGarticleZ-DNADNA methylationnuclease-freesingle-molecule FRETmethylcytosine sensitivenatural DNA methyltransferase inhibitorsBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 11990, p 11990 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Z-DNA DNA methylation nuclease-free single-molecule FRET methylcytosine sensitive natural DNA methyltransferase inhibitors Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	Z-DNA DNA methylation nuclease-free single-molecule FRET methylcytosine sensitive natural DNA methyltransferase inhibitors Biology (General) QH301-705.5 Chemistry QD1-999 Sook Ho Kim Hae Jun Jung Seok-Cheol Hong Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay
description	Methylcytosines in mammalian genomes are the main epigenetic molecular codes that switch off the repertoire of genes in cell-type and cell-stage dependent manners. DNA methyltransferases (DMT) are dedicated to managing the status of cytosine methylation. DNA methylation is not only critical in normal development, but it is also implicated in cancers, degeneration, and senescence. Thus, the chemicals to control DMT have been suggested as anticancer drugs by reprogramming the gene expression profile in malignant cells. Here, we report a new optical technique to characterize the activity of DMT and the effect of inhibitors, utilizing the methylation-sensitive B-Z transition of DNA without bisulfite conversion, methylation-sensing proteins, and polymerase chain reaction amplification. With the high sensitivity of single-molecule FRET, this method detects the event of DNA methylation in a single DNA molecule and circumvents the need for amplification steps, permitting direct interpretation. This method also responds to hemi-methylated DNA. Dispensing with methylation-sensitive nucleases, this method preserves the molecular integrity and methylation state of target molecules. Sparing methylation-sensing nucleases and antibodies helps to avoid errors introduced by the antibody’s incomplete specificity or variable activity of nucleases. With this new method, we demonstrated the inhibitory effect of several natural bio-active compounds on DMT. All taken together, our method offers quantitative assays for DMT and DMT-related anticancer drugs.
format	article
author	Sook Ho Kim Hae Jun Jung Seok-Cheol Hong
author_facet	Sook Ho Kim Hae Jun Jung Seok-Cheol Hong
author_sort	Sook Ho Kim
title	Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay
title_short	Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay
title_full	Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay
title_fullStr	Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay
title_full_unstemmed	Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay
title_sort	z-dna as a tool for nuclease-free dna methyltransferase assay
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/336da33dc9c1470fa98fc7120e7531db
work_keys_str_mv	AT sookhokim zdnaasatoolfornucleasefreednamethyltransferaseassay AT haejunjung zdnaasatoolfornucleasefreednamethyltransferaseassay AT seokcheolhong zdnaasatoolfornucleasefreednamethyltransferaseassay
_version_	1718432110024327168

Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay

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