Detection of regional DNA methylation using DNA-graphene affinity interactions

Md Hakimul Haque; Vinod Gopalan; Sharda Yadav; Md Nazmul Islam; Ehsan Eftekhari; Qin Li; Laura G. Carrascosa; Nam-Trung Nguyen; Alfred K. Lam; Muhammad J. A. Shiddiky

doi:10.1016/j.bios.2016.09.016

Detection of regional DNA methylation using DNA-graphene affinity interactions

Md Hakimul Haque
, Vinod Gopalan
, Sharda Yadav
, Md Nazmul Islam
, Ehsan Eftekhari
, Qin Li
, Laura G. Carrascosa
, Nam-Trung Nguyen
, Alfred K. Lam
, Muhammad J. A. Shiddiky

Research output: Contribution to journal › Article › peer-review

Abstract

We report a new method for the detection of regional DNA methylation using base-dependent affinity interaction (i.e., adsorption) of DNA with graphene. Due to the strongest adsorption affinity of guanine bases towards graphene, bisulfite-treated guanine-enriched methylated DNA leads to a larger amount of the adsorbed DNA on the graphene-modified electrodes in comparison to the adenine-enriched unmethylated DNA. The level of the methylation is quantified by monitoring the differential pulse voltammetric current as a function of the adsorbed DNA. The assay is sensitive to distinguish methylated and unmethylated DNA sequences at single CpG resolution by differentiating changes in DNA methylation as low as 5%. Furthermore, this method has been used to detect methylation levels in a collection of DNA samples taken from oesophageal cancer tissues.

Original language	English
Pages (from-to)	615-621
Journal	Biosensors & Bioelectronics
Volume	87
Early online date	5 Sept 2016
DOIs	https://doi.org/10.1016/j.bios.2016.09.016
Publication status	Published - 15 Jan 2017

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10.1016/j.bios.2016.09.016

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title = "Detection of regional DNA methylation using DNA-graphene affinity interactions",

abstract = "We report a new method for the detection of regional DNA methylation using base-dependent affinity interaction (i.e., adsorption) of DNA with graphene. Due to the strongest adsorption affinity of guanine bases towards graphene, bisulfite-treated guanine-enriched methylated DNA leads to a larger amount of the adsorbed DNA on the graphene-modified electrodes in comparison to the adenine-enriched unmethylated DNA. The level of the methylation is quantified by monitoring the differential pulse voltammetric current as a function of the adsorbed DNA. The assay is sensitive to distinguish methylated and unmethylated DNA sequences at single CpG resolution by differentiating changes in DNA methylation as low as 5\%. Furthermore, this method has been used to detect methylation levels in a collection of DNA samples taken from oesophageal cancer tissues.",

author = "Haque, \{Md Hakimul\} and Vinod Gopalan and Sharda Yadav and Islam, \{Md Nazmul\} and Ehsan Eftekhari and Qin Li and Carrascosa, \{Laura G.\} and Nam-Trung Nguyen and Lam, \{Alfred K.\} and Shiddiky, \{Muhammad J. A.\}",

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doi = "10.1016/j.bios.2016.09.016",

language = "English",

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T1 - Detection of regional DNA methylation using DNA-graphene affinity interactions

AU - Haque, Md Hakimul

AU - Gopalan, Vinod

AU - Yadav, Sharda

AU - Islam, Md Nazmul

AU - Eftekhari, Ehsan

AU - Li, Qin

AU - Carrascosa, Laura G.

AU - Nguyen, Nam-Trung

AU - Lam, Alfred K.

AU - Shiddiky, Muhammad J. A.

PY - 2017/1/15

Y1 - 2017/1/15

N2 - We report a new method for the detection of regional DNA methylation using base-dependent affinity interaction (i.e., adsorption) of DNA with graphene. Due to the strongest adsorption affinity of guanine bases towards graphene, bisulfite-treated guanine-enriched methylated DNA leads to a larger amount of the adsorbed DNA on the graphene-modified electrodes in comparison to the adenine-enriched unmethylated DNA. The level of the methylation is quantified by monitoring the differential pulse voltammetric current as a function of the adsorbed DNA. The assay is sensitive to distinguish methylated and unmethylated DNA sequences at single CpG resolution by differentiating changes in DNA methylation as low as 5%. Furthermore, this method has been used to detect methylation levels in a collection of DNA samples taken from oesophageal cancer tissues.

AB - We report a new method for the detection of regional DNA methylation using base-dependent affinity interaction (i.e., adsorption) of DNA with graphene. Due to the strongest adsorption affinity of guanine bases towards graphene, bisulfite-treated guanine-enriched methylated DNA leads to a larger amount of the adsorbed DNA on the graphene-modified electrodes in comparison to the adenine-enriched unmethylated DNA. The level of the methylation is quantified by monitoring the differential pulse voltammetric current as a function of the adsorbed DNA. The assay is sensitive to distinguish methylated and unmethylated DNA sequences at single CpG resolution by differentiating changes in DNA methylation as low as 5%. Furthermore, this method has been used to detect methylation levels in a collection of DNA samples taken from oesophageal cancer tissues.

UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000390499600087&KeyUID=WOS:000390499600087

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M3 - Article

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SP - 615

EP - 621

JO - Biosensors & Bioelectronics

JF - Biosensors & Bioelectronics

ER -

Detection of regional DNA methylation using DNA-graphene affinity interactions

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