Methylsorb: A simple method for quantifying DNA methylation using DNA-gold affinity interactions

Muhammad J.A. Shiddiky, Abu Ali Ibn Sina, Laura G. Carrascosa, Ramkumar Palanisamy, Sakandar Rauf, Matt Trau

Research output: Book chapter/Published conference paperConference paperpeer-review

2 Citations (Scopus)

Abstract

The analysis of DNA methylation is becoming increasingly important both in the clinic and also as a research tool to unravel key epigenetic molecular mechanisms in biology. Current methodologies for the quantification of regional DNA methylation are largely affected by comprehensive DNA sequencing methodologies which tend to be expensive, tedious, and time-consuming for many applications. Herein, we report an entirely new DNA methylation detection method referred to as 'Methylsorb', which is based on the inherent affinity of DNA bases to the gold surface (i.e., the trend of the affinity interactions is adenine > cytosine ≥ guanine > thymine) [1]. Since the degree of gold-DNA affinity interaction is highly sequence-dependent, it provides a new capability to detect DNA methylation by simply monitoring the relative adsorption of bisulfite treated DNA sequences onto a gold chip. Because the selective physical adsorption of DNA fragments to gold enable a direct read-out of regional DNA methylation, the current requirement for DNA sequencing is obviated. To demonstrate the utility of this method we present data on the regional methylation status of two CpG clusters located in the EN1 and MIR200B genes in MCF7 and MDA-MB-231 cells. The methylation status of these regions was obtained from the change in relative mass on gold surface with respect to relative adsorption of an unmethylated DNA source and this was detected using surface Plasmon resonance (SPR) in a label-free and real-time manner. We anticipate that the simplicity of this method, combined with the high level of accuracy for identifying the methylation status of cytosines in DNA, could find broad application in biology and diagnostics.

Original languageEnglish
Title of host publication8th International Conference on Electrical and Computer Engineering
Subtitle of host publicationAdvancing Technology for a Better Tomorrow, ICECE 2014
Place of PublicationUnited States
PublisherIEEE, Institute of Electrical and Electronics Engineers
Pages17-20
Number of pages4
ISBN (Electronic)9781479941667
DOIs
Publication statusPublished - 28 Jan 2015
Event8th International Conference on Electrical and Computer Engineering, ICECE 2014 - Dhaka, Bangladesh
Duration: 20 Dec 201422 Dec 2014

Publication series

Name8th International Conference on Electrical and Computer Engineering: Advancing Technology for a Better Tomorrow, ICECE 2014

Conference

Conference8th International Conference on Electrical and Computer Engineering, ICECE 2014
Country/TerritoryBangladesh
CityDhaka
Period20/12/1422/12/14

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