Issue 2, 2012
From the journal:

Lab on a Chip

Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine

Christopher L. Warren,†ab   Jianfei Zhao,c   Kimberly Glass,d   Vikas Rishi,c   Aseem Z. Ansaribe  and  Charles Vinson*c  

* Corresponding authors

a McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA

b Department of Biochemistry, University of Wisconsin, Madison, WI, USA

c Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
E-mail: vinsonc@mail.nih.gov
Fax: +301-494-8419
Tel: +301-496-8753

d Department of Physics, University of Maryland, College Park, MD, USA

e The Genome Center, University of Wisconsin, Madison, WI, USA

Abstract

We synthesized customized double-stranded DNA microarrays including methyl-5-cytosine at CpG dinucleotides and produced all 163,555 possible 8-mers (un-, hemi-, and di-methylated) to gain insight into how methylation affects transcription factor binding. An antibody to methyl-5-cytidine showed greater binding to the methylated DNA, demonstrating efficient incorporation of methyl-5-cytosine into the synthesized DNA. In contrast, binding of the transcription factor CREB was inhibited by CpG methylation. This platform represents a powerful new technology to evaluate the effect of DNA methylation on protein binding in any sequence context.

Graphical abstract: Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine

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Article information

DOI
https://doi.org/10.1039/C1LC20698B
Article type
Technical Note
Submitted
28 Jul 2011
Accepted
14 Nov 2011
First published
05 Dec 2011

Lab Chip, 2012,12, 376-380

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Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine

C. L. Warren, J. Zhao, K. Glass, V. Rishi, A. Z. Ansari and C. Vinson, Lab Chip, 2012, 12, 376 DOI: 10.1039/C1LC20698B

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