title: Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine.
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.
authors.affiliation: McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Warren
authors.forename: Jianfei
authors.initials: J
authors.lastname: Zhao
authors.forename: Kimberly
authors.initials: K
authors.lastname: Glass
authors.forename: Vikas
authors.initials: V
authors.lastname: Rishi
authors.forename: Aseem Z
authors.initials: AZ
authors.lastname: Ansari
authors.forename: Charles
authors.initials: C
authors.lastname: Vinson
mesh_terms: D044503:5-Methylcytosine / Q000276:immunology / Q000378:metabolism*; D000906:Antibodies / Q000276:immunology; D018899:CpG Islands; D017362:Cyclic AMP Response Element-Binding Protein / Q000235:genetics; D004247:DNA / Q000378:metabolism*; D019175:DNA Methylation; D024202:Electrophoretic Mobility Shift Assay / Q000295:instrumentation; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation*
chemical_list: D000906:Antibodies; D017362:Cyclic AMP Response Element-Binding Protein; D044503:5-Methylcytosine; D004247:DNA