TCB Publications - Abstract

Jiwook Shim, Gwendolyn I. Humphreys, Bala Murali Venkatesan, Jan Marie Munz, Xueqing Zou, Chaitanya Sathe, Klaus Schulten, Farhad Kosari, Ann M. Nardulli, George Vasmatzis, and Rashid Bashir. Detection and quantification of methylation in DNA using solid-state nanopores. Scientific Reports, 3:1389, 2013. (8 pages). (PMC: 3593219)

SHIM2013 Epigenetic modifications in eukaryotic genomes occur primarily in the form of 5- methylcytosine (5mC). These modifications are heavily involved in transcriptional repression, gene regulation, development and progression of disease, including cancer. Here, we report a new single molecule assay for the detection of methylated DNA using solid-state nanopores. Methylated DNA in complex with truncated MBD1 (MBD-1x) protein had a 3 fold increase in blockage current relative to unmethylated DNA. Furthermore, the discrimination of methylated and unmethylated DNA is demonstrated with high fidelity in the presence of only a single bound protein, thereby giving a resolution of a single methylated CpG dinucleotide. The extent of methylation of a target molecule could also be coarsely quantified using this novel approach. This nanopore-based methylation sensitive assay circumvents the need for bisulfite conversion, fluorescent labeling, and PCR and could therefore prove very useful in studying the role of epigenetics in human disease.

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