Detection and Quantification of Methylation in DNA using Solid-State Nanopores

• DOI: 10.1038/srep01389
• Publication Date: 2013-03-11T10:02:08Z
• Authors: Jiwook Shim; Gwendolyn I. Hump...; Bala Murali Venka...; Jan Marie Munz; Xueqing Zou; Chaitanya Sathe; Klaus Schulten; Farhad Kosari; Ann M. Nardulli; George Vasmatzis; Rashid Bashir
• Keywords: Homeodomain Proteins; 0301 basic medicine; 570; Genetics and Genomics; DNA; DNA Methylation; Polymerase Chain Reaction; Article; 3. Good health; DNA-Binding Proteins; Nanopores; 03 medical and health sciences; Humans; CpG Islands; 5' Untranslated Regions; Biotechnology; Fluorescent Dyes; Transcription Factors

Epigenetic modifications in eukaryotic genomes occur primarily in the form of 5-methylcytosine (5 mC). These modifications are heavily involved in transcriptional repression, gene regulation, development and the progression of diseases including cancer. We report a new single-molecule assay for the detection of DNA methylation using solid-state nanopores. Methylation is detected by selectively labeling methylation sites with MBD1 (MBD-1x) proteins, the complex inducing a 3 fold increase in ionic blockage current relative to unmethylated DNA. Furthermore, the discrimination of methylated and unmethylated DNA is demonstrated 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.