Detection and Quantification of Methylation in DNA using Solid-State Nanopores
Open Access
- 11 March 2013
- journal article
- Published by Springer Science and Business Media LLC in Scientific Reports
- Vol. 3 (1), 1389
- https://doi.org/10.1038/srep01389
Abstract
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.This publication has 60 references indexed in Scilit:
- Controlled Translocation of Individual DNA Molecules through Protein Nanopores with Engineered Molecular BrakesNano Letters, 2011
- Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA MoleculesJournal of the American Chemical Society, 2010
- Direct DNA Methylation Profiling Using Methyl Binding Domain ProteinsAnalytical Chemistry, 2010
- DNA Sensing Using Nanocrystalline Surface‐Enhanced Al2O3 Nanopore SensorsAdvanced Functional Materials, 2010
- Single Molecule Epigenetic Analysis in a Nanofluidic ChannelAnalytical Chemistry, 2010
- Nanoelectromechanics of Methylated DNA in a Synthetic NanoporeBiophysical Journal, 2009
- Dlx1 and Dlx2 Control Neuronal versus Oligodendroglial Cell Fate Acquisition in the Developing ForebrainNeuron, 2007
- Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulationsJournal of Computational Chemistry, 2004
- All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of ProteinsThe Journal of Physical Chemistry B, 1998
- VMD: Visual molecular dynamicsJournal of Molecular Graphics, 1996