Detection and quantification of methylation in DNA using solid-state nanopores.

Authors

Jiwook Shim, Rowan UniversityFollow
Gwendolyn I Humphreys
Bala Murali Venkatesan
Jan Marie Munz
Xueqing Zou
Chaitanya Sathe
Klaus Schulten
Farhad Kosari
Ann M Nardulli
George Vasmatzis
Rashid Bashir

Document Type

Article

Version Deposited

Accepted for publication (PostPrint)

Publication Date

3-2013

Publication Title

Scientific Reports

DOI

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.

Comments

Postprint in PubMed Central with a Creative Commons license.

Recommended Citation

Shim, J., Humphreys, G. I., Venkatesan, B. M., Munz, J. M., Zou, X., Sathe, C., ... & Bashir, R. (2013). Detection and Quantification of Methylation in DNA using Solid-State Nanopores. Scientific Reports, 2013(3), 1389-1396.

Creative Commons License

This work is licensed under a Creative Commons Attribution 3.0 License.