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

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

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number1389
JournalScientific reports
Volume3
DOIs
StatePublished - Mar 25 2013

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Nanopores
DNA Methylation
Methylation
Epigenomics
5-Methylcytosine
DNA
Disease Progression
Proteins
Genome
Polymerase Chain Reaction
Genes
Neoplasms

ASJC Scopus subject areas

  • General

Cite this

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, 3, [1389]. https://doi.org/10.1038/srep01389

Detection and quantification of methylation in DNA using solid-state nanopores. / Shim, Jiwook; Humphreys, Gwendolyn I.; Venkatesan, Bala Murali; Munz, Jan Marie; Zou, Xueqing; Sathe, Chaitanya; Schulten, Klaus; Kosari, Farhad; Nardulli, Ann M.; Vasmatzis, George; Bashir, Rashid.

In: Scientific reports, Vol. 3, 1389, 25.03.2013.

Research output: Contribution to journalArticle

Shim, J, Humphreys, GI, Venkatesan, BM, Munz, JM, Zou, X, Sathe, C, Schulten, K, Kosari, F, Nardulli, AM, Vasmatzis, G & Bashir, R 2013, 'Detection and quantification of methylation in DNA using solid-state nanopores', Scientific reports, vol. 3, 1389. https://doi.org/10.1038/srep01389
Shim J, Humphreys GI, Venkatesan BM, Munz JM, Zou X, Sathe C et al. Detection and quantification of methylation in DNA using solid-state nanopores. Scientific reports. 2013 Mar 25;3. 1389. https://doi.org/10.1038/srep01389
Shim, Jiwook ; Humphreys, Gwendolyn I. ; Venkatesan, Bala Murali ; Munz, Jan Marie ; Zou, Xueqing ; Sathe, Chaitanya ; Schulten, Klaus ; Kosari, Farhad ; Nardulli, Ann M. ; Vasmatzis, George ; Bashir, Rashid. / Detection and quantification of methylation in DNA using solid-state nanopores. In: Scientific reports. 2013 ; Vol. 3.
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