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

doi:10.1038/srep01389

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 journal › Article › peer-review

139 Scopus citations

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 language	English (US)
Article number	1389
Journal	Scientific Reports
Volume	3
DOIs	https://doi.org/10.1038/srep01389
State	Published - 2013
Externally published	Yes

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10.1038/srep01389

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@article{33236606c5d74875aee2660fcc651a5b,

title = "Detection and quantification of methylation in DNA using solid-state nanopores",

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.",

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

note = "Funding Information: The authors would like to acknowledge support from the National Institutes of Health (R21 CA155863 to R.B. and NIDDK R01 053884 to A.M.N.). B.M.V. was a trainee supported by the Midwestern Cancer Nanotechnology Training Center (NIH-NCI R25 CA154015) at UIUC. J.S. was supported by NIH R21 CA155863. X.Z., C.S. and K.S. are grateful for the National Institutes of Health grant P41-RR005969. The authors would also like to acknowledge financial support from the Mayo Clinic/University of Illinois Strategic Alliance for Technology-Based Healthcare (http://mayoillinois.org/). The authors also gladly acknowledge supercomputer time provided by Extreme Science and Engineering Discovery Environment (XSEDE) MCA93S028 and the parallel computing resource Taub cluster provided by the Computational Science and Engineering Program at the University of Illinois. And finally, the authors also thank Drs. Adrian Bird for the MBD-1x expression vector, previously referred to as 1xMBD51, and Prof. Paul Soloway at (Cornell University) for technical advice on purification of the MBD-1x protein providing the coding sequence for MBD-1x.",

year = "2013",

doi = "10.1038/srep01389",

language = "English (US)",

volume = "3",

journal = "Scientific Reports",

issn = "2045-2322",

publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - Detection and quantification of methylation in DNA using solid-state nanopores

AU - Shim, Jiwook

AU - Humphreys, Gwendolyn I.

AU - Venkatesan, Bala Murali

AU - Munz, Jan Marie

AU - Zou, Xueqing

AU - Sathe, Chaitanya

AU - Schulten, Klaus

AU - Kosari, Farhad

AU - Nardulli, Ann M.

AU - Vasmatzis, George

AU - Bashir, Rashid

N1 - Funding Information: The authors would like to acknowledge support from the National Institutes of Health (R21 CA155863 to R.B. and NIDDK R01 053884 to A.M.N.). B.M.V. was a trainee supported by the Midwestern Cancer Nanotechnology Training Center (NIH-NCI R25 CA154015) at UIUC. J.S. was supported by NIH R21 CA155863. X.Z., C.S. and K.S. are grateful for the National Institutes of Health grant P41-RR005969. The authors would also like to acknowledge financial support from the Mayo Clinic/University of Illinois Strategic Alliance for Technology-Based Healthcare (http://mayoillinois.org/). The authors also gladly acknowledge supercomputer time provided by Extreme Science and Engineering Discovery Environment (XSEDE) MCA93S028 and the parallel computing resource Taub cluster provided by the Computational Science and Engineering Program at the University of Illinois. And finally, the authors also thank Drs. Adrian Bird for the MBD-1x expression vector, previously referred to as 1xMBD51, and Prof. Paul Soloway at (Cornell University) for technical advice on purification of the MBD-1x protein providing the coding sequence for MBD-1x.

PY - 2013

Y1 - 2013

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/84875192951

UR - https://www.scopus.com/pages/publications/84875192951#tab=citedBy

U2 - 10.1038/srep01389

DO - 10.1038/srep01389

M3 - Article

C2 - 23474808

AN - SCOPUS:84875192951

SN - 2045-2322

VL - 3

JO - Scientific Reports

JF - Scientific Reports

M1 - 1389

ER -

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

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