Cancer is a leading cause of death worldwide accounting for approximately 13% of all deaths in 2004. It is becoming more and more apparent that cancer is as much a disease of misdirected epigenetics as it is a disease of genetic mutations. Epigenetic alterations occur in the form of DNA methylation changes, an early and frequently observed event in carcinogenesis. Interestingly, cancer-specific methylated DNA from most tumor types is readily available in bodily fluids and biopsy specimens and also exists in the form of free-floating DNA shed by dead cancer cells. A technology capable of detecting aberrant methylation patterns in specific genes extracted from the serum of cancer patients would be of immense clinical value. We propose using solid-state nanopore sensors for the detection of robust cancer biomarkers (specifically DNA methylation patterns) at ultra low concentrations in human serum samples. Nanopore sensors use the principle of electrical current spectroscopy to interrogate individual DNA molecules, with the sensitivity to discern subtle structural motifs in single molecules. Nanopore technology is also well suited for gene based methylation analysis, capable of screening small panels of hypermethylation markers specific to a variety of cancers. Nanopore sensors could potentially play an important role in early cancer detection, risk assessment, disease monitoring, chemoprediction and patient prognosis. In working towards our goal of nanopore based methylation analysis, in this R21 we propose the following specific aims: (i) We will first explore the methylation detection capabilities of nanopore sensors using commercially available, fully methylated DNA fragments, and (ii) We will perform Methylation detection and quantification of methylated plasmid DNA. Depending on the outcomes of Aims 1 and 2, this technique may be extended in a follow on R01 to the analysis of pre-clinical and clinical samples, specifically the detection of aberrant methylation patterns in DNA isolated from the serum of prostate cancer patients.

Public Health Relevance

Direct detection of DNA methylation patterns in cancer genes can be very important in early cancer detection, risk assessment, disease monitoring, and patient prognosis. We propose the use of solid-state nanopore sensors for the detection of these methylation patterns.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Exploratory/Developmental Grants (R21)
Project #
Application #
Study Section
Nanotechnology Study Section (NANO)
Program Officer
Ossandon, Miguel
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Illinois Urbana-Champaign
Organized Research Units
United States
Zip Code
Shim, Jiwook; Banerjee, Shouvik; Qiu, Hu et al. (2017) Detection of methylation on dsDNA using nanopores in a MoS2 membrane. Nanoscale 9:14836-14845
Shim, Sangjo; Shim, Jiwook; Taylor, William R et al. (2016) Magnetophoretic-based microfluidic device for DNA Concentration. Biomed Microdevices 18:28
Hu, Huan; Banerjee, Shouvik; Estrada, David et al. (2015) Tip-Based Nanofabrication of Arbitrary Shapes of Graphene Nanoribbons for Device Applications. RSC Adv 5:37006-37012
Shim, Jiwook; Kim, Younghoon; Humphreys, Gwendolyn I et al. (2015) Nanopore-based assay for detection of methylation in double-stranded DNA fragments. ACS Nano 9:290-300
Banerjee, Shouvik; Wilson, James; Shim, Jiwook et al. (2015) Slowing DNA Transport Using Graphene-DNA Interactions. Adv Funct Mater 25:936-946
Shim, Jiwook; Humphreys, Gwendolyn I; Venkatesan, Bala Murali et al. (2013) Detection and quantification of methylation in DNA using solid-state nanopores. Sci Rep 3:1389
Shim, Jiwook; Rivera, Jose A; Bashir, Rashid (2013) Electron beam induced local crystallization of HfO2 nanopores for biosensing applications. Nanoscale 5:10887-93
Banerjee, Shouvik; Shim, Jiwook; Rivera, Jose et al. (2013) Electrochemistry at the edge of a single graphene layer in a nanopore. ACS Nano 7:834-43
Venkatesan, Bala Murali; Estrada, David; Banerjee, Shouvik et al. (2012) Stacked graphene-Al2O3 nanopore sensors for sensitive detection of DNA and DNA-protein complexes. ACS Nano 6:441-50
Venkatesan, Bala Murali; Bashir, Rashid (2011) Nanopore sensors for nucleic acid analysis. Nat Nanotechnol 6:615-24

Showing the most recent 10 out of 11 publications