New Nanopore Sensor Simplifies Analysis of Methylated DNA
DNA methylation, the addition of a methyl group to specific locations on a DNA strand, plays a critical role in determining which genes are active in a cell at any given time. It plays an important role in embryonic development, cell growth and reproduction, and many diseases, including cancer. Now, researchers collaborating at the Mayo Clinic and the University of Illinois in Urbana-Champaign have developed a novel single molecule test for detecting DNA methylation that should greatly simplify and advance the study of this important genomic process.
The details of this new test appear in a paper published in the journal Scientific Reports. This study was led by George Vasmatzis, co-leader of the Mayo Clinic’s Biomarker Discovery Program in the Center for Individualized Medicine, and Rashid Bashir, co-principal investigator of the Midwest Cancer Nanotechnology Training Center at the University of Illinois, part of the National Cancer Institute’s Alliance for Nanotechnology in Cancer.
The new method relies on solid-state nanopores, nanometer-sized holes created using standard semiconductor processing technologies in membranes made of a particular type of insulating material known as a dielectric. Electrical signals from the dielectric change in specific patterns when molecules, such as DNA pass through the nanopore. In this case, the collaborating teams labeled methylated regions of DNA with a specific methyl DNA binding protein known as MBD1.Whenever the protein-labeled region of DNA passes through a nanopore, the electrical current changes by a factor of three compared to when unlabeled regions of DNA pass through the pore, an easily observed change.
"While nanopores have been studied for genomic sequencing and screening analysis, this new assay can potentially circumvent the need for some of the current processes in evaluating epigenetics-related diseases," says Dr. Vasmatzis. He says the assay could eliminate the need for bisulfite conversion of DNA, fluorescent labeling, and polymerase chain reaction (PCR), the standard method for detecting methylated DNA. While this method is useful, its limitation is that it requires large quantities of DNA.
In its current form, this new technique can detect single instances of DNA methylation with high fidelity and determine the total number of methylation sites per DNA molecule. According to Dr. Bashir, "The next step in this research is to increase the spatial resolution by incorporating thinner membranes and by integrating the same preparation steps." Such improvements would then enable researchers to create high-resolution methylation maps that would be useful for characterizing so-called epigenetic diseases, including cancer.
The investigators note that "cancer-specific methylated DNA from most tumor types are known to be present in biopsy specimens and in patient serum at very low concentrations. A rapid, accurate, and amplification free assay to detect these biomarkers from minute sample volumes could prove invaluable in the early detection of disease, monitoring disease progression, and prognosis. With continued development, solid-state nanopores could meet this unmet technological and clinical need."
This research, which is detailed in a paper titled "Detection and quantification of methylation in DNA using solid-state nanopores," was funded in part by the NCI Alliance for Nanotechnology in Cancer, a comprehensive initiative designed to accelerate the application of nanotechnology to the prevention, diagnosis, and treatment of cancer. A free copy of the full paper is available at the journal’s website.View full paper