Collaborators from Mayo-Illinois Alliance for Technology Based Healthcare have developed a new, single molecule test for detecting methylated DNA. Methylation — the addition of a methyl group of molecules to a DNA strand — is one of the ways gene expression is regulated. The findings appear in the journal Scientific Reports (Nature Publishing Group).
“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 George Vasmatzis, Ph.D., co-leader of Mayo’s Biomarker Discovery Program in the Center for Individualized Medicine and co-lead author on the article. He says the assay could eliminate the need for bisulfite conversion of DNA, fluorescent labeling, and polymerase chain reaction (PCR).
“Next steps include increasing the spatial resolution by incorporating thinner membranes and by integrating the same preparation steps,” says Rashid Bashir, Ph.D., professor of bioengineering, director of the Micro and Nanotechnology Laboratory, and co-lead author of the study at the University of Illinois at Urbana-Champaign.
A nanopore, in this case, is a very small hole in an artificial membrane, that allows only a single molecule to be located and identified. Researchers say this is useful as methylation in promoter sequences can indicate tumor development in most major types of cancer and may be a better biomarker than many genetic markers. Scientists are now able to differentiate methylated from non-methylated DNA by attaching a protein on the methylated nucleotides measuring ionic electrical current via a solid-state nanopore.
The findings are part of a larger formal collaboration, the Mayo-Illinois Alliance for Technology Based Healthcare. The collaboration in part supported the research. Other support came from the National Institutes of Health (R21 CA155863, NIDDK R01 053884, NCI R25 CA 154015, NIH R21 CA155863, and P41-RR005969). Co-authors include Jiwook Shim, Ph.D.; Gwendolyn Humphreys; Bala Murali Venkatesan, Ph.D.; Xueqing Zou, Ph.D.; Chaitanya Sathe; Klaus Schulten, Ph.D.; Ann Nardulli, Ph.D.; and Rashid Bashir, Ph.D. of the University of Illinois; and Jan Marie Munz and Farhad Kosari, Ph.D., both of Mayo Clinic.