New Technology Helps Detect Epigenetic Changes Important to Disease

Professor of Molecular and Integrative Physiology Ann M. Nardulli and colleagues at the University of Illinois and the Mayo Clinic have created a new technique for identifying methylated DNA, a modification to our genetic material that has been shown to correlate with the disease severity and metastasis ability of various types of cancers.

Professor of Molecular and Integrative Physiology Ann M. Nardulli and colleagues at the University of Illinois and the Mayo Clinic have created a new technique for identifying methylated DNA, a modification to our genetic material that has been shown to correlate with the disease severity and metastasis ability of various types of cancers.

Genetics has been a hot topic among biologists since Watson and Crick first discovered the structure of DNA, the molecule that encodes the information in all living things. As important as the DNA itself is, scientists are now finding that the study of epigenetics, a word that literally means “on top of genetics” and refers to additional chemical modifications to DNA, may give us clues to the causes of human diseases.

Methylation, the addition of a –CH3 group to a molecule, is one of the most highly characterized epigenetic modifications. The addition of this little group has been shown to cause changes in gene expression, and often contributes to the induction and development of certain diseases like cancer.

While the analysis of these methylation patterns may point to novel ways to diagnose and treat these diseases, the current techniques for these analyses are labor intensive and require large sample volumes of DNA for accuracy.

The researchers have now developed a single-molecule test for DNA methylation using a synthetic membrane with a hole in it, known as a nanopore, which lets only one molecule pass through it to be identified. DNA is negatively charged and is able to pass through a nanopore due to charge differences on either side of the membrane. The side of the membrane that the DNA begins on is negatively charged, which repels the similarly-charged DNA, while the side that the DNA is supposed to go to is positively charged, which attracts the DNA through the nanopore. This movement creates a characteristic electrical current reading.

The scientists were able to label methylated DNA bases with a protein called MBD1 which binds to these modified bases, while leaving unmethylated DNA bases unlabeled. Because DNA bound to the MBD1 protein has a larger diameter than the nanopore’s diameter, it will not migrate through the pore, creating a different electrical current reading than that shown when the non-methylated, unlabeled DNA passes through the nanopore. This allows scientists to differentiate non-methylated and methylated DNA simply by measuring the electrical current.

While more research and development of this test is necessary to refine the process, the future clinical applications for this technology will be invaluable. Scientists may soon be able to quantify and map the locations of the MBD-1 proteins bound to target DNA molecules, providing more information and a detection method for diseases that have a characteristic methylation pattern.

The paper, “Detection and Quantification of Methylation in DNA using Solid-State Nanopores,” appears in Scientific Reports.
Read more about the Mayo-Illinois Alliance.

March 28, 2013 All News