By Will Soutter
Researchers at Cornell University have developed a nanofluidic device that can be used to analyze epigenetic changes in the DNA by studying one molecule at a time.
Nanofludic sorting of DNA (Photo provided by Craighead Lab)
Epigenetics is the study of changes inherited in gene expressions caused by chemical changes in the DNA but with the underlying DNA sequence remaining intact without changes. The most common of the epigenetic changes is DNA methylation, which is a biochemical change caused by the addition of a methyl group or Carbon-Hydrogen group to the DNA. Current methods of study entail large samples of DNA molecules most of which get destroyed in the extraction process. The nanofluidic device developed at Cornell facilitates DNA study with a small sample by isolating one molecule at a time.
The research is funded by the National Cancer Institute, the National Institutes of Health and the Cornell Center for Invertebrate Genetics. The process involves an arrangement that carries out color sorting at the molecular level. The device is capable of sorting 500 molecules per minute. Methylated DNA molecules are appended with a fluorescent tag by means a of a biochemical reaction. The molecules are then forced one by one through a 250 nm wide channel in a nanofluidic medium. A laser beam is used to excite the molecules to cause fluorescence in the nanofluidic stream just before the channel splits into a Y. A detector generates an electric pulse every time it senses a fluorescent molecule and pushes this down one arm of the Y. Thus methylated molecules are separated from the other molecules and can be directed to further treatment in microfluidic systems for establishing the gene sequence. To test the integrity of their method, the researchers checked for fluorescence in both the arms of the Y channel and also subjected the collected methylated sample to amplification using a polymerized chain reaction. The results showed just 1-2% of false positives for methylation. Lead researcher Ben Cipriany added that this technique of color coding and molecule sorting could be extended to study other epigenetic characteristics as well as to other molecule-separation tasks.