28 May 2012

Epigenetics down to the molecule

The nanofluidic device allows for molecular sorting of methylated DNA

Roman Ivanov, Computer

Nanotechnologists from Cornell University (USA) have developed a new tool for studying epigenetic changes in DNA molecules that are responsible for the occurrence of cancer and other diseases. The invention is a nanoscale liquid device that sorts and collects DNA molecules in one cycle of operation.

Epigenetics studies chemical changes in the structure of DNA molecules that do not affect the genetic code, but can affect gene expression (for example, slow down as a result of methylation that once occurred) and are capable of inheritance during further cell division. One of the most important and frequently observed epigenetic changes is the methylation of DNA molecules, when methyl groups attach to cytosine in DNA (about 1% of genomic DNA is methylated in humans). For a more detailed study of this process and its consequences, biologists conduct chemical precipitation of methylated molecules. Unfortunately, this method requires a lot of raw material and often leads to damage and loss of the very methylated molecules that were supposed to be found.

On the contrary, nanofluidic devices are capable of sampling individual molecules from an extremely small amount of source material taken for analysis. One such device, developed in the laboratory of Harold Craighead, is described in the journal Proceedings of the National Academy of Sciences (Cipriany et al., Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel).

A few details. The process begins with a biochemical reaction in which a fluorescent marker is selectively attached to a methylated DNA molecule. The sample is then pushed along a nanofluidic channel with a diameter of 250 nm, narrow enough to pass only one DNA molecule at a time. The laser beam illuminates the channel all the time, causing the luminescence of the marker. When a glowing molecule passes by the detector, an electric field trigger is triggered, and an electric pulse deflects the molecule, pushing it to one side right in front of the Y-shaped fork. As a result, the methylated molecules go to one collection point, and all the others go to another.

DNA molecules labeled with a fluorescent marker are sorted by an electric pulse,
pushing them in the direction of one of the two branches (diagrams from the article in PNAS)

According to the developers, the device functions so fast that it is able to sort more than 500 molecules per minute.

Fluorescent sorting is a well—known phenomenon. In fact, researchers from Cornell University have not invented anything fundamentally new, but they were able to miniaturize and make it possible to separate individual molecules.

Sorted methylated molecules can be further studied using traditional microfluidic sequencing devices.

Prepared based on the materials of Cornell University:
Nanofluidics sorts DNA one molecule at a time to study cancer-causing changes.

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