01 June 2017

Minutes instead of hours

Microfluidic chip will accelerate the separation of DNA fragments by an order of magnitude

Grigory Kopiev, N+1

Scientists from The University of Twente has developed a microfluidic chip capable of separating DNA fragments along the length in a few minutes, unlike the widespread gel electrophoresis method, which requires several hours for this. In addition, the presented method is much cheaper and simpler than electrophoresis. This technology can significantly accelerate research and commercial applications in the field of genetics. The study was published in the journal Microsystems and Nano Engineering (Gumuscu et al., Exploiting biased reptation for continuous flow preparatory DNA fractionation in a versatile microfluidic platform).

In many genetic processes, DNA is broken down into fragments several thousand nucleotides long. In order to sort and arrange them by length, electrophoresis is usually used. This process can be represented as follows. First, a gel with agarose is prepared, which is placed in a special chamber with electrodes at the ends. A sample with DNA fragments of different lengths and a fluorescent dye for visualization is placed on the edge of the chamber. Since DNA molecules are negatively charged, they begin to move from the cathode to the anode under the influence of an electric field. The method is based on the fact that fragments, depending on their length, move along the gel at different speeds, because longer fragments are more inhibited by the gel. Due to this, at the end of the process, scientists receive several strips in the gel, each of which contains fragments of similar length.

The main problem with this method is the sorting time, which takes several hours or even tens of hours for long fragments. Scientists have solved this problem with a new microfluidic chip. It consists of a gel chamber and an array of adjacent channels with a width of 50 micrometers. The difference between this method and classical electrophoresis is that it uses not only the dependence of the movement of fragments of DNA molecules on their size and field strength, but also the dependence of the speed of their reorientation when changing the direction of the field on the size.

Figure from the article by Gumuscu et al.

Scientists created two alternating electric fields of different strengths in perpendicular directions. The ratio of the longitudinal electric field strength to the perpendicular one varied from 2.4 to 3. The researchers selected such a frequency of the alternating field that the molecules were oriented and moved generally in a longitudinal direction, but not in a straight line, but along a trajectory resembling a zigzag, with shorter and lighter molecules deviating more from the trajectory. 

Thus, at the output, fragments of different lengths, which ranged from 500 to 10 thousand nucleotide bases, fell into different channels corresponding to fragments with different numbers of nucleotides.

The method allows the separation of DNA fragments in just a few minutes instead of the hours required for conventional electrophoresis. It also allows you to separate DNA molecules from their accompanying substances obtained during the preparation and isolation of DNA fragments.

You can read more about the technologies that allow you to read DNA in our material "Sequence it".

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