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The Netherlands: Nano Engineering DNA Fractioning Within Minutes

| Editor: Alexander Stark

Researchers at the University of Twente developed a glass microchip for ultrafast separation and purification of DNA fragments. According to the scientists, the new chip is capable of fractionating DNA fragments within just a few minutes.

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A new chip developed by scientists at the University of Twente is capable of fractionating DNA fragments within just a few minutes.
A new chip developed by scientists at the University of Twente is capable of fractionating DNA fragments within just a few minutes.
(Source: University of Twente)

Enschede/The Netherlands — The chip allows for DNA fractioning in high resolution and also purifies the fragments by removing other salts in the DNA sample. Tiny amounts of DNA, like in medical diagnostics or in forensics, are sufficient. The fragments are typically in the size range of second generation DNA sequencing, the next step after the well-known Human Genome Project.

UT scientist Burcu Gumuscu and her colleagues achieved this high speed and resolution by inventing a new approach to the common technique of gel electrophoresis. In the conventional approach, the DNA moves in a gel by an applied electric field. Larger fragments will move slower than small ones, and in this way size separation is possible. But the electric field has one direction and the molecules move in a straight line. The scientists varied the field by periodically applying an electric field of different magnitudes in the perpendicular direction. The fragments also respond to this method. They don’t just move in a straight line now, but somewhere in between the two field directions. As large fragments respond differently to the fields than small ones, the fragments can be separated.

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For collecting the fragments, the chip is equipped with arrays of micro channels on the sides of a square separation chamber with the size of about one square centimeter. Next to that, there are a DNA reservoir and electrodes for applying the electric fields. The chip is easy to produce using fundamental cleanroom techniques of the Mesa+ NanoLab, and cheap, the scientists claim. It is also versatile, as the type and concentration of gel and the electric fields can be adjusted to the application. Protein separation is one of further possible application areas.

The research shows that DNA fragments between 0,5 kbp and 10 kpb (1 kbp= 1,000 base pairs) can be fractionated within two minutes, at high resolution. These are typically the smaller fragments, essential for the second generation DNA sequencing. Speeding up the separation is also a major step forward in medical applications.

The research has been done in the Bios Lab-on-a-chip group, part of the Mesa+ and MIRA research institutes of the University of Twente.

The paper, titled ‘Exploiting biased reptation for continuous flow preparative DNA fractionation in a versatile microfluidic platform’ by Burcu Gümüşcü, Johan Bomer, Hans de Boer, Albert van den Berg and Jan Eijkel, is published by Nature Microsystems and Nano-Engineering.

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