Capturing DNA molecules in a nanochannel

An electric voltage can be used to propel DNA molecules through a channel a few nanometers deep, or to stop them in their tracks.

In a strong electric field the molecules judder along the channel, while in weaker fields they move more smoothly. This enables DNA fragments to be ‘captured’ on a chip and separated for analysis. University of Twente researchers will soon publish details of this work in Nano Letters.

The researchers found that, when forced through extremely shallow channels just 20 nanometers deep and a few micrometers wide, DNA molecules behave very differently than they do in free solution. In the latter situation they tend to form clumps, while molecules in the channels are forced into an elongated straitjacket.

This effect alone produces a difference in mobility between long and short molecules. Moreover, exposure to an electric field has now been shown to have a substantial effect. This presents a range of new options for the separation of fragments (and entire molecules) of DNA. The previous technique, known as gel electrophoresis, involved the use of micro-channels filled with a gel.

According to researcher Georgette Salieb-Beugelaar, the laborious and time-consuming process of pouring in the gel can be rendered obsolete by the new method.

Roughness
In their Nano Letters article, the researchers ascribe the difference in mobility to factors such as the roughness of the channels’ surfaces. A DNA molecule can easily be 1000 times longer than the channels are deep. As a result, it encounters minute surface irregularities at many different points, an effect that is reinforced by the electric field. This seems to be the cause of the stagnation in mobility that occurs in strong fields. It presents an opportunity to capture fragments and – using weaker fields – to accurately control their onward motion. This is the first demonstration of varying mobility in electric fields of differing strengths.