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DNA pinball machine

Posted August 18, 2015

DNA sequencing requires DNA molecules in the right concentration. A microfluidic device shaped as a pinball machine with micrometre-sized pins with micro-gaps between them can do the job. The balls of the game consist of coils of DNA, with the special twist that the user controls the size of these balls.

dna dtu

Over the last decade microfluidic devices have served as a technology for particle separation based on physical principles rather than chemistry. In one design, particles flow through an array of pins. The pins have been positioned so that whenever a particle passes between two pins, it encounters an obstacle in the form of a third pin, which it circumvents by moving sideward.

Particles larger than a critical size will mostly move to the same side at every pin, while smaller particles will go either way and consequently zigzag through the device. Thus, larger particles are concentrated, as they exit the device through a few outlets only, while the solvent and the smaller particles flow out of all outlets.

The technology works well for the separation of near-spherical particles, but the separation of DNA molecules presents a challenge. A DNA molecule in a fluid forms a soft coil that easily elongates in the shear flow between pins, with the result that it follows the flow instead of being concentrated. This challenge was met recently at Princeton University (USA) in a collaboration that involved researchers at DTU Nanotech.

Add small molecules to pack large molecules

machineThe challenge was met by adding smaller molecules to the fluid containing the DNA molecules. This forces the DNA molecules into a more compact shape, which can be concentrated by the device.

“When particles of different sizes are dispersed in a fluid, the larger particles will attract each other with a so-calleddepletion force,” explains Researcher Jonas Nyvold Pedersen. “Like a gas in an inflated party balloon tries to expand the balloon by stretching its rubber skin, so the smaller particles try to expand their accessible volume by pressing the larger particles together” adds Associate Professor Henrik Flyvbjerg.

Compact and collect
Depletion forces are used extensively. Waste water, e.g., is not easily filtered. The polluting particles are too small. By adding yet smaller particles, the larger particles form large aggregates that are easily filtered with clean water as the result. Some wine production methods comprise the clearing of the wine in a similar manner.

The present device concentrates DNA, up to a factor 17, and it does this fast and continuously in time. Moreover, this filter does not need to be emptied. It empties itself continuously. Purification of DNA from enzymatic reactions for next-generation DNA-sequencing libraries will be an important application.

Source: DTU

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