Electroacoustic DNA chip synthesis

By Dr Matt Wilkinson

- Last updated on GMT

Related tags: Dna

A new tool for creating DNA microarrays using a directional
acoustic droplet ejector has been developed that circumvents the
problem of blocked nozzles when using inkjet printing techniques.

Led by Professor Eun Sok Kim, researchers from the University of Southern California have developed a device that uses an ultrasonic ejector that requires no nozzle to eject droplets of DNA bases on demand and allows the synthesis of any random DNA sequence. So far the device has only been used to create oligmers of 15 bases in length (15-mers) but Kim believes that the synthesis of 30-mers would be possible. "The limiting factor right now comes from how DNA is synthesised and behaves - DNA folding could cause problems when making longer oligomers,"​ said Kim. The research will be published in an upcoming issue of the Journal of Micro-Electro-Mechanical Systems​ and the group has patents pending on the process. There are two main ways of commercially producing arrays; the first is used by Affymetrix to make its GeneChips. This costly photolithography method requires a long turnaround time when producing custom arrays. Nimblegen and Xeotron have offered maskless photolithography techniques that use a digital micromirror array, but the method is still limited by the photolabile-protecting group chemistry. Agilent and Rosetta have developed a more flexible method that allows faster construction of DNA microarrays by dispensing phosphoramidite monomers from multi-channel ink-jet print heads. The smallest droplet size depends on the size of the print-heads, but these cannot be miniaturised too far for fear of the phosphamidite precipitating on the print heads. The new device consists of a two by two array of ejectors that precisely eject droplets that converge on a single point about 2mm above the device and adhere to the surface of a slide. Each of the ejectors can be run individually and if they contain small amounts of the DNA bases A, T, C, and G can create DNA sequences in a 70µm in diameter spot on the surface. Kim believes that the system would be very scalable and the addition of microchannels to deliver the bases would allow various spots to be synthesised at once. "The technique could be used to coalesce droplets in the air and as they propagate they mix and this could lead to exciting applications,"​said Kim "These may include protein synthesis in microreaction chambers; we have been looking at ejecting oil droplets and conducting biochemical reactions inside the droplet."

Related topics: Contract Manufacturing & Logistics

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