Product Survey: Automated nucleic acid extraction

One Size Doesn’t Fit All
by Harald Zähringer, Labtimes 02/2013

Systems for automated extraction of DNA or RNA are available in many different formats and price levels. Choosing the right one can rack your brain.

Brave new DNA extraction world: just load the samples and walk away.

Have you ever estimated how much time you spend in the lab extracting DNA or RNA? Ok, if you are working in a protein lab it might not be that much; however, if your interest lies in gene expression, genotyping or forensics, it’s probably more than you ever wish. Manual nucleic acid extraction can be very wearisome and, if done the old way with classical chloroform-phenol, it is also a hazardous task. Even if you apply one of the popular extraction kits based on silica columns or magnetic beads, it still involves a lot of repetitive pipetting work. Hence, not only RNA or DNA high throughput labs but also ordinary labs more often indulge in automated nucleic acid extraction systems. If the repetitive pipetting issue doesn’t bother your boss, however, there is another argument that speaks for extraction robots: yields and quality of automatically extracted DNA or RNA are usually more consistent compared to manually extracted nucleic acids.

Spoilt for choice

Once you have persuaded your lab head to invest in an extraction platform, the next question will be: which one? Puh, that’s a hard question to answer. Unless your lab suffers a severe budget crisis, which would boil down the selection to a few semi-automatic instruments, there is a fairly wide choice. It ranges from small, affordable, semi-automatic bench-top devices to full-blown, completely automatic walk-away systems.

Most extraction platforms are designed similar to ordinary liquid handlers with one or more robot arms moving a pipetting head back and forth and, if necessary, up and down to the appropriate microplates, which are arranged on a work desk. The robot arms of fully automatic, high throughput extractors usually work behind a sheet enclosure or translucent hood made of plastic. Other more basic instruments without enclosure may be placed within a standard laminar flow hood. Nucleic acid extraction with these instruments is based on pipetting, albeit extremely fast and precise, but still, ordinary pipetting. There are also systems available using another extraction approach. If one takes a closer look at the heads of these machines, the difference is immediately obvious: they are not equipped with pipetting tips but with magnetisable metal rods. The idea behind rod head extractors, which are used for nucleic acid extraction based on magnetic particle separation, is pretty straightforward.

Similar to manual extraction with magnetic beads, nucleic acids are bound to paramagnetic beads after cell lysis. The bead solution is dispensed into well plates and the disposable-tip-covered rods are immersed into the bead suspension. A magnetic field magnetises the rods, which immediately attract the nucleic acid-covered paramagnetic particles. Similar to metal pieces lifted by a magnetic-crane on a scrap yard, the DNA-laden beads are transferred by the magnetised rods to another well plate filled with wash buffer. The magnet is subsequently switched off and the rods start to rotate to efficiently re-suspend the particles. Finally, the beads are again magnetically collected by the rods and carried into elution buffer to elute the nucleic acids.

Rod head extractors are especially qualified for larger scale extractions. However, it is hard to predict, which type of extraction system is best suited to a certain application. Barry Fields’ group at the University of Atlanta, USA, asked themselves, which of six commercial extraction systems works best to purify DNA and RNA from human nasal wash specimens spiked with respiratory pathogens, amongst them bacteria and RNA viruses (Yang et al., J Virol Methods., 171(1):195-9.). A simple question that led to less simple answers.

One thing that the group could define rather easy was the cost per extraction, which is in the range of three to seven euro. And all systems yielded extracts free of contamination and RT-PCR inhibitors. That’s the good news; the bad news is, according to Yang et al., “The systems differed in nucleic acid recovery, reproducibility and linearity in a pathogen specific manner.” Two distinct models, for example, coming from the same company, based on the same extraction chemistry showed different extraction efficiencies for influenza A and RS-virus, respectively. Bottom line of the paper: no system was superior for all agents tested.

Same difference

A recent publication, coming from a forensic lab, tells a similar story (Legal Medicine, 14, 36-9). The team compared the performance of three automatic extraction systems, using a variety of forensic samples, ranging from blood and hair roots to bones and teeth. The conclusion of the authors is almost identical to that of the above-mentioned paper: “All three platforms performed reasonably well on most samples but each showed different strengths and limitations based on the sample type processed.”

So, the answer to the initial question above is fairly simple: check out as many extraction systems as possible and choose one that performs best with your most frequently used samples.

First published in Labtimes 02/2013. We give no guarantee and assume no liability for article and PDF-download.

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