Automating Nucleic Acid Extraction

Whether determining the presence or sequence of a gene, altering that sequence, or creating a new vaccine, all of molecular biology and much of modern medicine are fundamentally about manipulating nucleic acids. To do so, these RNAs and DNAs need to be isolated from the matrix in which they’re found, purified, and brought to a useful concentration.

More and more, researchers are turning to automation to ease and speed the extraction of nucleic acids, incorporating some or all of the lysis, binding, washing, and elution steps, and perhaps some of the upstream sample preparation and processing and downstream applications as well. Here we look at some of the options available for automating nucleic acid extraction, with some tips and advice on choosing the best system for your lab’s needs and making the most of it along the way.

Automated nucleic acid extraction

“Nucleic acid extraction can be quite tedious and time-consuming,” points out Rick Grygiel, a supervisor on Promega’s Field Support Scientists team.

”All of the steps in a manual nucleic acid extraction involve moving liquids between tubes and wells, and with automation, the analyst doesn’t get fatigued or worn down by performing so many pipetting steps,” adds Carol Loring, Field Applications Specialist with INTEGRA Biosciences. That’s also “where mistakes can happen: errors in pipetting, whether it’s a volume error, or an error in transferring from the wrong tube or mislabeling. … The advantage of the instrumentation is that those errors don’t happen, because machines don’t make mistakes—they always move to the correct tube, and they always pipette the correct volume.”

You also get day-to-day consistency, repeatability, and reproducibility, notes Grygiel. Instrumentation can often shorten turn-around times, and allow technicians to walk away, devoting time to other tasks.

Depending on the types of instrumentation employed, automation can also allow for easier tracking of samples, ensure that steps were carried out correctly, and establish chain of custody—therefore aiding in regulatory compliance, adds Uwe Jäntges, Senior Director of Products of Revvity's chemagen Business.

Types of instrumentation

Automating nucleic acid extraction generally requires more complex processing than automating something like a PCR setup, which is typically just liquid handling, notes Grygiel. It requires a lot of mixing, for example, which is usually accomplished either through tip mixing (trituration) or with some type of orbital shaking device. Most often, magnetic beads are employed to make things more automatable, requiring a magnetic separation device to separate the beads from the supernatant.

Automation equipment can run the gamut from a handheld electronic pipette to an all-encompassing system delivering walkaway end-to-end performance.

A step up from the electronic pipette might be a dedicated or a fully-user programmable (open platform) pipetting robot whose task it is to pick up liquid from one point—a trough, tubes, or a multiwell plate, for example—and deliver it to another. This can be done serially, with multiple iterations.

Sometimes a lab is simply looking for automation to accomplish repetitive tasks, and a small, inexpensive, easy-to-program pipetting robot to ease up on some of the labor in the laboratory may be the answer, Loring says. Other steps, such as moving plates onto a shaker or heater, can be done manually, or the pipetting robot could be integrated with other instrumentation.

There are also instruments that can accomplish the entire nucleic acid extraction, and perhaps (some of) the upstream preparation steps and downstream assays and analyses, without any manual interventions.

Considerations

A lab that processes enough samples would likely profit from automation. Number and frequency of samples are just two things to consider when looking into what instrumentation to opt for. Type and volume of sample, throughput, and the concentration of output required, are others.

Overall cost should be taken into account. Jäntges believes that “the reason why people are not looking for the highest degree of automation is simply the budget.”

Open platforms allow for the user to choose their own reagents and consumables, while closed systems may mandate the use of specific kits. Oftentimes a closed platform will be sold at cost or even at a loss because “our revenue stream is the reagent flow,” explains Jäntges.

Size is another factor. “In some labs space is at a premium, and larger automation can be two meters in length and half a meter or more deep,” notes Eric Vincent, a Promega product manager overseeing high-throughput purification chemistry. On the other hand, points out Loring, a pipetting robot “may fit on the bench or inside a biosafety cabinet.”

Other considerations have to do with expertise and comfort with preparing and employing the instruments, as well as the flexibility required. If a lab specializes in a single task—say, preparing whole blood samples for next-generation sequencing library preparation—then a custom-made, purpose-built instrument will probably be more straightforward to program and set up, to use, and to troubleshoot. On the other hand, labs requiring instrumentation to perform multiple tasks—nucleic acid extraction one day, and ELISA the next, for example—may benefit from a more open platform. “An open platform may have more complexity to it because it’s not as turnkey,” says Grygiel. “But with the open platforms you can do, essentially, whatever you would want to do within your budgetary constraints.”

Troubleshooting

When people are struggling to automate something, Grygiel often advises “to narrow down potentially what step may be causing trouble,” isolating the problem by performing the automated protocol with one of the steps done manually. If that doesn’t fix the problem, then repeat with a different manual step, and so forth. “Then you can see what step the instrument is not reproducing what can be done manually.”

For example, “when I’m determining liquid-handling parameters for an instrument I will use a manual pipette to see how the solution actually moves. How fast can you draw it up in the tip? How fast can you dispense it from a tip? If it’s something viscous and it moves slowly, you may have to add an aspiration delay … or even a blow to make sure you get everything out. Or if you have something that’s volatile and you see it start to drip out of the tip, you may have to add a trailing air gap,” he explains. “There is a good deal of art to go along with your science.”