The Need for Efficiencies in the DNA Cleanup Workflow

Genetic engineering has advanced tremendously over the last few decades, benefiting numerous fields, ranging from industrial biotechnology to medicine. However, the development of associated laboratory techniques has often not matched this pace, leaving many methods out of date and in need of reform.

Technology Networks spoke with Brittany Niccum, commercial product manager at Beckman Coulter Life Sciences, to learn about the limitations of column-based DNA cleanup – a key technique used in genetic engineering – and explore alternative, modernized options. In this interview, Brittany also shares her thoughts on the biggest trends and advances in the genetic engineering space and what she envisions future technology will look like.

Anna MacDonald (AM): From your perspective as someone in genetic engineering, what have been some of the major advances in the field over the last 20 years?

Brittany Niccum (BN): A lot has happened in the last couple of decades. A big area when I was coming into the field was making biofuels. I rotated in lab where we worked on engineering bacteria to produce hydrogen. The problem is that natural oils were still pretty cheap, and making these organisms is not, so that trend faded a bit. But what’s come out of it is engineering organisms to make compounds that are in high demand and also have a difficult natural method: for instance, the malaria treatment, artemisinin, used to be extracted from the bark of the wormwood tree. Now we can engineer microorganisms to produce the chemical and don’t have to rely on extracting it from bark. So, shifting away from chemicals that have a bigger price point or are too ecologically damaging has been really important.

Genetic engineering just has so many applications in science and in medicine. Jennifer Doudna won the Nobel Prize last year for developing the CRISPR/Cas9 tool that’s really been a foundation of genetic engineering in recent years. Researchers have applied it to disease states and genetic disorders, including sickle cell disease, blindness, cancer and even COVID-19.

The funny thing is that despite all these advances, in many cases, we’re still using lab techniques that were discovered in the 1940s. Even newer methods, like Gibson and Golden Gate, have been around since the early 2000s and haven’t changed much. So there’s this disconnect between what we can do conceptually and the lab techniques we’re still using to support it.

AM: What are some examples of outdated lab techniques or technologies that have not kept up with the progress? 

BN: Some things have obviously updated, like sequencing techniques, flow cytometry, ultracentrifugation, and what we can do with computer analysis in the lab. But some basic techniques haven’t changed. I always had older mentors in school, so learned the techniques they had used 30 and 40 years earlier (one mentor recalled that in her days in school she’d have a pipette in one hand and a cigarette in the other, so it was a different time!). Some things had changed by the time I was in grad school, of course, like pipettes and petri dishes were plastic instead of glass, and petri dishes came with the medium. But in many ways, if you were in a lab 20 or 30 years ago and walked back in today, you wouldn’t notice a difference.

One technique that hasn’t change a lot is column or silica-based DNA cleanup, which is used for DNA and plasmid purification, and first developed in the 1980s. The cleanup step is essential for almost any molecular biology, genetic engineering, and synthetic biology workflow. Column cleanups have been on the market since 1991 and haven’t really changed since then. It’s funny, we haven’t used floppy disks since 1991, so why are so many of us still using this old method?

AM: Are outdated techniques more of a problem for lab technicians or the workflow itself?

BN: For normal PCR cleanup, the maximum number of samples you can do is 24 or 36 because that’s all that will fit in your centrifuge. It does take time: you have to add liquids, take it over to the centrifuge (which is usually at the end of the bench and is almost always shared equipment), put samples inside, spin for a minute, take it out, and dump it and then repeat. It’s almost always about 30 minutes, give or take. It’s not that it’s hard or complicated, it’s just heavily involved and can be mind-numbing—you really have to stay with it. There are over 300 touchpoints for 24 samples. And I am quite clumsy, so I’ve dropped samples, which isn’t good if it’s a precious one. It’s also common to skip a sample by losing count, or either doubling when adding wash buffers or forgetting to put in elution.

Many technicians are doing cleanup multiple times per day—for synthetic biology workflows, you have four or five cleanup steps. That means you’re spending at least two hours that could be used for something else. When my company, Beckman Coulter Life Sciences, did a survey of staff scientists and others who work in labs, we found that after transferring samples from well to well, PCR cleanup came in second for disliked tasks in the lab. We also found that over 46% of respondents do 1-24 DNA or plasmid prep cleanups and over 12% do more than 97 cleanups per week. That’s a lot of time spent on cleanups, and it can get painful physically. My biggest pipette hand injury was during my postdoc, when I was in the lab from 8 a.m. to 3 a.m. the next morning. My hand was basically useless the next day.

AM: What is the alternative to column cleanup?

BN: There are now instruments that are modernizing DNA cleanup and plasmid purification and making it a semi-automated process, like the EMnetik System, which Beckman Coulter Life Sciences developed. It’s about the size of a toaster. The reagent kits are composed of a magnetic bead technology, SuperSPRI, which is highly reactive to magnetic fields. This, combined with a magnetic mixer allows for semi-automated magnetic bead DNA cleanup. The plasmid purification kit uses the same technology to purify plasmids from bacterial culture.

The EMnetik System reduces touchpoints from 300 to fewer than 50, and allows cleanup to be done in less than 16 minutes. It’s also really easy to use: The user interface tells you exactly what to do and when to do it. So it could be really helpful for students who don’t have a lot of experience. Depending on how many cleanups you do, you could potentially cut a day off your experiment. And if you’re in industry, making constructs or products for synthetic biology, it could put you a day ahead of competing companies.

AM: What are some other trends in the space and what will future technology look like?

BN: In the 1980s and 1990s, people could sequence a gene, but the process was so labor-intensive that one sequence would be their entire PhD thesis. For my own dissertation, I sequenced the genomes of 500 strains of E. coli, and I was able to do it within five years. So while it’s hard to imagine what we’ll be capable of in 10 or 20 years, I would say that things will follow this trajectory and become even more automated and streamlined.

In genetic engineering, it may not ever be a situation where you add one ingredient and walk away forever! And that’s probably good, since the human capital component is really essential. But instruments like the EMnetik System and future methods do mean using people’s time better and more efficiently. They free up time to be applied in different ways, like solving problems, rather than at the bench doing the monotonous work. I remember in grad school, planning my day around cleanup. So while instruments like the EMnetik System might not have helped me get done with my PhD faster, maybe it would be one less thing to worry about and have to plan my days around. And definitely one less pipette hand injury.

Brittany Niccum was speaking to Anna MacDonald, Science Writer for Technology Networks.