A peek into a DNA-robotics laboratory

As has escaped nobody’s attention, there is currently a pandemic going on. I’m currently in my 8th week of lockdown. The first few weeks were fine, I dare say even a nice change of pace. Plenty of opportunity to focus on the office tasks of doing a lab-centered PhD: updating your labbook, writing future protocols, and reflecting on your projects in general. However, for the past 6 weeks the walls have been closing in on me and I cannot wait until I can finally get back into the lab (or attend a BBQ). If you were to ask my parents, “the lab” is this mysterious alchemy-like place where I mix one brightly colored substance with another, and where we will eventually find the cure for all diseases. That’s unfortunately not the case; the substances I mix all kind of look like water. However, the lab is still a super exciting place. In this blogpost, I will give you a tour and tell you about my experience visiting another lab. What a lab exactly contains tends to differ greatly between groups and specializations. For instance, although at first glance an organic synthesis lab might look similar to a cell lab (it’s the fume hoods), their contents are vastly distinct. I’m part of the Gothelf lab, but my main project falls a bit outside of our group’s specialization. This means that the equipment and expertise I need is sometimes not readily accessible in our lab. However, one of the great things about being part of the DNA-robotics training network, is that we can easily go on secondments to our collaborators. Last autumn I visited the lab of prof. Hendrik Dietz at the Technische Universität München. Being in the lab there, I felt like a kid in a candy shop: There were common stocks of nearly all the buffers I use, a NanoDrop that could measure eight samples simultaneously, and a freezer with literal liters of origami scaffolds. I could go on, but let us start the tour where I start my experiments.

A typical day starts by pipetting together all the components required to make our DNA nanostructures. This folding mixture needs to be incubated in an hours-long temperature ramp. The exact specifications of the ramp might require optimization:  beginning and ending temperature, ramping speed, step size, and numerous other variables can impact the folding of our structures. Each set of variables requires its own incubation in a separate PCR machine, so a thorough optimization (if required) can take a long time. Unless, of course, there are many PCR blocks available in parallel. Cue the tetrads; Frankenstein-ish assemblies of recycled PCR machines.  They are loud and proud and there are six of them in total (each with four PCR blocks). And you still need to finish mixing on time, because often all the blocks are taken by the afternoon.

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Figure 1. The tetrads

 

Then, after the temperature ramp, we need to analyze our structures to see if they have folded correctly. The first step in this process is gel electrophoreses, where a current separates our samples into different sections in an agarose gel. I think my favorite part of the Dietz lab was the gel area. There were so many gel chambers and they were incredibly easy to use. I especially loved the monster gels, which were gigantic gels where you could load in 50 samples. After running and scanning the gel, you can opt to purify the different sections. It is in this part of the experiments where I found perhaps the greatest ease-of-handling improvement; pipet tips made for the extraction of gel samples. No more fiddling around with a scalpel, just pierce the gel with your pipet and expunge the separated section in a spin column. It literally takes less than a minute. Now if only the supplier of these amazing tips would sell them to labs outside of Germany.

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Figure 2. The gel area. The gels are kept in a water bath during the electrophoresis, to prevent local heating.
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Figure 3. The Transmission Electron Microscope

We incubated our mixtures, confirmed the presence of folded structures, and purified them. Now, we want to see what they look like. There are multiple ways to go about this. For instance, flat structures tend to look best under an atomic force microscope (AFM). In contrast, bulky structures can be studied better with transmission electron microscopy (TEM). We have both available back in Aarhus, but unlike the AFM, the TEM is not property of the Gothelf lab and has a long waiting list (at least a few weeks). The Dietz lab has two TEMs for themselves, in addition to two CRYO-EMs. I could often book a time slot only a few days in advance, no problem. Both AFM and TEM require quite a bit of practice and optimization of the imaging conditions, but the results are worth it: a gel only confirms whether a structure has folded, but there’s nothing like seeing your teeny tiny structures for real.

Of course, the contents and equipment of the lab are only one part of a secondment experience. Another is the expertise of the people there. I have asked so many questions and gotten so much valuable input on my project.  The opportunity to compare protocols of even routine experiments is indispensable. Finally, there’s the people themselves, who’ve made my time in and outside of the Dietz lab incredibly enjoyable. Whether it be the Mensa lunches with the group, the wine-and-Bob-Ross afternoons with Alba, or the sushi-movie-nights with Michi, I have a lot of great memories to look back on. So, all in all, the secondment was a great success. I look forward to the next one! (when we are allowed to travel again).

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