Opentrons Customer Interview | Northwestern University

Michael Rourke is a PhD researcher in chemistry at Northwestern University where he uses OT-2 and the Opentrons protocol editor to advance organic chemistry research.

Dr. Michael Rourke was deeply inspired by automation. In order to improve the accuracy and precision of experiments and reduce the burden of tedious and repetitive manual tasks on his team, he led the organic chemistry laboratory at Northwestern University to successfully transform into laboratory automation. and by using the user-friendly Opentrons Protocol EditorUses the Opentrons OT-2 automated pipetting platform and Opentrons' open source software platform to Improve laboratory safety.

Opentrons: Please introduce your research background.

Michael Rourke: I am a synthetic chemist. I have a degree in biochemistry from the University of Colorado, where I studied synthetic chemistry, focusing on the modification of carbohydrates. Now I'm at Northwestern University as a PhD candidate doing synthesis methodology in Scheidt's research group. When I came here, I worked primarily on photoredox catalytic reactions using high-throughput equipment in a 96-well plate format in the MBRAUN glove box.

Opentrons: It sounds like your job requires a lot of manual pipetting.

Michael Rourke: Indeed. Say you have two substrates, A and B, and combine them to form AB - there are several variables you want to change (e.g. you might want to make six photocatalysts, four solvents, four bases, etc. ). These variables can add up quickly. And the more complex the reaction, or the more variables you consider, the smaller the slots on the corresponding orifice plate will be. When your focus becomes smaller, it becomes less easy to determine the precise location of the operation and when to start and stop the operation.

Opentrons: So how did you manage this complexity before you had OT-2?

Michael Rourke: We use manual pipettes and use cards to record the progress of each well. Frankly, doing it manually is error-prone. And it’s uncomfortable to hold a pipette in the glove box for hours on end. I reviewed it with my advisor and told him that the high-throughput technology was effective, but that there was room for improvement in our accuracy and precision.

Opentrons: Was that when you first thought about using automation?

Michael Rourke: Yes. My boss was enthusiastic about it, and my advisor suggested I shop around to see what was available. But when you come back with an offer of $250,000, you’re not going to get very far in the center of academic funding! However, our biggest concern was the durability of the pipette. We use Opentrons electronic pipettes, which are made from carbonate-based polymers. The possibility of their degradation in organic solvents is the biggest foreseeable challenge or difficulty in our workflow. We saw an article about a professor in Michigan who had an OT-2 automated pipetting platform in his glove box, and we found that the price of the pipettes required for the OT-2 was similar to the pipettes we were already using. . So in January 2021, we made the decision and ordered an OT-2 and put it in an inert gas glove box.

Opentrons: How was your experience setting up the OT-2?

Michael Rourke: I measured it to see if it would fit, and it does! Since I didn't know how well WiFi would work in an enclosed space, I ran the USB port through the glovebox's sealed cover. But it turned out that this wasn't actually necessary because I put the OT-2 in and sealed it, and the WiFi still worked pretty well.

Opentrons: How does the OT-2 perform in your lab?

Michael Rourke: It performed well. The first time I used it, I wore one pipette slightly because the necessary air gap was not retained at the top of the tip. But my volume with organic solvents is about two-thirds, so 150-200 microliters in the pipette. I placed our own plate—the Paradox 96-well reaction plate for photoreduction catalysis—on to the pipetting platform and used Opentrons Labware Libraryincorporates them into the protocol. I placed a blower next to the pipetting platform to blow down the well plate. I used some reservoirs and I tried to increase the number of vertical columns especially the vertical columns of reaction solvents so that I could use the reservoirs instead for this experiment. I have prepared many reagents in 2-dram scintillation vials. We are both professional organic chemists but lack Python programming experience, so we are using the Protocol Editor interface to create our protocols .

Opentrons: How does the OT-2 pipette perform in your experimental work?

Michael Rourke: We don't have any problems with fluid aspiration and injection. Many of the chemical reactions I do now use organic solvents such as acetonitrile, tetrahydrofuran, dimethylformamide (DMF) - and methylene chloride, which are all very volatile. We couple it with liquid chromatography-mass spectrometry (LCMS) and gas chromatography-mass spectrometry (GCMS) so that I can put a standard in before the reaction or I can take it back and let the pipetting The platform is removed from the scintillation vial and a known amount is added to each well.

Opentrons: What is the most significant benefit of automated pipetting for you?

Michael Rourke: I think consistency is important. Everyone who manually handles well plates has wondered, “Didn’t I just add something to that plate?” Now, the process is perfectly replicable. This is the biggest advantage of automated pipetting.

Opentrons: What areas do you think the OT-2 still needs to improve on?

Michael Rourke: We suggested to our boss that the purpose of automated pipetting is to increase throughput, but also to improve accuracy and precision. There's nothing worse than spending a day working on a reaction and then realizing you missed something. Opentrons Protocol Designer can color-code entries, but colored printer cartridges are not common in academic labs. So to ensure accuracy, we can only print out a screenshot of the starting deck conditions and write the coding on it using ChemDraw. It would be great if you could add a numeric or letter code as a note in Protocol Designer to keep track of the solvent or reagent in the container - a little suggestion.

Opentrons: How does automating your workflow differ from the way you were doing it manually?

Michael Rourke: The workflow in our laboratory is often customized, and everyone designs experiments according to their own needs. You have to get creative in how you experiment with layout. I have never set up an experiment without using microchannels, but some of my colleagues still only use single-channel pipettes; while single-channel pipettes are more accurate and precise than manual pipetting, they are not the same as manual pipetting. The flow and speed of operation are similar. I completed 300 reactions in two and a half hours using both single-channel and microchannel operations.

Opentrons: How does having an automated pipetting platform handle all pipetting work in the glovebox increase your throughput?

Michael Rourke: The automated pipetting platform has really improved our throughput. We used to do 96 samples a day. Now, I can do 300 a day. Regarding the work we do in the glove box, there are certain tasks that are done on a regular basis, but for some jobs that require large-scale preparation of everything at once, you can spend one day setting it all up and then the next The sky will move again. I used to be able to process only one well plate per day, but now I can process up to four at the same time, and with enough reagents and other supplies, we might even be able to process eight well plates in a day, or leave the pipetting platform overnight run. This greatly improves our work efficiency. Also, now I can do the screening in the initial stages and then allow time to analyze all the data points, rather than having to stand in front of the glove box for five days in a row and analyze it a week or two later.

Opentrons: Is there anything else you’d like to share?

Michael Rourke: I became a chemist to analyze data and come up with new ideas, and to share ideas with colleagues and younger students. It's hard to communicate verbally and think when I'm working in the glove box. You can only count the numbers silently because talking makes you lose count. This only hinders the creativity and happiness of scientific work. Nowadays, we no longer need to do tasks such as filling reagent bottles ourselves. Since we have automated pipetting platforms, no one has to physically handle a well plate. I am excited that undergraduate students in our lab will be trained and begin using the OT-2 this summer. I think a lot of the projects in the lab can be automated over time. For example, we take safety very seriously at Northwestern University: organic solvents are flammable and using them is risky. Transitioning the reaction setup to an automated system in a controlled environment like a glove box has clear advantages. In addition, our laboratory equipment enables pipetting platforms to perform preparative-scale reactions in 20 ml and 40 ml bottles. As organic chemists, we take ensuring safety very seriously, and I believe that in the near future, laboratory automation will make a significant contribution to risk mitigation in both industrial and academic laboratories.