Dr. Thorsten Dieckmann, University of Waterloo Associate Professor in Chemistry and Biochemistry, has used Nicoya’s OpenSPR to recently publish “Structural Consequences of Calmodulin EF Hand Mutations” with M. Piazza, V. Taiakina, and J. G. Guillemette. With over 40 publications, we interviewed Dr. Dieckmann about his RNA-ligand research and experience using OpenSPR. He is now expanding from using an OpenSPR in his lab to using one in a teaching lab so that he can provide a “far greater impact and learning advantage” for his students.
Tell us a bit about yourself and how you are using OpenSPR in your research.
My lab is interested in nucleic acids mostly, and in that area in ribonucleic acid or RNA. We look at small molecule – RNA interactions which we want to exploit in long run in order to build a detection module for biosensors. Among other things, that involves characterizing the behaviour of ribonucleic acid module, a so-called RNA aptamer which is an RNA that has been designed and developed in order to bind to a very specific ligand, a process called SELEX, essentially an in vitro evolution process. You start with a large library of random RNA sequences then try to fish out the ones that have the desired property.
In order to do this, we need to learn how the RNA molecule interacts with its target molecule, the ligand. In our case, these are typically fluorescent small molecules, organic dyes, along the lines of Fluorescein and Malachite green. We basically study the interactions between the two and use that information as a starting point for the design of sensor building blocks.
Where OpenSPR comes in, is that one of the things we’re interested in is to learn how fast or slow the direction between the RNA and ligand happens. We can measure that directly using the Open SPR system; the information we get is the binding kinetics of the system.
You have a collaborative relationship with Nicoya Lifesciences. Can you talk to us about that?
We heard about it through Ryan Denomme, Nicoya’s founder. We started out collaborating as part of a six-month NSERC mini-project because they were looking for people with ongoing research projects, interested in the kind of services the OpenSPR can provide. That allowed us to try the system which ended up helping us publish our research. It’s been very collaborative. In the past, we’ve told them when we think things could be different and they’ve modified the general design or software. It’s a very strong feedback relationship that we’ve both benefited from. We like that Nicoya continuously improves their products by seeking honest feedback and complete transparency from their customers.
What do you think are some advantages for using the OpenSPR in your research and teaching lab?
The more traditional way uses a system that is typically a Biacore, but they cost $150,000 or so a piece. Naturally, if you find them in industry or at universities, they’re typically in central facilities. That’s fine if you have to do a lot of routine things, but what intrigued us with OpenSPR is it’s a system where you can have your own, in your own lab, that you can actually push a little harder because it’s a little more open. There are possibilities to modify the way it runs which is, for research applications, a real bonus because it can adapt to the kind of research we want to do.
Another significant advantage is that both the system itself and the supplies are less expensive than for the industry standard version. That’s a huge plus if you’re in academic research, because resources are limited. With the OpenSPR, we can do many more experiments for essentially the same amount of money. So there’s a strong financial aspect, as well as a strong research aspect.
Why do you have an OpenSPR in your UW Biochemistry Teaching Lab? What advantage will it give your students?
I’m currently involved in that because I teach the course that runs parallel to the lab, so I will introduce SPR as part of my course. Our lab instructor is working at the moment to put together an experiment with very high reliability that can be performed, analyzed and done on the SPR in the six-hour instruction block. This will give students a huge learning advantage. With Biacore, if you could afford it, you wouldn’t want it being run buy 50 undergrads, so a technician would probably run it. That would be a very different experience for the student. With OpenSPR, they can actually do the work themselves in small groups, giving them a far greater impact and learning advantage. They can work with the system themselves; that’s really cool.
The OpenSPR system is less expensive and significantly easier to operate in many ways. It’s a much shorter learning curve for students. My graduate students learned in a few hours how to handle it.
You can read more about Dr. Dieckmann’s research here:
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