Ohio State and Otterbein researchers collaborate to bring DNA origami to students of all grade levels

Posted: April 5, 2023
Output of the MiniOne gel electrophoresis system waiting for analysis
MiniOne gel electrophoresis system

An Ohio State Department of Mechanical and Aerospace Engineering Professor and alum published research in September 2022 and again in March 2023 that could bring DNA origami experiments to the middle school, high school and undergraduate classroom.

Dr. Carlos E. Castro, PhD., a professor at the Department of Mechanical and Aerospace Engineering, and Dr. Michael W. Hudoba, PhD., an associate professor and Chair at the Otterbein University Department of Engineering and Computer Science, have taken a typical DNA nanotechnology experiment that can cost upwards of $40,000 and take anywhere from days or weeks to complete and successfully translated it to a repeatable in-classroom experiment that can be completed in less than two hours for under $300 and with readily-available lab equipment like hot plates and water baths.

Through these experiments, the pair hopes to introduce the relatively new and growing DNA origami field to students at a younger age. To do this, Castro and Hudoba created a step-by-step procedure that can be followed by students of all ages, with slight variations based on grade-level and experience in the lab.

“State-of-the-art research like DNA origami is usually limited to graduate studies,” Hudoba said. “We hope that this work will establish a basis to expose students to DNA origami nanotechnology, introducing them to DNA nanotechnology and related fields earlier in their educational careers. Ideally, this will inspire more students to grow their interest in STEM, and pursue undergraduate degrees, graduate degrees, and careers in these emerging and exciting fields.”

Typically, DNA origami nanostructures are created through three common steps: design, fabrication and analysis.

Experiment being run with students at Otterbein

In this educational setting, Castro and Hudoba originally decided to forgo the design process for students since it requires commonly inaccessible design software that takes time to learn. Instead, they included a previously published device that was stored in a solution that could be melted and used for fabrication and analysis along with some additional material to teach DNA origami design in a related lesson to students who complete the experiment.

The classroom fabrication is done using a typical set of lab beakers, a hot plate and some tap water. The test tube of prepared solution containing the designed DNA origami nanostructures are put in a heated beaker of water to melt the solution and then transferred to a beaker of colder water for the folding process. Once the folding process is finished, the solution is moved to an ice bucket to set the structure.

For the analysis of the fabricated structures, the class will then perform a type of agarose gel electrophoresis using a cheap kit called the MiniOne gel electrophoresis system. In this system, the set solution is mixed with a dye and then set into an agarose gel. This gel is then electrocuted at 40 volts for 42 minutes and analyzed under a blue LED light.

The publication in September of 2022 focused on the methods of an experiment using nanorod structure that is being developed as a drug delivery usually referred to as the “Horse”. The March 2023 publication focuses on analyzing the “Compliant Hinge Joint”.

Mike Hudoba
Mike Hudoba

Although being able to translate such a complex lab experiment to the classroom did not come without its challenges, Castro and Hudoba went through several versions of this experiment before they were able to find something that worked. They even made small tweaks to some of the methods from the 2022 publication to the 2023 version.

One of the major challenges was to ensure that the results from the classroom protocol were verifiable with previous published research, Hudoba pointed out. 

“Results in the laboratory can be verified with the use of an electron microscope, which can vary in cost from $100,000 to upwards of $10,000,000,” he said. “Since classrooms could obviously not be expected to use electron microscopy systems, confirmation and analysis comes through comparing gel electrophoresis images with gel images we provide that were confirmed with electron microscopy.”

Carlos Castro
Carlos Castro

This made for a unique challenge, however, because results initially were inconsistent with what was expected, according to Hudoba.  In these experiments, things such as salt concentration, the limitations of the classroom electrophoresis kit, and the purity of the water used have a drastic effect on the results.

“In a sense, we had to work backwards,” Hudoba said. “Instead of performing experiments to analyze results, we had to analyze results to develop the experiments.  It was only once we were able to get the same electrophoresis output using both setups (classroom and laboratory equipment) — that was able to be verified using electron microscopy — that we were confident in our results and the protocol.”

As two of the leading experts in the field, Castro and Hudoba found it both humbling and exciting that an experiment that used to take weeks to complete now can be done in a classroom at such a young age.

Ohio State students running the experiment

“As someone who has worked in DNA nanotechnology research for a long time, it has been really exciting to see the progression from rigorous optimization of DNA origami folding protocols that could take up to a week, to now with this work making it possible to make and perform basic characterization DNA origami structures in just about any classroom,” Castro said. “There are still big challenges that many labs are working on to continue to drive the research field forward to societal impact, but it has been fun to break down barriers that allow a broader range of students to learn about and access DNA origami. I have found it is also very rewarding for researchers in my lab. They get excited about being able to teach younger students about this emerging technology and it is a fun challenge to think about how to make an experiment that we developed in the lab as simple and cost-effective as possible so it can be carried out in a classroom. It has allowed us to challenge some things we have taken for granted.”

Castro and Hudoba hope is that research labs become more accessible to younger students, both figuratively and literally. 

“We want any student to think that they can become a research scientist if that is where their passion takes them,” Hudoba said. “We want to be available to educators to help bring our work into their classroom so that students can have a hands-on experience with cutting-edge science.”

Castro and Hudoba both stressed that they would be happy to work with anyone interested in bringing this into their classroom and would love to hear from any teachers interested.

“The published research shows that the science works, meaning you can create DNA origami nanostructures with low-cost equipment and reagents,” Hudoba said. “But the goal of the research is more than that.  The goal is to actually bring this work into the classrooms, so it is not quite successful until we have educators implement these experiments in their own curricula.”