Ohio State, Otterbein researchers make DNA origami accessible for K-12 classrooms

Posted: 

An Ohio State University engineering professor and an alumnus published research in September 2022 and again in March 2023 that could broaden access to DNA origami concepts to the middle school, high school and undergraduate classroom.

Ohio State Mechanical and Aerospace Engineering Professor Carlos Castro and alumnus Michael Hudoba, now associate professor and chair of Otterbein University's Department of Engineering and Computer Science, have translated a very costly and timely nanotechnology experiment to a repeatable in-classroom experiment that can be completed in less than two hours for under $300. And it only requires readily-available lab equipment like hot plates and water baths.

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.

Students conducting experiment in the lab
Ohio State students performing the annealing phase of the experiment where their DNA origami structures are loaded onto a gel for analysis.

“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.”

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

For the classroom 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 is 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 an inexpensive kit made by MiniOne . In this system, the set solution is mixed with a dye and then set into an agarose gel, which is electrocuted at 40 volts for 42 minutes and analyzed under a blue LED light.

The publication in September 2022 focused on the methods of an experiment using nanorod structure previously developed for drug delivery applications. The March 2023 publication focuses on analyzing a compliant hinge joint.

Mike Hudoba
Hudoba

Although being able to translate complex lab experiments to the classroom did not come without its challenges, Castro and Hudoba went through several iterations before they were able to find something that worked. They even made small tweaks to some of the methods in between the two journal articles.

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.”

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.”

Carlos Castro
Castro

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.

“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."

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.”

modified version of original article by Jake Rahe, Dept. of Mechanical and Aerospace Engineering