Biomolecules, such as DNA and proteins, are not static structures. They undergo complex conformational changes that are essential to their functioning and the signaling pathways they belong to. Understanding these changes is pivotal to a deeper comprehension of how the body works and could eventually shed light on certain diseases that afflict us.
Recent advancements in DNA nanotechnology provide insight into the subtle role of biomolecules. Channeling DNA’s chemical and physical properties will aid the study of other structures. For example, new DNA origami technologies have allowed researchers to fold DNA strands into any shape they choose on a nanoscopic scale.
In a paper recently published in Nature Communications, researchers harnessed this ability by using DNA nanotweezers to test a label-free detection method for conformational changes in biomolecular assemblies using microwave microfluidics.
These nanotweezers were fabricated by reconfiguring strands of DNA, and they have two states: open and closed. In the past, this change between states has been triggered by a burst of ultraviolet light.
Nicholas Stephanopoulos, an assistant professor in the Biodesign Center for Molecular Design and Biomimetics and the School of Molecular Sciences, and his postdoc, Minghui Liu, teamed up with Angela Stelson and the Radio Frequency Electronics Group of the National Institute of Standards and Technology to evaluate the effectiveness of this method.
This collaboration originated from a conference that both Stephanopoulos and Stelson attended. When the two found themselves discussing their projects at a conference dinner one night, Stephanopoulos proposed that she use the DNA nanotweezers his lab had developed to test her detection method.
“We had this microwave microfluidic device, and basically, all we had measured was salt water. We were confident that it would work, but we didn’t have a system in mind,” Stelson said. “I was talking to Nick, and I said that I wanted a system with a simplistic conformational change, so he said, ‘If you want a simple change, we have these DNA nanotweezers that we think would work well with your project.’”
This microfluidic device essentially measured the electromagnetic properties of the solution in which the DNA nanotweezers were suspended for both their open and closed state. The change noted between the two states confirmed that the method could be used in detection.
“This project highlights the fact that a chemical change induces a change in the electrical property,” Stelson added.
Currently, to measure conformational changes, researchers label structures with fluorescent dye, but this can upset the natural properties of the assemblies, and processing these samples is a lengthy and potentially costly process.
“For many proteins, especially membrane proteins, it’s very difficult to label them,” Liu said. “When you do, you introduce an extra molecule that changes its surface charge and its composition. But with this method, you don’t need any labelling.”
These pre-existing methods typically only capture one end-state of the conformational change, like a snapshot, but this microfluidic process could provide a real-time depiction of conformational changes, shedding even more light on how these biomolecules work.
According to Stelson, the associated device that measures these electromagnetic properties is portable, cheap and safe to use in any lab environment.
“That is an advantage that we want to emphasize. Anyone could use this in their lab.”
Although this paper is a proof-of-concept for a novel method, the researchers believe it won’t be long before the detection method will be available for new applications.
“What I would like to do is ask how you can use this to measure interesting things,” Stephanopoulos said. “What are some interesting protein-based systems we can use, and how can we use a DNA system that will amplify the signal? Using this method, we could probe things we wouldn’t otherwise probe.”
The researchers are currently in the process of attaching two different proteins to these nanotweezers and using the method to measure the associated protein-protein interactions.
“We’ve got some plans to do some in situ measurement where we attach proteins to the end of the tweezers, and we are trying to understand what chemical mechanism of the opening of the tweezers causes the electrical changes.”
Along with these studies, the researchers will continue to refine the protocol, improving the time resolutions of its measurements and reducing its cost.
A better understanding of these assemblies’ structure and the interactions between them could confer down-the-line applications in diagnostics, treatments and the synthetic assembly of naturally occurring proteins.
Although this paper’s findings confirmed an easier method for detection, it is also a testament to the community of researchers who are open to collaboration.
“This project is a perfect example of why you should go to conferences and talk to people you wouldn’t otherwise talk to,” Stephanopoulos said. “If I sat three seats down, I would have never spoken with Angela. It’s a funny sort of serendipity of the meeting of the minds—she had never heard of DNA nanotechnology. That’s the fun part of science: meeting people from different disciplines and being able to collaborate with them.”