Scientists at Caltech have developed a technique using DNA origami that could pave the way for affordable, reusable biomarker sensors capable of rapidly detecting proteins in bodily fluids—potentially eliminating the need for lab-based testing.
A coarse-grained model of the DNA origami lilypad used in the study. The tails hanging down indicate where redox reporters are located. For scale, the diameter of the disk is approximately 80 nm. Image Credit: Matteo Guareschi/Caltech
Our work provides a proof-of-concept showing a path to a single-step method that could be used to identify and measure nucleic acids and proteins.
Paul Rothemund, Visiting Associate, Computing and Mathematical Sciences, and Computation and Neural Systems, Caltech
A paper detailing the research was recently published in Proceedings of the National Academy of Sciences. The lead authors are former Caltech postdoctoral scholar Byoung-jin Jeon and current graduate student Matteo M. Guareschi, who completed the work in Rothemund's lab.
DNA origami, first introduced by Rothemund in 2006, allows for precise molecular design at the nanoscale using self-assembling DNA strands. This method enables long DNA strands to fold into specific shapes by binding with shorter complementary DNA sequences that act as "staples." Over the years, researchers have used this approach to create nanoscale shapes, including a map of the Americas and even functional transistors.
In this latest research, the team used DNA origami to construct a lilypad-like structure—a flat, circular surface about 100 nanometers in diameter—tethered by a DNA linker to a gold electrode. Both the lilypad and the electrode were equipped with short DNA strands designed to bind with an analyte, a target molecule in a solution. When an analyte binds to these strands, the lilypad is pulled toward the gold surface, bringing 70 redox reporter molecules into contact with the electrode. These molecules lose electrons in a reaction, generating an electric current. A stronger current indicates a higher concentration of the target molecule.
Previously, similar biosensors were developed using single DNA strands rather than DNA origami. That work was led by Kevin W. Plaxco (PhD '94) of UC Santa Barbara, who is also a co-author of the current study.
Guareschi notes that the larger size of the lilypad origami offers key advantages over single DNA strands.
That means it can fit 70 reporters on a single molecule and keep them away from the surface before binding. Then when the analyte is bound and the lilypad reaches the electrode, there is a large signal gain, making the change easy to detect.
Matteo M. Guareschi, Graduate Student, Caltech
This larger structure also allows the system to detect larger molecules, such as proteins.
The team demonstrated that the lilypad could be adapted to sense proteins by modifying the short DNA strands with biotin, enabling detection of streptavidin. Additionally, they incorporated a DNA aptamer—designed to bind to platelet-derived growth factor BB (PDGF-BB), a protein linked to conditions like cirrhosis and inflammatory bowel disease.
We just add these simple molecules to the system, and it's ready to sense something different. It's large enough to accommodate whatever you throw at it—that could be aptamers, nanobodies, fragments of antibodies—and it doesn't need to be completely redesigned every time.
Matteo M. Guareschi, Graduate Student, Caltech
Another key advantage of the sensor is its reusability. The researchers demonstrated that the system could be repurposed multiple times by swapping out adapters for different detections. While performance slightly declines over time, the current version can be reused at least four times.
Looking ahead, the team envisions applications in proteomics, the large-scale study of proteins and their concentrations.
“You could have multiple sensors at the same time with different analytes, and then you could do a wash, switch the analytes, and remeasure. And you could do that several times. Within a few hours, you could measure hundreds of proteins using a single system,” said Guareschi.
Journal Reference:
Jeon, B., et al. (2024) Modular DNA origami–based electrochemical detection of DNA and proteins. Proceedings of the National Academy of Sciences. doi.org/10.1073/pnas.2311279121