An innovative approach called DNA origami has paved the way for scientists at the California Institute of Technology (Caltech) to develop a technique that could revolutionize biomarker sensors. These sensors, which detect proteins in bodily fluids, promise to be more affordable and reusable, potentially eliminating the need to send samples out to lab centers for testing.

A Path to Simplified Biomarker Detection

This revolutionary development offers a proof-of-concept for a single-step method to identify and measure nucleic acids and proteins. The study, recently published in the Proceedings of the National Academy of Sciences, was led by a visiting associate at Caltech, Paul Rothemund, focusing on computing and mathematical sciences, and computation and neural systems.

“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,” said Paul Rothemund (BS ’94), a visiting associate at Caltech in this field.

DNA origami, a technique pioneered by Rothemund in 2006, allows for precise control over the design of molecular structures at the nanoscale. This technique involves folding long strands of DNA through self-assembly into any desired shape. Researchers begin with a scaffold of DNA in a solution, which is then folded into shape by hundreds of short sequences of complementary DNA that act as “staples.” The technique enables the creation of structures ranging from nanoscale transistors to intricate maps of the Americas. In 2006, Rothemund used this method to craft miniature DNA smiley faces measuring 100 nanometers across and 2 nanometers thick, exemplified his groundbreaking work.

Creating Nanoscale Biosensors

The latest work by Rothemund and his colleagues involved using DNA origami to create a lilypad-like structure. This flat, circular surface, about 100 nanometers in diameter, is tethered to a gold electrode by a DNA linker. Both the lilypad and the electrode are equipped with short DNA strands designed to bind with an analyte, a molecule of interest in solution, such as DNA, a protein, or an antibody.

When the analyte binds to these DNA strands, the lilypad is pulled down to the gold surface, bringing 70 reporter molecules on the lilypad into contact with the surface. These reporter molecules can easily lose electrons and set off an electric current that can be measured, offering new tools for early disease diagnosis and research.

Previous attempts at similar biosensors used single DNA strands rather than DNA origami structures. This prior work, led by Kevin W. Plaxco of UC Santa Barbara, had similar goals which demonstrates a significant advancement in the new origami technique by Rothemund.

Guareschi, a graduate student at Caltech, commented“The new lilypad origami is large compared to the other DNA strands. It can fit 70 reporters on a single molecule and keep them” away from the surface before binding.

This allows for easy signal detection which helps in identifying diseases and virus mutations.

The relatively large size of the lilypad origami also means that the system can readily accommodate and detect larger molecules, such as large proteins. Researchers at Caltech showed that the two short DNA strands on the lilypad and the gold surface could serve as adapters, turning the system into a sensor for proteins rather than for DNA.

The Caltech researchers then added biotin to those short DNA strands to turn the system into a strepavidin sensor. With further testing the researchers used an aptamer to test for a protein indicative helpful in diagnosing cirrhosis and inflammatory bowel disease, Platelet-derived Growth Factor BB (PDGF-BB).

Adaptable and Reusable Sensing Technology

As Guareschi notes, this creativity widens the possibilities. “We add these simple molecules to the system, and it’s ready to sense something different,” he said. This broadening of application shows how scalable this new technique is.

The lilypad bends readily, making them suitable for larger proteins. The researchers demonstrated the aptamers made this huge potentiality possible.

A Major Breakthrough in Early Cancer Detection

With the new contribution, DNA origami could lead the way in identifying proteins that act as tumor markers thus enabling early cancer detection. Such markers for identifying early-stage cancers are critically where this method shows their potential. It promises precision and consistency in protein identification,” argued a Caltech biochemist.

New Wave of Protemics

At present they are not designed for real-world use, but frame given the tech the suite of tools their breakthrough will pave the way for future protein detection tech.

In the future, the team hopes to extend the system to proteomics, the study that determines which proteins are in a sample and at what concentrations. This advancement could drastically impact an array of fields, from cancer research to personalized medicine.

Additional authors of the paper, “Modular DNA origami-based electrochemical detection of DNA and proteins,” include Jaimie M. Stewart of UCLA; Emily Wu and Ashwin Gopinath of MIT, Netzahualcóyotl Arroyo-Currás of Johns Hopkins University School of Medicine, Philippe Dauphin-Ducharme of the Université de Sherbrooke in Canada; and Philip S. Lukeman of St. John’s University in New York.

The work was supported by the Army Research Office, the Office of Naval Research, the National Science Foundation, and the Life Sciences Research Foundation supported by Merck Research Laboratories.