A ‘DNA origami’ sensor to detect cancer biomarkers in blood

By engineering structures out of DNA, NCCR Bio-Inspired Materials researchers at the University of Fribourg have developed a biosensor that produces a fluorescent signal upon binding molecules found in some types of tumors. The DNA-based sensor could one day help screen a drop of blood for cancer biomarkers.

To detect cancer early on without having to do invasive surgical procedures such as tumor biopsies, scientists worldwide are racing to develop tests that detect tumor-derived nucleic acids, including DNA and short snippets of RNA called miRNAs, which are present in low abundance in the blood of cancer patients. However, the most common methods to detect these molecules are costly, time-consuming, and require trained personnel and specific chemical supplies.

To develop a more efficient strategy for cancer biomarker detection, researchers led by NCCR principal investigators Guillermo Acuña and Curzio Rüegg at the University of Fribourg turned to a technique called ‘DNA origami,’ which relies on the ability of the DNA molecule to fold into intricate shapes and structures.

“DNA molecules are quite fascinating because, on the one side, they carry genetic information,” Rüegg says. On the other hand, he adds, because complementary sequences of DNA can bind to one another, it’s possible to engineer three-dimensional structures with programmable functions. DNA can bind other molecules, serving as a scaffold for complex nanomachinery.

Using DNA origami, the researchers designed a rectangle-shaped sensor made of three building blocks containing sequences that can bind target molecules. The team then coated each building block with different fluorophores — fluorescent molecules that can re-emit light upon excitation.

As the biosensor is produced, its building blocks snap together to form a fully closed book-like structure. However, the presence of target molecules can displace the sequences that keep the structure closed, causing it to open. This structural modification leads to changes in the fluorescence emitted by the fluorophores that decorate the ‘book’ — a signal that can be easily detected with a microscope.

The book-like biosensor could detect, at the same time, two different miRNAs from breast cancer cells within minutes and down to 600,000 molecules per microliter, the researchers reported in the journal Nanoscale.

The collaboration between Acuña and Rüegg, who are both part of the NCCR Bio-Inspired Materials program, continues to this day. Funded by an Innosuisse grant, Rüegg is working towards developing bioassays that could be used in blood tests for breast cancer monitoring. Acuña is filing a patent application to manufacture portable devices that would allow the detection of these bioassays using a smartphone. “All the experiments in our studies are performed in the lab with expensive equipment by highly trained personnel,” Acuña says. In the future, he adds, “we want to use these biosensors in an affordable, portable device.”

However, more work is needed to take the assays from the lab to the real world. For one, the sensors have to be more sensitive in order to detect lower amounts of miRNAs from cancer cells, Rüegg says. His team is now testing specific molecules that could improve the sensors’ sensitivity. Another approach may involve isolating miRNAs from larger volumes of blood to add to the sensor, he says.

To develop cancer diagnostic tests that are as easy as a pregnancy test would also require separating the liquid portion of blood from a blood drop before analyzing it. “That would be a challenge, but it’s doable,” Rüegg says. “The portable device could be an application that would add a unique value to this sensor.”

Reference: Domljanovic, I.; Loretan, M.; Kempter, S.; Acuna, G.P.; Kocabey, S.; Ruegg, C. DNA origami book biosensor for multiplex detection of cancer-associated nucleic acids, Nanoscale, 2022, 14, 15432–15441. https://doi.org/10.1039/D2NR03985K (open access)