Art by Aastha Paudel
The geometric reasoning skills used to construct Lego structures—a grocery store, a single-family home, or even the Louvre—rarely apply in the realm of biosensors and genomics, where there is a stronger focus on mechanisms of membrane systems and pharmaceutical pathways. But for a team of Caltech researchers behind a recently published paper in the Proceedings of the National Academy of Sciences, the intersection of these two seemingly disparate disciplines yielded a new molecule revolutionizing the quantification of the relative concentrations and activities of nucleic acids and proteins: the lily pad sensor. This reagentless biosensor capable of detecting biomarkers continuously is built from DNA origami, a material synthesis technique that folds DNA into precise, nanoscale shapes. It is like a molecular spy: adaptable, relentless, and poised to transform medicine.
For first co-author Matteo Guareschi, a PhD candidate at Caltech’s Rothemund Lab, DNA origami symbolized the optimal combination of the best parts of biological and physical engineering. Coming from an electrical engineering background that did not provide specific training in biochemistry or biophysics, Guareschi stumbled on the field nearly by accident.
“I realized many things you can do with DNA, you can also do in the silicon electron world,” he said. “I got really interested in biological sensing with the idea of taking a molecule like DNA, which we usually think about as a molecule of life, and re-engineering it for completely different purposes such as treating it as a material or as a computation device.” In bridging his engineering background with the molecular intricacies of biology, Guareschi embodies the very fusion that DNA origami represents—where structural imagination meets biochemical precision, enabling a new era of biosensing.
So, what exactly is DNA origami? Picture a microscopic Lego: DNA strands folded and assembled together into custom-designed structures, all at a scale so small it boggles the mind. “What is really unique is the very sort of fine-grain resolution that we have on a DNA origami molecule,” Guareschi said. “We can end up deciding or programming things at the sub-nanometer level.” This level of precision is typically beyond reach for the silicon chip, an advantage that makes the DNA origami technique so special.
The device itself, dubbed the “lily pad sensor,” is a flat, disk-shaped DNA origami tethered to a gold electrode by a long, flexible DNA leash. This biosensor relies on the DNA origami structure to detect the presence of an analyte through a carefully designed interplay of binding and signaling mechanisms. In its resting state, the sensor floats far from the surface, quiet and unassuming. But when a target molecule—a biomarker like DNA, RNA, or a protein—shows up, it binds to the origami and causes structural changes that bring the origami closer to the electrode, producing a measurable electrical current. This motion brings dozens of tiny reporter molecules called methylene blue (MB) near enough to the surface to generate an electrical signal. The system is akin to a drawbridge lowering to let the signal cross.
The origami is anchored to the surface by a long DNA linker, which serves a dual purpose. First, the linker acts as a tether, preventing the origami from being washed away during experimental steps such as adding or removing solutions from the chip. Second, it maintains a sufficient distance between the origami and the surface in the absence of the analyte, ensuring a low baseline “off” signal. This design balances the need for stability with the requirement for a clear distinction between the “on” and “off” states of the sensor.
“The idea behind the sensor was to maximize the contrast between the off and on state,” Guareschi said. “Keep it very far from the surface in the off state—very low signal; bring it very close to the surface in the on state—very high signal.”
Utilizing the design combining the lily pad DNA origami with the anchored to gold electrodes, the team achieved a stunning one thousand percent boost in signal—outmatching more traditional methods like electrochemical DNA and aptamer-based sensors that typically yield only two hundred to four hundred percent signal gains.
Traditional tests like the enzyme-linked immunosorbent assay or polymerase chain reaction are the lab coat-clad tortoises of the biosensing world: slow, expensive, and reliant on skilled hands to add chemicals step-by-step. This new sensor, though, is a hare—reagent-less and needs no extra ingredients to work. “Your blood or any other biological fluid could flow in our sensor, and over time, it keeps getting measured without an external operator,” Guareschi said. It’s a device that could one day sit inside a patient, continuously tracking biomarkers like a glucose monitor does for diabetics.
But the device’s real superpower is its versatility. Unlike older sensors that need a bespoke redesign for every new molecule they detect, this one’s modular. Swap out a few DNA pieces, and it’s ready for a new target. “The other big thing for us was that it can be adapted to a large range of analytes,” Guareschi said. The team proved this concept by testing it on everything from nucleic acids to proteins like streptavidin (a protein isolated from the bacteria widely used in biotechnology) and platelet-derived growth factor-BB, a biomarker tied to cancer and tissue repair.
Building this molecular marvel wasn’t all smooth sailing. One headache was the MB reporters. The team wanted as many as possible—up to two hundred per origami—for a stronger signal. However, too many MBs caused the origami to clump together like overzealous party guests. “We found that only once we went down to seventy and took a lot of other precautions […] we could see good origami formation,” Guareschi said.
Unlike Guareschi’s initial expectations, the team observed that the origami didn’t lie flat over the single-stranded DNA, but rather curled up at the edges. This deformed mechanism was caused by MB-laden strands flapping around in Brownian motion—random, jiggling movement of tiny particles suspended in fluid—which bent the structure into a U-shape.
“It’s that point where you understand that the cartoon sketch you have of something is not quite the reality of the system,” Guareschi said. “Since this is a modular sensor, we knew we needed to adapt it to different analytes, but it’s not ‘quite snap your fingers and that’s done’. We need to think about the geometry of these techniques.”
To make the origami adaptable to analytes of different sizes, the team tweaked the “curtain” of DNA strands holding the MBs—a method akin to adjusting a shower curtain rod to fit the tub. For bigger molecules, a longer curtain was key to ensuring the MBs could still reach the electrode.
Looking ahead, Guareschi said the goal is to turn the lily pad DNA origami into a self-contained system that can measure nucleic acids and protein levels in a lab setting without needing dedicated personnel to run it. Further experiments will continue to optimize the biocompatibility of DNA with other biomolecular materials such as plasma and components of cells’ plasma membranes.
“The optimization of the [DNA origami system] is one of the things I’m most proud about in the paper because I really enjoy the insight that comes from trying to understand what is happening at the molecular level,” Guareschi said. “We only get the readout of the issue, and we don’t know which reason we can attribute it to. There’s all sorts of things that are happening that we don’t see. So being able to play with these geometric parameters was really interesting to understand what is happening on a more biomolecular level.”