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'Dancing DNA' Leads to 100-Fold Noise Reduction for Sensitive Molecular Detection


NEW YORK – Biosensors are increasingly being used in nucleic acid detection technologies — including in diagnostics devices — but the inherent noisiness of the signal has challenged all-electronic approaches to date. A team at the University of Massachusetts Amherst has now discovered that synchronizing the movement of tethered capture molecules can improve detection and reduce noise.

Jinglei Ping, senior researcher on the project, said in an interview that the team's noise-reduction method leads to a 100-fold improvement in the detection limit of its all-electronic system.

Biological samples are a soup of charged molecules. While researchers have long sought to reduce noise in all-electrical biosensor technologies, Ping said the discovery of the nanoelectromechanical method was actually the result of a moment of insight away from the laboratory.

While attending one of his daughter's swim meets last year, Ping said he got stuck sitting quite far from the pool and was having trouble at first finding his child among the swimmers. But, "I realized that I could easily find her by her unique swimming style, or movement pattern," he said. "I thought, why can't we drive a DNA strand to move in a specific pattern, then we just need to recognize the pattern."

Back at the lab, Ping and his team found success by tethering DNA probes to nanostructures on graphene sheets and making them vibrate in electric fields. This produces a signature waveform, or nanomechanoelectrical fingerprint, of DNA, and hybridization of target DNA oligomers with probe DNA oligonucleotides modulates the current. Because single-stranded and double-stranded DNA have different flexibilities, they move differently, allowing for detection of hybridization.

Essentially, "we just make the DNA dance, and we can identify the target based on the unique dancing pattern," Ping explained.

In a study published earlier this year in PNAS, Ping and his colleagues found that spacing miniaturized pyramidal structures on the graphene sheet was an optimal approach, as the tethered DNA pieces would not bump each other when waggling in the A/C field.

Charlie Johnson, a professor of physics at the University of Pennsylvania, said in an email that the nanomechanoelectrical approach is "very creative and novel."

While the use of all-electronic transduction of DNA binding using graphene devices is well established, Johnson said he was not aware of other efforts to detect molecular binding by an electromechanical measurement of the biomolecule itself.

Furthermore, "the demonstration of a 100X improvement in detection limit is extremely impressive and important," Johnson said. While there may be a good bit of development work yet to be done, to his mind, "there is definitely a pathway to applications in future diagnostic systems for improved performance."

The use of biosensors in nucleic acid detection technologies is on the rise. For example, Aptitude Medical uses electrochemical probes and a simple biosensor in its core technology, while Cambridge Nucleomics incorporates biosensors with its nanobait approach. Researchers have recently paired biosensors with DNA nanoballs, and DiagMetrics pairs biosensors with nanoCLAMPs. Graphene-based sensor technologies are also part of the core technologies at IdentifySensors and GrapheneDx, for example.

According to Arvind Balijepalli, a project leader in the physical measurement laboratory at the National Institute of Standards and Technology (NIST), the accelerated popularity of electronic detection tech has been supported by recent advances in the manufacture of graphene — a hexagonal arrangement of single carbon atoms. Only one atom thick, graphene sheets are extremely conductive and strong.

"There are a few pivotal changes that are allowing more companies to commercialize graphene devices," Balijepalli said. Synthesis of graphene has become more advanced, he said, resulting in the ability to purchase large sheets that support the fabrication of highly reproducible sensors without the high upfront cost that was previously required for research-grade graphene devices, or ones that relied on silicon.

"Because we can make these in large batches, you can get thousands if not hundreds of thousands of sensors in a single run, and that has the potential to reduce the cost per device," Balijepalli said.

With his team at NIST, Balijepalli has also been pursuing biosensors for DNA detection. Earlier this year, the team developed a method that sequesters the reaction from the readout circuitry to make the costliest piece of the detector reusable. The system enables low noise detection with a limit of detection of approximately 100 femtomolar. More recently, the team has also been looking into using a different A/C technique to further improve the signal-to-noise ratio.

In the case of the UMass nanomechanoelectrical system, Ping said it differs from reported techniques that are simply nanomechanical. "The vibration is actually not physically isolated from the electrical detection part; it's actually entangled with the electrical part," he explained.

The approach bears some tangential similarities to a method that was described in a public presentation by researchers at the Air Force Research Lab specializing in graphene field-effect transistor-based biosensors to detect stress biomarkers in sweat and interstitial fluids, as well as to an approach previously described in publications in PNAS and the Journal of the American Chemical Society that is reportedly being commercialized by German firm Dynamic Biosensors in a technology called SwitchSense.

Although these projects also drive vibration of molecules using A/C, "in my research, the emphasis is on discerning the 'dance' pattern from the electrical signal," Ping explained.

The nanomechanoelectrical approach can now potentially be used for different nucleic acid detection needs. For example, "the technology is promising for point-of-care diagnosis of various diseases, particularly COVID, concussion, and even cancer," Ping said.

The team is now assessing its intellectual property options for the method and is also considering commercializing the technology with industry partners, Ping said.

Overall, recent technological advancements are poised to make biosensors a more prominent part of the diagnostics ecosystem.

"With different nanomaterials and electrical biosensing techniques, we are now capable of producing nucleic acid sensors that are inexpensive, miniaturized, easy to use, and rapid, without compromising sensitivity," said Ping.