Digital Assays Detect Nucleic Acids to Identify Clinical Pathogens

On September 6, 2023, researchers from the Karolinska Institute published a study in Science Advances detailing a new pathogen detection assay that uses DNA nanoballs. The study was a collaborative effort between the institute, Rutgers University, and the Stanford Genome Technology Center, with funding from the Knut and Alice Wallenberg Foundation. 

Unlike currently available protein-based diagnostics, this novel approach eliminates the need for developing high-quality antibodies to detect pathogens.  

"The methodology involves combining molecular biology (DNA nanoball generation) and electronics (electric impedance-based quantification) to yield a pioneering detection tool," Vicent Pelechano, principal investigator and associate professor at the Karolinska Institute Department of Microbiology, said in a press release.  

The researchers modified existing methods, loop-mediated isothermal amplification (LAMP), to generate DNA nanoballs in the presence of pathogens. The modified mechanisms use compaction oligonucleotides to promote the assembly of the nanoballs.  

After isolating the nanoballs in the presence of pathogens, the researchers passed the nanoballs through a microfluidic impedance cytometer using capillary-driven flow. By measuring the changes in flow resistance, the cytometer could provide a quantified readout of nanoballs.  

“In summary, we demonstrated a passive flow impedance-based detection of novel label-free DNA nanoballs targeting SARS-CoV-2 and later various pathogens of both viral and bacterial origin. It potentially provides a sensitive (10 copies), cheap, fast (<60 min), and scalable POC system to help address the growing pathogen detection challenges in the coming decades,” concluded researchers in the study.  

The researchers note that this system can be repurposed to detect DNA or RNA targets for multiple diseases, including HIV, the β-lactamase gene, and more. 

The COVID-19 pandemic has highlighted the importance of pathogen detection for public health and minimizing disease spread. Despite the availability of tools from previous research, clinical investigators are constantly looking for more effective and accurate detection tools, as available tools are not unequivocally accurate.  

A new, inexpensive, and accurate diagnostic tool may improve disease detection. Additionally, the tool’s adaptability may be helpful as new variants emerge.  

“This new method, offering label-free detection, could hasten the rollout of new diagnostic kits. Integrating affordable mass-produced electronics with lyophilized reagents, the technology possesses the potential to provide a cheap, widely deployed, and scalable point-of-care device,” stated the press release.  

The researchers are exploring the device’s utility in environmental monitoring, food safety, and virus or antimicrobial resistance detection.