Nanopore-Based Fingerprint Immunoassay Based on Rolling Circle Amplification and DNA Fragmentation

In recent years, nanopore-based sequencers have become robust tools with unique advantages for genomics applications. However, progress toward applying nanopores as highly sensitive, quantitative diagnostic tools has been impeded by several challenges. One major limitation is the insufficient sensitivity of nanopores in detecting disease biomarkers, which are typically present at pM or lower concentrations in biological fluids, while a second limitation is the general absence of unique nanopore signals for different analytes. To bridge this gap, we have developed a strategy for nanopore-based biomarker detection that utilizes immunocapture, isothermal rolling circle amplification, and sequence-specific fragmentation of the product to release multiple DNA reporter molecules for nanopore detection. These DNA fragment reporters produce sets of nanopore signals that form distinctive fingerprints, or clusters. This fingerprint signature therefore allows the identification and quantification of biomarker analytes. As a proof of concept, we quantify human epididymis protein 4 (HE4) at low pM levels in a few hours. Future improvement of this method by integration with a nanopore array and microfluidicsbased chemistry can further reduce the limit of detection, allow multiplexed biomarker detection, and further reduce the footprint and cost of existing laboratory and point-of-care devices.

Automated summary

In recent years, nanopore-based sequencers have shown great potential as robust tools in genomics applications. However, challenges remain in using nanopores for sensitive and quantitative diagnostic tools. One major limitation is the lack of sensitivity to detect disease biomarkers at low concentrations, while another limitation is the absence of unique nanopore signals for different analytes. To address these challenges, a strategy has been developed that utilizes immunocapture, amplification, and fragmentation techniques to release multiple DNA reporter molecules for nanopore detection. This approach allows for the identification and quantification of biomarker analytes. Future improvements can include integration with a nanopore array and microfluidics-based chemistry to enhance detection sensitivity, enable multiplexed biomarker detection, and reduce the size and cost of diagnostic devices.