Single-molecule techniques make it possible to digitally count even extremely rare biomarker molecules, providing greatly improved sensitivity for early disease detection. However, in standard setups, there is a necessary balance: if the concentration is too high, molecules overlap and become unreadable; if too low, there are not enough events for robust analysis. To overcome this, probes can be arranged on a surface at well‑defined, nanometer-scale distances ensuring each probe can capture and report on at least one biomarker molecule without signal confusion.
A practical, low-cost way to build such nanoarrays is nanosphere lithography (NSL), which enables precise control over probe placement for clear, single-molecule readouts. However, the usefulness of these arrays depends on how consistent and uniform the colloidal mask is: irregularities can undermine detection quality. Finally, the arrangement of the probes is determined by the nanosphere diameter, which can make it challenging to guarantee that each probe area holds only one molecule critical for unambiguous digital counting, especially as you try to increase the distance between probes for better optical resolution.
Researchers at the Biodesign Institute at Arizona State University have introduced a cost-effective strategy for constructing DNA origami nanoarrays. This approach (SiMPLE) utilizes the high mechanical rigidity of silica nanoparticles to generate nanoscale adhesive patches on substrates through a cleanroom-free, scalable self-assembly method. As a result, it becomes possible to pattern DNA origami pedestals with precise control and high throughput, minimizing molecular overlap to maximize single-molecule detection sensitivity using standard optical techniques. By bypassing expensive lithography, the approach addresses key bottlenecks of traditional patterning, enabling digital biomarker quantification at ultra-low concentrations and paving the way for rapid, high-throughput assays in diagnostics, and drug discovery. The method helps democratize nanoarray fabrication, placing single-molecule analytical tools within reach of most research labs without compromising the data quality or experimental throughput essential for modern biosensing applications.
Potential Applications
- Early cancer and infectious disease diagnostic kits
- Genetic testing and biomarker detection platforms
- High-throughput drug screening and drug-target interaction studies
- Targeted drug delivery system development
- Fabrication of advanced nanophotonic devices and optical materials
- Production of nanomaterial biosensors for research and clinical use
Benefits and Advantages
- Cleanroom-free and scalable fabrication process
- Cost-effective compared to traditional lithography methods
- High precision and deterministic placement of biomolecules
- Enhanced single-molecule detection sensitivity with minimal overlap
- Compatible with standard optical imaging systems
- Facilitates multiplexed detection with sub-femtomolar sensitivity
- User-friendly protocols suitable for typical laboratory settings
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