Using encoded hydrogel microparticles in a 96-well filter plate system for enhanced rinsing efficiency in multiplexed nucleic acid detection

Accurate and efficient nucleic acid detection is crucial for biomedical applications, including disease diagnostics and molecular-level insights into disease mechanisms. Among various detection methods, hydrogel microparticle-based assays have garnered significant attention for their high sensitivity and multiplexing capability. However, these assays are often hindered by time-consuming, non-reproducible, and unstable rinsing steps, which compromise sensitivity and reliability. While filter plates hold great potential for streamlining the rinsing process, challenges such as sample evaporation and difficulty in temperature control have limited their integration into hydrogel microparticle-based nucleic acid assays. In this study, we present a 96-well filter plate-based detection system incorporating evaporation-minimizing films and printed circuit board heaters. This system enables nucleic acid assays within a filter plate while ensuring uniform temperature control across wells and significantly enhancing rinsing efficiency. Additionally, our platform demonstrates a two-fold improvement in the limit of detection compared to conventional tube-based assays, while maintaining high reproducibility across wells. By addressing the key challenges associated with integrating hydrogel microparticle-based assays with filter plates, this system provides a facile, rapid, reliable, and sensitive approach for multiplex nucleic acid detection.