FRET-Plex: Plug-and-Play Encoded Beads for Multiplex Nucleic Acid Detection

Cytometric bead assay (CBA) plays a critical role in multiplex bioassays; however, the rapid and cost-effective preparation of encoded beads remains challenging. Herein, we propose a plug-and-play strategy for DNA-encoded beads that enables the modulation of Förster resonance energy transfer (FRET) efficiency through on-demand self-assembly of fluorescently labeled DNA on the bead surface, thereby achieving bead encoding followed by rapid, high-throughput decoding via flow cytometry. This platform allows encoding to occur concurrently with target capture, eliminating the need for preconstructing an encoded bead library and substantially reducing both assay complexity and cost. Using this approach, we successfully generated eight types of encoded beads and validated the platform's utility through qualitative and quantitative detection of multiple nucleic acid targets. Collectively, this platform provides a strategy for the preparation of encoded beads and a method for the rapid, high-throughput detection of multiple nucleic acids.