Polydopamine nanoparticle-based multicolor proximity immunoassays for ultrasensitive, multiplexed analysis of proteins using isothermal quadratic amplification

Simple, rapid and selective methods for simultaneous determination of ultralow amount of multiple protein biomarkers in complicated biological samples are in great demand for early-stage diagnostics and biomedical research. Herein, we present a novel polydopamine nanoparticle (PDANP)-based multicolor fluorescent proximity immunoassay for ultrasensitive and multiplexed analysis of proteins in a single solu- lion using isothermal quadratic amplification (IQA). The assay system consists of DNA tethered-antibody pairs for different protein targets, different fluorophore-labeled DNA hairpin probes, DNA polymerase, T7 exonuclease and PDANPs. The DNA tethered- antibodies and fluorophore-labeled hairpin probes can coexist stably, and fluorophore- labeled DNA hairpin probes are adsorbed onto the PDANPs, leading to the significant quenching of the fluorescence of all fluorophores. When target proteins enter into the system, each pair of DNA tethered-antibodies simultaneously binds to a specific protein target and forms the proximate complexes via proximity-dependent DNA hybridization. The formed proximate complexes can then unfold the hairpin structures of the respective probes, leading to DNA polymerase/T7 exonuclease-catalyzed recycling of both proximate complexes and DNA strands to achieve IQA. This IQA results in the di- gestion of many fluorophore-labeled hairpin probes, causing a substantial increase in the fluorescence of corresponding fluorophores for detection of target proteins. As a proof of concept, we demonstrate that a three-color proximity immunoassay can si- multaneously detect prostate-specific antigen (PSA), carcinoembryonic antigen (CEA) and alpha-fetoprotein (AFP) with ultralow attomolar detection limits, high specificity and 6-log dynamic range. Furthermore, the application of this assay for direct and simultaneous determination of multiple proteins in clinical sera has also been demonstrated. Our newly proposed assay can be expected to provide a generic method platform for multiplexed analysis of a variety of low-abundance proteins.