Optically Encoded Suspension Microarrays: Materials, Design Strategies, and Future Directions for Multiplexed Bioanalysis

Abstract

Suspension microarrays based on optically encoded microbeads have become one of the most versatile platforms for multiplexed bioanalysis because they combine solution-phase reaction kinetics, flexible assay design, and high-throughput detection. However, despite more than two decades of intense research, no consensus has emerged regarding the optimal strategies for particle encoding, surface functionalization, and signal decoding. Progress has mainly been driven by incremental improvements in individual materials rather than by systematic comparison of competing technological concepts. This review critically evaluates the main approaches to the fabrication of optically encoded microbeads, including post-synthetic (swelling and layer-by-layer assembly) and in situ encoding strategies, and proposes a mechanistic classification of in situ methods of particle formation into polymerization-driven and confinement-controlled ones. Instead of comparing the fabrication methods solely in terms of encoding capacity, we assess their relative merits in terms of structural control, code stability, scalability, compatibility with biofunctionalization, and suitability for clinical implementation. We further examine the strengths and limitations of organic fluorophores, aggregation-induced emission luminogens, semiconductor quantum dots, and upconversion nanoparticles and show that no encoding material is universally optimal and that performance is determined by trade-offs between optical properties, manufacturing complexity, and stability in biological media. We argue that future progress will depend not as much on increasing the theoretical number of optical codes as on improving the code reproducibility, minimizing spectral crosstalk and nonspecific interactions, and employing microfluidic fabrication, antifouling surface chemistry, automated spectral decoding, and artificial intelligence-assisted data analysis. These developments are expected to transform suspension microarrays from multiplexed analytical tools into standardized lab-on-a-microbead platforms suitable for next-generation clinical diagnostics.