Advances in Conventional and Extended Fluorescence Correlation Spectroscopy for the Analysis of Biological Clusters and Aggregates

Biological clusters, encompassing proteins, nucleic acids, and lipids, represent functional assemblies that underpin cellular physiology and contribute to disease pathogenesis. Their detection and characterization remain technically challenging due to their multistep, heterogeneous, and often transient nature. Fluorescence correlation spectroscopy (FCS) has become a powerful tool for quantifying particle numbers, diffusion states, and brightness changes, thereby providing direct insights into finite molecular assemblies. Applications include diverse oligomers and complexes of proteins, lipids, and nucleic acids, underscoring both physiological and pathological relevance. Recent methodological extensions—including multi-color cross-correlation FCS, image- and super-resolution-based approaches, and brightness analyses—have expanded the capacity to resolve complex molecular interactions. Transient state (TRAST) monitoring provides additional sensitivity to photophysical state transitions of fluorophores and to their physicochemical environments. Looking ahead, integration with AI promises to lower technical barriers and accelerate broader adoption. This review highlights the conceptual framework, recent advances, and future opportunities of FCS in probing biological clusters and aggregates.