Accurate and Robust Measurement of Single-Molecule Fluorescence Spectral Heterogeneity

Abstract Understanding single-molecule fluorescence spectral heterogeneity (smFLUSH) is vital for developing new probes for multidimensional super-resolution microscopy and decoding nanoscopic environments. However, traditional analysis methods distort the data and fail to distinguish random background noise for actual spectral differences between the single molecules. To overcome this bottleneck, we developed a Monte Carlo simulation and an adaptive signal processing framework inspired by balanced detection in spectral domain optical coherence tomography that employs a dynamically scaling, molecule-specific spectral boundary to effectively decouple intrinsic molecular fluctuations from instrumental noise, achieving an exceptional subnanometer precision floor. We experimentally validated this framework using a tailor-designed library of Boron Dipyrromethene (BODIPY) dyes engineered with systematically tuned degrees of conformational freedom. This adaptive pipeline revealed a distinct structural bifurcation: in a subseries of dyes, targeted molecular rigidification monotonically suppressed smFLUSH, whereas steric crowding and core predistortion in a phenyl- and ethyl-containing subseries caused spectral variance to plateau at an elevated baseline regardless of additional rotor count. Furthermore, correlating smFLUSH with excited-state relaxation dynamics revealed that spectral heterogeneity aligns with shorter fluorescence lifetimes and larger Stokes shifts, demonstrating that matrix-coupled structural adjustments simultaneously accelerate nonradiative deactivation. Ultimately, this framework establishes a robust workflow for single-molecule photophysics and delivers a rational synthetic blueprint for designing single-molecule spectrally stable probes.