BPS2026 – Efficient imaging fluorescence fluctuation spectroscopy analysis through vision transformers

In fluorescence correlation spectroscopy (FCS) and photon counting histogram (PCH) analysis, the same experimental fluorescence intensity fluctuations are used, but each analytical method focuses on a different property of the signal. The time-dependent decay of the correlation of fluorescence fluctuations is measured in FCS yielding molecular diffusion coefficients and triplet-state parameters such as fraction and decay time. The amplitude distribution of these fluctuations is calculated by PCH analysis yielding the molecular brightness. Both FCS and PCH give information about the molecular concentration. Here we describe a global analysis protocol that simultaneously recovers relevant and common parameters in model functions of FCS and PCH from a single fluorescence fluctuation trace. Application of a global analysis approach allows increasing the information content available from a single measurement that results in more accurate values of molecular diffusion coefficients and triplet-state parameters and also in robust, time-independent estimates of molecular brightness and number of molecules.

Towards a better understanding of the dissociation behavior of liposome-oligonucleotide complexes in the cytosol of cells

We compare the accuracy of a variety of Fluorescence Fluctuation Spectroscopy (FFS) methods for the study of Förster Resonance Energy Transfer (FRET) assays. As an example, the cleavage of a doubly labeled, FRET-active peptide substrate by the protease Trypsin is monitored and analyzed using methods based on fluorescence intensity, Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Intensity Distribution Analysis (FIDA). The presented fluorescence data are compared to High-Pressure Liquid Chromatography (HPLC) data obtained from the same assay. The HPLC analysis discloses general disadvantages of the FRET approach, such as incomplete labeling and the need for aliquots. However, the simultaneous use of two photon detectors monitoring the fluorescence signal of both labels significantly improves the analysis. In particular, the two global analysis tools Two-Dimensional Fluorescence Intensity Distribution Analysis (2D-FIDA) and Two-Color Global Fluorescence Correlation Spectroscopy (2CG-FCS) highlight the potential of a combination of FFS and FRET. While conventional FIDA and FCS auto- or cross-correlation analysis leaves the user with drawbacks inherent in two-color and FRET applications, these effects are overcome by the global analysis on the molecular level. Furthermore, it is advantageous to analyze the unnormalized as opposed to the normalized correlation data when combining any fluorescence correlation method with FRET, since the analysis of the unnormalized data introduces more accuracy and is less sensitive to the experimental drawbacks.

The interactions between a cationic polymer, poly(2-dimethylamino)ethyl methacrylate (pDMAEMA), and negatively charged rhodamine-labeled 25-mer phosphodiester oligonucleotides (Rh-ONs) were studied by fluorescence fluctuation spectroscopy and other techniques. The composition of the pDMAEMA/Rh-ON complexes was investigated as a function of the charge ratio (+/-) by increasing the pDMAEMA concentration and keeping the Rh-ON concentration constant. We applied two different methods for analyzing the fluorescence fluctuation profiles of the pDMAEMA/Rh-ON complexes, which depended on their composition. First, we analyzed the data with the photon counting histogram (PCH) technique, which determines the molecular brightness and the concentration of fluorophores (Chen et al, 1999). A particular challenge for the data analysis is the occurrence of sudden fluorescence bursts in the fluorescence fluctuation profiles, which are linked to the appearance of multimolecular complexes (i. e. when several Rh-ONs were present in one complex). A quantitative interpretation of the analysis for the complexes remains challenging and is connected to the rarity of the fluorescent bursts, which do not provide sufficient data statistics. To specifically address the problem of the fluorescent bursts we employed a method described by Van Craenenbroeck et al. (1999). This method, applicable only when data were integrated over much longer time bins, allowed us to estimate the number of fluorescence bursts which could be considered as a relative measure of the amount of multimolecular complexes present. When monomolecular complexes were formed, i. e. at high values of the charge ratio, highly intense fluorescence peaks were not present and the interpretation of the PCH analysis was more straightforward. The molecular brightness of the species (epsilon), as revealed from PCH analysis, was greater than epsilon for the free Rh-ONs, indicating that the Rh-ONs were attached to pDMAEMA chains.

Fluorescence Fluctuation Spectroscopy (FFS) studies the fluctuating fluorescent signal from a small illumination volume and extracts the concentration and dynamical information of fluorophores. Detecting the fluorescence in two detector channels introduces the possibility of differentiating the fluorophores based on color. We introduce bivariate cumulant analysis for Two-Color Fluorescence Fluctuation Spectroscopy and derive an analytical expression for the bivariate factorial cumulants of photon counts at arbitrary sampling times. Fits of the data to the analytical model determine the brightness of each channel, occupation number and diffusion time of each fluorescent species. The statistical accuracy of each cumulant is described by its variance, which we calculate by the moments-of-moments technique. The theory is experimentally verified using model dye system. We also performed first experiments in living cells, and develop a model that takes nonideal detector effects into account. This technique is useful for optimizing the spectroscopic separation of heterogeneous biological samples by FFS.

Cells secrete extracellular vesicles (EVs) into their microenvironment that act as mediators of intercellular communication under physiological conditions and in this context also actively participate in spreading various diseases. Large efforts are currently made to produce reliable EV samples and to develop, improve, and standardize techniques allowing their biophysical characterization. Here, we used ultrafiltration and size-exclusion chromatography for the isolation and a model-free fluorescence fluctuation analysis for the investigation of the physical and biological properties of EVs secreted by mammalian cells. Our purification strategy produced enriched samples of morphologically intact EVs free of extravesicular proteins and allowed labeling of marker molecules on the vesicle surface for single-vesicle analysis with single-molecule sensitivity. This novel approach provides information on the distribution profile of both EV size and relative expression level of a specific exosomal marker, deciphering the overall heterogeneity of EV preparations.

Molecular Brightness Characterization of EGFP In Vivo by Fluorescence Fluctuation Spectroscopy

Self Assembly of Rubisco Activase Monitored by Fluorescence Fluctuation Spectroscopy

Fluorescence Fluctuation Spectroscopy in the Presence of Hydrodynamic Flow to Determine Protein Stoichiometry at Ultra Low Concentrations

We demonstrate that photoswitchable markers enable fluorescence fluctuation spectroscopy at high molecular concentration. Reversible photoswitching allows precise control of the density of fluorescing entities, because the equilibrium between the fluorescent ON- and the dark OFF-state can be shifted through optical irradiation at a specific wavelength. Depending on the irradiation intensity, the concentration of the ON-state markers can be up to 1,000 times lower than the actual concentration of the labeled molecular entity. Photoswitching expands the range of single-molecule detection based experiments such as fluorescence fluctuation spectroscopy to large entity concentrations in the micromolar range.

Fluorescence fluctuation spectroscopy (FFS) offers a window to observe and investigate dynamics of bio-molecular organisation. Furthermore, FFS acquisitions uniquely allow obtaining insights into other properties of the sample such as concentration and brightness (counts per molecule) of the fluorescently labelled species simultaneously. Here, we exploit the large number of measurements and statistics obtained from scanning fluorescence fluctuation spectroscopy (sFFS) acquisitions to elucidate bio-molecular organisation. We demonstrate the versatility and sensitivity of the approach using computer simulations, synthetic biological membranes and living cells.

Dopamine Receptor Signaling in MIN6 β-Cells Revealed by Fluorescence Fluctuation Spectroscopy

Brightness Analysis of Cytoplasmic HTLV-1 and HIV-1 Gag in the Presence of Membrane-Bound Gag Complexes by Dual-Color Z-Scan Fluorescence Fluctuation Spectroscopy

Protein Conformational Dynamics Detected Via Fluorescence Fluctuation Spectroscopy

The Photon Counting Histogram in Fluorescence Fluctuation Spectroscopy with Non-Ideal Photodetectors