Time-resolved molecule counting by photon statistics across the visible spectrum

Dual-Label Single-Molecule Imaging Method for Quantifying Apparent Fluorescence Efficiency of Fluorescent Proteins

Fluorescent proteins (FPs) are indispensable tools for life science research, crucial for quantitative analyses, such as protein stoichiometry determination, signal transduction, and protein-protein interactions. In this work, we introduce a new method of dual-color single-molecule imaging to assess the apparent fluorescence efficiency of FPs (DC-FEFP). By integrating high signal-to-noise ratio (SNR) FPs or self-labeling tags, this approach enables us to precisely quantify the fluorescence efficiency of various FPs at the single-molecule level in both living and fixed cells. With DC-FEFP, we found that mNeonGreen has the highest fluorescence efficiency among three commonly used FPs in living cells, as well as the significant impact of fixation on the photophysical properties of FPs. DC-FEFP is a high-precision and versatile tool for quantifying the fluorescence efficiency of FPs. It is capable of providing accurate information to calibrate protein stoichiometry based on single-molecule imaging.

Super-resolution microscopy based on the inherent fluctuations of dye molecules

Fluorescence microscopy is a critical tool across various disciplines, from materials science to biomedical research, yet it is limited by the diffraction limit of resolution. Advanced super-resolution techniques such as localization microscopy and stimulated-emission-depletion microscopy often demand considerable resources. These methods depend heavily on elaborate sample-staining, complex optical systems, or prolonged acquisition periods, and their application in 3D and multicolor imaging presents significant experimental challenges. In the current work, we provide a complete demonstration of a widely accessible super-resolution imaging approach capable of 3D and multicolor imaging based on super-resolution optical fluctuation imaging (SOFI). We replace the confocal pinhole with an array of single-photon avalanche diodes and use the microsecond-scale fluctuations of dye molecules as a contrast mechanism. This contrast is transformed into a super-resolved image using a robust and deterministic algorithm. Our technique utilizes natural fluctuations inherent to organic dyes, thereby it does not require engineering of the blinking statistics. Our robust, versatile super-resolution method opens the way to next-generation multimodal imaging and facilitates on-demand super-resolution within a confocal architecture.

ProDOL: a general method to determine the degree of labeling for staining optimization and molecular counting

Determining the label to target ratio, also known as the degree of labeling (DOL), is crucial for quantitative fluorescence microscopy and a high DOL with minimal unspecific labeling is beneficial for fluorescence microscopy in general. Yet robust, versatile and easy-to-use tools for measuring cell-specific labeling efficiencies are not available. Here we present a DOL determination technique named protein-tag DOL (ProDOL), which enables fast quantification and optimization of protein-tag labeling. With ProDOL various factors affecting labeling efficiency, including substrate type, incubation time and concentration, as well as sample fixation and cell type can be easily assessed. We applied ProDOL to investigate how human immunodeficiency virus-1 pathogenesis factor Nef modulates CD4 T cell activation measuring total and activated copy numbers of the adapter protein SLP-76 in signaling microclusters. ProDOL proved to be a versatile and robust tool for labeling calibration, enabling determination of labeling efficiencies, optimization of strategies and quantification of protein stoichiometry.

Electric-Field Fluctuations as the Cause of Spectral Instabilities in Colloidal Quantum Dots

Spectral diffusion (SD) represents a substantial obstacle toward implementation of solid-state quantum emitters as a source of indistinguishable photons. By performing high-resolution emission spectroscopy for individual colloidal quantum dots at cryogenic temperatures, we prove the causal link between the quantum-confined Stark effect and SD. Statistically analyzing the wavelength of emitted photons, we show that increasing the sensitivity of the transition energy to an applied electric field results in amplified spectral fluctuations. This relation is quantitatively fit to a straightforward model, indicating the presence of a stochastic electric field on a microscopic scale, whose standard deviation is 9 kV/cm, on average. The current method will enable the study of SD in multiple types of quantum emitters such as solid-state defects or organic lead halide perovskite quantum dots, for which spectral instability is a critical barrier for applications in quantum sensing.

How Blinking Affects Photon Correlations in Multichromophoric Nanoparticles

A single chromophore can only emit a maximum of one single photon per excitation cycle. This limitation results in a phenomenon commonly referred to as photon antibunching (pAB). When multiple chromophores contribute to the fluorescence measured, the degree of pAB has been used as a metric to "count" the number of chromophores. But the fact that chromophores can switch randomly between bright and dark states also impacts pAB and can lead to incorrect chromophore numbers being determined from pAB measurements. By both simulations and experiment, we demonstrate how pAB is affected by independent and collective chromophore blinking, enabling us to formulate universal guidelines for correct interpretation of pAB measurements. We use DNA-origami nanostructures to design multichromophoric model systems that exhibit either independent or collective chromophore blinking. Two approaches are presented that can distinguish experimentally between these two blinking mechanisms. The first one utilizes the different excitation intensity dependence on the blinking mechanisms. The second approach exploits the fact that collective blinking implies energy transfer to a quenching moiety, which is a time-dependent process. In pulsed-excitation experiments, the degree of collective blinking can therefore be altered by time gating the fluorescence photon stream, enabling us to extract the energy-transfer rate to a quencher. The ability to distinguish between different blinking mechanisms is valuable in materials science, such as for multichromophoric nanoparticles like conjugated-polymer chains as well as in biophysics, for example, for quantitative analysis of protein assemblies by counting chromophores.

Photobleaching step analysis for robust determination of protein complex stoichiometries

The counting of discrete photobleaching steps in fluorescence microscopy is ideally suited to study protein complex stoichiometry in situ. The counting range of photobleaching step analysis has been significantly improved with more-sophisticated algorithms for step detection, albeit at an increasing computational cost and with the necessity for high-quality data. Here, we address concerns regarding robustness, automation, and experimental validation, optimizing both data acquisition and analysis. To make full use of the potential of photobleaching step analysis, we evaluate various labeling strategies with respect to their molecular brightness, photostability, and photoblinking. The developed analysis algorithm focuses on automation and computational efficiency. Moreover, we validate the developed methods with experimental data acquired on DNA origami labeled with defined fluorophore numbers, demonstrating counting of up to 35 fluorophores. Finally, we show the power of the combination of optimized trace acquisition and automated data analysis by counting labeled nucleoporin 107 in nuclear pore complexes of intact U2OS cells. The successful in situ application promotes this framework as a new resource enabling cell biologists to robustly determine the stoichiometries of molecular assemblies at the single-molecule level in an automated manner.

An update on molecular counting in fluorescence microscopy

Quantitative assessment of protein complexes, such as receptor clusters in the context of cellular signalling, has become a pressing objective in cell biology. The advancements in the field of single molecule fluorescence microscopy have led to different approaches for counting protein copy numbers in various cellular structures. This has resulted in an increasing interest in robust calibration protocols addressing photophysical properties of fluorescent labels and the effect of labelling efficiencies. Here, we want to give an update on recent methods for protein counting with a focus on novel calibration protocols. In this context, we discuss different types of calibration samples and identify some of the challenges arising in molecular counting experiments. Some recently published applications offer potential approaches to tackle these challenges.

Picosecond time-resolved photon antibunching measures nanoscale exciton motion and the true number of chromophores

The particle-like nature of light becomes evident in the photon statistics of fluorescence from single quantum systems as photon antibunching. In multichromophoric systems, exciton diffusion and subsequent annihilation occurs. These processes also yield photon antibunching but cannot be interpreted reliably. Here we develop picosecond time-resolved antibunching to identify and decode such processes. We use this method to measure the true number of chromophores on well-defined multichromophoric DNA-origami structures, and precisely determine the distance-dependent rates of annihilation between excitons. Further, this allows us to measure exciton diffusion in mesoscopic H- and J-type conjugated-polymer aggregates. We distinguish between one-dimensional intra-chain and three-dimensional inter-chain exciton diffusion at different times after excitation and determine the disorder-dependent diffusion lengths. Our method provides a powerful lens through which excitons can be studied at the single-particle level, enabling the rational design of improved excitonic probes such as ultra-bright fluorescent nanoparticles and materials for optoelectronic devices.

Multiple-Labeled Antibodies Behave Like Single Emitters in Photoswitching Buffer

The degree of labeling (DOL) of antibodies has so far been optimized for high brightness and specific and efficient binding. The influence of the DOL on the blinking performance of antibodies used in direct stochastic optical reconstruction microscopy (dSTORM) has so far attained limited attention. Here, we investigated the spectroscopic characteristics of IgG antibodies labeled at DOLs of 1.1-8.3 with Alexa Fluor 647 (Al647) at the ensemble and single-molecule level. Multiple-Al647-labeled antibodies showed weak and strong quenching interactions in aqueous buffer but could all be used for dSTORM imaging with spatial resolutions of ∼20 nm independent of the DOL. Single-molecule fluorescence trajectories and photon antibunching experiments revealed that individual multiple-Al647-labeled antibodies show complex photophysics in aqueous buffer but behave as single emitters in photoswitching buffer independent of the DOL. We developed a model that explains the observed blinking of multiple-labeled antibodies and can be used for the development of improved fluorescent probes for dSTORM experiments.

Super-resolution microscopy reveals majorly mono- and dimeric presenilin1/γ-secretase at the cell surface

γ-Secretase is a multi-subunit enzyme whose aberrant activity is associated with Alzheimer’s disease and cancer. While its structure is atomically resolved, γ-secretase localization in the membrane in situ relies mostly on biochemical data. Here, we combined fluorescent tagging of γ-secretase subunits with super-resolution microscopy in fibroblasts. Structured illumination microscopy revealed single γ-secretase complexes with a monodisperse distribution and in a 1:1 stoichiometry of PSEN1 and nicastrin subunits. In living cells, sptPALM revealed PSEN1/γ-secretase mainly with directed motility and frequenting ‘hotspots’ or high track-density areas that are sensitive to γ-secretase inhibitors. We visualized γ-secretase association with substrates like amyloid precursor protein and N-cadherin, but not with its sheddases ADAM10 or BACE1 at the cell surface, arguing against pre-formed megadalton complexes. Nonetheless, in living cells PSEN1/γ-secretase transiently visits ADAM10 hotspots. Our results highlight the power of super-resolution microscopy for the study of γ-secretase distribution and dynamics in the membrane.

Mouse Heterochromatin Adopts Digital Compaction States without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation

The formation of silenced and condensed heterochromatin foci involves enrichment of heterochromatin protein 1 (HP1). HP1 can bridge chromatin segments and form liquid droplets, but the biophysical principles underlying heterochromatin compartmentalization in the cell nucleus are elusive. Here, we assess mechanistically relevant features of pericentric heterochromatin compaction in mouse fibroblasts. We find that (1) HP1 has only a weak capacity to form liquid droplets in living cells; (2) the size, global accessibility, and compaction of heterochromatin foci are independent of HP1; (3) heterochromatin foci lack a separated liquid HP1 pool; and (4) heterochromatin compaction can toggle between two “digital” states depending on the presence of a strong transcriptional activator. These findings indicate that heterochromatin foci resemble collapsed polymer globules that are percolated with the same nucleoplasmic liquid as the surrounding euchromatin, which has implications for our understanding of chromatin compartmentalization and its functional consequences.

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HP1 has only a weak capacity to form droplets in living cells

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Size, accessibility, and compaction of heterochromatin foci are independent of HP1

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Heterochromatin compaction is “digital” and can toggle between two distinct states

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Methodological framework to assess hallmarks of phase separation in living cells

Photon arrival time tagging with many channels, sub-nanosecond deadtime, very high throughput, and fiber optic remote synchronization

Time-Correlated Single Photon Counting (TCSPC) and time tagging of individual photon detections are powerful tools in many quantum optical experiments and other areas of applied physics. Using TCSPC, e.g., for the purpose of fluorescence lifetime measurements, is often limited in speed due to dead-time losses and pileup. We show that this limitation can be lifted by reducing the dead-time of the timing electronics to the absolute minimum imposed by the speed of the detector signals while maintaining high temporal resolution. A complementing approach to speedy data acquisition is parallelization by means of simultaneous readout of many detector channels. This puts high demands on the data throughput of the TCSPC system, especially in time tagging of individual photon arrivals. Here, we present a new design approach, supporting up to 16 input channels, an extremely short dead-time of 650 ps, very high time tagging throughput, and a timing resolution of 80 ps. In order to facilitate remote synchronization of multiple such instruments with highest precision, the new TCSPC electronics provide an interface for White Rabbit fiber optic networks. Beside fundamental research in the field of astronomy, such remote synchronization tasks arise routinely in quantum communication networks with node to node distances on the order of tens of kilometers. In addition to showing design features and benchmark results of new TCSPC electronics, we present application results from spectrally resolved and high-speed fluorescence lifetime imaging in medical research. We furthermore show how pulse-pileup occurring in the detector signals at high photon flux can be corrected for and how this data acquisition scheme performs in terms of accuracy and efficiency.

Higher-Order Photon Correlation as a Tool To Study Exciton Dynamics in Quasi-2D Nanoplatelets

Colloidal semiconductor nanoplatelets, in which carriers are strongly confined only along one dimension, present fundamentally different excitonic properties than quantum dots, which support strong confinement in all three dimensions. In particular, multiple excitons strongly confined in just one dimension are free to rearrange in the lateral plane, reducing the probability for multibody collisions. Thus, while simultaneous multiple photon emission is typically quenched in quantum dots, in nanoplatelets its probability can be tuned according to size and shape. Here, we focus on analyzing multiexciton dynamics in individual CdSe/CdS nanoplatelets of various sizes through the measurement of second-, third-, and fourth-order photon correlations. For the first time, we can directly probe the dynamics of the two, three, and four exciton states at the single nanocrystal level. Remarkably, although higher orders of correlation vary substantially among the synthesis' products, they strongly correlate with the value of second order antibunching. The scaling of the higher-order moments with the degree of antibunching presents a small yet clear deviation from the accepted model of Auger recombination through binary collisions. Such a deviation suggests that many-body contributions are present already at the level of triexcitons. These findings highlight the benefit of high-order photon correlation spectroscopy as a technique to study multiexciton dynamics in colloidal semiconductor nanocrystals.

Cotranslational Incorporation into Proteins of a Fluorophore Suitable for smFRET Studies

Single-molecule FRET (smFRET) is a powerful tool to investigate conformational changes of biological molecules. In general, smFRET studies require protein samples that are site-specifically double-labeled with a pair of donor and acceptor fluorophores. The common approaches to produce such samples cannot be applied when studying the synthesis and folding of the polypeptide chain on the ribosome. The best strategy is to incorporate two fluorescent amino acids cotranslationally using cell-free protein synthesis systems. Here, we demonstrate the cotranslational site-specific incorporation into a model protein of Atto633, a dye with excellent photophysical properties, suitable for single molecule spectroscopy, together with a second dye using a combination of the sense cysteine and the nonsense amber codon. In this work we show that cotranslational incorporation of good fluorophores into proteins is a viable strategy to produce suitable samples for smFRET studies.