Triplet-State Investigations of Fluorescent Dyes at Dielectric Interfaces Using Total Internal Reflection Fluorescence Correlation Spectroscopy

Multisite phosphorylation and binding alter conformational dynamics of the 4E-BP2 protein

Intrinsically disordered proteins (IDPs) play critical roles in regulatory protein interactions, but detailed structural/dynamic characterization of their ensembles remain challenging, both in isolation and when they form dynamic "fuzzy" complexes. Such is the case for mRNA cap-dependent translation initiation, which is regulated by the interaction of the predominantly folded eukaryotic initiation factor 4E (eIF4E) with the intrinsically disordered eIF4E binding proteins (4E-BPs) in a phosphorylation-dependent manner. Single-molecule Förster resonance energy transfer showed that the conformational changes of 4E-BP2 induced by binding to eIF4E are non-uniform along the sequence; while a central region containing both motifs that bind to eIF4E expands and becomes stiffer, the C-terminal region is less affected. Fluorescence anisotropy decay revealed a non-uniform segmental flexibility around six different labeling sites along the chain. Dynamic quenching of these fluorescent probes by intrinsic aromatic residues measured via fluorescence correlation spectroscopy report on transient intra- and inter-molecular contacts on nanosecond-to-microsecond timescales. Upon hyperphosphorylation, which induces folding of ∼40 residues in 4E-BP2, the quenching rates decreased at most labeling sites. The chain dynamics around sites in the C-terminal region far away from the two binding motifs significantly increased upon binding to eIF4E, suggesting that this region is also involved in the highly dynamic 4E-BP2:eIF4E complex. Our time-resolved fluorescence data paint a sequence-level rigidity map of three states of 4E-BP2 differing in phosphorylation or binding status and distinguish regions that form contacts with eIF4E. This study adds complementary structural and dynamics information to recent studies of 4E-BP2, and it constitutes an important step toward a mechanistic understanding of this important IDP via integrative modeling.

Measuring Photophysical Transition Rates with Fluorescence Correlation Spectroscopy and Antibunching

We present a new method that combines fluorescence correlation spectroscopy (FCS) on the microsecond time scale with fluorescence antibunching measurements on the nanosecond time scale for measuring photophysical rate constants of fluorescent molecules. The antibunching measurements allow us to quantify the average excitation rate of fluorescent molecules within the confocal detection volume of the FCS measurement setup. Knowledge of this value allows us then to quantify, in an absolute manner, the intersystem crossing rate and triplet state lifetime from the microsecond temporal decay of the FCS curves. We present a theoretical analysis of the method and estimate the maximum bias caused by the averaging of all quantities (excitation rate and photophysical rates) over the confocal detection volume, and we show that this bias is smaller than 5% in most cases. We apply the method for measuring the photophysical rate constants of the widely used dyes Rhodamine 110 and ATTO 655.

[Research on Photoimmunotherapy Based on Photochemical Property of Molecules]

Photoimmunotherapy (PIT) is a new cancer therapy that uses near-infrared (NIR) light and a conjugate of an antibody and a photosensitizer (IR700). Since both NIR light and the conjugate are not toxic for human, PIT has attracted attention as a promising cancer therapy with less side effects. However, there is no photosensitizer for PIT other than IR700. To improve the therapeutic effect, more light-sensitive dye is needed. To this end, we have studied the cytotoxic mechanism of PIT, showing that the hydrophilic axial ligand cleavage of IR700 by NIR light irradiation is important for the cytotoxicity. Herein, I focused on the triplet state (T1) of IR700 because the light-induced axial ligand cleavage reaction is thought to occur via the T1. First, the quantum yield of intersystem crossing, which is the transition efficiency from the excited singlet state (S1) to T1, was determined by analysis of the T1 kinetics using fluorescence correlation spectroscopy (FCS). Also, I examined whether the cytotoxicity of IR700 can be changed in the presence of a triplet quencher. The findings obtained here will be important information for the design of a new photosensitizer for PIT in the future.

Photoimmunotherapy: A new cancer treatment using photochemical reactions

Photoimmunotherapy (PIT) is a new molecular-targeted phototherapy in which administration of an antibody conjugated to IR700 (Ab-IR700, a phthalocyanine derivative) is followed by irradiation with near-infrared light. PIT induces cell death due to cell membrane damage, and the formation of IR700 aggregates on the cell membrane triggered by photochemical reactions is an important mechanism of cell killing. Specifically, water-soluble axial ligands of IR700 are cleaved by the photochemical reaction, and the phthalocyanine stacks up due to the π-π interaction, resulting in the formation of aggregates. In addition, the formation of IR700 radical anions and their protonation are essential for the progress of this photochemical reaction. The elucidation of these mechanisms may lead to the development of more effective compounds in the future. In addition, the optical properties of phthalocyanine are expected to expand the medical application of phthalocyanine derivatives in the future.

Dibenzo[hi,st]ovalene as Highly Luminescent Nanographene: Efficient Synthesis via Photochemical Cyclodehydroiodination, Optoelectronic Properties, and Single-Molecule Spectroscopy

Dibenzo[hi,st]ovalene (DBOV), as a new nanographene, has demonstrated promising optical properties, such as red emission with a high fluorescence quantum yield of 79% and stimulated emission, as well as high thermal stability and photostability, which indicated its promise as a light-emitting and optical gain material. However, the previous synthetic routes required at least 12 steps. This obstructed access to different derivatives, e.g., to obtain crystals suitable for X-ray diffraction analysis and to tune the optoelectronic properties. Here, we report an efficient synthetic pathway to DBOV based on a sequential iodination-benzannulation of bi(naphthylphenyl)diyne, followed by photochemical cyclodehydroiodination (PCDHI). This protocol included a fused bischrysene as a key intermediate and furnished scalable amounts of meso-substituted DBOV derivatives with different substituents. DBOV with 2,6-dimethylphenyl groups could be used for single-crystal X-ray analysis, revealing the precise structure of the DBOV core. The optoelectronic properties of the DBOV derivatives were investigated by UV-vis absorption and fluorescence spectroscopy, cyclic voltammetry, and density functional theory calculations. Single-molecule spectroscopy at room and low temperatures provided novel insights into the photophysics of DBOV embedded in a polymer film. As a result of weak coupling of the optical transitions to the matrix, single-molecule emission spectra at 4.5 K showed narrow vibronic lines. The fluorescence autocorrelation function covering 9 orders of magnitude in time displayed high contrast photon antibunching and bunching, from which the fluorescence decay rate and the triplet population and depopulation rates could be retrieved. Remarkably, the intersystem crossing rate into the triplet state decreased by more than an order of magnitude at low temperature, demonstrating that temperature can be a crucial parameter to boost single photon emission of an aromatic hydrocarbon.

Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification

Single-molecule techniques for protein sequencing are making headway towards single-cell proteomics and are projected to propel our understanding of cellular biology and disease. Yet, single cell proteomics presents a substantial unmet challenge due to the unavailability of protein amplification techniques, and the vast dynamic-range of protein expression in cells. Here, we describe and computationally investigate the feasibility of a novel approach for single-protein identification using tri-color fluorescence and plasmonic-nanopore devices. Comprehensive computer simulations of denatured protein translocation processes through the nanopores show that the tri-color fluorescence time-traces retain sufficient information to permit pattern-recognition algorithms to correctly identify the vast majority of proteins in the human proteome. Importantly, even when taking into account realistic experimental conditions, which restrict the spatial and temporal resolutions as well as the labeling efficiency, and add substantial noise, a deep-learning protein classifier achieves 97% whole-proteome accuracies. Applying our approach for protein datasets of clinical relevancy, such as the plasma proteome or cytokine panels, we obtain ~98% correct protein identification. This study suggests the feasibility of a method for accurate and high-throughput protein identification, which is highly versatile and applicable.

Macromolecules identification methods are central for most biological and biomedical studies, and while the field of genomics advanced to single-molecule resolution, the proteomic field still relies on bulk and costly techniques. We describe a solution for single protein identification, based on the analysis of optical traces obtained from fluorescently-labeled proteins threaded through a nanopore and processed by a pattern recognition algorithm. To evaluate the feasibility of our method we constructed computer simulations of the system, producing and analyzing nearly 10⁸ individual protein translocations from the human Swiss-Prot database. Our results suggest protein identification of >95% for the whole human proteome, even under non-ideal conditions. These results constitute the basis for a novel whole proteome identification method, with single molecule resolution.

Building, Characterization, and Applications of Cuvette-FCS in Denaturant-Induced Expansion of Globular and Disordered Proteins

Fluorescence correlation spectroscopy (FCS) is a single-molecule sensitive technique with widespread applications in biophysics. However, conventional microscope-based FCS setups have limitations in performing certain experiments such as those requiring agitations such as stirring or heating, and those involving measurements in solvents with the mismatch of refractive indices. We have recently developed an FCS setup that is suitable for performing measurements inside regular cuvettes. The cuvette-FCS is suitable for performing single-molecule measurements in experiments that are regularly performed in spectrofluorometers but are generally avoided in microscope-based FCS. Here we describe building and characterization of the performance of the cuvette-FCS setup in detail. Finally, we have used a natively folded protein and an intrinsically disordered protein to demonstrate and describe how cuvette-FCS can be applied conveniently to measure urea-dependent expansion of hydrodynamic size of proteins.

Rotational and translational diffusion of size-dependent fluorescent probes in homogeneous and heterogeneous environments

Macromolecular crowding effects on diffusion depend on the fluorophore structure, the concentration of crowding agents, and the technique employed.

Determination of equilibrium and rate constants for complex formation by fluorescence correlation spectroscopy supplemented by dynamic light scattering and Taylor dispersion analysis

The equilibrium and rate constants of molecular complex formation are of great interest both in the field of chemistry and biology. Here, we use fluorescence correlation spectroscopy (FCS), supplemented by dynamic light scattering (DLS) and Taylor dispersion analysis (TDA), to study the complex formation in model systems of dye-micelle interactions. In our case, dyes rhodamine 110 and ATTO-488 interact with three differently charged surfactant micelles: octaethylene glycol monododecyl ether C₁₂E₈ (neutral), cetyltrimethylammonium chloride CTAC (positive) and sodium dodecyl sulfate SDS (negative). To determine the rate constants for the dye-micelle complex formation we fit the experimental data obtained by FCS with a new form of the autocorrelation function, derived in the accompanying paper. Our results show that the association rate constants for the model systems are roughly two orders of magnitude smaller than those in the case of the diffusion-controlled limit. Because the complex stability is determined by the dissociation rate constant, a two-step reaction mechanism, including the diffusion-controlled and reaction-controlled rates, is used to explain the dye-micelle interaction. In the limit of fast reaction, we apply FCS to determine the equilibrium constant from the effective diffusion coefficient of the fluorescent components. Depending on the value of the equilibrium constant, we distinguish three types of interaction in the studied systems: weak, intermediate and strong. The values of the equilibrium constant obtained from the FCS and TDA experiments are very close to each other, which supports the theoretical model used to interpret the FCS data.

Transient state imaging of live cells using single plane illumination and arbitrary duty cycle excitation pulse trains

We demonstrate the applicability of Single Plane Illumination Microscopy to Transient State Imaging (TRAST), offering sensitive microenvironmental information together with optical sectioning and reduced overall excitation light exposure of the specimen. The concept is verified by showing that transition rates can be determined accurately for free dye in solution and that fluorophore transition rates can be resolved pixel-wise in live cells. Furthermore, we derive a new theoretical framework for analyzing TRAST data acquired with arbitrary duty cycle pulse trains. By this analysis it is possible to reduce the overall measurement time and thereby enhance the frame rates in TRAST imaging.

Transient state microscopy probes patterns of altered oxygen consumption in cancer cells

Altered cellular metabolism plays an important role in many diseases, not least in many forms of cancer, where cellular metabolic pathways requiring lower oxygen consumption are often favored (the so-called Warburg effect). In this work, we have applied fluorescence-based transient state imaging and have exploited the environment sensitivity of long-lived dark states of fluorophores, in particular triplet state decay rates, to image the oxygen consumption of living cells. Our measurements can resolve differences in oxygen concentrations between different regions of individual cells, between different cell types, and also based on what metabolic pathways the cells use. In MCF-7 breast cancer cells, higher oxygen consumption can be detected when they rely on glutamine instead of glucose as their main metabolite, predominantly undergoing oxidative phosphorylation rather than glycolysis. By use of the high triplet yield dye Eosin Y the irradiance requirements during the measurements can be kept low. This reduces the instrumentation requirements, and harmful biological effects from high excitation doses can be avoided. Taken together, our imaging approach is widely applicable and capable of detecting subtle changes in oxygen consumption in live cells, stemming from the Warburg effect or reflecting other differences in the cellular metabolism. This may lead to new diagnostic means as well as advance our understanding of the interplay between cellular metabolism and major disease categories, such as cancer.

Fluorescence correlation spectroscopy study of protein transport and dynamic interactions with clustered-charge peptide adsorbents

Ion-exchange chromatography relies on electrostatic interactions between the adsorbent and the adsorbate and is used extensively in protein purification. Conventional ion-exchange chromatography uses ligands that are singly charged and randomly dispersed over the adsorbent, creating a heterogeneous distribution of potential adsorption sites. Clustered-charge ion exchangers exhibit higher affinity, capacity, and selectivity than their dispersed-charge counterparts of the same total charge density. In the present work, we monitored the transport behavior of an anionic protein near clustered-charge adsorbent surfaces using fluorescence correlation spectroscopy. We can resolve protein-free diffusion, hindered diffusion, and association with bare glass, agarose-coated, and agarose-clustered peptide surfaces, demonstrating that this method can be used to understand and ultimately optimize clustered-charge adsorbent and other surface interactions at the molecular scale.

Permeability of anti-fouling PEGylated surfaces probed by fluorescence correlation spectroscopy

The present work reports on in situ observations of the interaction of organic dye probe molecules and dye-labeled protein with different poly(ethylene glycol) (PEG) architectures (linear, dendron, and bottle brush). Fluorescence correlation spectroscopy (FCS) and single molecule event analysis were used to examine the nature and extent of probe-PEG interactions. The data support a sieve-like model in which size-exclusion principles determine the extent of probe-PEG interactions. Small probes are trapped by more dense PEG architectures and large probes interact more with less dense PEG surfaces. These results, and the tunable pore structure of the PEG dendrons employed in this work, suggest the viability of electrochemically-active materials for tunable surfaces.

Measuring surface binding thermodynamics and kinetics by using total internal reflection with fluorescence correlation spectroscopy: practical considerations

The combination of total internal reflection illumination and fluorescence correlation spectroscopy (TIR-FCS) is an emerging method useful for, among a number of things, measuring the thermodynamic and kinetic parameters describing the reversible association of fluorescently labeled ligands in solution with immobilized, nonfluorescent surface binding sites. However, there are many parameters (both instrumental and intrinsic to the interaction of interest) that determine the nature of the acquired fluorescence fluctuation autocorrelation functions. In this work, we define criteria necessary for successful measurements and then systematically explore the parameter space to define conditions that meet the criteria. The work is intended to serve as a guide for experimental design, in other words, to provide a methodology to identify experimental conditions that will yield reliable values of the thermodynamic and kinetic parameters for a given interaction.

Rapid prototyping of nanofluidic systems using size-reduced electrospun nanofibers for biomolecular analysis

Biomolecular transport in nanofluidic confinement offers various means to investigate the behavior of biomolecules in their native aqueous environments, and to develop tools for diverse single-molecule manipulations. Recently, a number of simple nanofluidic fabrication techniques has been demonstrated that utilize electrospun nanofibers as a backbone structure. These techniques are limited by the arbitrary dimension of the resulting nanochannels due to the random nature of electrospinning. Here, a new method for fabricating nanofluidic systems from size-reduced electrospun nanofibers is reported and demonstrated. As it is demonstrated, this method uses the scanned electrospinning technique for generation of oriented sacrificial nanofibers and exposes these nanofibers to harsh, but isotropic etching/heating environments to reduce their cross-sectional dimension. The creation of various nanofluidic systems as small as 20 nm is demonstrated, and practical examples of single biomolecular handling, such as DNA elongation in nanochannels and fluorescence correlation spectroscopic analysis of biomolecules passing through nanochannels, are provided.

Electrostatic interactions of fluorescent molecules with dielectric interfaces studied by total internal reflection fluorescence correlation spectroscopy

Electrostatic interactions between dielectric surfaces and different fluorophores used in ultrasensitive fluorescence microscopy are investigated using objective-based Total Internal Reflection Fluorescence Correlation Spectroscopy (TIR-FCS). The interfacial dynamics of cationic rhodamine 123 and rhodamine 6G, anionic/dianionic fluorescein, zwitterionic rhodamine 110 and neutral ATTO 488 are monitored at various ionic strengths at physiological pH. As analyzed by means of the amplitude and time-evolution of the autocorrelation function, the fluorescent molecules experience electrostatic attraction or repulsion at the glass surface depending on their charges. Influences of the electrostatic interactions are also monitored through the triplet-state population and triplet relaxation time, including the amount of detected fluorescence or the count-rate-per-molecule parameter. These TIR-FCS results provide an increased understanding of how fluorophores are influenced by the microenvironment of a glass surface, and show a promising approach for characterizing electrostatic interactions at interfaces.