Applications of fluorescence correlation spectroscopy

Variational calculus approach to Zernike polynomials with application to FCS

Zernike polynomials are a sequence of orthogonal polynomials that play a crucial role in optics and, in particular, modeling microscopy systems. Introduced by Frits Zernike in 1934, they are particularly useful in expressing wavefront aberrations and, thus, imperfections of imaging systems. However, their origin and properties are rarely discussed and proven. Here, we present a novel approach to Zernike polynomials using variational calculus and apply them to describe aberrations in fluorescence microscopy. In particular, we model the impact of various optical aberrations on the performance of one-photon and two-photon excitation fluorescence microscopy.

Conformational distortion in a fibril-forming oligomer arrests alpha-Synuclein fibrillation and minimizes its toxic effects

The fibrillation pathway of alpha-Synuclein, the causative protein of Parkinson's disease, encompasses transient, heterogeneous oligomeric forms whose structural understanding and link to toxicity are not yet understood. We report that the addition of the physiologically-available small molecule heme at a sub-stoichiometric ratio to either monomeric or aggregated α-Syn, targets a His50 residue critical for fibril-formation and stabilizes the structurally-heterogeneous populations of aggregates into a minimally-toxic oligomeric state. Cryo-EM 3D reconstruction revealed a 'mace'-shaped structure of this monodisperse population of oligomers, which is comparable to a solid-state NMR Greek key-like motif (where the core residues are arranged in parallel in-register sheets with a Greek key topology at the C terminus) that forms the fundamental unit/kernel of protofilaments. Further structural analyses suggest that heme binding induces a distortion in the Greek key-like architecture of the mace oligomers, which impairs their further appending into protofilaments and fibrils. Additionally, our study reports a novel mechanism of prevention as well as reclamation of amyloid fibril formation by blocking an inter-protofilament His50 residue using a small molecule.

Fluorescence correlation spectroscopy study on the effects of the shape and size of a protein on its diffusion inside a crowded environment

Fluorescence correlation spectroscopy (FCS) has been commonly used to study the diffusional and conformational fluctuations of labeled molecules at single-molecule resolution. Here, we explored the applications of FCS inside a polyacrylamide gel to study the effects of molecular weight and molecular shape in a crowded environment. To understand the effect of molecular weight, we carried out FCS experiments with four model systems of different molecular weights in the presence of varying concentrations of acrylamide. The correlation curves were fit adequately using a model containing two diffusing components: one representing unhindered diffusion and one representing slow hindered diffusion in the gel phase. A large number of measurements carried out at different randomly chosen spots on a gel were used to determine the most probable diffusion time values using Gaussian distribution analysis. The variation of the diffusivity with the molecular weight of the model systems could be represented well using the effective medium model. This model assumes a combination of hydrodynamic and steric effects on solute diffusivity. To study the effects of solute shape, FCS experiments were carried inside a urea gradient gel to probe the urea-induced unfolding transition of Alexa488Maleimide-labeled bovine serum albumin. We showed that the scaling behavior, relating the hydrodynamic radius and the number of amino acids, changes inside an acrylamide gel for both folded and unfolded proteins. We showed further that crowding induced by a polyacrylamide gel increases the resolution of measuring the difference in hydrodynamic radii between the unfolded and folded states.

Filtered FCS: species auto- and cross-correlation functions highlight binding and dynamics in biomolecules

An analysis method of lifetime, polarization and spectrally filtered fluorescence correlation spectroscopy, referred to as filtered FCS (fFCS), is introduced. It uses, but is not limited to, multiparameter fluorescence detection to differentiate between molecular species with respect to their fluorescence lifetime, polarization and spectral information. Like the recently introduced fluorescence lifetime correlation spectroscopy (FLCS) [Chem. Phys. Lett. 2002, 353, 439-445], fFCS is based on pulsed laser excitation. However, it uses the species-specific polarization and spectrally resolved fluorescence decays to generate filters. We determined the most efficient method to generate global filters taking into account the anisotropy information. Thus, fFCS is able to distinguish species, even if they have very close or the same fluorescence lifetime, given differences in other fluorescence parameters. fFCS can be applied as a tool to compute species-specific auto- (SACF) and cross- correlation (SCCF) functions from a mixture of different species for accurate and quantitative analysis of their concentration, diffusion and kinetic properties. The computed correlation curves are also free from artifacts caused by unspecific background signal. We tested this methodology by simulating the extreme case of ligand-receptor binding processes monitored only by differences in fluorescence anisotropy. Furthermore, we apply fFCS to an experimental single-molecule FRET study of an open-to-closed conformational transition of the protein Syntaxin-1. In conclusion, fFCS and the global analysis of the SACFs and SCCF is a key tool to investigate binding processes and conformational dynamics of biomolecules in a nanosecond-to-millisecond time range as well as to unravel the involved molecular states.

Fluorescence correlation spectroscopy in biology, chemistry, and medicine

This review describes the method of fluorescence correlation spectroscopy (FCS) and its applications. FCS is used for investigating processes associated with changes in the mobility of molecules and complexes and allows researchers to study aggregation of particles, binding of fluorescent molecules with supramolecular complexes, lipid vesicles, etc. The size of objects under study varies from a few angstroms for dye molecules to hundreds of nanometers for nanoparticles. The described applications of FCS comprise various fields from simple chemical systems of solution/micelle to sophisticated regulations on the level of living cells. Both the methodical bases and the theoretical principles of FCS are simple and available. The present review is concentrated preferentially on FCS applications for studies on artificial and natural membranes. At present, in contrast to the related approach of dynamic light scattering, FCS is poorly known in Russia, although it is widely employed in laboratories of other countries. The goal of this review is to promote the development of FCS in Russia so that this technique could occupy the position it deserves in modern Russian science.

Optical and non-optical methods for detection and characterization of microparticles and exosomes

Microparticles and exosomes are cell-derived microvesicles present in body fluids that play a role in coagulation, inflammation, cellular homeostasis and survival, intercellular communication, and transport. Despite increasing scientific and clinical interest, no standard procedures are available for the isolation, detection and characterization of microparticles and exosomes, because their size is below the reach of conventional detection methods. Our objective is to give an overview of currently available and potentially applicable methods for optical and non-optical determination of the size, concentration, morphology, biochemical composition and cellular origin of microparticles and exosomes. The working principle of all methods is briefly discussed, as well as their applications and limitations based on the underlying physical parameters of the technique. For most methods, the expected size distribution for a given microvesicle population is determined. The explanations of the physical background and the outcomes of our calculations provide insights into the capabilities of each method and make a comparison possible between the discussed methods. In conclusion, several (combinations of) methods can detect clinically relevant properties of microparticles and exosomes. These methods should be further explored and validated by comparing measurement results so that accurate, reliable and fast solutions come within reach.

Separation of the rotational contribution in fluorescence correlation experiments

The theory of fluorescence correlation spectroscopy is reexamined with the aim of separating the contribution of rotational diffusion. Under constant excitation, fluorescence correlation experiments are characterized by three polarizations: one of the incident beam and two of the two photon detectors. A set of experiments of different polarizations is proposed for study. From the results of the experiments the isotropic factor of the fluorescence intensity correlation functions can be determined, which is independent of the rotational motion of the sample molecule. This function can be used to represent each fluorescence intensity correlation function as the product of the isotropic and the rotational factors. The theory is illustrated by an experiment in which rotational diffusion of porcine pancreatic lipase labeled with Texas Red was observed Texas Red is a label that allows precise fluorescence correlation experiments even in the nanosecond time range.

Diffusion in supported lipid bilayers: influence of substrate and preparation technique on the internal dynamics

The diffusion law of DMPC and DPPC in Supported Lipid Bilayers (SLB), on different substrates, has been investigated in details by Fluorescence Recovery After Patterned Photobleaching (FRAPP). Over micrometer length scales, we demonstrate the validity of a purely Brownian diffusive law both in the gel and the fluid phases of the lipids. Measuring the diffusion coefficient as a function of temperature, we characterize the gel-to-liquid phase transition of DMPC and DPPC. It is shown that, depending on the type of substrate and the method used for bilayer preparation, completely different behaviours can be observed. On glass substrates, using the Langmuir-Blodgett deposition technique, both leaflets of the bilayer have the same dynamics. On mica, the dynamics of the proximal leaflet is slower than the dynamics of the distal leaflet, although the transition temperature is the same for both layers. Preparing bilayers from vesicle fusion in same conditions leads to more random behaviours and shifted transition temperatures.

Direct observation of single molecule mobility in semidilute polymer solutions

We determine the mobility of dye-labeled polystyrene molecules in solution by fluorescence correlation spectroscopy (FCS) over a wide range of concentrations and molecular weights (ranging from 3.9 x 10{3} to 1550 x 10{3} g/mol ). In order to obtain absolute values of the diffusion coefficient, which can be compared to diffusion coefficients determined by other methods, the size of the focal volume has been determined by independent experiments and theoretical calculations. All data demonstrate that FCS is uniquely suited to explore polymer dynamics in solution. The mobility of the chains as expressed through the self-diffusion coefficient is significantly slowed down above the overlap concentration c{*}. The dependence of c{*} on molecular weight is well described by the power law c{*} proportional, variant M{w};{1-3nu} ( nu: Flory exponent). A comparison with the data taken from the literature demonstrates that the overlap concentration presents a robust concept that holds for a wide range of molecular weights.

Imaging single events at the cell membrane

The ability to sense and respond to the environment is a hallmark of living systems. These processes occur at the levels of the organism, cells and individual molecules. Sensing of extracellular changes could result in a structural or chemical alteration in a molecule, which could in turn trigger a cascade of intracellular signals or regulated trafficking of molecules at the cell surface. These and other such processes allow cells to sense and respond to environmental changes. Often, these changes and the responses to them are spatially and/or temporally localized, and visualization of such events necessitates the use of high-resolution imaging approaches. Here we discuss optical imaging approaches and tools for imaging individual events at the cell surface with improved speed and resolution.

Direct observation of spatiotemporal dependence of anomalous diffusion in inhomogeneous fluid by sampling-volume-controlled fluorescence correlation spectroscopy

The direct observation of a spatiotemporal behavior of anomalous diffusion in aqueous polymer [hyaluronan (HA)] solution was achieved by fluorescence correlation spectroscopy (FCS) using a modified instrument, enabling continuous change of the confocal volume of a microscope, namely, sampling-volume-controlled (SVC) FCS (SVC-FCS). Since HA chains form a mesh structure with a pore size of about 10-40 nm, the observed diffusion coefficient (Dobs) is markedly dependent on the diffusion distance (L). By SVC-FCS, the curve of the distance dependence of diffusion coefficient was directly obtained as a continuous profile in L = 245-600 nm showing evidence of anomalous diffusion. On plotting Dobs against either of the sampling time (tauobs) or the diffusion distance (L), Dobs turnover was observed near the anomalous diffusion area. The appearance of this turnover is attributed to the nonuniform mesh structure that can be observed only by a fast observation and that should be dynamically averaged by polymer motions with large tauobs. This behavior is similar to that revealed in glass, colloidal systems, and gel solutions using dynamic light scattering, neutron scattering, and other techniques.

Focal volume optics and experimental artifacts in confocal fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) can provide a wealth of information about biological and chemical systems on a broad range of time scales (<1 micros to >1 s). Numerical modeling of the FCS observation volume combined with measurements has revealed, however, that the standard assumption of a three-dimensional Gaussian FCS observation volume is not a valid approximation under many common measurement conditions. As a result, the FCS autocorrelation will contain significant, systematic artifacts that are most severe with confocal optics when using a large detector aperture and aperture-limited illumination. These optical artifacts manifest themselves in the fluorescence correlation as an apparent additional exponential component or diffusing species with significant (>30%) amplitude that can imply extraneous kinetics, shift the measured diffusion time by as much as approximately 80%, and cause the axial ratio to diverge. Artifacts can be minimized or virtually eliminated by using a small confocal detector aperture, underfilled objective back-aperture, or two-photon excitation. However, using a detector aperture that is smaller or larger than the optimal value (approximately 4.5 optical units) greatly reduces both the count rate per molecule and the signal-to-noise ratio. Thus, there is a tradeoff between optimizing signal-to-noise and reducing experimental artifacts in one-photon FCS.

Muscovite (mica) allows the characterisation of supported bilayers by ellipsometry and confocal fluorescence correlation spectroscopy

We demonstrate for the first time that ellipsometry and confocal fluorescence correlation spectroscopy (FCS) are complementary methods for the characterisation of supported planar phospholipid bilayers (SPBs) formed on mica, a mineral used in atomic force microscopy investigations of SPBs. Addition of small unilamellar vesicles containing 20% dioleoyl-phosphatidylserine (DOPS) and 80% dioleoyl-phosphatidylcholine (DOPC) to an oxidised borosilicate surface, on the other hand, results in a planar lipid system characterised by lateral diffusion coefficients which are three time smaller than those obtained for SPBs. Moreover, seven labelled phospholipids were tested for their suitability in the FCS characterisation of vesicles as well as of SPBs.

Fluorescence correlation spectroscopy: inception, biophysical experimentations, and prospectus

Fluorescence correlation spectroscopy examines the chemical and the photophysical dynamics of dilute molecular solutions by measurement of the dynamic optical fluctuations of the fluorescence of a few molecules, even averaging less than one molecule at a time, in open focal volumes that are usually less than a femtoliter (<10(-18) m(3)). It applies the same principles of statistical thermodynamics as does quasi-elastic light scattering. Molecular interactions, conformational changes, chemical reactions, and photophysical dynamics that are not ordinarily detectable by quasi-elastic light scattering can be analyzed by fluorescence correlation spectroscopy in cases in which molecular fluorescence changes in the dynamic range 10(-7)-10(2) s.

Intramolecular dynamics of chain molecules monitored by fluctuations in efficiency of excitation energy transfer. A theoretical study

The fluorescence quantum yield of a polymer molecule to which an energy donor chromophore and an energy acceptor chromophore are attached depends on the distance between the donor and acceptor chromophores. If this distance fluctuates with time, the fluorescence intensity is expected to fluctuate as well, and the time course of the intensity fluctuations will be correlated with the time course of the changes in the interchromophore distance. The intensity fluctuations are experimentally measurable if the number of illuminated molecules is small. A theoretical treatment of such fluorescence intensity fluctuations is presented in terms of a parameter that describes the polymer chain dynamics. Computer simulations were performed to illustrate the dependence of the autocorrelation function of the intensity fluctuations on the polymer chain conformation, the interchromophore energy transfer properties, and the macromolecular dynamics. These simulations demonstrate that the intensity fluctuations due to nonradiative energy transfer between chromophores attached to polymer chains can be large enough to be experimentally useful in the study of intramolecular dynamics of macromolecules.

Thermal fluctuations of large cylindrical phospholipid vesicles

The time correlation function of the shape fluctuations of large (greater than 10 micron), cylindrical, hydrated, phospholipid-membrane vesicles consisting of one bimolecular layer was measured. The restoring force of the membrane was due to the excess curvature of a membrane element. A value for the curvature elastic modulus, Kc, was obtained from the mean-square amplitude of the normal modes of the fluctuations using the equipartition theorem. An expression for the correlation time was found by solving the dynamics of the membrane's relaxation against the low Reynolds number viscous drag of the surrounding fluid. The amplitudes and correlation times of the fundamental bending mode of the cylindrical vesicles both yield Kc = 1-2 X 10(-12) ergs.

Lateral diffusion of lipids and glycophorin in solid phosphatidylcholine bilayers. The role of structural defects

The lateral mobility of the lipid analog N-4-nitrobenzo-2-oxa-1,3 diazole phosphatidylethanolamine and of the integral protein glycophorin in giant dimyristoylphosphatidylcholine vesicles was studied by the photobleaching technique. Above the temperature of the chain-melting transition (Tm = 23 degrees C), the diffusion coefficient, Dp, of the protein [Dp = (4 +/- 2) X 10(-8) cm2/s at 30 degrees C] was within the experimental errors equal to the corresponding values DL of the lipid analog. In the P beta 1 phase the diffusion of lipid and glycophorin was studied as a function of the probe and the protein concentration. (a) At low lipid-probe content (cL less than 5 mmol/mol of total lipid), approximately 20% of the probe diffuses fast (D approximately equal to 10(-8) - 10(-9) cm2/s), while the mobility of the rest is strongly reduced (D less than 10(-10) cm2/s). At a higher concentration (cp approximately 20 mmol), all probe is immobilized (D less than 10(-10) cm2/s). (b) Incorporation of glycophorin up to cp = 0.4 mmol/mol of total lipid leads to a gradual increase of the fraction of mobile lipid probe due to the lateral-phase separation into a pure P beta 1 phase and a fraction of lipid that is fluidized by strong hydrophilic lipid-protein interaction. (c) The diffusion of the glycophorin molecules is characterized by a slow and a fast fraction. The latter increases with increasing protein content, which is again due to the lateral-phase separation caused by the hydrophilic lipid-protein interaction. The results are interpreted in terms of a fast transport along linear defects in the P beta 1 phase, which form quasi-fluid paths for a nearly one dimensional and thus very effective transport. Evidence for this interpretation of the diffusion measurements is provided by freeze-fracture electron microscopy.

Fast diffusion along defects and corrugations in phospholipid P beta, liquid crystals

The diffusion of a fluorescent lipid analogue in liquid crystals of the anisotropic P beta, phase of dimyristoylphosphatidylcholine (DMPC) had been found to be highly variable, suggesting structural defect pathways. Fluorescence photobleaching recovery (FPR) experiments imply two effective diffusion pathways with coefficients differing by at least 100. This is consistent with fast diffusion along submicroscopic bands of disordered material ("defects") in the bilayer corrugations characteristic of this phase. Due to strains during transformation from the L alpha phase, the axis of the corrugations is ordinarily disrupted by mosaic patches rotationally disoriented within the mean plane of the molecular bilayers, although larger oriented domains are sometimes adventitiously aligned into microscopically visible striped textures. The corrugations are also systematically aligned along positive disclinations pairs or "oily streaks." Thus, fast diffusion occurs parallel to the disclination lines and along the textured stripes. FPR results yield an upper limit on the effective diffusion in the ordered material of D less than or equal to 2 X 10(-16) cm2/s at 22 degrees C, D less than or equal to 3 X 10(-17) cm2/s at 13 degrees C. In contrast the diffusion coefficient along defect pathways where disordered ribbons are aligned is D approximately 4 X 10(-11) cm2/s at 16 degrees C.

Measurement of submicron laser beam radii

Three methods for direct measurement of the intensity distribution in laser beams focused by microscope optics to waists of submicron width are described and compared. They use scans of the beam waist with (1) a knife-edge, (2) a submicroscopic point fluorescent source, and (3) convolution scans generated by the photobleached pattern of the focused beam. An indirect photographic technique is also evaluated. The laser beam is found to propagate ideally down to a minimum size usually limited by the aberrations of the optics.

The use of fluorescence correlations spectroscopy to probe chromatin in the cell nucleus

All systems in thermodynamic equilibrium are subject to spontaneous fluctuations from equilibrium. For very small system, the fluctuations can be made apparent, and can be used to study the behavior of the system without introducing any external perturbations. The mean squared amplitude of these fluctuations contains information about the absolute size of the system. The characteristic time of the fluctuation autocorrelation function contains kinetic information. In the experiments reported here, these concepts are applied to the binding equilibrium between ethidium bromide and DNA, a system where the fluorescence properties of the dye greatly enhance the effect of spontaneous fluctuations in the binding equilibrium. Preliminary experiments employ well-characterized DNA preparations, including calif thymus DNa, SV40 DNA, and calf thymus nucleohistone particles. Additional measurements are described which have been made in small regions of individual nuclei, isolated from green monkey kidney cells, observing as few as 5000 dye molecules. The data indicate that the strength of dye binding increases in nuclei isolated from cells which have been stimulated to enter the cell growth cycle. The viscosity of nuclear material is inferred to be between one and two orders of magnitude greater than that of water, and it decreases as the cells leave the resting state and enter the cell growth cycle. Washing the nuclei also lowers the viscosity. These experiments demonstrate that fluorescence correlation spectroscopy can provide information at the subnuclear level that is otherwise unavailable.

Rates of cholesterol exchange between human erythrocytes and plasma lipoproteins

Rates of exchange of labelled cholesterol between human erythrocytes and three plasma lipoprotein species, LDL, HDL2 and HDL3, were measured over a range of lipoprotein concentrations and temperatures. The exchange rates reached limiting, concentration-independent values, which were the same for the three lipoproteins. The temperature dependencies correspond to activation energies of 12 kcal in the limiting rate region, and at lower lipoprotein concentrations to activation energies of 11 to 22 kcal. Calculations based on simple collision theory indicate that energetic barriers to the exchange are far smaller than indicated by these activation energies and that no particular orientation of lipoprotein molecules is required for the exchange. The occurrence of a limiting rate may be a result of the adsorption of lipoprotein molecules onto a limited number of sites on the cell surface, or of a slow process occurring in the membrane, possibly the diffusion of cholesterol. Present data do not permit a choice between these models.

Fluorescence spectroscopic investigations of the dynamic properties of proteins, membranes and nucleic acids

Fluorescence spectroscopy can reveal the dynamic properties of proteins, membranes and nucleic acids on the nanosecond timescale. Dynamic processes which can affect the fluorescence spectral characteristics of biopolymer-bound fluorophores include dipolar relaxation around excited state dipoles, rotational diffusion of fluorophores, and permeation of bipolymers of fluorescence quenchers. The occurrence of these processes is revealed by the time-dependence of the Stokes's shifts, the time dependence of fluorescence anisotropies and the quenching of fluorescence, respectively. We will describe each of these processes in detail using examples of data obtained for membrane-bound fluorophores. In addition, we will review the fluorescence spectral evidence for nanosecond structural fluctuations in proteins and nucleic acids. In total, fluorescence spectroscopy indicates that both proteins and membranes fluctuate rapidly on the nanosecond and subnanosecond timescale. In contrast, base pairs in double-helical DNA appear to be immobile on this timescale.

Hydrodynamic evidence in support of spacer regions in chromatin

Quasi-elastic light scattering and sedimentation velocity methods were used to study the hydrodynamic properties of purified dimer subunits obtained from partial digestion of chicken erythrocyte chromatin with staphylococcal nuclease. The experimental value of 1.87 +/- 0.08 X 10(-7) gram per second for the friction factor of these dimer subunits in low ionic strength buffer cannot be reasonably interpreted in terms of a contiguous sphere model. Analysis by means of an equivalent dimer method suggests that the spacer region accounts for a maximum of 19 percent of the friction properties of the dimer.