From Fluorescence Correlation Spectroscopy Research Articles

Rotational and translational diffusion of biomolecules in complex liquids and HeLa cells.

Diffusive motion accompanies many physical and biological processes. The Stokes-Sutherland-Einstein relation for the translational diffusion coefficient, DT, agrees with experiments done in simple fluids but fails for complex fluids. Moreover, the interdependence between DT and rotational diffusion coefficient, DR, also deviates in complex fluids from the classical relation of DT/DR = 4r2/3 known in simple fluids. Makuch et al. Soft Matter, 2020, 16, 114-124 presented a generalization of the classical translational and rotational diffusion theory for complex fluids. In this work, we empirically verify this model based on simultaneous translational and rotational diffusion measurements. We use fluorescently stained cowpea chlorotic mottle virus (CCMV) particles as monodisperse probes and aqueous polyethylene glycol (PEG) solutions as a model complex fluid. The theory and experimental data obtained from fluorescence correlation spectroscopy (FCS) measurements agreed. Finally, we used the same model and analyzed the diffusion of Yo-Pro-1 stained large ribosomal subunits (LSU) in the cytoplasm and nucleus of living HeLa cells.

Probing Viscosity of Co-Polymer Hydrogel and HeLa Cell Using Fluorescent Gold Nanoclusters: Fluorescence Correlation Spectroscopy and Anisotropy Decay.

Fluorescence dynamics of gold nanoclusters (Au9 and Au25 ) are studied in the complex and crowded environment of a triblock co-polymer (F127) hydrogel and inside cervical cancer cell, HeLa. In the hydrogel, spherical micelles of F127 remain immobilized with a hydrophobic core (PPO) and a hydrophilic corona (PEO) region. The fluorescence anisotropy decay suggests that the timescale of rotational relaxation in the hydrogel is similar to that in bulk water (viscosity ∼1 cP). From fluorescence correlation spectroscopy (FCS) it is inferred that the local viscosity in the hydrogel is 12 cP for Au9 and 18 cP for Au23 . These results indicate that gold nanoclusters (AuNCs) localize in the corona region of the hydrogel. Evidently, frictions against rotation and translation are different inside the gel. It is suggested that rotation of the AuNCs senses the immediate water-like "void" region while translation motion involves in-and-out movement of the AuNCs at the periphery of the gel. Finally, the gold nanoclusters are used for cell imaging and estimation of intracellular viscosity of HeLa cells.

Spectroscopic and Microscopic Approach to Monitor the Changes in Bilayer Rigidity during Cell Penetrating Peptide Induced Self-Reproduction of Phospholipid Vesicles

Understanding peptide-membrane interaction in view of structural change of lipid bilayer is essential to develop new therapeutic strategies. Though different mechanisms are proposed for cell penetrating peptides (CPPs) penetration in lipid bilayer, the exact mechanism of cellular uptake of CPPs remains a significant unanswered piece of puzzle. Here, we report a novel observation that model phospholipid vesicles self-reproduce to generate unilamellar daughter vesicles in presence of a CPP, nonaarginine (R9). Fluorescence lifetime image analysis (FLIM) exquisitely captures the changes of L-α-phosphatidylcholine (LAPC) bilayer in different times and also quantifies the changes through valuable lifetime distributions obtained. Mean square displacement (MSD) calculations from FLIM images of single vesicle trajectory establish CPP induced self-reproduction of LAPC vesicles. Heterogeneous nature of lipid bilayer after 1 hour of R9 addition is observed from fluorescence correlation spectroscopy (FCS) which supposed to consider as the starting point of “mother vesicles” reproduction. Solvation dynamic study delineates the change in dynamics of the encapsulated water inside vesicles which also states different rigidity of lipid bilayer in different states of vesicle self-reproduction. Fluorescence anisotropy image analysis provides information regarding change in lipid bilayer rigidity by quantifying the rotational motion of the fluorophore in presence of perturbation of CPPs. From these experimental observations, we are able to establish phospholipid vesicles self-reproduction in presence of CPPs which may be considered as a possible route of CPPs action to deliver cargos to cell interior through hydrophobic barriers. Overall, our results provide an experimental underpinning of the role of lipid bilayer structural changes in self-reproduction which can exhibit great potential to interpret the protein-lipid interaction in emergence of life.

Inhibiting the Fibrillation of Serum Albumin Proteins in the Presence of Surface Active Ionic Liquids (SAILs) at Low pH: Spectroscopic and Microscopic Study.

One of the key necessary steps to prevent human neurological disorders is the efficient disruption of protein aggregation or amyloid fibril. In this article, we have explored the effect of three amphiphilic surface active ionic liquids (SAILs), namely 1-methyl-3-octylimidazolium chloride ([C8mim]Cl), 1-dodecyl-3-methyllimidazolium chloride ([C12mim]Cl), and 1-hexadecyl-3-methyllimidazolium chloride ([C16mim]Cl) having concentrations of 5.8, 0.29, and 0.08 mM, respectively, on bovine serum albumin (BSA) and human serum albumin (HSA) fibril. These SAILs have different alkyl chain length attached to the cationic imidazolium headgroups. Interestingly, it is observed that all of the three SAILs exhibit fibril inhibition at room temperature itself as initially evidenced from thioflavin T (ThT) fluorescence assay study. However, C16mimCl is found as the most efficient quencher having highest quenching constant than the other two analogues. In addition, circular dichroism (CD) data give valuable insights into the conformational changes of BSA fibril as a consequence of interaction with SAILs. The field emission scanning electron microscopy (FESEM) and fluorescence lifetime imaging microscopy (FLIM) confirm the inhibitory effect of SAILs. It is evident from fluorescence correlation spectroscopy (FCS) study that 62% fibril is ruptured in the presence of C8mimCl while C12mimCl and C16mimCl completely destroy the fibrillar morphology. So the inhibition efficiency is related to the hydrophobicity associated with the long alkyl chain attached with the cationic imidazolium headgroup of SAILs.

Encapsulation and Residency of a Hydrophobic Dye within the Water-Filled Interior of a PAMAM Dendrimer Molecule.

Tightly confined water within a small droplet behaves differently from bulk water. This notion is obtained on the basis of several reports showing unusual behaviors of water droplet residing at the core of a reverse micelle. In this study, we have shown a well-known hydrophobic dye, coumarin 153 (C153), which prefers to reside at the water-rich region inside the dendrimer molecule. Optical density (OD) measurement at the absorption peak of C153 shows that it is almost insoluble in bulk water but highly soluble in aqueous dendrimer solution. The OD of C153 increases several times in the latter case as compared to that in the former. We found the most interesting observation when we compared the data from fluorescence correlation spectroscopy (FCS) with the fluorescence anisotropy decay of C153 in aqueous dendrimer solution. The FCS measurement reveals a much slower translational diffusion time (τD) of C153 attached to a dendrimer molecule as compared to that of free C153 in bulk water in the absence of dendrimer. The slower τD in the former case is commensurate with the size of the dendrimer molecule. This is possible only when C153 is encapsulated by the dendrimer molecule. In contrast to the FCS study, the fluorescence anisotropy decay of C153 in water remains largely invariant after addition of the dendrimer. This can happen if a bulk-water-like environment at the C153 surroundings is preserved within the C153-dendrimer complex. This supports our institutive expectation that C153 resides within the water-rich peripheral cavities of the dendrimer molecule. A more expected binding of C153 to the hydrophobic core of dendrimer may not be possible here because of an inadequate size of the dendrimer core.

Frequency Extrapolation of Mechanical Properties Obtained from Brillouin Scattering Measurements in Biological Samples

Brillouin Light Scattering Microspectroscopy (BLSM) is an all optical technique that can be used to yield information on the high frequency (GHz) mechanical properties of materials (Longitudinal Modulus, Shear Modulus). Results from BLSM measurements are thus distinct from those obtained using lower frequency perturbation or correlation based approaches, often yielding their interpretation or direct comparison challenging. Here we compare studies of the frequency dependence of the mechanical parameters (Shear Modulus) up to the MHz-range - derived from Fluorescence Correlation Spectroscopy (FCS) studies - to the corresponding BLSM obtained elastic parameters, for a range of biological samples.

Fluorescence correlation spectroscopy in thin films at reflecting substrates as a means to study nanoscale structure and dynamics at soft-matter interfaces.

Structure and dynamics at soft-matter interfaces play an important role in nature and technical applications. Optical single-molecule investigations are noninvasive and capable to reveal heterogeneities at the nanoscale. In this work we develop an autocorrelation function (ACF) approach to retrieve tracer diffusion parameters obtained from fluorescence correlation spectroscopy (FCS) experiments in thin liquid films at reflecting substrates. This approach then is used to investigate structure and dynamics in 100-nm-thick 8CB liquid crystal films on silicon wafers with five different oxide thicknesses. We find a different extension of the structural reorientation of 8CB at the solid-liquid interface for thin and for thick oxide. For the thin oxides, the perylenediimide tracer diffusion dynamics in general agrees with the hydrodynamic modeling using no-slip boundary conditions with only a small deviation close to the substrate, while a considerably stronger decrease of the interfacial tracer diffusion is found for the thick oxides.

Mean squared displacement from fluorescence correlation spectroscopy.

Under certain conditions, the mean squared displacement (MSD) can be retrieved from fluorescence correlation spectroscopy (FCS) measurements. However, in the general case this procedure is not valid, and the apparent MSD obtained from FCS data may substantially differ from the true one. In this work we discuss under which conditions this procedure can be applied. Furthermore, we use computer simulations to obtain the MSD and the apparent MSD for the diffusion of a single polymer chain under various approximations. Based on the simulation results we discuss the reliability of the apparent MSD obtained from FCS, showing that it systematically deviates from the true MSD. We also propose a general procedure to verify the reliability of the apparent MSD by measurements at various focal spot sizes.

Excited state proton transfer in the lysosome of live lung cells: normal and cancer cells.

Dynamics of excited state proton transfer (ESPT) in the lysosome region of live lung cells (normal and cancer) is studied by picosecond time-resolved confocal microscopy. For this, we used a fluorescent probe, pyranine (8-hydroxy-pyrene-1,3,6-trisulfonate, HPTS). From the colocalization of HPTS with a lysotracker dye (lysotracker yellow), we confirmed that HPTS resides in the lysosome for both of the cells. The diffusion coefficient (Dt) in the lysosome region was obtained from fluorescence correlation spectroscopy (FCS). From Dt, the viscosity of lysosome is estimated to be ∼40 and ∼30 cP in the cancer and normal cells, respectively. The rate constants of the elementary steps of ESPT in a normal lung cell (WI38) are compared with those in a lung cancer cell (A549). It is observed that the time constant of the initial proton transfer process in a normal cell (τ(PT) = 40 ps) is similar to that in a cancer cell. The recombination of the geminate ion pair is slightly faster (τ(rec) = 25 ps) in the normal cell than that (τ(rec) = 30 ps) in a cancer cell. The time constant of the dissociation (τ(diss)) of the geminate ion pair for the cancer cell (τ(diss) = 80 ps) is 1.5 times faster compared to that (τ(diss) = 120 ps) in a normal cell.

Physiological environment induces quick response – slow exhaustion reactions

In vivo environments are highly crowded and inhomogeneous, which may affect reaction processes in cells. In this study we examined the effects of intracellular crowding and an inhomogeneity on the behavior of in vivo reactions by calculating the spectral dimension (ds), which can be translated into the reaction rate function. We compared estimates of anomaly parameters obtained from fluorescence correlation spectroscopy (FCS) data with fractal dimensions derived from transmission electron microscopy (TEM) image analysis. FCS analysis indicated that the anomalous property was linked to physiological structure. Subsequent TEM analysis provided an in vivo illustration; soluble molecules likely percolate between intracellular clusters, which are constructed in a self-organizing manner. We estimated a cytoplasmic spectral dimension ds to be 1.39 ± 0.084. This result suggests that in vivo reactions initially run faster than the same reactions in a homogeneous space; this conclusion is consistent with the anomalous character indicated by FCS analysis. We further showed that these results were compatible with our Monte-Carlo simulation in which the anomalous behavior of mobile molecules correlates with the intracellular environment, leading to description as a percolation cluster, as demonstrated using TEM analysis. We confirmed by the simulation that the above-mentioned in vivo like properties are different from those of homogeneously concentrated environments. Additionally, simulation results indicated that crowding level of an environment might affect diffusion rate of reactant. Such knowledge of the spatial information enables us to construct realistic models for in vivo diffusion and reaction systems.

Direct Measurement of Association and Dissociation Rates of DNA Binding in Live Cells by Fluorescence Correlation Spectroscopy

Measurement of live-cell binding interactions is vital for understanding the biochemical reactions that drive cellular processes. Here, we develop, characterize, and apply a new procedure to extract information about binding to an immobile substrate from fluorescence correlation spectroscopy (FCS) autocorrelation data. We show that existing methods for analyzing such data by two-component diffusion fits can produce inaccurate estimates of diffusion constants and bound fractions, or even fail altogether to fit FCS binding data. By analyzing live-cell FCS measurements, we show that our new model can satisfactorily account for the binding interactions introduced by attaching a DNA binding domain to the dimerization domain derived from a site-specific transcription factor (the vitellogenin binding protein (VBP)). We find that our FCS estimates are quantitatively consistent with our fluorescence recovery after photobleaching (FRAP) measurements on the same VBP domains. However, due to the fast binding interactions introduced by the DNA binding domain, FCS generates independent estimates for the diffusion constant (6.7 ± 2.4 μm2/s) and the association (2 ± 1.2 s−1) and dissociation (19 ± 7 s−1) rates, whereas FRAP produces only a single, but a consistent, estimate, the effective-diffusion constant (4.4 ± 1.4 μm2/s), which depends on all three parameters. We apply this new FCS method to evaluate the efficacy of a potential anticancer drug that inhibits DNA binding of VBP in vitro and find that in vivo the drug inhibits DNA binding in only a subset of cells. In sum, we provide a straightforward approach to directly measure binding rates from FCS data.

Sequence Sensitivity of Breathing Dynamics in Heteropolymer DNA

We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a biological sequence of the T7 bacteriophage. Quantitative agreement with data from fluorescence correlation spectroscopy is demonstrated.

A New Photostable Terrylene Diimide Dye for Applications in Single Molecule Studies and Membrane Labeling

A new terrylene diimide-based dye (WS-TDI) that is soluble in water has been synthesized, and its photophysical properties are characterized. WS-TDI forms nonfluorescing H-aggregates in water that show absorption bands being blue-shifted with respect to those of the fluorescing monomeric form. The ratio of monomeric WS-TDI to aggregated WS-TDI was determined to be 1 in 14 400 from fluorescence correlation spectroscopy (FCS) measurements, suggesting the presence of a large amount of soluble, nonfluorescent aggregates in water. The presence of a surfactant such as Pluronic P123 or CTAB leads to the disruption of the aggregates due to the formation of monomers in micelles. This is accompanied by a strong increase in fluorescence. A single molecule study of WS-TDI in polymeric films of PVA and PMMA reveals excellent photostability with respect to photobleaching, far above the photostability of other common water-soluble dyes, such as oxazine-1, sulforhodamine-B, and a water-soluble perylenediimide derivative. Furthermore, labeling of a single protein such as avidin is demonstrated by FCS and single molecule photostability measurements. The high tendency of WS-TDI to form nonfluorescent aggregates in water in connection with its high affinity to lipophilic environments is used for the fluorescence labeling of lipid membranes and membrane containing compartments such as artificial liposomes or endosomes in living HeLa cells. The superior fluorescence imaging quality of WS-TDI in such applications is demonstrated in comparison to other well-known membrane staining dyes such as Alexa647 conjugated with dextran and FM 4-64 lipophilic styryl dye.

Photobleaching, Mobility, and Compartmentalisation: Inferences in Fluorescence Correlation Spectroscopy

In living cells the transport and diffusion of molecules is constrained by compartments of various sizes. This paper is an attempt to show that the size of these compartments can in principle be estimated experimentally from Fluorescence Correlation Spectroscopy (FCS) combined with the measurement of the photobleaching rate. In this work, confocal fluorescence microscopy experiments have been carried out on giant unilamellar vesicles, a system that mimics cellular compartmentalisation. We have developed numerical and analytical models to describe the fluorescence decay due to photobleaching in this geometry, which has enabled us to point out two regimes depending on the value of the parameter P(B) = sigma(B)P/D (where sigma(B) is the photobleaching cross section of the dye, D its diffusion constant, and P the laser power (in photon/s)). In particular, when P(B) << 1 (i.e. in the fast diffusion regime), the photobleaching rate is independent of the diffusion constant and scales like sigma(B)P/R2, in agreement with the experimental results. On the other hand, the standard diffusion models used to analyse the FCS data do not take into account the effects of the fluorescence decay on the autocorrelation curve. We show here how to correct the raw data for these drawbacks.

Applications of Fluorescence Correlation Spectroscopy: Polydispersity Measurements

The method of histograms is applied to the determination of polydispersity of particles and molecules in solution from fluorescence correlation spectroscopy (FCS) data. This is an ill-posed problem, which can be overcome by using a common strategy for imposed regularization and constraint conditions. The method developed for evaluating the polydispersity is tested on both computer-generated correlation curves and real FCS data. The results obtained show that FCS measurements can be successfully used for the determination of polydispersity of suspensions, with an efficiency comparable to that of photon correlation spectroscopy (PCS). The advantage of FCS, however, is its better sensitivity to small particles (size <50 nm) and molecules in dilute solutions, as well as its better selectivity. The usefulness of FCS for environmental chemistry is discussed with regard to the obtained results.