Fluorescence Intensity Fluctuations Research Articles

A new method for measurement and quantification of tracer diffusion in nanoconfined liquids.

We report development of a novel instrument to measure tracer diffusion in water under nanoscale confinement. A direct optical access to the confinement region, where water is confined between a tapered fiber and a flat substrate, is made possible by coating the probe with metal and opening a small aperture (0.1 μm-1 μm) at its end. A well-controlled cut using an ion beam ensures desired lateral confinement area as well as adequate illumination of the confinement gap. The probe is mounted on a tuning-fork based force sensor to control the separation between the probe and the substrate with nanometer precision. Fluctuations in fluorescence intensity due to diffusion of a dye molecule in water confined between the probe and the sample are recorded using a confocal arrangement with a single photon precision. A Monte Carlo method is developed to determine the diffusion coefficient from the measured autocorrelation of intensity fluctuations which accommodates the specific geometry of confinement and the illumination profile. The instrument allows for measurement of diffusion laws under confinement. We found that the diffusion of a tracer molecule is slowed down by more than 10 times for the probe-substrate separations of 5 nm and below.

Aptamer-Anchored Rubrene-Loaded Organic Nanoprobes for Cancer Cell Targeting and Imaging

Aptamer-Anchored Rubrene-Loaded Organic Nanoprobes for Cancer Cell Targeting and Imaging

Fluorescence correlation spectroscopy as a tool for the study of the intracellular dynamics and biological fate of protein corona

In biological fluids, nanoparticles (NPs) are in contact with proteins and other biomolecules. Proteins adsorb to NPs and form a coating called a protein corona (PC). The PC is known to greatly affect the interaction of NPs with biological systems. A comprehensive knowledge of the protein nanoparticle interaction is essential to understand the biological fate of NPs and for the design of NPs for biomedicine. Fluorescence correlation spectroscopy (FCS) and fluorescence cross-correlation spectroscopy (FCCS) are sensitive spectroscopy techniques that measure fluorescence intensity fluctuations of single molecules inside a femtoliter confocal volume. Both techniques are suitable for studying the formation of protein corona around NPs and for examining corona stability in situ in biological matrixes. In this review we provide a short description of FCS/FCCS and their application in PC studies, highlighting results from our work about the impact of surface chemistry of NPs on corona formation and NP intracellular fate.

A general method to quantify ligand-driven oligomerization from fluorescence-based images.

Here, we introduce fluorescence intensity fluctuation spectrometry for determining the identity, abundance and stability of protein oligomers. This approach was tested on monomers and oligomers of known sizes and was used to uncover the oligomeric states of the epidermal growth factor receptor and the secretin receptor in the presence and absence of their agonist ligands. This method is fast and is scalable for high-throughput screening of drugs targeting protein-protein interactions.

Near-infrared fluorescent probe for fast track of cyclooxygenase-2 in Golgi apparatus in cancer cells

Cyclooxygenase-2 (COX-2) has been used as an excellent traceable biomarker, and exists maximally in Golgi apparatus (Cancer cells). Celecoxib (CCB) is a selective inhibitor for COX-2, and has been used as one of non-steroidal anti-inflammatory drug. Herein we report the conjugation of nile blue (NB) with CCB via a six-carbon linkage to form a fluorescence probe NB-C6-CCB for the detection of COX-2. NB-C6-CCB displays strong fluorescence with the emission peak centered at near-infrared wavelength (700 nm) in tumor cells or tumor tissues with high expression of COX-2. Importantly, NB-C6-CCB can discriminate cancer cells (MCF-7) fluorescence intensity from normal ones (COS-7) in the co-culture medium under confocal microscope. Subcellular localization of the NB-C6-CCB preferentially points to the Golgi apparatus and increases the fluorescent intensity. The competitive analysis (with CCB) and Native-PAGE analysis confirmed that NB-C6-CCB shows selective binding affinity towards COX-2 enzyme. Competitive analysis with CCB (flow cytometry assay) revealed the fluorescence intensity fluctuation due to pretreatment of CCB with different concentrations, indicating that the NB-C6-CCB is a precise or sensitive probe for the COX-2. Tumor tissue (depth: 500 µm), organs and mice imaging tests show excellent near-infrared visualization, specific localization and identification of tumors.

Measuring Mobility in Chromatin by Intensity-Sorted FCS

The architectural organization of chromatin can play an important role in genome regulation by affecting the mobility of molecules within its surroundings via binding interactions and molecular crowding. The diffusion of molecules at specific locations in the nucleus can be studied by fluorescence correlation spectroscopy (FCS), a well-established technique based on the analysis of fluorescence intensity fluctuations detected in a confocal observation volume. However, detecting subtle variations of mobility between different chromatin regions remains challenging with currently available FCS methods. Here, we introduce a method that samples multiple positions by slowly scanning the FCS observation volume across the nucleus. Analyzing the data in short time segments, we preserve the high temporal resolution of single-point FCS while probing different nuclear regions in the same cell. Using the intensity level of the probe (or a DNA marker) as a reference, we efficiently sort the FCS segments into different populations and obtain average correlation functions that are associated to different chromatin regions. This sorting and averaging strategy renders the method statistically robust while preserving the observation of intranuclear variations of mobility. Using this approach, we quantified diffusion of monomeric GFP in high versus low chromatin density regions. We found that GFP mobility was reduced in heterochromatin, especially within perinucleolar heterochromatin. Moreover, we found that modulation of chromatin compaction by ATP depletion, or treatment with solutions of different osmolarity, differentially affected the ratio of diffusion in both regions. Then, we used the approach to probe the mobility of estrogen receptor-α in the vicinity of an integrated multicopy prolactin gene array. Finally, we discussed the coupling of this method with stimulated emission depletion FCS for performing FCS at subdiffraction spatial scales.

Amyloidogenic Nanoplaques in Blood Serum of Patients with Alzheimer's Disease Revealed by Time-Resolved Thioflavin T Fluorescence Intensity Fluctuation Analysis.

Background:Biomarkers are central to current research on molecular mechanisms underlying Alzheimer’s disease (AD). Their further development is of paramount importance for understanding pathophysiological processes that eventually lead to disease onset. Biomarkers are also crucial for early disease detection, before clinical manifestation, and for development of new disease modifying therapies.Objective:The overall aim of this work is to develop a minimally invasive method for fast, ultra-sensitive and cost-effective detection of structurally modified peptide/protein self-assemblies in the peripheral blood and in other biological fluids. Specifically, we focus here on using this method to detect structured amyloidogenic oligomeric aggregates in the blood serum of apparently healthy individuals and patients in early AD stage, and measure their concentration and size.Methods:Time-resolved detection of Thioflavin T (ThT) fluorescence intensity fluctuations in a sub-femtoliter observation volume element was used to identify in blood serum ThT-active structured amyloidogenic oligomeric aggregates, hereafter called nanoplaques, and measure with single-particle sensitivity their concentration and size.Results:The concentration and size of structured amyloidogenic nanoplaques are significantly higher in the blood serum of individuals diagnosed with AD than in control subjects.Conclusion:A new method with the ultimate, single-particle sensitivity was successfully developed. The proposed approach neither relies on the use of immune-based probes, nor on the use of radiotracers, signal-amplification or protein separation techniques, and provides a minimally invasive test for fast and cost-effective early determination of structurally modified peptides/proteins in the peripheral blood, as shown here, but also in other biological fluids.

Evaluation of gamma-ray disturbing effect on readout of charged particle tracks using fluorescent nuclear track detectors (FNTDs)

In this study, we aimed to identify the reasons for track misrecognition caused by gamma-rays in the FNTD (fluorescent nuclear track detector) system. FNTDs were irradiated with fluence-controlled 241Am alpha-particles at 0°. The irradiated FNTDs were scanned by a commercial reader to obtain fluorescence images of uniform shape tracks and a reader-counted track density per unit area [mm−2]. The track density was good agreement with manually eye-counted track density. Then, the FNTDs irradiated with alpha-particles were additionally irradiated with 137Cs gamma-rays and scanned by the reader in order to monitor transition of the reader-counted track density with gamma dose. Track counting efficiency, which is defined as the reader-counted density divided by the eye-counted density, was reliable with until 33 mSv of gamma dose with ± 30% accuracy. However, with the higher dose of gamma-rays at 95 and 242 mSv, the efficiency fluctuated over the accuracy because of track misrecognition. To clarify the reasons for the track misrecognition, fluorescence track images were compared before and after gamma irradiations. On the fluorescence images with gamma-rays, the non-uniform signal caused by secondary electrons were observed (Sykora et al., 2010a). Especially with 242 mSv of gamma dose, the non-uniform signal formed “track-like” spots. To analyze the characteristics of the non-uniform signal, fluorescence intensity (FI) per pixel was analyzed for track and background (BG) areas separately. The FIs at both track and BG areas showed linearity to gamma dose. In the analysis of FI distributions, the fluctuation of FIs at BG area increased with gamma doses while the fluctuation of FIs at track areas did not change significantly. As a result, the difference of FI values between track and BG areas was smaller with the higher dose of gamma-rays. This phenomenon caused the difficulty of detecting tracks under gamma-ray exposure.

Schlieren two-photon microscopy for phase-contrast imaging.

While simultaneous phase-contrast and two-photon fluorescence imaging in microscopy can bring abundant biomedical information, it is difficult to retrieve phase information from conventional two-photon microscopes. To realize low-cost, in situ phase-contrast and two-photon fluorescence imaging, we propose Schlieren two-photon microscopy, a method that implements phase-contrast imaging on two-photon microscopes. This method involves spatially modulated fluorescence plates, which are made of two-photon fluorescence dyes or upconversion nanoparticles. We demonstrate that the fluorescence intensity fluctuation reflects the phase gradients of the specimen via theoretical analysis, simulations, and experiments. The proposed method is fully compatible with commercial two-photon microscopes, thus enabling widespread applications in live tissue imaging.

Measuring Fluctuations in the Intensity of a Single Point-Like Luminescence Emitter: Artifacts in Processing Microscopic Images

The processing of images of point-like fluorescing objects, obtained by a matrix detector in the scheme of a luminescent microscope, is considered. Analysis of model images with parameters close to experimental images of flickering single CdSe/ZnS quantum dots is presented. A scheme for obtaining information on fluctuations in fluorescence intensity is proposed.

Changes in biophysical characteristics of PFN1 due to mutation causing amyotrophic lateral sclerosis.

Single amino acid mutations in profilin 1 (PFN1) have been found to cause amyotrophic lateral sclerosis (ALS). Recently, we developed a mouse model for ALS using a PFN1 mutation (glycine 118 to valine, G118V), and we are now interested in understanding how PFN1 becomes toxically lethal with only one amino acid substitution. Therefore, we studied mutation-related changes in the PFN1 protein and hypothesized that such changes significantly disturb its structure. Initially, we expressed and studied the purified PFN1WT and PFN1G118V proteins from bacterial culture. We found that the PFN1G118V protein has a different mean residue ellipticity, as measured by far-UV circular dichroism, accompanied by a spectral shift. The intrinsic fluorescence of PFN1G118V showed a small fluctuation in maximum fluorescence absorption and intensity. Moreover, we examined the time course of PFN1 aggregation using SDS-PAGE, western blotting, and MALDI-TOF/TOF and found that compared with PFN1WT, PFN1G118V had an increased tendency to form aggregates. Dynamic light scattering data confirmed this, showing a larger size distribution for PFN1G118V. Our data explain why PFN1G118V tends to aggregate, a phenotype that may be the basis for its neurotoxicity.

Fluorescence lifetime correlation spectroscopy: Basics and applications

This chapter presents a concise introduction into the method of Fluorescence Lifetime Correlation Spectroscopy (FLCS). This is an extension of Fluorescence Correlation Spectroscopy (FCS) that analyses fluorescence intensity fluctuations from small detection volumes in samples of ultra-low concentration. FCS has been widely used for investigating diffusion, conformational changes, molecular binding/unbinding equilibria, or chemical reaction kinetics, at single molecule sensitivity. In FCS, this is done by calculating intensity correlation curves for the measured intensity fluctuations. FLCS extends this idea by calculating fluorescence-lifetime specific intensity correlation curves. Thus, FLCS is the method of choice for all studies where a parameter of interest (conformational state, spatial position, molecular environmental condition) is connected with a change in the fluorescence lifetime. After presenting the theoretical and experimental basis of FLCS, the chapter gives an overview of its various applications.

Velocity landscape correlation resolves multiple flowing protein populations from fluorescence image time series

Molecular, vesicular and organellar flows are of fundamental importance for the delivery of nutrients and essential components used in cellular functions such as motility and division. With recent advances in fluorescence/super-resolution microscopy modalities we can resolve the movements of these objects at higher spatio-temporal resolutions and with better sensitivity. Previously, spatio-temporal image correlation spectroscopy has been applied to map molecular flows by correlation analysis of fluorescence fluctuations in image series. However, an underlying assumption of this approach is that the sampled time windows contain one dominant flowing component. Although this was true for most of the cases analyzed earlier, in some situations two or more different flowing populations can be present in the same spatio-temporal window. We introduce an approach, termed velocity landscape correlation (VLC), which detects and extracts multiple flow components present in a sampled image region via an extension of the correlation analysis of fluorescence intensity fluctuations. First we demonstrate theoretically how this approach works, test the performance of the method with a range of computer simulated image series with varying flow dynamics. Finally we apply VLC to study variable fluxing of STIM1 proteins on microtubules connected to the plasma membrane of Cystic Fibrosis Bronchial Epithelial (CFBE) cells.

Carbon Dots for Single-Molecule Imaging of the Nucleolus

Carbon dots are newly discovered bright fluorescent biolabeling probes that nonspecifically bind to multiple cellular structures. Here we report yellow-orange emissive carbon dots that spontaneously localize inside the nucleolus of HeLa cells, specifically binding to the RNA. Single-particle measurements of carbon dots show fluorescence-intensity fluctuations with superior brightness and photostability. These optical properties were used for performing blinking-assisted localization microscopy that shows organization of the nucleolar RNA with improved resolution. Our study opens up the opportunity for single-molecule imaging and super-resolution microscopy applications using fluorescent carbon dots.

Probing the conformational dynamics of photosystem I in unconfined and confined spaces.

The fluorescence dynamics of Photosystem I (PSI) in bulk water and inside a confined environment like a liposome have been investigated using time resolved confocal microscopy. In bulk water, PSI exhibits a major emission peak at ∼680 nm, while in the liposome it exhibits a markedly blue shifted emission maximum at ∼485 nm. This is indicative of conformational changes due to entrapment and emergence of a stressed conformation of PSI inside the liposome. The observed time constants for the fluorescence lifetime of PSI inside the liposome are significantly high as opposed to PSI in bulk water. More interestingly, the fluorescence intensity of PSI in bulk water exhibits strong fluctuations with many high intensity jumps and these are anti-correlated with the fluorescence lifetime of PSI. In contrast, inside the liposome, no such anti-correlated behaviour is observed. We further demonstrated that PSI exhibits at least two conformational states in bulk water, whereas a single conformation is observed inside the liposome, indicating the conformational rigidity and locking of the PSI complex inside a liposome.

Single plane illumination microscopy as a tool for studying nucleome dynamics.

Single plane illumination microscopy (SPIM) is a new optical method that has become extremely important in recent years. It is based on the formation of a "light slice" in the specimen in which fluorescently tagged molecules are observed. The spatial resolution is close to that of confocal optics, but without the disadvantages inherent to scanning or high laser irradiation doses. A recent development is light sheet fluctuation microscopy, which exploits the dynamic information contained in the fluorescence intensity fluctuations of each image pixel. Here we review the principles of this method and show some recent applications to the dynamics of transcription factors and chromatin. We show that the dimerization of Fos and Jun proteins is directly linked to their binding to DNA; that nuclear receptor activation changes their intranuclear dynamics; and that the viscoelastic behavior of interphase chromatin strongly depends on the presence of lamin A.

Reference-free path length interferometry of random media with the intensity moments analysis.

Stochastic interference of partially coherent light multiple scattered by a random medium is considered. The relationship between the second- and third-order moments of intensity fluctuations in random interference patterns, the coherence function of probe radiation, and the probability density of path differences for the interfering partial waves in the medium are established. The obtained relationships were verified using the statistical analysis of spectrally selected fluorescence radiation emitted by the laser-pumped dye-doped random medium. Rhodamine 6G water solution was applied as the doping agent for the ensembles of densely packed silica grains which were pumped by the CW radiation (532 nm) from the diode-pumped solid state laser. Experimentally observed abrupt decay of the second- and third-order moments of fluorescence intensity fluctuations for the wavelengths ranging from 620 nm to 680 nm is interpreted in terms of amplification of spontaneous emission at large dye concentrations. This paper discusses the new optical probe of random media defined as "the reference-free path length interferometry with the intensity moments analysis".

Correction to "Artifact-Free and Detection-Profile-Independent Higher-Order Fluorescence Correlation Spectroscopy for Microsecond-Resolved Kinetics. 2. Mixtures and Reactions".

Fluorescence correlation spectroscopy (FCS) is a primary tool in the time-resolved analysis of nonreacting or reacting molecules in solution, based on fluorescence intensity fluctuations. However, conventional FCS alone is insufficient for a complete determination of reaction or mixture parameters. In an accompanying article, a technique for the computation of artifact-free higher-order correlations with microsecond time resolution was described. Here, we demonstrate the applications of the technique to analyze the systems of fast and slow reactions. As an example of non- or slow-reacting systems, the technique is applied to resolve two-component mixtures of labeled oligonucleotides. Next, the protonation reaction of fluorescein isothiocyanate in phosphate buffer is analyzed as an example of fast reactions (relaxation time <1 μs). By reference to an (apparent) nonreacting system, the simple factorized form of cumulant-based higher-order correlations is exploited to remove the dependence on the molecular d...

Artifact-Free and Detection-Profile-Independent Higher-Order Fluorescence Correlation Spectroscopy for Microsecond-Resolved Kinetics. 2. Mixtures and Reactions.

Fluorescence correlation spectroscopy (FCS) is a primary tool in the time-resolved analysis of nonreacting or reacting molecules in solution, based on fluorescence intensity fluctuations. However, conventional FCS alone is insufficient for a complete determination of reaction or mixture parameters. In an accompanying article, a technique for the computation of artifact-free higher-order correlations with microsecond time resolution was described. Here, we demonstrate the applications of the technique to analyze the systems of fast and slow reactions. As an example of non- or slow-reacting systems, the technique is applied to resolve two-component mixtures of labeled oligonucleotides. Next, the protonation reaction of fluorescein isothiocyanate in phosphate buffer is analyzed as an example of fast reactions <10 μs (actual time scale ∼6 μs). By reference to an (apparent) nonreacting system, the simple factorized form of cumulant-based higher-order correlations is exploited to remove the dependence on the molecular detection function (MDF). Therefore, there is no need to model and characterize the experimental MDF, and the precision and the accuracy of the technique are enhanced. It is verified that the higher-order correlation analysis enables a complete and simultaneous determination of the number and brightness parameters of mixing or reacting molecules, the reaction relaxation time, and forward and reverse reaction rates.

Artifact-Free and Detection-Profile-Independent Higher-Order Fluorescence Correlation Spectroscopy for Microsecond-Resolved Kinetics. 1. Multidetector and Sub-Binning Approach.

Fluorescence correlation spectroscopy (FCS) is a powerful tool in the time-resolved analysis of nonreacting or reacting molecules in solution, based on fluorescence intensity fluctuations. However, conventional (second-order) FCS alone is insufficient to measure all parameters needed to describe a reaction or mixture, including concentrations, fluorescence brightnesses, and forward and reverse rate constants. For this purpose, correlations of higher powers of fluorescence intensity fluctuations can be calculated to yield additional information from the single-photon data stream collected in an FCS experiment. To describe systems of diffusing and reacting molecules, considering cumulants of fluorescence intensity results in simple expressions in which the reaction and diffusion parts factorize. The computation of higher-order correlations in experiments is hindered by shot-noise and common detector artifacts, the effects of which become worse with increasing order. In this article, we introduce a technique to calculate artifact-free higher-order correlation functions with improved time resolution, and without any need for modeling and calibration of detector artifacts. The technique is formulated for general multidetector experiments and verified in both two-detector and single-detector configurations. Good signal-to-noise ratio is achieved down to 1 μs in correlation curves up to order (2, 2). This capability makes possible a variety of new measurements including multicomponent analysis and fast reaction kinetics, as demonstrated in a companion article (10.1021/acs.jpcb.7b00408).