Detection of single-molecule DNA hybridization by using dual-color total internal reflection fluorescence microscopy

We examined the use of prism-type simultaneous dual-color total internal reflection fluorescence microscopy (TIRFM) to probe DNA molecules at the single-molecule level. The system allowed the direct detection of the complementary interactions between single-stranded probe DNA molecules (16-mer) and various lengths of single-stranded target DNA molecules (16-mer and 55-mer) that had been labeled with different fluorescent dyes (Cy3, Cy5, and fluorescein). The polymer-modified glass substrate and the extent of DNA probe immobilization were easily characterized either with standard TIRFM or with atomic force microscopy. However, only dual-color TIRFM could provide unambiguous images of individual single-stranded target DNA molecules hybridized with the correct sequence in the range of fM–aM. Succinic anhydride showed low RMS roughness and was found to be an optimal blocking reagent against non-specific adsorption, with an efficiency of 92%. This study provides a benchmark for directly monitoring the interactions and the detection of co-localization of two different DNA molecules and can be applied to the development of a nanoarray biochip at the single-molecule level.     

Translational motion of a spherical particle near a planar liquid-fluid interface

The translational electrophoretic motion of a colloidal spherical particle parallel to a planar liquid-fluid interface is analyzed by using the reciprocal theorem developed by Yariv and Brenner [E. Yariv, H. Brenner, J. Fluid Mech. 484 (2003) 85]. Based on the thin electric double layers assumption, analytical solutions of the forces acting on the particle are obtained, and the influence of the liquid-fluid interface on the electrophoretic velocity of the particle is studied. It is found that the speed of the particle's electrokinetic motion will increase as the separation distance between the particle and the interface decreases. This enhancement of electrophoretic mobility becomes more significant when the viscosity of the fluid phase becomes larger.     

Steric repulsion by adsorbed polymer layers studied with total internal reflection microscopy

Total internal reflection microscopy (TIRM) was applied to measure the interaction potential between charge-stabilized polystyrene latex spheres and a glass wall in dependence on the concentration of additional poly(ethylene oxide). The influence of the polymer can be described by steric repulsion between polymer layers, which are physically adsorbed onto the surfaces of the polystyrene sphere and the glass wall. The expected attractive contribution to the potential due to polymer depletion was not observed. An increase of the polymer bulk concentration is shown to strengthen the steric repulsion. At the highest polymer concentrations studied, it is possible to accurately describe the experimental data for the steric contribution to the total interaction potential with the Alexander-de Gennes model for brush repulsion.     

应用全内反射单分子荧光成像研究蛋白复合物亚基组成

细胞的生化过程大都是由蛋白复合物完成的,研究蛋白复合物亚基的组成对于了解蛋白质的结构和生物学功能具有重要的意义,然而如何准确确定蛋白复合物中蛋白质亚基的数量（stoichiometry）仍然是一个挑战.近年来,活细胞体系单分子荧光成像技术的不断发展为原位实时动态地研究蛋白质的结构和性质提供了新的手段.本文主要介绍了应用活细胞全内反射单分子荧光成像技术表征细胞膜区蛋白复合物组成的3种方法,包括单分子漂白步数分析、荧光强度统计分布以及蛋白运动分析,并结合其基本原理介绍了这几种方法在活细胞体系膜蛋白研究中的应用.     

Depletion interaction mediated by a polydisperse polymer studied with total internal reflection microscopy

Total internal reflection microscopy (TIRM) was applied to measure depletion forces between a charged colloidal sphere and a charged solid wall induced by dextran, a nonionic nonadsorbing polydisperse polysaccharide. The polymer size polydispersity is shown to greatly influence the depletion potential. Using the theory for the depletion interaction due to ideal polydisperse polymer chains, we could accurately describe the experimental data with a single adjustable parameter.     

A versatile total internal reflection photometric detection cell for flow analysis

A total internal reflection (TIR) flow-through cell that is highly tolerant of schlieren effects, has limited hydrodynamic dispersion and does not trap gas bubbles, and which is suitable for sensitive photometric measurements in flow analysis, is described. Light from an optical fibre is introduced into a short length of quartz capillary through the sidewall at an incident angle of ca. 53°. Under this condition, incident light undergoes total internal reflection from the external air-quartz interface and is propagated by successive reflections from the external walls through the aqueous liquid core of the cell. Detection of the transmitted beam is enabled by intentionally introducing an optical coupling medium at a predetermined distance along the capillary wall, which allows the internally reflected light to be captured by a second optical fibre connected to a charge-couple device detector.This configuration embodies a number of the desirable features of a liquid core waveguide cell (i.e. total internal reflection), a multi-reflection (MR) flow cell (i.e. minimum susceptibility to schlieren effects, low hydrodynamic dispersion and little tendency to trap bubbles), and a conventional Z-cell (wide dynamic range). When employed with a flow injection system, a limit of detection of 2.0 μg PL⁻¹ was achieved for the determination of reactive phosphate using the TIR cell, compared with LOD values of 3.8 μg PL⁻¹ and 4.9 μg PL⁻¹ obtained using the MR and Z-cells with same manifold.The combined advantages of schlieren-tolerance and lack of bubble entrapment of the MR cell with the higher S/N ratio and wider dynamic range of a conventional Z-cell, make the TIR cell eminently useful for photometric measurements of samples with widely differing refractive indices.     

Self-assembling protein platform for direct quantification of circulating microRNAs in serum with total internal reflection fluorescence microscopy

MicroRNA (miRNA) has recently emerged as a new and important class of cellular regulators. Strong evidences showed that aberrant expression of miRNA is associated with a broad spectrum of human diseases, such as cancer, diabetes, cardiovascular and psychological disorders. However, the short length and low abundance of miRNA place great challenges for conventional techniques in the miRNA quantification and expression profiling. Here, we report a direct, specific and highly sensitive yet simple detection assay for miRNA without sample amplification. A self-assembled protein nanofibril acted as an online pre-concentrating sensor to detect the target miRNA. Locked nucleic acid (LNA) of complimentary sequence was served as the probe to capture the target miRNA analyte. The quantification was achieved by the fluorescence intensity measured with total internal reflection fluorescence microscopy. A detection limit of 1 pM was achieved with trace amount of sample consumption. This assay showed efficient single-base mismatch discrimination. The applicability of quantifying circulating mir-196a in both normal and cancer patient’s serums was also demonstrated.     

In situ measurements of the dynamics of single giant DNA molecules at the toluene-trioctylamine/water interface by total internal reflection fluorescence microscopy

The dynamics of single giant deoxyribonucleic acid (T4GT7DNA, 165 600 base pairs) molecules was examined near and at the toluene/water, toluene-trioctylamine mixtures/water, and trioctylamine/water interfaces by total internal reflection fluorescence microscopy. The results were considerably affected by the trioctylamine content. With pure toluene or mixtures of lower trioctylamine volume contents (%VA), the randomly coiled DNA molecules diffused to near the interfaces. With mixtures of higher %VA (9 and 50%), the DNA molecules were stretched and adsorbed at the interfaces. There are a large number of anionic phosphate groups ((-O)2PO2-) in the DNA molecule that have an electrostatic affinity to protonated trioctylamine existing at the interface. In the case of pure trioctylamine, globular DNA molecules were adsorbed at the interface and also existed in the aqueous phase.     

Electron transfer reaction in a single protein molecule observed by total internal reflection fluorescence microscopy

To observe an electron transfer (ET) process in a single protein molecule, we constructed a model system, Alexa-HCytb5, in which cytochrome b5 (Cytb5) is modified with a fluorescent probe, Alexa Fluor 647 dye. In this model system, intramolecular transfer of an electron from the Alexa dye to heme in Cytb5 is supposed to oxidize the probe and quench its fluorescence, and the ET reaction at the single-molecule level can be monitored as the intermittent change in the fluorescence intensity. Alexa-HCytb5 was fixed on the glass surface, and illumination of laser light by the total internal reflection resulted in blinking of the fluorescence from the single Alexa-HCytb5 molecule in the time scale of several hundred milliseconds. Each Alexa-HCytb5 molecule is characterized by its own rate constant of the blinking, corresponding to the ET rate constant at the single-molecule level, and its variation ranges between 1 and 10 s(-1). The current system thus enables us to visualize the ET reaction in the single protein molecule, and the protein ET reaction was found to be explained by the distribution of the rate constants. On the basis of the Marcus theory, we suggest that the origin of this rate distribution is the distance change associated with the structural fluctuation in the protein molecule.     

Evaluation of lateral resolution of scanning surface microscopy by total internal reflection with thermal lens effect

We have developed a novel method for in situ and non-destructive surface analyses, or a total internal reflection with thermal lens spectroscopy (TIR-TLS), which has sufficient sensitivity to monitor phenomena in thin films, such as lipid bilayers. In this study, we applied TIR-TLS to microscopy for surface analyses, and we experimentally obtained its lateral resolution using the edge of a chromium film made by a photolithography technique. The obtained resolution was 20 microm, which was 60% of the diameter of an excitation beam at the interface. The estimated resolution with a simple model agreed with the experimental one, and from this model, TIR-TLS microscopy has the same resolution as that of ordinary optical microscopy. The microscopy by TIR-TLS was applied to a sample whose contrast was too weak to be visually seen, and an image of the sample was obtained without any loss of resolution.     

Effect of surface tension and surface elasticity of a fluid-fluid interface on the motion of a particle immersed near the interface

The motion of a particle immersed in a fluid near a fluid-fluid interface is studied on the basis of the linearized Navier-Stokes equations. The motion is influenced by surface tension, dilatational surface elasticity modulus, and surface shear modulus, as well as by gravity. The backflow at the location of the particle after a sudden impulse has some universal features that are the same as for a rigid wall with stick boundary conditions. At short times the flow depends only on the mass densities of the two fluids. The nature of the short-time flow is calculated from potential flow theory. At a somewhat later time the particle shows a pronounced rebound. The maximum value of the rebound and the time at which the maximum occurs depend on the elastic properties of the interface.     

Adsorption of a protein-porphyrin complex at a liquid-liquid interface studied by total internal reflection synchronous fluorescence spectroscopy

Interfacial analysis has attracted more and more attention owing to its fundamental and biological importance. Total internal reflection fluorescence (TIRF) spectroscopy is a useful method to study interfacial properties. The synchronous scanning fluorescence technique provides a selective tool to analyze a specific component in a complex system. The interaction and adsorption of bovine serum albumin (BSA) and meso-tetrakis(4-sulfonatophenyl)porphyrin (TPPS) at toluene-water interface were studied successfully by the coupling technique of total internal reflection synchronous fluorescence (TIRSF). New methods are provided for the determination of the critical micelle concentration (cmc), apparent adsorption equilibrium constant (K_ad) and maximum amount of adsorption (f_max) at the liquid-liquid interface. The results indicated that BSA could adsorb onto the toluene-water interface as a complex of BSA-TPPS in a ratio of 1:1 ratio based on Langmuir adsorption isothermal model. The cmc, apparent K_ad and f_max for BSA at pH 3.1 were determined to be 1.0 × 10⁻⁴ mol L⁻¹, 1.15 × 10⁵ L mol⁻¹ and 1.14 × 10⁻⁹ mol cm⁻², respectively.     

A method for visualization of biomolecules labeled by a single quantum dot in living cells by a combination of total internal reflection fluorescence microscopy and intracellular fluorescence microscopy

We developed a simple fluorescence microscopy for acquisition of high-resolution images of single quantum dots (QDs) labeled to biomolecules on apical plasma membrane, in cell interior and on basal plasma membrane of living cells. The method was a combination of total internal reflection fluorescence microscopy (TIRFM) at apical cell surface and intracellular microscopy coupled with focusing objective. Insulin conjugated to single QD (insulin-QD) was chosen as the model system. In order to bind insulin-QDs to insulin receptors on the plasma membrane through the interaction between insulin and its receptor, as well as internalize them, the cells attached on a coverslip were incubated with biotinylated insulin and QD-streptavidin conjugate at 37 °C. Next, fluorescent molecules in the cells were photobleached by illuminating the cells using a 100-W mercury lamp with the wavelengths from 460 to 490 nm. Then, the incident angle of a laser beam was adjusted to produce total internal reflection at the apical surface of a single cell. In this case, the insulin-QDs in the whole cell were excited, and the fluorescent molecules outside the cell were not illuminated. Finally, the images of single insulin-QDs on the apical plasma membrane, in the cell interior and on the basal plasma membrane of the cell were taken by focusing the objective to different positions, respectively. The resolution and contrast of the fluorescent spots in the images were much higher than those obtained by using epi-fluorescence microscopy and comparable to those obtained by using the conventional TIRFM. The method improved the image acquisition speed for the images on the apical and basal plasma membrane using the conventional TIRFM, and could acquire the high-resolution images in the cell interior quickly.     

Investigation of short-time particle dynamics near an interface in the presence of nonadsorbed macro-ions

The optical technique of total internal reflection microscopy was used to study the normal Brownian motion of a single colloidal particle near an interface. The measurements were made using a recently developed technique in which the diffusion coefficient was determined by the variance of the short-time (Deltat --> 0) motion of the particle. Experiments were performed in solutions containing either silica nanospheres or clay platelets (Laponite RD) to investigate the effect of nonadsorbed material on the dynamics of near-contact particle motion. The change in the diffusion coefficient with separation distance between the particle and plate in solutions containing nonadsorbed macro-ions was well-described by the theory developed for simple fluids. These results suggest that, in dilute solutions of nonadsorbed material in which the bulk rheological properties remain similar to those of the pure fluid, the mobility and diffusion coefficient correction factors developed for simple fluids remain valid.     

Simultaneous investigation of sedimentation and diffusion of a single colloidal particle near an interface

We describe here a new procedure for the simultaneous investigation of sedimentation and diffusion of a colloidal particle in close proximity to a solid, planar wall. The measurements were made using the optical technique of total internal reflection microscopy, coupled with optical radiation pressure, for dimensionless separation distances (gap width/radius of particle) ranging from 0.01 to 0.05. In this region, the hydrodynamic mobility and diffusion coefficient are substantially reduced below bulk values. The procedure involved measuring the mean and the variance of vertical displacements of a Brownian particle settling under gravity toward the plate. The spatially varying diffusion coefficient was calculated from the displacements at small times (where diffusive motion was dominant). The mobility relationship for motion normal to a flat plate was tested by measuring the average distance of travel versus time as the particle settled under the constant force of gravity. For the simple Newtonian fluid used here (aqueous salt solution), the magnitude of the diffusion coefficient and mobility, plus their dependence on separation distance, showed excellent agreement with predictions. This new technique could be of great value in measuring the mobility and diffusion coefficient for near-contact motion in more complex fluids for which the hydrodynamic correction factors are not known a priori, such as shear-thinning fluids.     

Quantitative detection of antibody based on single-molecule counting by total internal reflection fluorescence microscopy with quantum dot labeling

We presented a sensitive method to quantify antibody based on single-molecule counting by total internal reflection fluorescence microscopy with quantum dot labeling. In this method, the biotinylated monoclonal anti-human IgG molecules were immobilized on the silanized glass substrate surface. By the strong biotin-streptavidin affinity, streptavidin-coated quantum dots were labeled to the target molecules as fluorescent probe. Then, images of fluorescent spots in the evanescent wave field were obtained by a high-sensitivity electron multiplying charge-coupled device. Finally, the number of fluorescent spots corresponding to single molecules in the subframe images was counted, one by one. The linear range of 8.0 × 10⁻¹⁴ to 5.0 × 10⁻¹² mol L⁻¹ was obtained between the number of single molecules and the sample concentration.     

Total internal reflection imaging of microorganism adhesion using an oil immersion objective

In this paper, we report the results of total internal reflection microscopy investigations of the interaction of two types of microorganisms: Saccharomyces cerevisiae and Escherichia coli with substrates. It is shown that with this method qualitative and quantitative information about cells-substrate interaction can be obtained. One can easily make a difference between attached and non-attached as well as between dead and alive cells, and more generally can follow the dynamics of the process of cells' attachment to substrates. Quantitative information about the cell size and cell-substrate distance is obtained by using a model in which yeast cells and bacteria are approximated by ellipsoids, and multiple reflections of the evanescent waves between the cells and the substrate are neglected.     

Time-resolved total internal reflection fluorescence spectroscopy. Part I. Photophysics of Coumarin 343 at liquid/liquid interface

Pico-second time-resolved time-correlated single photon counting (TCSPC) technique under the total internal reflection (TIR) condition has been used to study the photophysical properties of Coumarin 343 (C343) dye molecules adsorbed at the water/1,2-dichloroethane (DCE) interface. The fluorescence decay profile of C343 under TIR condition at the water/DCE interface was non-exponential and fitted to the double exponential decay function with the fluorescence lifetimes 0.3 and 3.6 ns, which proved the existence of two different forms of C343 species having largely different lifetimes at the interface. The longer fluorescence lifetime component of C343 at the interface is attributed to the emission from the monomeric form of the dye molecules and the shorter lifetime component is due to the aggregation of dye molecules. The penetration depth dependence of decay curves indicated no change in the fluorescence lifetime components, however, the amplitude corresponding to the lifetime of aggregate increased and the amplitude corresponding to the lifetime of monomer decreased with the decrease in penetration depth of the aqueous phase from the interface. Aggregation is significant in the interfacial layer. The decrease in monomer lifetime at the interface compared to that in the bulk solution is interpreted in terms of excitation energy migration between the dye molecules.     

A new total reflection X-ray fluorescence vacuum chamber with sample changer analysis using a silicon drift detector for chemical analysis

There are several TXRF spectrometers commercially available for chemical analysis as well as for wafer surface analysis, but there is up to now no spectrometer for chemical analysis available that allows to measure samples under vacuum conditions. Simply a rough vacuum of 10⁻² mbar for the sample environment reduces the background due to scattering from air, thus to improve the detection limits. The absorption of low energy fluorescence radiation from low Z elements is reduced and therefore extends the elemental range to be measured down to Na. Finally evacuation of the chamber removes the Ar K-lines from the spectrum.The new vacuum chamber for TXRF named WOBISTRAX is equipped with a 12-position sample changer, a 10-mm² silicon drift detector (SDD) with an 8-μm Be entrance window and electrical cooling by Peltier effect, so no LN₂ is required. The chamber was designed to be attached to a diffraction tube housing. WOBISTRAX can be operated with a 3 kW long fine focus Mo-X-ray tube and uses a Mo/Si multilayer for monochromatization. The modified software is performing the motion control between sample changer and MCA features.The performance is expressed in terms of detection limits which are 700 fg Rb for Mo Kα excitation with 50 kV, 40 mA excitation conditions, 1000 s livetime. Using a Cr-X-ray tube for excitation of Al the achieved detection limits are 52 pg. So it could be shown that with the same measuring chamber and using an SDD with 8 μm Be window and a Cr-tube for excitation, low Z elements can be also measured with good detection limits.