Exponentially modified Gaussian relevance to the distributions of translocation events in nanopore-based single molecule detection

Nanopore technique plays an important role in single molecule detection, which illuminates the properties of an individual molecule by analyzing the blockage durations and currents. However, the traditional exponential function is lack of efficiency to describe the distributions of blockage durations in nanopore experiments. Herein, we introduced an exponentially modified Gaussian （EMG） function to fit the duration histograms of both simulated events and experimental events. In comparison with the traditional exponential function, our results demonstrated that the EMG provides a better fit while covers the entire range of the distributions. In particular, the fitted parameters of EMG could be directly used to discriminate the sequence length of the oligonucleotides at single molecule level.     

Distribution of single molecules in polymer thin films

Distribution of fluorescent dye molecules in polymer thin (100 nm) films was investigated using far-field single-molecule video microscopy, by varying concentrations of dye molecules mixed in the polymer. Histograms of fluorescence photocounts of individual fluorescent spots showed wide distribution, varying in the number of fluorescent spots composed of one, two, three or group of molecules. The number of the molecules present in the fluorescent spots was also ascertained by fluorescence photobleaching experiments. Photocounts associated with maxima of the histograms were found to be independent of the concentrations; however, the number of occurrences associated with more than one molecule decreased with decreasing concentration. By reducing concentration as well as by mixing dye molecules into a polymer solution, fluorescent spots grouping more than one molecule were separated considerably into fluorescent spots including a single-molecule.     

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.     

Effect of aggregation state, temperature and phospholipids on photobleaching of photosynthetic pigments in spinach Photosystem II core complexes

Photosystem II (PSII) complex activity is known to decrease under strong white light illumination, and this photoinhibition phenomenon is connected to the photobleaching of the PSII photosynthetic pigments. In this work the pigment photobleaching has been studied on PSII core complexes, by observing the effects of different factors such as the aggregation state (PSII monomers and dimers were used), temperature (20 degrees C and 10 degrees C temperatures were tested) and the presence of the exogenous phospholipids (cardiolipin and phosphatidylglycerol). In particular, PSII resistance against white light stress was studied by means of UV/VIS Absorption and Fluorescence Emission measurements. It was found that PSII dimers resulted more resistant against photobleaching and that lower temperature reduces the pigment photodestruction. Moreover, the presence of phosphatidylglycerol or cardiolipin enhanced the PSII resistance to the photobleaching phenomenon, mainly at lower temperatures.     

The electrochemical behavior of a system with a limited number of molecules

In this paper, based on Einstein relationship between diffusion and random walk, the electrochemical behavior of a system with a limited number of molecules was simulated and explored theoretically. The transition of the current vs time responses from discrete to continuous was clearly obtained as the number of redox molecules increased from 10 to 10⁶. By correlation analysis between the simulation results and the results of analytical expressions, a quantized extent parameter was proposed to investigate the underlying rules of these discrete signals, which looked stochastic. The results revealed that this parameter would be useful to describe such systems.     

Investigation of the carrier saturation in facilitated transport of unsaturated hydrocarbons

Single-component facilitated transports of ethylbenzene, styrene, cyclohexene and 1-hexene were carried out using the feed concentrations ranging from 0.5 M to pure. Equilibrium constants of the Ag⁺-solute complex formation, determined by distribution method, were 0.7, 2.2, 32.0, 129.1 M⁻¹, respectively. Carrier saturation was not found with the membrane incorporated with 2.67 M Ag⁺-ion. As the carrier concentration was reduced to 0.51 M, increase in the feed concentration beyond 4.5 M had very little effect on ethylbenzene flux, suggesting the onset of carrier saturation. Styrene and cyclohexene underwent the carrier saturation when the carrier loading was 0.25 M, while a complete saturation was not observed with 1-hexene. Extraction of solute from the membranes revealed that less than 50% of Ag⁺-ions were occupied when the carrier saturation occurred. It was also found that the ability of solute to use available Ag⁺-ions in the membrane was dependent on the equilibrium constant.     

Determination of Gossypol in Trace Level by Flow Injection Analysis with Chemiluminescence Detection

Gossypol, [1, 1′, 6, 6′, 7,7′-hexahydroxyl-5,5′-diisopropyl-3,3′-dimethyl-(2,2′-binaphtha- lene)-8,8′-dicarboxaldehyde] is a polyphenolic yellow compound naturally occurring in various parts of cotton plants1. The compound has been associated with     

光漂白全过程中聚合物薄膜折射率和厚度的实时分析

在基于衰减全反射原理的基础上提出一种新的测量方法, 动态研究漂白动力学过程, 即利用波导的衰减全反射吸收峰对聚合物材料的折射率和厚度敏感的特性, 实时测量聚合物材料的折射率和厚度. 实验系统采用CCD摄像头将标志波导模式的一组暗线显示在计算机屏幕上, 然后根据暗线的移动, 可以精确测量每一时刻波导薄膜的折射率和膜厚. 利用这种技术, 对聚合物薄膜的光漂白过程进行了实时监控. 发现在光漂白全过程中, 聚合物薄膜的折射率和厚度的变化同时存在化学和物理两种变化过程.     

Fluorescence energy transfer-sensitized photobleaching of a fluorescent label as a tool to study donor-acceptor distance distributions and dynamics in protein assemblies: studies of a complex of biotinylated IgM with streptavidin and aggregates of concanavalin A

A photokinetic method of detection of fluorescence resonance energy transfer (FRET) between special fluorescent labels is applied to study time-averaged spatial distribution of labeled proteins in protein assemblies. Prolonged irradiation of a sample at the absorption maximum of the energy donor initiates FRET-sensitized fluorescence photobleaching of the energy acceptor label, which was monitored by steady-state fluorimetric measurements. Kinetics of the acceptor photobleaching and kinetics of decreasing the efficiency of FRET from donors to unbleached acceptors were determined. The FRET efficiency was found from measuring sensitization of acceptor fluorescence. Analysis of the photokinetic data permits to estimate the time-averaged distribution of acceptors on donor-acceptor distances in the range of characteristic distances of FRET. Dynamic processes influencing donor-acceptor distances can be also investigated by the method. Application of the method is demonstrated by the studies of a complex of biotinylated IgM with streptavidin and aggregates composed of concanavalin A and sodium dodecyl sulphate. A new thiadicarbocyanine dye was used as the acceptor label. R-phycoerythrin and tetramethylrhodamine isothiocyanate were the donor labels. In the IgM-streptavidin complex, 16% of acceptors most contributed to FRET provided 90% of FRET efficiency, whereas acceptors made about the same time-averaged contribution to FRET in the concanavalin A aggregates.     

Dependence on effective saturation of numbers of singlet peaks in one- and two-dimensional separations

The average numbers of singlet peaks in one-dimensional (1D) and two-dimensional (2D) separations of randomly distributed peaks are predicted by statistical-overlap theory and compared against the effective saturation. The effective saturation is a recently introduced metric of peak crowding that is more practitioner-friendly than the usual metric, the saturation. The effective saturation absorbs the average minimum resolution of statistical-overlap theory, facilitating the comparison of 1D and 2D separations by traditional metrics of resolution and peak capacity. In this paper, singlet peaks are identified with maxima produced by a single mixture constituent. Their effective saturations are calculated from published equations for the average minimum resolution of 1D singlet peaks, and from equations derived here for the average minimum resolution of 2D singlet peaks. The fractions of peaks that are singlets in 1D and 2D separations are predicted by statistical-overlap theory as functions of saturation but are compared as functions of effective saturation. The two fractions differ by no more than 0.033 at any effective saturation between 0 and 6, when the distribution of peak heights is exponential and the edge effect is neglected. This result shows that 1D and 2D separations of randomly distributed peaks are about the same in their ability to separate singlet peaks as maxima, when assessed relative to effective saturation. Empirical equations in effective saturation are reported for the fractions of peaks that are singlets. It is argued that the effective saturation is a good metric for comparing separations having different average minimum resolutions.     

Self-assembling bacterial pores as components of nanobiosensors for the detection of single peptide molecules

Nano-sized bacterial pores were inserted into a lipid membrane as a nanobiosensor for the detection of single peptide molecules. Due to the intrinsic properties of single-channel conductance, the transit of individual molecules through the pore can be studied. The analysis of both the blockage current and duration is able to provide specific structural information and allows the detection of specific peptides in bulk mixtures. Supported by the National Natural Science Foundation of China (Grant No. 20875030) and the Shuguang Project of Shanghai (Grant No. 07SG36)     

The detection of tetrahydrofuran hydrate formation and saturation using magnetic resonance imaging technique

Tetrahydrofuran (THF) hydrate was formed in bulk as well as in glass beads pack with a mean diameter of 3.0 mm by controlling the temperature under ambient pressure. Images of THF hydrate formation procedure were obtained using the magnetic resonance imaging (MRI) technique. The experiment results showed that MRI is an effective method for the detection of hydrate formation. Saturation of hydrate formed both in bulk and glass beads can be confirmed by intensity integration of MRI images.     

Spectral imaging of single molecules by transmission grating-based epi-fluorescence microscopy

A spectral imaging method of single protein molecules labeled with a single fluorophore is presented. The method is based on a transmission grating and a routine fluorescence microscope. The bovine serum alubmin (BSA) and antiBSA molecules labeled with Alexa Fluor 488 and Alexa Fluor 594, respectively, are used as the model proteins. The fluorescence of single molecules is dispersed into zeroth-order spectrum and first-order spectrum by the transmission grating. Results show that the fluorescence emission spectrum of single molecule converted from the first-order spectral imaging is in good agreement with the bulk fluorescence spectrum. The spectral resolution of 2.4 nm/pixel is obtained, which is sufficient for identifying the molecular species in a multicomponent system.     

Probing lipid vesicles by bimolecular association and dissociation trajectories of single molecules

Vesicles prepared by DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) and SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) lipid molecules having sizes smaller than the diffraction-limited focused laser beam have been used to confine single molecules in the laser focus. The confinement of single molecules in a volume smaller than the focused laser beam leads to a Gaussian distribution of single molecule fluorescence intensity. The interactions of single Nile Red molecules with DMPC and SOPC lipid bilayers were studied by single molecule fluorescence confocal microscopy. Nile Red molecules were observed to associate with and dissociate from individual DMPC and SOPC vesicles adsorbed on a glass surface, generating on-and-off fluctuations in a fluorescence signal representing a very low noise two-state trajectory. Off-time statistics were used to investigate the mean radius of the vesicles and the size distribution functions. The means of the on-time distributions of Nile Red in DMPC and SOPC vesicles were significantly different. The association and dissociation reactions of single Nile Red molecules with a vesicle have been studied. Features of the bimolecular interaction between the probe Nile Red and the vesicle were evaluated from the uncorrelated mean on-time and vesicle radius distributions, and the linear Nile Red concentration dependence of the mean off-time. Nile Red is shown to be a useful probe of the structural fluctuations and heterogeneity of these membrane structures, and it is a useful model with which to directly study a diffusion-influenced reversible bimolecular reaction.     

Investigation of fluorinated surfaces by means of radio-labelled probe molecules

Acid-base reactions and interactions are at the heart of inorganic fluorine chemistry and are now recognised as forming a very important part of the chemistry, catalytic or non-catalytic, that occurs on inorganic fluorinated surfaces. This review traces the use that has been made of radioactive isotopes, particularly the short-lived β⁺ emitter, fluorine-18, and the very long-lived chlorine-36, which is a β⁻ emitter, to investigate a variety of surface-related phenomena. Attention is concentrated on solid Lewis acids, including aluminium(III) fluoride derivatives, fluorinated γ-alumina and fluorinated chromia.     

Identification of individual DNA molecule of Mycobacterium tuberculosis by nested PCR-RFLP and capillary electrophoresis

The improvement of sensitivity and differentiation in rapidly identifying a small amount of mycobacteria in sputum has significant implications for reducing tuberculosis transmission. We previously applied the conventional PCR and capillary electrophoresis (CE) to establish the restriction fragment length polymorphism (RFLP) pattern of mycobacterial 65-kDa heat shock protein (hsp65) gene from colony specimens. However, the previous analysis did not provide enough sensitivity for sputum specimens in which the limitation of analysis might be hindered by PCR inhibitors and primer-dimers formation during amplification. In the current study, nested PCR (nPCR) had been redesigned for PCR-RFLP analysis (PRA) of mycobacterial hsp65 gene using CE. The results show both Mycobacterium tuberculosis complex and mycobacteria other than tuberculosis could be identified in the presence of PCR inhibitors. The interference due to primer-dimers was also minimized. Based on the Poisson distribution, the repeatability of single DNA molecule detection was greatly affected by sampling probability and might be improved significantly by increasing the sample loading. The PRA using nPCR and CE is not only able to detect the individual mycobacterial DNA molecule but also potentially differentiate the species.     

Controllable distribution of single molecules and peptides within oligomer template investigated by STM

This communication provides a facile method for distributing and dispersing molecules within a molecular template. Using the self-assembled template of oligo(phenylene-ethynylene) (OPE), organic molecules such as coronene (COR) and biomolecules such as tripeptide are controllably distributed and dispersed within this molecular template on highly oriented pyrolytic graphite (HOPG) surfaces. COR molecules were controllably distributed into various regular arrays by simply adjusting the molecular molar ratio, while tripeptide molecules were uniformly positioned at the vacancies of the OPE template.     

Determination of homogeneous vibronic spectra and the inhomogeneous distribution function of impurity molecules in solids by fluorescence saturation

Methods are developed for determining homogeneous vibronic spectra and the inhomogeneous distribution function of impurity molecules in low-temperature solid matrices by optical saturation of no-phonon transitions. The possibilities are demonstrated with solid solutions of perylene in benzophenone and n-hexane at 4.2 K.     

Temperature dependence of ligand-protein complex formation as reflected by saturation transfer difference NMR experiments

We show that temperature is an important parameter for the sensitivity of saturation transfer difference (STD) spectroscopy. A decreased intensity of STD signals is observed for lactose binding to growth-regulatory galectin7 (p53-induced gene 1), as well as for nucleotide binding to annexin A6, when the temperature is increased from 281 to 298-310 K. Opposite temperature effects on STD intensity are observed for S-peptide binding to S-protein to reconstitute RNase S. However, the STD signals for tryptophan binding to downstream regulatory element antagonist modulator of the human prodynorphin gene (DREAM)are relatively unaffected between 281 and 298 K. The known kinetics of the binding of ATP by the uncoupling protein from brown adipose tissue mitochondria (UCP1) predicted an observable STD at 310 K, but rapid sample degradation limits the experiments to much lower temperatures. Temperature strongly influences the kinetics and affinity constant of various types of complex formation and in so doing influences the observed STD effects. Therefore, temperature can be exploited to facilitate the optimization of STD-based applications, and at the same time minimize the number of test samples. STD-based screening protocols to detect new target-specific compounds may yield a larger number of potential ligands if screened at various temperatures.