Probing redox proteins on a gold surface by single molecule fluorescence spectroscopy

The interaction between the fluorescently labeled redox protein, azurin, and a thin gold film is characterized using single-molecule fluorescence intensity and lifetime measurements. Fluorescence quenching starts at distances below 2.3 nm from the gold surface. At shorter distances the quantum yield may decrease down to fourfold for direct attachment of the protein to bare gold. Outside of the quenching range, up to fivefold enhancement of the fluorescence is observed on average with increasing roughness of the gold layer. Fluorescence-detected redox activity of individual azurin molecules, with a lifetime switching ratio of 0.4, is demonstrated for the first time close to a gold surface.     

Probing multivalent interactions in a synthetic host-guest complex by dynamic force spectroscopy

Multivalency is present in many biological and synthetic systems. Successful application of multivalency depends on a correct understanding of the thermodynamics and kinetics of this phenomenon. In this Article, we address the stability and strength of multivalent bonds with force spectroscopy techniques employing a synthetic adamantane/β-cyclodextrin model system. Comparing the experimental findings to theoretical predictions for the rupture force and the kinetic off-rate, we find that when the valency of the complex is increased from mono- to di- to trivalent, there is a transition from quasi-equilibrium, with a constant rupture force of 99 pN, to a kinetically dependent state, with loading-rate-dependent rupture forces from 140 to 184 pN (divalent) and 175 to 210 pN (trivalent). Additional binding geometries, parallel monovalent ruptures, single-bound divalent ruptures, and single- and double-bound trivalent ruptures are identified. The experimental kinetic off-rates of the multivalent complexes show that the stability of the complexes is significantly enhanced with the number of bonds, in agreement with the predictions of a noncooperative multivalent model.     

Intercalation interactions between dsDNA and acridine studied by single molecule force spectroscopy

In this letter, we report on the direct measurement of the intercalation interactions between acridine and double-stranded DNA (dsDNA) using single molecule force spectroscopy. The interaction between acridine and dsDNA is broken by force of 36 pN at a loading rate of 5.0 nN/s. The most probable rupture force between acridine and dsDNA is dependent on the loading rate, indicating that the binding of acridine and dsDNA is a dynamic process. The combination of SMFS experimental data with the theoretical model clearly suggests the presence of two energy barriers along with an unbinding trajectory of acridine-dsDNA.     

Probing the initial events in the spontaneous emulsification of trans-anethole using dynamic NMR spectroscopy

The spontaneous emulsification of alcoholic solutions of trans-anethole (t-A) in water is investigated using EXSY and DOSY NMR techniques. The system investigated (5-10 mM t-A in 5% EtOH/H2O solution) is exceptional in providing sharp, clearly resolved signals for both t-A that is dissolved in the aqueous phase (free t-A) and t-A that is incorporated in aggregates (3-6 nm diameter) thus allowing both fractions to be probed simultaneously. This feature is utilized to explore the initial events that occur during the spontaneous emulsification process. Upon mixing, the majority of the t-A (ca. 75%) undergoes nucleation to form small aggregates (ca. 10 nm diameter), while 15% (corresponding to [t-A] = 7.5 x 10(-4) M) is dissolved in the aqueous phase. The kinetic rates governing the exchange process between aggregated and free t-A are found to be time-dependent and slow on the NMR time scale (k = 0.8-2 s(-1)). DOSY experiments indicate that the initially formed small aggregates undergo rapid coalescence to form larger droplets. Ostwald ripening of these droplets at the expense of the remaining small aggregates is responsible for the subsequent, slower time-evolution of the system.     

Heterogeneous dynamics and dynamic heterogeneities at the glass transition probed with single molecule spectroscopy

We studied the temperature dependence of the structural relaxation in poly(vinyl acetate) near the glass transition temperature with single molecule spectroscopy from Tg-1 K to Tg+12 K. The temperature dependence of the observed relaxation times matches results from bulk experiments; the observed relaxation times are, however, 80-fold slower than those from bulk experiments at the same temperature. We attribute this factor to the size of the probe molecule. The individual relaxation times of the single molecule environments are distributed normally on a logarithmic time scale, confirming that the dynamics in poly(vinyl acetate) is heterogeneous. The width of the distribution of individual relaxation times is essentially independent of temperature. The observed full width at half maximum (FWHM) on a logarithmic time axis is approximately 0.7, corresponding to a factor of about 5-fold, significantly narrower than the dielectric spectrum of the same material with a FWHM of about 2.0 on a logarithmic time axis, corresponding to a factor of about 100-fold. We explain this narrow width as the effect of temporal averaging of single molecule fluorescence signals over numerous environments due to a limited lifetime of the probed heterogeneities, indicating that heterogeneities are dynamic. We determine a loose upper limit for the ratio of the structural relaxation time to the lifetime of the heterogeneities (the rate memory parameter) of Q<80 for the range of investigated temperatures.     

Single molecule study of perylene orange photobleaching in thin sol-gel films

The paper reports on photobleaching mechanisms of perylene orange embedded in thin sol-gel films, derived from single molecule studies. The experimental configuration uses wide-field illumination and one photon excitation of the molecules. Measurements have been performed both at ambient conditions and under vacuum in order to get information on the influence of oxygen on photobleaching in such porous samples. We have also recorded the evolution of photobleaching with respect to the excitation intensity. The results demonstrate that photobleaching from excited states higher than the first singlet and triplet states has a nonnegligible contribution as soon as the excitation energy exceeds a few hundred W/cm2 and that this process is favored in the presence of air. The study also demonstrates that perylene orange in sol-gel films is not a very efficient emitter but that photobleaching can be slow, which explains the interest for perylene orange as a good candidate to produce long lifetime solid-state lasers when embedded in monoliths of sol-gel.     

Probing local effects in silica sol-gel media by fluorescence spectroscopy of p-DASPMI

Stillbazolium salts present remarkable potential for application in several scientific areas. Their versatile behavior is explained by invoking the "twisted intramolecular charge-transfer" (TICT) mechanism, a model that describes the multiple fluorescence of DASPMI (4-(4-(dimethylamino)styryl)- N-methylpyridiniumiodine). One feature of their behavior is the sensitivity of the fluorescence lifetime to viscosity, thus identifying them as suitable probes for microheterogeneous systems, such as cells and sol-gel derived media. Because of their optical transparency, sol-gel matrices are light addressable and therefore appropriate for performing spectroscopic studies. The sol-gel process has been successfully used to produce hosts to biomolecules like proteins, for biosensor applications; however, these systems have to be optimized. Therefore, in this study modification of the matrices was performed through the incorporation of either silanes or polymers. (Aminopropyl)triethoxysilane, trimethoxypropylsilane, or (glycidyloxypropyl)triethoxysilane were added. The modification was also extended to the incorporation of the polymers poly(ethylene glycol) (molecular weight 300 and 20000) and Gelrite. The effect of these modifiers upon the gelation and aging processes was examined via the study of the photophysics of p-DASPMI by using both steady-state and time-resolved fluorescence. It was possible to discriminate the dominant dye-host interactions in each of the main steps of the preparation of modified sol-gel matrices.     

Supramolecular research by single molecule force spectroscopy

Single molecule force spectroscopy (SMFS) is a new kind of technique based on atomic force microscope, which allows detecting force as low as pico-newtons directly. Herein based on our recent work, we want to demonstrate the investigation of supramolecular structures and interactions in polymer systems by SMFS, such as desorption force between polymer and substrate, identifiability of polymer micelle and its interaction with surfactant, splitting force of ion-induced helical structure in polysaccharide. It shows well that SMFS is a powerful tool in the study of supramolecular science.     

Enhanced fluorescence of Cy5-labeled oligonucleotides near silver island films: a distance effect study using single molecule spectroscopy

We investigated fluorescence enhancements and lifetime reductions of Cy5 probe molecules at various distances from the deposited silver island film surface using single molecule spectroscopic methods. The proximity of fluorophore molecules to the surface was controlled by alternating layers of biotinylated bovine serum albumin (BSA-biotin) and avidin, followed by binding of Cy5-labeled oligonucleotides to the top of a BSA-biotin layer structure. We observed dramatically varied brightness of fluorophores with distances from metal structures as well with reduced blinking in the presence of silver island films. In addition, distributions of fluorescence lifetimes and apparent emission intensities from individual molecules indicate an inhomogeneous nature of local matrix surface near metallic nanostructures. These studies illustrate the exclusive information that is otherwise hidden in ensemble measurements.     

Probing the binding kinetics of proinflammatory cytokine-antibody interactions using dual color fluorescence cross correlation spectroscopy

Dual color fluorescence cross correlation spectroscopy (FCCS) was used to investigate quantitatively the binding kinetics of tumor necrosis factor (TNFα) with TNFα antibody (anti-TNFα) following fluorescent labeling. Through the analysis of the auto correlation curves of fluorescence correlation spectroscopy (FCS), diffusion coefficients of 100.06 ± 4.9 μm(2) s(-1) and 48.96 ± 2.52 μm(2) s(-1) for Alexa488-TNFα and Atto647N-anti-TNFα were obtained. In addition, the calculated hydrodynamic diameters of the Alexa488-TNFα and Atto647N-anti-TNFα were approximately 4.89 ± 0.24 nm and 9.99 ± 0.52 nm, respectively, which agrees with the values of 5.20 ± 1.23 nm and 9.28 ± 0.86 nm for the native TNFα and the anti-TNFα as determined from dynamic light scattering measurements. For the binding kinetics, association (k(on)) and dissociation (k(off)) rate constants were (1.13 ± 0.08) × 10(4) M(-1) s(-1) and (1.53 ± 0.19) × 10(-3) s(-1) while the corresponding dissociation constant (K(d)) at 25 °C was (1.36 ± 0.10) × 10(-7) M. We believe this is the first report on the binding kinetics for TNFα-antibody recognition in the homogeneous phase. Using this technology, we have shown that controlled experiments can be performed to gain insight into molecular mechanisms involved in the immune response.     

Probing chitosan and phospholipid interactions using Langmuir and Langmuir-Blodgett films as cell membrane models

The interaction between chitosan and Langmuir and Langmuir-Blodgett (LB) films of dimyristoyl phosphatidic acid (DMPA) is investigated, with the films serving as simplified cell membrane models. At the air-water interface, chitosan modulates the structural properties of DMPA monolayers, causing expansion and decreasing the monolayer elasticity. As the surface pressure increased, some chitosan molecules remained at the interface, but others were expelled. Chitosan could be transferred onto solid supports alongside DMPA using the LB technique, as confirmed by infrared spectroscopy and quartz crystal microbalance measurements. The analysis of sum-frequency vibration spectroscopy data for the LB films combined with surface potential measurements for the monolayers pointed to chitosan inducing the ordering of the DMPA alkyl chains. Furthermore, the morphology of DMPA LB films, studied with atomic force microscopy, was affected significantly by the incorporation of chitosan, with the mixed chitosan-DMPA films displaying considerably higher thickness and roughness, in addition to chitosan aggregates. Because chitosan affected DMPA films even at pressures characteristic of cell membranes, we believe this study may help elucidate the role of chitosan in biological systems.     

Elucidating interactions of ionic liquids with polymer films using confocal Raman spectroscopy

We report on the molecular interactions between room-temperature ionic liquids (RTILs) and Nafion and PDMS membranes, proving that in contact with these polymers RTILs behave like electrolytes rather than solvents.     

Probing paeonol-pluronic polymer interactions by 1H NMR spectroscopy

By using a combination of 1H NMR spectroscopy, two-dimensional heteronuclear single-quantum coherence-resolved (1)H{(13)C} and homonuclear rotating-frame Overhauser enhancement NMR correlation experiments with diffusion ordered spectroscopy (DOSY), the location and distribution of a hydrophobic drug, paeonol, have been established with respect to the methyl groups of the poly(ethylene oxide)-poly(propylene oxide) -poly(ethylene oxide) (PEO-PPO-PEO) triblock copolymer. The interaction between them is adjustable according to the different temperature-dependent hydrophilicities or hydrophobicities of the triblock copolymer components. On the other hand, such interactions influence the self-assembly properties of the block copolymer amphiphiles in solution. The amount of anhydrous methyl groups of PPO segments shows an increase with increasing paeonol concentration. It was also demonstrated that the shell-crosslinking of the Pluronic polymer has an effect in increasing the amount of anhydrous methyl groups and thus increasing the hydrophobicity of Pluronic micelles. This might be the deeper reason underlying the increase in drug-loading capacity and prolongation in release time of Pluronic micelles for drug delivery after the shell-crosslinking. Changes in self-diffusion coefficients of paeonol with varying copolymer concentrations and types were also determined by the diffusion-based NMR DOSY technique, and values of K(a), DeltaG, and n were calculated.     

Single molecule force spectroscopy using polyproteins

In recent years single molecule force spectroscopy has emerged as a powerful new tool to explore the mechanical stability and folding pathways of individual proteins. This technique is used to apply a stretching force between two points of a protein, unfolding the protein to an extended state. By measuring the unfolding and folding trajectories of individual proteins, insight can be gained into the physical mechanisms of protein folding. In this tutorial review we introduce the reader to single molecule force spectroscopy using the atomic force microscope (AFM), and explain the two main modes of operation of the AFM for force spectroscopy: force-extension and force-clamp. We introduce the approach of using polyproteins to obtain a clear mechanical fingerprint for monitoring the response of proteins to an applied mechanical force. In addition, we provide an informative and representative review of recent research on proteins using single molecule force spectroscopy. We focus on areas which have made a significant contribution to the single molecule protein folding field and highlight emerging areas of research which have wider implications for the general scientific community.     

Evidence for resonance optical trapping of individual fluorophore-labeled antibodies using single molecule fluorescence spectroscopy

We report single molecule fluorescence studies of the diffusion of individual multiple fluorophore-labeled antibodies in solution, which show that a trapping potential of about 3.6 k(B)T can be obtained at laser powers below 1 mW with resonant excitation. Individual antibodies can be trapped for up to 140 ms, and bound antibodies can also be used to trap a single virion for up to 1 s. Selective resonance trapping to sort and manipulate fluorophore-labeled biomolecules and complexes may be possible.     

Single molecule fluorescence correlation spectroscopy of single apoptotic cells using a red-fluorescent caspase probe

The detection of single molecules in single cells has enabled biochemical analyses to be conducted with high sensitivity and high temporal resolution. In this work, detection of apoptosis was studied by single molecule fluorescence correlation spectroscopy (FCS) in single living cells. Caspase activity was assayed using a new red fluorogenic probe that avoids the spectral overlap of green fluorescent probes and cell autofluorescence. This new probe, 2SBPO-Casp, was synthesized by coupling a water-soluble Nile Blue derivative (2SBPO) to an aspartic acid residue. Upon apoptosis induction and caspase activation, free 2SBPO dye is shown to accumulate inside the cell after probe cleavage. In previous work in our lab, single molecule fluorescence in single apoptotic cells was detected 45 min after induction using a rhodamine 110-based probe. However, significant statistical analysis was needed to exclude false positives. The use of 2SBPO-Casp overcomes the autofluorescence problem and offers a steady fluorescence signal. In our single molecule FCS measurements, Ramos cells were determined apoptotic on the basis of their correlation coefficient value (R(2)). Cells that contain an R(2) ≥ 0.65 were identified as highly correlated and therefore determined to be apoptotic. Single apoptotic cells identified in this manner were found as early as 30 min after induction and the number of apoptotic cells reached a peak value at the 3rd hour, which is consistent with other techniques. Using single molecule techniques and a new apoptosis probe, the temporal dynamics were elucidated with better sensitivity and resolution than in previous studies.     

Single molecule spectroscopy as a probe for dye-polymer interactions

Experimental (Single Molecule Spectroscopy) and theoretical (quantum-chemical calculations and Monte Carlo and molecular dynamics simulations) techniques are combined to investigate the behavior and dynamics of a polymer-dye molecule system. It is shown that the dye molecule of interest (1,1'-dioctadecyl-3,3,3',3'-tetramethylindo-dicarbocyanine) adopts two classes of conformations, namely planar and nonplanar ones, when embedded in a poly(styrene) matrix. From an in-depth analysis of the fluorescence lifetime trajectories, the planar conformers can be further classified according to the way their alkyl side chains interact with the surrounding poly(styrene) chains.     

Probing riboswitch-ligand interactions using thiamine pyrophosphate analogues

The Escherichia coli thiM riboswitch forms specific contacts with its natural ligand, thiamine pyrophosphate (TPP or thiamine diphosphate), allowing it to generate not only nanomolar binding affinity, but also a high degree of discrimination against similar small molecules. A range of synthetic TPP analogues have been used to probe each of the riboswitch-ligand interactions. The results show that the pyrimidine-sensing helix of thiM is exquisitely tuned to select for TPP by recognising the H-bonding donor and acceptors around its aminopyrimidine ring and also by forming π-stacking interactions that may be sensitive to the electronics of the ring. The central thiazolium ring of TPP appears to be more important for ligand recognition than previously thought. It may contribute to binding via long-range electrostatic interactions and/or by exerting an electron withdrawing effect on the pyrimidine ring, allowing its presence to be sensed indirectly and thereby allowing discrimination between thiamine (and its phosphate esters) and other aminopyrimidines found in vivo. The pyrophosphate moiety is essential for submicromolar binding affinity, but unexpectedly, it does not appear to be strictly necessary for modulation of gene expression.