Can Dissipative Properties of Single Molecules Be Extracted from a Force Spectroscopy Experiment?

We performed dynamic force spectroscopy of single dextran and titin I27 molecules using small-amplitude and low-frequency (40-240 Hz) dithering of an atomic force microscope tip excited by a sine wave voltage fed onto the tip-carrying piezo. We show that for such low-frequency dithering experiments, recorded phase information can be unambiguously interpreted within the framework of a transparent theoretical model that starts from a well-known partial differential equation to describe the dithering of an atomic force microscope cantilever and a single molecule attached to its end system, uses an appropriate set of initial and boundary conditions, and does not exploit any implicit suggestions. We conclude that the observed phase (dissipation) signal is due completely to the dissipation related to the dithering of the cantilever itself (i.e., to the change of boundary conditions in the course of stretching). For both cases, only the upper bound of the dissipation of a single molecule has been established as not exceeding 3⋅10(-7)kg/s. We compare our results with previously reported measurements of the viscoelastic properties of single molecules, and we emphasize that extreme caution must be taken in distinguishing between the dissipation related to the stretched molecule and the dissipation that originates from the viscous damping of the dithered cantilever. We also present the results of an amplitude channel data analysis, which reveal that the typical values of the spring constant of a I27 molecule at the moment of module unfolding are equal to 4±1.5mN/m, and the typical values of the spring constant of dextran at the moment of chair-boat transition are equal to 30-50mN/m.

Probing fibronectin-antibody interactions using AFM force spectroscopy and lateral force microscopy.

The first experiment showing the effects of specific interaction forces using lateral force microscopy (LFM) was demonstrated for lectin-carbohydrate interactions some years ago. Such measurements are possible under the assumption that specific forces strongly dominate over the non-specific ones. However, obtaining quantitative results requires the complex and tedious calibration of a torsional force. Here, a new and relatively simple method for the calibration of the torsional force is presented. The proposed calibration method is validated through the measurement of the interaction forces between human fibronectin and its monoclonal antibody. The results obtained using LFM and AFM-based classical force spectroscopies showed similar unbinding forces recorded at similar loading rates. Our studies verify that the proposed lateral force calibration method can be applied to study single molecule interactions.

Nanoscale spatially resolved infrared spectra from single microdroplets.

Droplet microfluidics has emerged as a powerful platform allowing a large number of individual reactions to be carried out in spatially distinct microcompartments. Due to their small size, however, the spectroscopic characterisation of species encapsulated in such systems remains challenging. In this paper, we demonstrate the acquisition of infrared spectra from single microdroplets containing aggregation-prone proteins. To this effect, droplets are generated in a microfluidic flow-focussing device and subsequently deposited in a square array onto a ZnSe prism using a micro stamp. After drying, the solutes present in the droplets are illuminated locally by an infrared laser through the prism, and their thermal expansion upon absorption of infrared radiation is measured with an atomic force microscopy tip, granting nanoscale resolution. Using this approach, we resolve structural differences in the amide bands of the spectra of monomeric and aggregated lysozyme from single microdroplets with picolitre volume.

MAR-mediated integration of plasmid vectors for in vivo gene transfer and regulation.

BACKGROUND: The in vivo transfer of naked plasmid DNA into organs such as muscles is commonly used to assess the expression of prophylactic or therapeutic genes in animal disease models. RESULTS: In this study, we devised vectors allowing a tight regulation of transgene expression in mice from such non-viral vectors using a doxycycline-controlled network of activator and repressor proteins. Using these vectors, we demonstrate proper physiological response as consequence of the induced expression of two therapeutically relevant proteins, namely erythropoietin and utrophin. Kinetic studies showed that the induction of transgene expression was only transient, unless epigenetic regulatory elements termed Matrix Attachment Regions, or MAR, were inserted upstream of the regulated promoters. Using episomal plasmid rescue and quantitative PCR assays, we observed that similar amounts of plasmids remained in muscles after electrotransfer with or without MAR elements, but that a significant portion had integrated into the muscle fiber chromosomes. Interestingly, the MAR elements were found to promote plasmid genomic integration but to oppose silencing effects in vivo, thereby mediating long-term expression. CONCLUSIONS: This study thus elucidates some of the determinants of transient or sustained expression from the use of non-viral regulated vectors in vivo.

Photocatalytic and phototoxic properties of TiO2-based nanofilaments: ESR and AFM assays.

There is uncertainty in understanding of the relationship between physico-chemical parameters of nanosized titanium dioxide (nano-TiO(2)) and its toxicity when brought into contact with living cells. This study provides a multidisciplinary experimental insight into the toxicity and phototoxicity of the custom-made TiO(2)-based nanowires (TiO(2)-NWs). We employed electron spin resonance (ESR) to detect reactive oxygen species (ROS) generated in aqueous suspensions of TiO(2)-NWs and combined these results with atomic force microscopy (AFM) to trace the onset of toxic effects towards human melanoma cells. The cells were treated with low concentrations (∼2.5 µg/ml) of TiO(2)-NWs and Degussa P25. High-resolution AFM surface topography and cell elasticity measurements revealed toxic effects both in cells incubated with TiO(2)-NWs in the dark and exposed to the photo-oxidative stress under UVA radiation. In contrast to ROS generation efficacy in the absence of cells in vitro, no direct correlation was found between the physical parameters of nano-TiO(2) and cell toxicity.

Characterization of N-cadherin unbinding properties in non-malignant (HCV29) and malignant (T24) bladder cells.

The expression of N-cadherin, characteristic of various cancers, very often leads to changes in the cells' adhesive properties. Thus, we sought to find out if N-cadherin expressed in various, but cancer-related cells, differs in its functional properties that could contribute to variations in cells' phenotypes. In our work, measurements of an unbinding force of a single N-cadherin molecule, probed with the same antibody both on a surface of living non-malignant (HCV29) and malignant cells (T24) of bladder cancer, were carried out with the use of an atomic force microscopy. The results show the enhanced N-cadherin level in T24 malignant cells (8.7% vs. 3.6% obtained for non-malignant one), confirmed by the Western blot and the immunohistochemical staining. The effect was accompanied by changes in unbinding properties of an individual N-cadherin molecule. Lower unbinding force values (26.1 ± 7.1 pN) in non-malignant cells reveal less stable N-cadherin complexes, as compared to malignant cells (61.7 ± 14.6 pN). This suggests the cancer-related changes in a structure of the binding site of the antibody, located at the extracellular domain of N-cadherin.

Gene-mediated restoration of normal myofiber elasticity in dystrophic muscles.

Dystrophin mediates a physical link between the cytoskeleton of muscle fibers and the extracellular matrix, and its absence leads to muscle degeneration and dystrophy. In this article, we show that the lack of dystrophin affects the elasticity of individual fibers within muscle tissue explants, as probed using atomic force microscopy (AFM), providing a sensitive and quantitative description of the properties of normal and dystrophic myofibers. The rescue of dystrophin expression by exon skipping or by the ectopic expression of the utrophin analogue normalized the elasticity of dystrophic muscles, and these effects were commensurate to the functional recovery of whole muscle strength. However, a more homogeneous and widespread restoration of normal elasticity was obtained by the exon-skipping approach when comparing individual myofibers. AFM may thus provide a quantification of the functional benefit of gene therapies from live tissues coupled to single-cell resolution.

Fibrogenic fibroblasts increase intercellular adhesion strength by reinforcing individual OB-cadherin bonds.

We have previously shown that the switch from N-cadherin to OB-cadherin expression increases intercellular adhesion between fibroblasts during their transition from a migratory to a fibrogenic phenotype. Using atomic force microscopy we here show that part of this stronger adhesion is accomplished because OB-cadherin bonds resist approximately twofold higher forces compared with N-cadherin junctions. By assessing the adhesion force between recombinant cadherin dimers and between native cadherins in the membrane of spread fibroblasts, we demonstrate that cadherin bonds are reinforced over time with two distinct force increments. By modulating the degree of lateral cadherin diffusion and F-actin organization we can attribute the resulting three force states to the single-molecule bond rather than to cadherin cluster formation. Notably, association with actin filaments enhances cadherin adhesion strength on the single-molecule level up to threefold; actin depolymerization reduces single-bond strength to the level of cadherin constructs missing the cytoplasmic domain. Hence, fibroblasts reinforce intercellular contacts by: (1) switching from N- to OB-cadherin expression; (2) increasing the strength of single-molecule bonds in three distinct steps; and (3) actin-promoted intrinsic activation of cadherin extracellular binding. We propose that this plasticity adapts fibroblast adhesions to the changing mechanical microenvironment of tissue under remodeling.

Motion of a colloidal particle in an optical trap.

Thermal position fluctuations of a colloidal particle in an optical trap are measured with microsecond resolution using back-focal-plane interferometry. The mean-square displacement and power spectral density are in excellent agreement with the theory for a Brownian particle in a harmonic potential that accounts for hydrodynamic memory effects. The motion of a particle is dominated at short times by memory effects and at longer times by the potential. We identify the time below which the particle's motion is not influenced by the potential, and find it to be approximately tau(k)/20 , where tau(k) is the relaxation time of the restoring force of the potential. This allows us to exclude the existence of free diffusive motion, proportional to t, even for a sphere with a radius as small as 0.27 microm in a potential as weak as 1.5 microN/m. As the physics of Brownian motion can be used to calibrate an optical trap, we show that neglecting memory effects leads to an underestimation of more than 10% in the detector sensitivity and the trap stiffness for an experiment with a micrometer-sized particle and a sampling frequency above 200kHz . Furthermore, these calibration errors increase in a nontrivial fashion with particle size, trap stiffness, and sampling frequency. Finally, we present a method to evaluate calibration errors caused by memory effects for typical optical trapping experiments.

Diameter-dependent elastic modulus supports the metastable-catalyst growth of carbon nanotubes.

We measured the elastic modulus of individual multiwalled carbon nanotubes (MWCNTs) grown by catalytic chemical vapor deposition (CVD) over a broad diameter range (10-25 nm). Alternating current (ac) dielectrophoresis was used for efficient tube deposition, and atomic force microscope (AFM) force-displacement curve technique was used for stiffness measurements. The elastic modulus exhibits a strong diameter dependence, showing a difference of nearly 2 orders of magnitude in the 10-20 nm diameter range (thinner MWCNTs have higher elastic modulus). Our results support the metastable-catalyst model in which the catalyst's molten skin plays a key role.

Specific detection of glycans on a plasma membrane of living cells with atomic force microscopy.

Among the many alterations of cancer cells is the expression of different surface oligosaccharides. In this work, oligosaccharide expression in living cells (cancer and reference ones) was studied with atomic force microscopy by using lectins as probes. The unbinding force obtained for the same lectin type (concanavalin A or Sambucus nigra) suggested slightly dissimilar structures of binding sites of the same ligand type. For the lectin from Phaseolus vulgaris, a much larger unbinding force indicated a distinct structure of the binding site in cancer cells. The unbinding probability confirmed a higher content of both sialic acid and mannose-containing ligands in cancer and reference cells, respectively. These results demonstrate the potential of atomic force microscopy to directly probe the presence of molecules on a living cell surface, together with the quantitative description of their expression.

Lectin-carbohydrate affinity measured using a quartz crystal microbalance.

The association of two molecules is described by two parameters, association equilibrium and association rate constants, which are characteristic for a given type of interaction. Usually, they are determined for interacting molecules dissolved in solution. However, for many applications one type of molecules is immobilized on a substrate, which may influence the binding kinetics. The studied complex of concanavalin A and carboxypeptidase Y belongs to the lectin-carbohydrate type of interaction involving the recognition of oligosaccharide moieties. The concanavalin A was immobilized on a gold electrode of quartz crystal, while carboxypeptidase Y was added to a buffer (Tris-buffered saline). The constants describing the association of the investigated molecules were determined on the basis of measurements performed using a quartz crystal microbalance in liquid. The obtained values were (0.59+/-0.01)x10(6) M(-1) for the association equilibrium constant and (5.6+/-0.1)x10(4) M(-1)s(-1) for the association rate constant. The saturation binding experiment gave another value of the association constant, (2.7+/-0.02)x10(6) M(-1). The comparison of obtained values with previously published ones verifies that the molecule orientation and binding site accessibility for specific ligands could influence the association equilibrium constant value. The presented measurements demonstrate the ability of a quartz crystal microbalance to detect and to evaluate the association process occurring between molecules.

Catalytically grown carbon nanotubes of small diameter have a high Young's modulus.

Experimental studies of carbon nanotubes (CNTs) obtained through different synthesis routes show considerable variability in their mechanical properties. The strongest CNTs obtained so far had a high Young's modulus of 1 TPa but could only be produced in gram scale quantities. The synthesis by catalytic chemical vapor deposition, a method that holds the greatest potential for large-scale production, gives CNTs with a high defect density. This leads to low Young's modulus values below 100 GPa for multiwall CNTs. Here we performed direct measurements of the mechanical properties of catalytically grown CNTs with only a few walls and find a Young's modulus of 1 TPa. This high value is confirmed for CNTs grown under two different growth conditions where the synthesis parameters such as the hydrocarbon source, catalyst material, and the synthesis temperature were varied. The results indicate that the observed difference in the Young's modulus for the catalytically grown CNTs with high and low numbers of walls is probably related to the growth mechanism of CNT.

Friction force microscopy as an alternative method to probe molecular interactions.

Friction force microscopy was applied to study protein-carbohydrate interactions that are important in many cellular recognition processes. The expression and structure of carbohydrates can be investigated using lectins as molecular probes since they recognize different types of sugar molecules. Lectins (concanavalin A and lentil lectin, recognizing mannose-type carbohydrates) were attached to the probing tip and carboxypeptidase Y (possessing complementary carbohydrates) was immobilized on a modified glass surface using microcontact printing. The results obtained from friction force maps and dependencies on the loading rate (measured in a physiological buffer) were divided in two distinct groups. The first group of results obtained for lectin-protein complexes was assigned to molecular recognition events, whereas the other including all control measurements was attributed to nonspecific interaction. All results presented here indicate that friction force microscopy can be successfully employed to study recognition processes.

Hydrogel microspheres: influence of chemical composition on surface morphology, local elastic properties, and bulk mechanical characteristics.

Hydrogel microspheres, beads, and capsules of uniform size, differing in their chemical composition, have been prepared by electrostatic complex formation of sodium alginate with divalent cations and polycations. These have served as model spheres to study the influence of the chemical composition on both surface characteristics and bulk mechanical properties. Resistance to compression experiments yielding the compression work clearly identified differences as a function of the composition, with forces at maximal compression in the range of 34-455 mN. The suitability and informative value of atomic force microscopy have been confirmed for the case where surface characterization is performed in a liquid environment equivalent to physiological conditions. Surface imaging and mechanical response to indentation revealed different average surface roughness and Young's moduli for all hydrogel types ranging from 0.9 to 14.4 nm and from 0.4 to 440 kPa, respectively. The hydrogels exhibited pure elastic behavior. Despite a relatively high standard deviation, resulting from both surface and batch heterogeneity, nonoverlapping ranges of Young's moduli were reproducibly identified for the selected model spheres. The findings indicate the reliability of contact mode atomic force microscopy to quantify local surface properties, which may have an impact on the biocompatibility of alginate-based hydrogel materials of different composition and conditions of preparation. Moreover, it seems that local elastic properties and bulk mechanical characteristics are subject to analogous composition influences.

Large fluctuations in the disassembly rate of microtubules revealed by atomic force microscopy.

Atomic force microscopy (AFM) in situ has been used to observe the cold disassembly dynamics of microtubules at a previously unrealised spatial resolution. Microtubules either electrostatically or covalently bound to aminosilane surfaces disassembled at room temperature under buffer solutions with no free tubulin present. This process was followed by taking sequential tapping-mode AFM images and measuring the change in the microtubule end position as a function of time, with an spatial accuracy down to +/-20nm and a temporal accuracy of +/-1s. As well as giving average disassembly rates on the order of 1-10 tubulin monomers per second, large fluctuations in the disassembly rate were revealed, indicating that the process is far from smooth and linear under these experimental conditions. The surface bound rates measured here are comparable to the rates for GMPCPP-tubulin microtubules free in solution, suggesting that inhibition of tubulin curvature through steric hindrance controls the average, relatively low disassembly rate. The large fluctuations in this rate are thought to be due to multiple pathways in the kinetics of disassembly with differing rate constants and/or stalling due to defects in the microtubule lattice. Microtubules that were covalently bound to the surface left behind the protofilaments covalently cross-linked to the aminosilane via glutaraldehyde during the disassembly process. Further work is needed to quantitatively assess the effects of surface binding on protofibril disassembly rates, reveal any differences in disassembly rates between the plus and minus ends and to enable assembly as well as disassembly to be imaged in the microscope fluid cell in real-time.