Correction of systematic errors in single-molecule force spectroscopy with polymeric tethers by atomic force microscopy

Single-molecule force spectroscopy has become a valuable tool for the investigation of intermolecular energy landscapes for a wide range of molecular associations. Atomic force microscopy (AFM) is often used as an experimental technique in these measurements, and the Bell-Evans model is commonly used in the statistical analysis of rupture forces. Most applications of the Bell-Evans model consider a constant loading rate of force applied to the intermolecular bond. The data analysis is often inconsistent because either the probe velocity or the apparent loading rate is being used as an independent parameter. These approaches provide different results when used in AFM-based experiments. Significant variations in results arise from the relative stiffness of the AFM force sensor in comparison with the stiffness of polymeric tethers that link the molecules under study to the solid surfaces. An analytical model presented here accounts for the systematic errors in force-spectroscopy parameters arising from the nonlinear loading induced by polymer tethers. The presented analytical model is based on the Bell-Evans model of the kinetics of forced dissociation and on the asymptotic models of tether stretching. The two most common data reduction procedures are analyzed, and analytical expressions for the systematic errors are provided. The model shows that the barrier width is underestimated and that the dissociation rate is significantly overestimated when force-spectroscopy data are analyzed without taking into account the elasticity of the polymeric tether. Systematic error estimates for asymptotic freely jointed chain and wormlike chain polymer models are given for comparison. The analytical model based on the asymptotic freely jointed chain stretching is employed to analyze and correct the results of the double-tether force-spectroscopy experiments of disjoining "hydrophobic bonds" between individual hexadecane molecules that are covalently tethered via poly(ethylene glycol) linkers of different lengths to the substrates and to the AFM probes. Application of the correction algorithm decreases the spread of the data from the mean value, which is particularly important for measurements of the dissociation rate, and increases the barrier width to 0.43 nm, which might be indicative of the theoretically predicted hydrophobic dewetting.     

基于原子力显微镜的单分子力谱在生物研究中的应用

原子力显微镜被广泛应用于生物研究领域,基于原子力显微镜的单分子力谱可以在单分子、单细胞水平上研究生物分子内和分子间的相互作用。 本文介绍了原子力显微镜单分子力谱在生物分子间相互作用、蛋白质去折叠、细胞表面生物分子、细胞力学性质和基于单分子力谱成像等研究中的最新进展。     

Energy Landscape of Aptamer/Protein Complexes Studied by Single‐Molecule Force Spectroscopy

Aptamers are single‐stranded nucleic acid molecules selected in vitro to bind to a variety of target molecules. Aptamers bound to proteins are emerging as a new class of molecules that rival commonly used antibodies in both therapeutic and diagnostic applications. With the increasing application of aptamers as molecular probes for protein recognition, it is important to understand the molecular mechanism of aptamer–protein interaction. Recently, we developed a method of using atomic force microscopy (AFM) to study the single‐molecule rupture force of aptamer/protein complexes. In this work, we investigate further the unbinding dynamics of aptamer/protein complexes and their dissociation‐energy landscape by AFM. The dependence of single‐molecule force on the AFM loading rate was plotted for three aptamer/protein complexes and their dissociation rate constants, and other parameters characterizing their dissociation pathways were obtained. Furthermore, the single‐molecule force spectra of three aptamer/protein complexes were compared to those of the corresponding antibody/protein complexes in the same loading‐rate range. The results revealed two activation barriers and one intermediate state in the unbinding process of aptamer/protein complexes, which is different from the energy landscape of antibody/protein complexes. The results provide new information for the study of aptamer–protein interaction at the molecular level.     

Atomic force microscopy measurement of heterogeneity in bacterial surface hydrophobicity

The structure and physicochemical properties of microbial surfaces at the molecular level determine their adhesion to surfaces and interfaces. Here, we report the use of atomic force microscopy (AFM) to explore the morphology of soft, living cells in aqueous buffer, to map bacterial surface heterogeneities, and to directly correlate the results in the AFM force-distance curves to the macroscopic properties of the microbial surfaces. The surfaces of two bacterial species, Acinetobacter venetianus RAG-1 and Rhodococcus erythropolis 20S-E1-c, showing different macroscopic surface hydrophobicity were probed with chemically functionalized AFM tips, terminating in hydrophobic and hydrophilic groups. All force measurements were obtained in contact mode and made on a location of the bacterium selected from the alternating current mode image. AFM imaging revealed morphological details of the microbial-surface ultrastructures with about 20 nm resolution. The heterogeneous surface morphology was directly correlated with differences in adhesion forces as revealed by retraction force curves and also with the presence of external structures, either pili or capsules, as confirmed by transmission electron microscopy. The AFM force curves for both bacterial species showed differences in the interactions of extracellular structures with hydrophilic and hydrophobic tips. A. venetianus RAG-1 showed an irregular pattern with multiple adhesion peaks suggesting the presence of biopolymers with different lengths on its surface. R. erythropolis 20S-E1-c exhibited long-range attraction forces and single rupture events suggesting a more hydrophobic and smoother surface. The adhesion force measurements indicated a patchy surface distribution of interaction forces for both bacterial species, with the highest forces grouped at one pole of the cell for R. erythropolis 20S-E1-c and a random distribution of adhesion forces in the case of A. venetianus RAG-1. The magnitude of the adhesion forces was proportional to the three-phase contact angle between hexadecane and water on the bacterial surfaces.     

Bubble colloidal AFM probes formed from ultrasonically generated bubbles

Here we introduce a simple and effective experimental approach to measuring the interaction forces between two small bubbles (approximately 80-140 microm) in aqueous solution during controlled collisions on the scale of micrometers to nanometers. The colloidal probe technique using atomic force microscopy (AFM) was extended to measure interaction forces between a cantilever-attached bubble and surface-attached bubbles of various sizes. By using an ultrasonic source, we generated numerous small bubbles on a mildly hydrophobic surface of a glass slide. A single bubble picked up with a strongly hydrophobized V-shaped cantilever was used as the colloidal probe. Sample force measurements were used to evaluate the pure water bubble cleanliness and the general consistency of the measurements.     

The relationship between nanobubbles and the hydrophobic force

The formation of nanobubbles on hydrophobic self-assembled monolayers has been examined in a binary ethanol/water titration using small angle X-ray scattering (SAXS) and atomic force microscopy (AFM). The AFM data demonstrates a localized force effect attributed to nanobubbles on an immersed hydrophobic surface. This evidence is arguably compromised by the possibility that the AFM tip actually nucleates nanobubbles. As a complementary noninvasive technique, SAXS has been used to investigate the interfacial region of the immersed hydrophobic surface. SAXS measurements reveal an electron density depletion layer at the hydrophobic interface, with changing air solubility in the immersing liquid, due to the formation of nanobubbles.     

Immobilization and surface characterization of NeutrAvidin biotin-binding protein on different hydrogel interlayers

For a number of potential applications, it is desirable to immobilize avidin class molecules onto solid supports and exploit their ability to bind biotinylated molecules with high affinity. NeutrAvidin molecules were surface immobilized in various ways. In this study, NeutrAvidin was covalently attached by carbodiimide chemistry onto carboxyl groups of polyacrylic acid and carboxymethyl-dextran hydrogel interlayers. A third strategy involved the affinity "docking" of NeutrAvidin onto a biotinylated poly(ethylene glycol) interlayer. These three interlayers were selected for their low nonspecific binding of proteins, which was expected to minimize surface binding of NeutrAvidin by nonspecific interfacial adsorption. X-ray photoelectron spectroscopy (XPS) analyses allowed detailed characterization of the multilayer fabrication steps. An ELISA assay was used to measure NeutrAvidin activity, which varied with the surface immobilization route. Atomic force microcopy (AFM) force measurements showed that the hydrogel interlayer contributed to a repulsive force and verified the specific interaction between biotinylated AFM tips and the NeutrAvidin surfaces. When a solution of free biotin was injected into the AFM liquid cell, the force curve changed substantially and became identical to that recorded between surfaces carrying no NeutrAvidin, indicating that the free solution biotin had displaced NeutrAvidin proteins off the PEG-biotin layer.     

Direct Identification of Protein–Protein Interactions by Single‐Molecule Force Spectroscopy

Single‐molecule force spectroscopy based on atomic force microscopy (AFM‐SMFS) has allowed the measurement of the intermolecular forces involved in protein‐protein interactions at the molecular level. While intramolecular interactions are routinely identified directly by the use of polyprotein fingerprinting, there is a lack of a general method to directly identify single‐molecule intermolecular unbinding events. Here, we have developed an internally controlled strategy to measure protein–protein interactions by AFM‐SMFS that allows the direct identification of dissociation force peaks while ensuring single‐molecule conditions. Single‐molecule identification is assured by polyprotein fingerprinting while the intermolecular interaction is reported by a characteristic increase in contour length released after bond rupture. The latter is due to the exposure to force of a third protein that covalently connects the interacting pair. We demonstrate this strategy with a cohesin–dockerin interaction.     

Self-localization of polyacrylic acid molecules on polar ZnO(0001)-Zn surfaces

The adsorption of single polyacrylic acid (PAAc) molecules was investigated on stepped hydroxide-stabilized polar ZnO(0001)-Zn surfaces using atomic force microscope (AFM) topography and force distance spectroscopy. Stepped surfaces of ZnO(0001)-Zn were prepared by a wet chemical etching procedure and PAAc molecules were adsorbed from aqueous NaClO(4) solutions. AFM single molecule topography studies could be utilized to show that polyacrylic acid molecules specifically adsorb on the non-polar (10-10) step edge faces at low ionic strengths. The radius of gyration of the dissolved PAAc in aqueous solution was measured by means of static light scattering experiments yielding a radius of gyration of R(g)=136 nm at pH 7.4 in 50 mM NaClO(4)/NaOH solution, which is in good agreement with the size of the adsorbed PAAc molecules as measured using AFM. The obtained results could be rationalized in terms of binding-site configurations at step edges and the effect of the chemical environment on both local electric double layer charge and molecular conformation of the PAAc molecules. The point of zero charge of the ZnO(10-10) surface was measured with chemical force microscopy to be pH(PZC)=10.2 ± 0.2. The specific adsorption of polyacrylic acid at non-polar ZnO step-edges can be explained by coordinative bonds formed between the carboxylic acid group and the Zn-surface atoms. On the hydroxide stabilized polar surface only weak hydrogen bonds can be formed in addition to van-der-Waals forces. Thus a "diffusion and trapping" mechanism keeps the adsorbed PAAc molecules mobile on the ZnO(0001)-Zn surface terraces due to small interaction forces until they are trapped at the (10-10) step faces by stronger coordinative bonds from the carboxylic groups to zinc atoms located in the first atomic layer of the crystal structure.     

The inevitable accumulation of large ions and neutral molecules near hydrophobic surfaces and small ions near hydrophilic ones

The present contribution offers a unified explanation to three central phenomena in physical chemistry of interfaces in contact with aqueous solution: (1) Accumulation of large anions at the air/water interface. (2) Accumulation of neutral gas molecules near hydrophobic surfaces and the resulting hydrophobic interaction between two such surfaces, and (3) The Hofmeister effect, namely, the enhanced propensity of small ions to hydrophilic surfaces and large ions to hydrophobic surfaces. The common thread linking these phenomena is the free energy balance between ion or molecule hydration in solution and the cost of localizing these objects at the water-surface interface. Comparing the results of an abstract lattice-gas model to force spectroscopy data collected by AFM we reveal the underlying principles and demonstrate their universality.     

Molecular hydrophobic attraction and ion-specific effects studied by molecular dynamics

Much is written about "hydrophobic forces" that act between solvated molecules and nonpolar interfaces, but it is not always clear what causes these forces and whether they should be labeled as hydrophobic. Hydrophobic effects roughly fall in two classes, those that are influenced by the addition of salt and those that are not. Bubble adsorption and cavitation effects plague experiments and simulations of interacting extended hydrophobic surfaces and lead to a strong, almost irreversible attraction that has little or no dependence on salt type and concentration. In this paper, we are concerned with hydrophobic interactions between single molecules and extended surfaces and try to elucidate the relation to electrostatic and ion-specific effects. For these nanoscopic hydrophobic forces, bubbles and cavitation effects play only a minor role and even if present cause no equilibration problems. In specific, we study the forced desorption of peptides from nonpolar interfaces by means of molecular dynamics simulations and determine the adsorption potential of mean force. The simulation results for peptides compare well with corresponding AFM experiments. An analysis of the various contributions to the total peptide-surface interactions shows that structural effects of water as well as van der Waals interactions between surface and peptide are important. Hofmeister ion effects are studied by separately determining the effective interaction of various ions with hydrophobic surfaces. An extension of the Poisson-Boltzmann equation that includes the ion-specific potential of mean force yields surface potentials, interfacial tensions, and effective interactions between hydrophobic surfaces. There, we also analyze the energetic contributions to the potential of mean force and find that the most important factor determining ion-specific adsorption at hydrophobic surfaces can best be described as surface-modified ion hydration.     

Cleaning and hydrophilization of atomic force microscopy silicon probes

The silicon surface of commercial atomic force microscopy (AFM) probes loses its hydrophilicity by adsorption of airborne and package-released hydrophobic organic contaminants. Cleaning of the probes by acid piranha solution or discharge plasma removes the contaminants and renders very hydrophilic probe surfaces. Time-of-flight secondary-ion mass spectroscopy and X-ray photoelectron spectroscopy investigations showed that the native silicon oxide films on the AFM probe surfaces are completely covered by organic contaminants for the as-received AFM probes, while the cleaning methods effectively remove much of the hydrocarbons and silicon oils to reveal the underlying oxidized silicon of the probes. Cleaning procedures drastically affect the results of adhesive force measurements in water and air. Thus, cleaning of silicon surfaces of the AFM probe and sample cancelled the adhesive force in deionized water. The significant adhesive force values observed before cleaning can be attributed to formation of a bridge of hydrophobic material at the AFM tip-sample contact in water. On the other hand, cleaning of the AFM tip and sample surfaces results in a significant increase of the adhesive force in air. The presence of water soluble contaminants at the tip-sample contact lowers the capillary pressure in the water bridge formed by capillary condensation at the AFM tip-sample contact, and this consequently lowers the adhesive force.     

Wettability of tri-block copolymer coated hydrophobic surfaces Predictions and measurements

Hydrophobic surfaces with adsorbed tri-block copolymers are wetted by oil in spite of the hydrophilic buoy groups of the block copolymer that are present near the surface. The effect of the buoy group length of the adsorbed molecules on the wettability of hydrophobic surfaces is studied by contact angle measurements and by computer modelling.

The computer model predicts an increase in interfacial free energy with increasing buoy group length for equilibrium adsorption of block copolymer from water. Molecules with large buoy groups occupy more lateral space; therefore the “bare” surface gets more exposed and the anchor groups contribute less to the interfacial free energy which thus increases with the buoy group length.

The calculations showed that the variation of the interaction parameter between solvent and buoy group hardly influences the interfacial free energy. In contrast the interaction parameter between solvent and surface influences the interfacial free energy to a large extent because the oil/surface interactions have a lower energetic value as compared to water/surface interactions and therefore the interfacial free energy is lower than in water. The interfacial free energy varies slightly with increasing buoy group length, depending on the value chosen for the solvent/surface interaction parameter.

Advancing and receding contact angles of hexadecane, sunflower oil and hydrolysate (partly hydrolysed sunflower oil) were measured on hydrophobic surfaces. All oil/water contact angles were small, indicating a hydrophobic apolar surface character. It was found that, for oils with a “good” interaction with the surface (hexadecane and sunflower oil), the contact angle has a minimum value at a certain buoy group length. For hydrolysate (less-strong interaction with the surface) the contact angle decreases monotonically with increasing buoy group length. The results for hexadecane, sunflower oil and hydrolysate are in reasonable agreement with the model predictions. The effect of increasing buoy group length is weak; both decreasing and increasing angles are found, depending on the type of oil used.     

Single DNA molecules as probes for interrogating silica surfaces after various chemical treatments

We examined the adsorption of single YOYO-1-labeled λ-DNA molecules at glass surfaces after treatment with various chemical cleaning methods by using total internal reflection fluorescence microscopy (TIRFM). The characteristics of these surfaces were further assessed using contact angle (CA) measurements and atomic force microscopy (AFM). By recording the real-time dynamic motion of DNA molecules at the liquid/solid interface, subtle differences in adsorption affinities were revealed. The results indicate that the driving force for adsorption of DNA molecules on glass surfaces is mainly hydrophobic interaction. We also found that surface topography plays a role in the adsorption dynamics.     

Feeling Inter‐ or Intramolecular Interactions with the Polymer Chain as Probe: Recent Progress in SMFS Studies on Macromolecular Interactions

Single‐molecule force spectroscopy (SMFS) opens new avenues for elucidating the structures and functions of large coiled molecules such as synthetic and biopolymers at the single‐molecule level. In addition, some of the features in the force–extension curves (i.e. force spectra) are closely related to primary/secondary structures of the molecules being stretched. For example, the long force plateau in the DNA stretching curve is related to the double‐helix structure. These features can be regarded as the force fingerprints of individual macromolecules. These force fingerprints can therefore be used as indicators/criteria of single‐molecule manipulation during the measurement of some unknown intra‐ or intermolecular interactions. By comparing the force spectra of a single polymer chain before and after interaction with other molecules, the mode/strength of such molecular interactions can be derived. This Review focuses on recent advances in AFM‐based SMFS studies on molecular interactions in both synthetic and biopolymer systems using a single macromolecular chain as probe, including interactions between nucleic acids and proteins, mechanochemistry of covalent bonds, conformation‐regulated enzymatic reactions, adsorption and desorption of biopolymers on a flat surface or from the nanopore of a carbon nanotube, and polymer interactions in the condensed state.     

基于原子力显微镜的高分子单分子力学研究

原子力显微镜(AFM)从根本上改变了人们对单个原子和分子的作用和认识方式。单分子力谱是基于原子力显微镜力的测量方法。概速了近年来利用基于原子力显微镜的单分子力谱研究单个高分子分子内及分子闻作用力的进展。     

Quantitative single molecule measurements on the interaction forces of poly(L-glutamic acid) with calcite crystals

The interaction between poly(L-glutamic acid) (PLE) and calcite crystals was studied with AFM-based single molecule force spectroscopy. Block copolymers of poly(ethylene oxide) (PEO) and PLE were synthesized and covalently attached to the tip of an AFM cantilever. In desorption measurements the molecules were allowed to adsorb on the calcite crystal faces and afterward successively desorbed. The corresponding desorption forces were detected with high precision, showing for example a force transition between the two blocks. Because of its importance in the crystallization process in biominerals, the PLE-calcite interaction was investigated as a function of the pH as well as the calcium concentration of the aqueous solution. The sensitivity of the technique was underlined by resolving different interaction forces for calcite (104) and calcite (100).     

Evidence of the synergetic role of charged species and atomic oxygen in the molecular etching of PTFE surfaces for hydrophobic surface synthesis

The transformation of a poly(tetrafluoroethylene) (PTFE) hydrophobic surface into a superhydrophobic one using a low pressure RF plasma is explored using optical emission spectrometry (OES), X-ray photoelectron spectroscopy (XPS), water contact angle (WCA) measurements, mass measurements, and atomic force microscopy (AFM). It is shown that the increase in contact angle is due to an increase of roughness provoked by a chemical etching of the surface. We propose a molecular mechanism for etching that requires the simultaneous presence of atomic oxygen and negatively charged species (electrons) at the PTFE surface.     

Dynamics of the interaction forces at the silver/solution interface during amine adsorption

The forces of interaction between a silver-coated particle and a flat silver surface in an aqueous medium were measured in the presence of a series of organic amines of varying concentrations. Atomic force microscopy (AFM) was used to quantify the replacement rate of adsorbed citrate molecules on the silver surfaces by a variety of amines, under conditions where the time scale of the amine adsorption was significantly slower than the time scale of the AFM measurements. The decay length of the electrostatic double-layer interaction between the silver surfaces was found to be time independent; thus, the change in surface change density (determined from the interaction forces) was used to quantify the replacement rate of adsorbed citrate by amine. In the absence of amine, the interaction force between the silver surfaces exhibited evidence of a multilayer structure of adsorbed citrate molecules on each silver surface. Upon addition of the amine, a decrease in the interaction force was always observed, where the dynamics of the force were dependent on both concentration and the molecular structure of the amine. These results are discussed with respect to formation of colloidal particles in synthesis routes where particle aggregation has a significant impact on the control of particle morphology and size.     

Direct measurements of the interaction between pyrene and graphite in aqueous media by single molecule force spectroscopy: understanding the pi-pi interactions

Pyrene derivatives can absorb onto the surface of carbon nanotubes and graphite particles through pi-pi interactions to functionalize these inorganic building blocks with organic surface moieties. Using single molecule force spectroscopy, we have demonstrated the first direct measurement of the interaction between pyrene and a graphite surface. In particular, we have connected a pyrene molecule onto an AFM tip via a flexible poly(ethylene glycol) (PEG) chain to ensure the formation of a molecular bridge. The pi-pi interaction between pyrene and graphite is thus indicated to be approximately 55 pN with no hysteresis between the desorption and adhesion forces.