The desorption process of macromolecules adsorbed on interfaces: the force spectroscopy approach

Atomic Force Microscopy of Hydrolysed Polyacrylamide Adsorption onto Calcium Carbonate

In this work, the interaction of hydrolysed polyacrylamide (HPAM) of two molecular weights (F3330, 11-13 MDa; F3530, 15-17 MDa) with calcium carbonate (CaCO3) was studied via atomic force microscopy (AFM). In the absence of polymers at 1.7 mM and 1 M NaCl, good agreement with DLVO theory was observed. At 1.7 mM NaCl, repulsive interaction during approach at approximately 20 nm and attractive adhesion of approximately 400 pN during retraction was measured, whilst, at 1 M NaCl, no repulsion during approach was found. Still, a significantly larger adhesion of approximately 1400 pN during retraction was observed. In the presence of polymers, results indicated that F3330 displayed higher average adhesion (450-625 pN) and interaction energy (43-145 aJ) with CaCO3 than F3530's average adhesion (85-88 pN) and interaction energy (8.4-11 aJ). On the other hand, F3530 exerted a longer steric repulsion distance (70-100 nm) than F3330 (30-70 nm). This was likely due to the lower molecular weight. F3330 adopted a flatter configuration on the calcite surface, creating more anchor points with the surface in the form of train segments. The adhesion and interaction energy of both HPAM with CaCO3 can be decreased by increasing the salt concentration. At 3% NaCl, the average adhesion and interaction energy of F3330 was 72-120 pN and 5.6-17 aJ, respectively, while the average adhesion and interaction energy of F3530 was 11.4-48 pN and 0.3-2.98 aJ, respectively. The reduction of adhesion and interaction energy was likely due to the screening of the COO- charged group of HPAM by salt cations, leading to a reduction of electrostatic attraction between the negatively charged HPAM and the positively charged CaCO3.

Nanoscale Pulling of Type IV Pili Reveals Their Flexibility and Adhesion to Surfaces over Extended Lengths of the Pili

Type IV pili (T4P) are very thin protein filaments that extend from and retract into bacterial cells, allowing them to interact with and colonize a broad array of chemically diverse surfaces. The physical aspects that allow T4P to mediate adherence to many different surfaces remain unclear. Atomic force microscopy (AFM) nanoscale pulling experiments were used to measure the mechanical properties of T4P of a mutant strain of Pseudomonas aeruginosa PAO1 unable to retract its T4P. After adhering bacteria to the end of an AFM cantilever and approaching surfaces of mica, gold, or polystyrene, we observed adhesion of the T4P to all of the surfaces. Pulling of single and multiple T4P on retraction of the cantilever from the surfaces could be described using the worm-like chain (WLC) model. Distinct peaks in the measured distributions of the best-fit values of the persistence length Lp on two different surfaces provide strong evidence for close-packed bundling of very flexible T4P. In addition, we observed force plateaus indicating that adhesion of the T4P to both hydrophilic and hydrophobic surfaces occurs along extended lengths of the T4P. These data shed new light, to our knowledge, on T4P flexibility and support a low-affinity, high-avidity adhesion mechanism that mediates bacteria-surface interactions.

Self-assembly of polysaccharides gives rise to distinct mechanical signatures in marine gels

Marine-gel biopolymers were recently visualized at the molecular level using atomic force microscopy (AFM) to reveal fine fibril-forming networks with low to high degrees of cross-linking. In this work, we use force spectroscopy to quantify the intra- and intermolecular forces within the marine-gel network. Combining force measurements, AFM imaging, and the known chemical composition of marine gels allows us to identify the microscopic origins of distinct mechanical responses. At the single-fibril level, we uncover force-extension curves that resemble those of individual polysaccharide fibrils. They exhibit entropic elasticity followed by extensions associated with chair-to-boat transitions specific to the type of polysaccharide at high forces. Surprisingly, a low degree of cross-linking leads to sawtooth patterns that we attribute to the unraveling of polysaccharide entanglements. At a high degree of cross-linking, we observe force plateaus that arise from unzipping, as well as unwinding, of helical bundles. Finally, the complex 3D network structure gives rise to force staircases of increasing height that correspond to the hierarchical peeling of fibrils away from the junction zones. In addition, we show that these diverse mechanical responses also arise in reconstituted polysaccharide gels, which highlights their dominant role in the mechanical architecture of marine gels.

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.

Study of Al(OH)3-polyacrylamide-induced pelleting flocculation by single molecule force spectroscopy

A nanocomposite polymer, Al(OH)3-polyacrylamide (Al-PAM) hybrid, was tested as a flocculant. This novel hybrid polymer was found to induce pellet-like floccules, leading to a more effective solid-liquid separation than common polyacrylamide (PAM)-based flocculants. To understand the mechanism of Al-PAM-induced pelleting flocculation, the molecular structure of this hybrid polymer was studied using an atomic force microscope (AFM). The interactions between Al-PAM molecules and a silica surface were measured using single molecule force spectroscopy (SMFS). The Al-PAM molecules were found to have a star-like structure with Al(OH)3 colloidal particles as cores connecting PAM chains. The SMFS results showed a strong attachment of the Al(OH)3 cores to the silica surface with an adhesion force of approximately 1250 pN, in contrast to a weaker adhesion force of only approximately 250 pN for PAM chains on the silica surface. The Al-PAM-induced pelleting flocculation is attributed to its star-like structure.

Interrogation of Single Synthetic Polymer Chains and Polysaccharides by AFM-Based Force Spectroscopy

This contribution reviews selected mechanical experiments on individual flexible macromolecules using single-molecule force spectroscopy (SMFS) based on atomic force microscopy. Focus is placed on the analysis of elasticity and conformational changes in single polymer chains upon variation of the external environment, as well as on conformational changes induced by the mechanical stress applied to individual macromolecular chains. Various experimental strategies regarding single-molecule manipulation and SMFS testing are discussed, as is theoretical analysis through single-chain elasticity models derived from statistical mechanics. Moreover, a complete record, reported to date, of the parameters obtained when applying the models to fit experimental results on synthetic polymers and polysaccharides is presented.

Friction of single polymers at surfaces

Atomic force microscope (AFM) single molecule force spectroscopy has been used to investigate the friction coefficient of individual polymers adsorbed onto a solid support. The polymer chains were covalently attached to an AFM tip and were allowed to adsorb on a mica surface. Different polymers (ssDNA, polyallylamine) were chosen to cover a range of friction coefficients. During the experiment, the AFM tip was retracted in- and off-plane which results, depending on the chosen conditions, in a desorption of the polymer from the surface, a sliding across the surface, or a combination of both. Thus, the obtained force-extension spectra reveal detailed information on the mobility of a polymer chain on a surface under experimentally accessible conditions. This study demonstrates that absorbed polymers with comparable desorption forces may exhibit drastically different in plane mobility.

Nanomechanical properties of desmin intermediate filaments

Desmin intermediate filaments play important role in the mechanical integrity and elasticity of muscle cells. The mechanisms of how desmin contributes to cellular mechanics are little understood. Here, we explored the nanomechanics of desmin by manipulating individual filaments with atomic force microscopy. In complex, hierarchical force responses we identified recurring features which likely correspond to distinct properties and structural transitions related to desmin's extensibility and elasticity. The most frequently observed feature is an initial unbinding transition that corresponds to the removal of approximately 45-nm-long coiled-coil dimers from the filament surface with 20-60 pN forces in usually two discrete steps. In tethers longer than 60 nm we most often observed force plateaus studded with bumps spaced approximately 16 nm apart, which are likely caused by a combination of protofilament unzipping, dimer-dimer sliding and coiled-coil-domain unfolding events. At high stresses and strains non-linear, entropic elasticity was dominant, and sometimes repetitive sawtooth force transitions were seen which might arise because of slippage within the desmin protofilament. A model is proposed in which mechanical yielding is caused by coiled-coil domain unfolding and dimer-dimer sliding/slippage, and strain hardening by the entropic elasticity of partially unfolded protofilaments.

Adhesion of single polyelectrolyte molecules on silica, mica, and bitumen surfaces

In a recent study (Energy Fuels 2005, 19, 936), a partially hydrolyzed polyacrylamide (HPAM) was used as a process aid to recover bitumen from oil sand ores. It was found that HPAM addition at the bitumen extraction step not only improved bitumen recovery but also enhanced fine solids settling in the tailings stream. To understand the role of HPAM, single-molecule force spectroscopy was employed for the first time to measure the desorption/adhesion forces of single HPAM molecules on silica, mica, and bitumen surfaces using an atomic force microscope (AFM). Silicon wafers with an oxidized surface layer and newly cleaved mica were used, respectively, to represent sand grains and clays in oil sands. The force measurements were carried out in deionized water and in commercial plant process water under equilibrium conditions. The desorption/adhesion forces of HPAM obtained on mica, silica, and bitumen surfaces were approximately 200, 40, and 80 pN in deionized water and approximately 100, 50, and 40 pN in the plant process water, respectively. The measured adhesion forces together with the zeta potential values of these surfaces indicate that the polymer would preferentially adsorb onto clay surfaces rather than onto bitumen surfaces. It is the selective adsorption of HPAM that benefits both bitumen recovery and tailings settling when the polymer was added directly to the bitumen extraction process at an appropriate dosage.

Functional polymers: scanning force microscopy insights

Scanning force microscopy (SFM) and related techniques make it possible to visualize polymer systems with a molecular resolution. Beyond imaging, they also enable the unveiling of a variety of (dynamic) physico-chemical properties of both isolated polymer chains and their supramolecular architectures, including structural, mechanical and electronic properties. This article reviews recent progress in the use of SFM on polymers, with a particular emphasis on the mechanical properties of copolymers and single polymer chains, as well as on the bottom-up fabrication of supramolecular polymeric (helical) nanostructures in particular based upon pi-conjugated macromolecules as building blocks for nanoelectronics. Through a detailed understanding of the polymer behavior, we propose solutions for the generation of organic functional (nano)systems.

Single-Chain Mechanical Property of Poly(N-vinyl-2-pyrrolidone) and Interaction with Small Molecules

The single-chain nanomechanical properties of poly(N-vinyl-2-pyrrolidone) (PVPr) and povidone-iodine (PVPr-I2) under different solution conditions have been investigated by using an atomic force microscopy based technique-single-molecule force spectroscopy. The force-extension curve (force curve) of PVPr in water is markedly deviated from that obtained in ethanol or tetrahydrofuran, suggesting a different interaction between PVPr and the solvents. Moreover, we have comparatively studied the force signals of PVPr-I2 and PVPr in an aqueous solution of KI or KI3 and found that only KI3 influences the elastic property of PVPr dramatically. These experimental results indicate that there exists a specific interaction between PVPr and KI3, which is also supported by Fourier transform infrared data. By the integration of the deviated area between the force curve and the modified freely jointed chain fitting curve, we estimate that the energy needed to destroy the interaction between PVPr and water is 5.3 kT and between PVPr and KI3 is 3.6 kT per repeating unit, respectively.

Topography and mechanical properties of single molecules of type I collagen using atomic force microscopy

Although the mechanical behavior of tendon and bone has been studied for decades, there is still relatively little understanding of the molecular basis for their specific properties. Thus, despite consisting structurally of the same type I collagen, bones and tendons have evolved to fulfill quite different functions in living organisms. In an attempt to understand the links between the mechanical properties of these collageneous structures at the macro- and nanoscale, we studied trimeric type I tropocollagen molecules by atomic force microscopy, both topologically and by force spectroscopy. High-resolution imaging demonstrated a mean (+/- SD) contour length of (287 +/- 35) nm and height of (0.21 +/- 0.03) nm. Submolecular features, namely the coil-pitch of the molecule, were also observed, appearing as a repeat pattern along the length of the molecule, with a length of approximately 8 nm that is comparable to the theoretical value. Using force spectroscopy, we established the stretching pattern of the molecule, where both the mechanical response of the molecule and pull-off peak are convoluted in a single feature. By interpreting this response with a wormlike chain model, we extracted the value of the effective contour length of the molecule at (202 +/- 5) nm. This value was smaller than that given by direct measurement, suggesting that the entire molecule was not being stretched during the force measurements; this is likely to be related to the absence of covalent binding between probe, sample, and substrate in our experimental procedure.

New tools for force spectroscopy

Force curves using atomic force microscopy have been proposed as a new tool to probe the conformation of adsorbed polymers and interactions between molecules through the analysis of the rupture distributions. We describe an algorithm for the computer-assisted detection of ruptures in force curves. This program allows us to automatically detect the ruptures. The algorithm is based on an analysis of the standard deviation in a sliding window along the length of the force. Automatic detection of ruptures constitutes an important step forward because the time required to analyse the curves is significantly reduced, thus allowing the user to perform multiple experiments. In addition, using these tools we can address the problem of the interpretation of rupture distributions.

Reversible Mechanical Unzipping of Amyloid β-Fibrils

Amyloid fibrils are self-associating filamentous structures, the deposition of which is considered to be one of the most important factors in the pathogenesis of Alzheimer's disease and various other disorders. Here we used single molecule manipulation methods to explore the mechanics and structural dynamics of amyloid fibrils. In mechanically manipulated amyloid fibrils, formed from either amyloid beta (Abeta) peptides 1-40 or 25-35, beta-sheets behave as elastic structures that can be "unzipped" from the fibril with constant forces. The unzipping forces were different for Abeta1-40 and Abeta25-35. Unzipping was fully reversible across a wide range of stretch rates provided that coupling, via the beta-sheet, between bound and dissociated states was maintained. The rapid, cooperative zipping together of beta-sheets could be an important mechanism behind the self-assembly of amyloid fibrils. The repetitive force patterns contribute to a mechanical fingerprint that could be utilized in the characterization of different amyloid fibrils.

Dynamics of the interaction between a fibronectin molecule and a living bacterium under mechanical force

Fibronectin (Fn) is an important mediator of bacterial invasions and of persistent infections like that of Staphylococcus epidermis. Similar to many other types of cell-protein adhesion, the binding between Fn and S. epidermidis takes place under physiological shear rates. We investigated the dynamics of the interaction between individual living S. epidermidis cells and single Fn molecules under mechanical force by using the scanning force microscope. The mechanical strength of this interaction and the binding site in the Fn molecule were determined. The energy landscape of the binding/unbinding process was mapped, and the force spectrum and the association and dissociation rate constants of the binding pair were measured. The interaction between S. epidermidis cells and Fn molecules is compared with those of two other protein/ligand pairs known to mediate different dynamic states of adhesion of cells under a hydrodynamic flow: the firm adhesion mediated by biotin/avidin interactions, and the rolling adhesion, mediated by L-selectin/P-selectin glycoprotein ligand-1 interactions. The inner barrier in the energy landscape of the Fn case characterizes a high-energy binding mode that can sustain larger deformations and for significantly longer times than the correspondent high-strength L-selectin/P-selectin glycoprotein ligand-1 binding mode. The association kinetics of the former interaction is much slower to settle than the latter. On this basis, the observations made at the macroscopic scale by other authors of a strong lability of the bacterial adhesions mediated by Fn under high turbulent flow are rationalized at the molecular level.

Staphylococcus epidermidis-fibronectin binding and its inhibition by heparin

Staphylococcus epidermidis is able to adhere onto biomaterials and to cause implant infections. Recently, host matrix proteins, which in vivo cover the implants, have been indicated as substrates for adhesion by specific bacterial adhesins. Here, the binding of S. epidermidis to fibronectin, a main protein of the extracellular matrix, and the effect of heparin on this interaction were studied by dynamic force spectroscopy (DFS). Novelties are that S. epidermidis strains analysed by DFS were clinical isolates from prosthesis-associated infections, genotyped and phenotyped for their adhesion properties to fibronectin and examined as living cells. Thus, fibronectin-binding staphylococci adhered to the fibronectin-coated substratum and formed a continuous layer assuring their contact with the fibronectin-coated cantilever tip during the approach-retraction cycles of the DFS measurements. Results show that only a single molecular binding site of fibronectin is involved in the interaction with S. epidermidis, that it takes place at the domain near the C-terminus and that it is specifically inhibited by heparin.

Force spectroscopy study of the adhesion of plasma proteins to the surface of a dialysis membrane: role of the nanoscale surface hydrophobicity and topography

A mechanochemical study of the process of adhesion of plasma proteins to the surface of dialysis membranes was carried out with a scanning force microscope (SFM) in the force spectroscopy mode. Three representative blood plasma proteins (fibronectin, fibrinogen, and albumin) covalently were grafted to a SFM probe, and the adhesion forces of these proteins to cellulosic and synthetic dialysis membranes were measured. The experiment was tailored to apply a controlled load on the protein molecules adsorbed onto the surface in order to simulate the squeezing forces exerted on them during blood filtration. The de-adhesion forces, measured using this new approach for studying the interaction between a protein and dialysis membranes, suggest that the membrane's topography, at a nanometer scale, plays a critical role in the adhesion process. This result was strongly supported by parallel experiments performed on a flattened glass surface with the same dominant hydrophilic character as dialysis membranes. In contrast, a hydrophobic polystyrene surface led to de-adhesion forces at least one order of magnitude greater, overwhelming any possible shape recognition process between the protein molecules and the surface.