Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level

While the theoretical implications of models of DNA tile self-assembly have been extensively researched and such models have been used to design DNA tile systems for use in experiments, there has been little research testing the fundamental assumptions of those models. In this paper, we use direct observation of individual tile attachments and detachments of two DNA tile systems on a mica surface imaged with an atomic force microscope (AFM) to compile statistics of tile attachments and detachments. We show that these statistics fit the widely used kinetic Tile Assembly Model and demonstrate AFM movies as a viable technique for directly investigating DNA tile systems during growth rather than after assembly.     

Reverse engineering of an affinity-switchable molecular interaction characterized by atomic force microscopy single-molecule force spectroscopy

Tunable and switchable interaction between molecules is a key for regulation and control of cellular processes. The translation of the underlying physicochemical principles to synthetic and switchable functional entities and molecules that can mimic the corresponding molecular functions is called reverse molecular engineering. We quantitatively investigated autoinducer-regulated DNA-protein interaction in bacterial gene regulation processes with single atomic force microscopy (AFM) molecule force spectroscopy in vitro, and developed an artificial bistable molecular host-guest system that can be controlled and regulated by external signals (UV light exposure and thermal energy). The intermolecular binding functionality (affinity) and its reproducible and reversible switching has been proven by AFM force spectroscopy at the single-molecule level. This affinity-tunable optomechanical switch will allow novel applications with respect to molecular manipulation, nanoscale rewritable molecular memories, and/or artificial ion channels, which will serve for the controlled transport and release of ions and neutral compounds in the future.     

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.     

Nonspecific protein adsorption at the single molecule level studied by atomic force microscopy

Liquid tapping atomic force microscopy was used to study the nonspecific adsorption of horse spleen ferritin at a bare gold surface at single molecule resolution. The majority of ferritin molecules adsorbed irreversible on gold surfaces in accordance with the random sequential adsorption (RSA) mechanism frequently used to describe irreversible adsorption processes. However, the time-resolved data also reveal events that go beyond the RSA model, i.e., lateral mobility and fragility of some molecules, resulting in desorption, chain formation, and subunit dissociation. Scanning effects of the AFM tip were observed, resulting in diminished protein coverage in the scanned area.     

Atomic force microscopy reveals hydroxyapatite-citrate interfacial structure at the atomic level

An approach to organic-inorganic interfacial structure at the atomic level is a great challenge in the studies of biomineralization. We demonstrate that atomic force microscopy (AFM) is powerful tool to discover the biomineral interface in detail. By using a model system of (100) hydroxyapatite (HAP) face and citrate, it reveals experimentally that only a side carboxylate and a surface calcium ion are involved in the binding effect during the citrate adsorption, which is against the previous understandings by using Langmuir adsorption and computer simulation. Furthermore, the adsorbed citrate molecules can use their free carboxylate and hydroxyl groups to be self-assembled on the HAP surface. AFM examination also finds that the presence of citrate molecules on the HAP crystal faces can enhance the adhesion force of the HAP surface. We suggest that the established AFM method can be used for a precise and direct understanding of biointerfaces at the atomic level.     

Optical characteristics of atomic force microscopy tips for single-molecule fluorescence applications.

Knowledge of the optical properties of atomic force microscopy (AFM) tips is relevant for the combination of optical and force spectroscopy. The luminescence properties of five commercial AFM tips were characterized using a combination of multiparameter fluorescence detection (MFD) and scanning confocal techniques. These include three Si3N4 tips, one silicon tip, and one high-density carbon (HDC) tip grown on top of a silicon tip. Time-decay histograms of the signal were analyzed to determine the strength of scatter, constant background, and fluorescence in the observed signal. Intensity and anisotropy images with optical resolution down to the diffraction limit were generated. The optical signal recorded from the apex of the Si3N4 tips ranged from 0.7 to 1.9 times the count rates from single Rhodamine 110 molecules under similar illumination conditions. The signal is predominantly composed of scatter and background (>85%), plus a small fluorescence component with lifetimes between 1 and 3 ns. The intensity of the recorded signal fell with increasing distance from the apex, and by 300 nm the signals fell below single-molecule levels for all Si3N4 cantilevers. Silicon cantilevers demonstrated very low count rates relative to single-molecule measurements under all conditions, and virtually no fluorescence. The high-density carbon tips also demonstrated low count rates, but the signal contained a short lifetime fluorescence component (0.7 ns). The intensity of the signals from each of the tips was geometry dependent, demonstrating the highest intensities at the edges and corners. Likewise, the anisotropy of all tip signals was observed to be geometry dependent, with the dependence varying on a case-by-case basis. The implications for using confocal illumination instead of total internal reflection are discussed.     

Visualization of hydrophobic polyelectrolytes using atomic force microscopy in solution

We have used atomic force microscopy to study the morphology of hydrophobic polyelectrolytes adsorbed on surfaces. The polyelectrolytes consisted of polystyrene sulfonate (PSS) chains made with three charge densities: 32%, 67%, and 92%. They were adsorbed on two types of surfaces: mica, and phospholipid bilayers made of mixed neutral and cationic lipids. We show that the chains with a low charge density (32%) are collapsed in spherical globules while highly charged chains (67% and 92%) are fully extended. End-to-end distances and contour lengths of the extended chains were measured. Statistical analysis shows that the persistence length of these chains depends on the surface where they adsorb. On lipid bilayers, highly ordered monolayers are formed upon increase of the proportion of cationic phospholipids. These results show that highly charged PSS chains behave in a similar manner than the stiffer, hydrophilic DNA when adsorbed on surfaces. It could lead to the design of new types of nanostructured surfaces using polyelectrolyte molecules synthesized with specific properties.     

SEBS aggregate patterning at a surface studied by atomic force microscopy

The morphologies of films spin coated from dilute block copolymer solution onto a mica substrate were studied by atomic force microscopy (AFM). Variables of interest were the polymer concentration, solvent, heating temperature, aging, and ultrasonic effect. It is shown that the solution concentration is the predominant factor in determining the shape of the aggregates displayed from spheres and rods to irregular patches with increasing concentration. The solubility parameter of the solvent plays an important role in modifying the distribution and the size of clusters at the surface. The structures of the aggregates at the surface are metastable, which could evolve with temperature from rodlike aggregates into regular stripes when annealed at a temperature higher than the order-disorder transition temperature of SEBS, whereas those in solution could evolve with aging and ultrasonic treatment into a more stable network structure.     

Visualization of complexes of Hoechst 33258 and DNA duplexes in solution by atomic force microscopy

Tertiary structure changes in DNA duplexes, induced by Hoechst 33258 binding, have been examined by the use of atomic force microscopy. Besides minor groove binding, which is an established mode of binding for this drug, Hoechst 33258 has now been found to show another binding mode, which causes an unwinding of the duplex. When the drug concentration is as high as 0.5 microg/ml, the Hoechst 33258 molecule seems to function as a clamp for two DNA chains and forms a condensate. The condensate was found to have a toroidal shape. By surveying more than 100 microscopic images of such condensates formed in I microg/ml drug solution, a mechanism of toroidal condensate formation has been proposed.     

Single-photon atomic force microscopy

In the last few years, an array of novel technologies, especially the big family of scanning probe microscopy, now often integrated with other powerful imaging tools such as laser confocal microscopy and total internal reflection fluorescence microscopy, have been widely applied in the investigation of biomolecular interactions and dynamics. But it is still a great challenge to directly monitor the dynamics of biomolecular interactions with high spatial and temporal resolution in living cells. An innovative method termed “single-photon atomic force microscopy” (SP-AFM), superior to existing techniques in tracing biomolecular interactions and dynamics in vivo, was proposed on the basis of the combination of atomic force microscopy with the technologies of carbon nanotubes and single-photon detection. As a unique tool, SP-AFM, capable of simultaneous topography imaging and molecular identification at the subnanometer level by synchronous acquisitions and analyses of the surface topography and fluorescent optical signals while scanning the sample, could play a very important role in exploring biomolecular interactions and dynamics in living cells or in a complicated biomolecular background.     

Capillary force in atomic force microscopy

Under ambient conditions, a water meniscus generally forms between a nanoscale atomic force microscope tip and a hydrophilic surface. Using a lattice gas model for water and thermodynamic integration methods, we calculate the capillary force due to the water meniscus for both hydrophobic and hydrophilic tips at various humidities. As humidity rises, the pull-off force rapidly reaches a plateau value for a hydrophobic tip but monotonically increases for a weakly hydrophilic tip. For a strongly hydrophilic tip, the force increases at low humidities (<30%) and then decreases. We show that mean-field density functional theory reproduces the simulated pull-off force very well.     

Single molecule charging by atomic force microscopy

AFM/KPM charging and charge mapping of polyamine charge carriers in a PMMA matrix is reported. Selective charging of the designed charge carrier is demonstrated at concentrations down to a single molecule. This works constitutes electrochemical charging and detection of single redox-active organic molecules in low dielectric matrices by probe microscopy.     

Halo-like structures studied by atomic force microscopy

Nanometer-sized clusters of copper have been produced in a hollow cathode sputtering source and deposited on SiO_x. Halo-like structures consisting of micrometer sized protrusions in the silicon oxide surface surrounded by thin rings of smaller particles are observed. The area in between seems to be depleted of particles. We propose that the halo-like structures are a result of electrostatic forces acting between the incoming charged clusters and charged regions on the surface. A simple computer simulation supports this suggestion.     

Measuring molecular weight by atomic force microscopy

Absolute-molecular-weight distribution of cylindrical brush molecules were determined using a combination of the Langmuir Blodget (LB) technique and Atomic Force Microscopy (AFM). The LB technique gives mass density of a monolayer, i.e., mass per unit area, whereas visualization of individual molecules by AFM enables accurate measurements of the molecular density, i.e., number of molecules per unit area. From the ratio of the mass density to the molecular density, one can determine the absolute value for the number average molecular weight. Assuming that the structure of brush molecules is uniform along the backbone, the length distribution should be virtually identical to the molecular weight distribution. Although we used only brush molecules for demonstration purpose, this approach can be applied for a large variety of molecular and colloidal species that can be visualized by a microscopic technique.     

Evaluation of interaction forces between profilin and designed peptide probes by atomic force microscopy

We evaluated the binding affinity of peptide probes for profilin (protein) using force curve measurement techniques and atomic force microscopy (AFM). The peptide probes designed and synthesized for this investigation were H-A3GP5GP5GP5G-OH (1), H-A3GP5G-OH (2), H-A3G7-OH (3), and H-A3G-OH (4). Each peptide probe was immobilized on a cantilever tip, and the interaction force to profilin, immobilized on a mica substrate, was examined by force curve measurements. The retraction forces obtained showed a sequence-dependent affinity of the peptide probe for profilin. The retraction force for peptide probe 1 was the largest of the four probes examined, and it confirmed that peptide probe 1 has high affinity for profilin. The single molecular retraction force between peptide probe 1 and profilin was estimated to be 96 pN, as determined by Gaussian fitting to the histogram of the retraction forces.     

Molecular layer of gaslike domains at a hydrophobic-water interface observed by frequency-modulation atomic force microscopy

It was numerically predicted that dissolved gas particles could enrich and adsorb at hydrophobic-liquid interfaces. Here we observe nucleation and growth of bright patches of ～0.45 nm high on the graphite surface in pure water with frequency-modulation atomic force microscopy when the dissolved gas concentration is below the saturation level. The bright patches, suspected to be caused by adsorption of nitrogen molecules at the graphite-water interface, are composed of domains of a rowlike structure with the row separation of 4.2 ± 0.3 nm. The observation of this ordered adlayer might underline the gas segregation at various water interfaces.     

Investigation of aerosol particles by atomic force microscopy

AFM has been applied for studying morphology and size distribution of nanometer-sized particles adsorbed on flat surfaces. In order to optimize imaging of these ultrafine particles different substrates were evaluated with respect to their roughness and stability under the influence of the sensing tip. Moreover, a method for calculating particle volumes from the three-dimensional AFM data is described. This greatly enhances the information content of AFM images, because a large number of particles in the raw data can be evaluated automatically in order to derive information on size distribution or surface coverage. This evaluation method has also been applied successfully to quantitatively describe changes on particles induced by different humidity of the surrounding atmosphere. Received: 15 July 1996 / Revised: 18 December 1996 / Accepted: 3 January 1997     

Pull-off force measurements between rough surfaces by atomic force microscopy

Direct measurements of the pull-off (adhesion) forces between pharmaceutical particles (beclomethasone dipropionate, a peptide-type material, and lactose) with irregular geometry and rough polymeric surfaces (series of polypropylene coatings, polycarbonate, and acrylonitrile-butadiene-styrene) were carried out using the atomic force microscope. These measurements showed that roughness of the interacting surfaces is the significant factor affecting experimentally measured pull-off forces. A broad distribution of pull-off force values was noted in the measurements, caused by a varying adhesive contact area for a particle located on rough substrate. The possibility of multiple points of contact between irregularly shaped pharmaceutical particles and substrate surfaces is demonstrated with nanoindentations of the particle in a fluoro-polymer film. Force-distance curves showing the "sawtooth" pattern are additional evidence that particles make contact with substrates at more than one point. Reduced adhesion of 10- to 14-microm-diameter lactose and peptide material particles to the polypropylene coatings with a roughness of 194 nm was found in this study. Similar pull-off force versus roughness relationships are also reported for the model spherical particles, silanized glass particle with a size of 10 microm and polystyrene particle with a diameter of 9 microm, in contact with polypropylene coatings of varying roughness characteristics. It was found that the model recently proposed by Rabinovich et al. (J. Colloid Interface Sci. 232, 1-16 (2000)) closely predicts the pull-off forces for glass and lactose particles. On the other hand, the adhesion of the peptide material and polystyrene particle to polypropylene is underestimated by about an order of magnitude with the theoretical model, in which the interacting substrates are treated as rigid materials. The underestimate is attributed to the deformation of the peptide material and polystyrene particles.