Imaging and nano-dissection of tobacco mosaic virus by atomic force microscopy

Tobacco mosaic virus (TMV) has been deposited on freshly cleaved mica substrates. The topography was investigated by contact, non-contact and lateral-force microscopy under ambient conditions in air. The results were in accord with known dimensions of TMV (i.e. 18 nm in diameter and 300 nm in length). However, convolution of tip shape with TMV morphology resulted in an apparent width of 80–140 nm in the lateral plane, a factor of 4–7 greater than the known diameter. Other artefacts - broadening and double images - were observed and ascribed to tip anomalies. High force loadings and slow repetitive scanning resulted in controlled removal of parts of the TMV structure. Accordingly, it was possible to reveal and image the central core channel of the TMV. The precision and resolution of dissection induced by AFM is currently limited by the shape of the tip, having a 40-nm radius of curvature for standard Si₃N₄ tips. It is estimated that sharper tips, with a radius of curvature of less than 10 nm, should be able to resolve, non-destructively, the protein subunits in the non-contact mode, and selectively remove single subunits in the contact mode.     

The mechanism of G-banding detected by atomic force microscopy

The morphologic changes occurring in human chromosomes during G-banding by trypsin treatment on the same metaphase were followed with the aid of an atomic force microscope (AFM). It was found that trypsin treatment alone caused a pattern of collapse in the chromosomes that was clearly dependent on the duration of trypsinization. The progressive pattern of collapse first indicated the loss of internal differentiation between chromatids, then bands, and finally all internal structures, except for edges running around the chromosomes' perimeter. When stained with Giemsa, the collapsed chromosomes partly regained their original form, and transverse ridges appeared that correspond to G-positive band regions. However, the treatment of fixed chromosomes with trypsin for 42 s diminished the chromosomal edges, and the z-dimensions could not be measured even with the subsequent application of Giemsa.     

Adhesion and friction properties of hydrogenated amorphous carbon films measured by atomic force microscopy

Atomic force microscopy has been used to measure adhesion and friction forces at the interface between an oxidized metal probe tip and amorphous carbon films of varying hydrogen contents (12.3–39.0 atomic percent hydrogen). The interface of an oxide surface and a hard carbon coating models the unlubricated head-disk interface of current hard disk products. Adhesion forces normalized by the radius of curvature of the contacting tip range from 1.09 to 8.53 N/m. Coefficients of friction values, measured as the slope of the friction versus load plot, range from 0.33 to 0.87. A trend of increasing adhesion forces and coefficients of friction is observed for increasing hydrogen content in the films. We attribute the increase in adhesion and friction to increases in the surface free energy of the carbon films with the incorporation of hydrogen.     

Investigation of nanoparticles by atomic and lateral force microscopy

Metallic nanoparticles have been produced on vitreous carbon substrates by means of thermal evaporation. From pictures of the particles, made by a high-resolution scanning electron microscope (HRSEM), a semispherical shape is suggested due to the total mass of deposited material. Atomic force microscopy (AFM) has been applied to this sample in order to get direct topographic information. The AFM has been operated with normal and super tips, the latter having a smaller cone angle and radius, thus following more precisely the contours of an object. Simultaneously lateral-force microscopic (LFM) images have been recorded. Major differences between the contents of HRSEM- and AFM-images are considered, emphasizing the important influence of the tips' geometry. Both the AFM and LFM line scans have been compared with and have qualitatively agreed with those calculated under simplifying assumptions.     

Effect of aging on the morphology of bitumen by atomic force microscopy

Effect of aging on the morphology of bitumen was investigated. Two bitumens were aged according to the thin film oven test (TFOT), pressure aging vessel (PAV) test and ultraviolet (UV) radiation, respectively. The morphology of the binders before and after aging was characterized by atomic force microscopy. The physical properties and chemical compositions of the binders were also measured. The results showed that aging affected the bitumen morphology significantly. Aging increased the overall surface stiffness of the bitumen and made the bitumen surface more solid-like. The extent of these changes was dependent on aging conditions. TFOT decreased the contrast between the dispersed domains and the matrix, which contributed to the single-phase trend of the binders. The effect of PAV aging on morphology of the binders was dependent on the base bitumen. In one case, it further accelerated the single-phase trend of bitumen in comparison with that after TFOT. In the other case, it caused the phase separation of bitumen. In both cases, PAV aging increased the surface roughness of the binders obviously. As a result of UV aging, the contrast between the matrix phase and dispersed phase was increased due to the difference in sensitivity to UV radiation of the bitumen molecules, which caused or further promoted the phase separation in the binders. Regardless of the aging procedure carried out, a strong correlation was observed between the changes in morphology and physical properties as well as chemical compositions of the binders before and after aging.     

Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy

Nucleosome is a fundamental structural unit of chromatin, and the exposure from or occlusion into chromatin of genomic DNA is closely related to the regulation of gene expression. In this study, we analyzed the molecular dynamics of poly-nucleosomal arrays in solution by fast-scanning atomic force microscopy (AFM) to obtain a visual glimpse of nucleosome dynamics on chromatin fiber at single molecule level. The influence of the high-speed scanning probe on nucleosome dynamics can be neglected since bending elastic energy of DNA molecule showed similar probability distributions at different scan rates. In the sequential images of poly-nucleosomal arrays, the sliding of the nucleosome core particle and the dissociation of histone particle were visualized. The sliding showed limited fluctuation within ∼50 nm along the DNA strand. The histone dissociation occurs by at least two distinct ways: a dissociation of histone octamer or sequential dissociations of tetramers. These observations help us to develop the molecular mechanisms of nucleosome dynamics and also demonstrate the ability of fast-scanning AFM for the analysis of dynamic protein–DNA interaction in sub-seconds time scale.     

Mechanical properties of L929 cells measured by atomic force microscopy: Effects of anticytoskeletal drugs and membrane crosslinking

To shed light on the architecture of the cytoskeleton, we used the atomic force microscope (AFM) to measure the elasticity, viscoelasticity, and plasticity of L929 cells. The initial elastic response (Young's modulus ～ 4,000 Pa) of the cells to an applied force was followed by a slow compression of the cytoskeleton (τ_1/2 ≈ 10 s). When force application was terminated, the cytoskeleton underwent a sudden partial decompression and a subsequent slow, incomplete recovery. The role of the cytoskeletal elements in cell mechanics was accessed in AFM measurements carried out on cells treated with cytochalasin D, nocodazole, or col-cemid. Cytochalasin D treatment reduced both elasticity (～45%) and cytoplasmic viscosity (～65%), whereas cells treated with nocodazole or colcemid exhibited a marked increase in elasticity (～100%) and a slight increase in viscosity (～15%). The AFM force measurements also provided evidence that the cell membrane and the cytoskeleton are mechanically coupled. Tightly adherent cells were stiffer than cells that were loosely attached. Moreover, cells crosslinked with either glutaraldehyde, 3,3 ‘-dithiobis’sul-fosuccinimidylpropionate] (DTSSP), or Concanavalin A were more rigid than untreated cells. It is of interest that cells crosslinked with Concanavalin A, but not DTSSP, displayed plastic behaviors that may reflect the induction of cytoskeletal reorganization by Concanavalin A.     

Imaging DNA molecules on mica surface by atomic force microscopy in air and in liquid

DNA molecules immobilized on mica surface by various methods have been observed by atomic force microscopy both in air and in liquid. Divalent cations and 3-aminopropyltriethoxysilane (APTES) modified mica surface have been used to immobilize the DNA molecules. Optimal DNA and divalent cations concentration for AFM imaging are presented. Among the different methods of modifying mica surface with APTES, the water solution modifying method appears to get the best results. When using high DNA concentration for AFM imaging, DNA networks can be formed. A simple method to extend long DNA molecules is demonstrated. The optimal imaging conditions and AFM operating techniques are discussed. Different DNA immobilizing methods have been compared and evaluated.     

3-D morphological characterization of the liver parenchyma by atomic force microscopy and by scanning electron microscopy

A comparative study of atomic force microscopy (AFM) and scanning electron microscopy (SEM) imaging of the healthy human liver parenchyma was carried out to determine the similarities and the differences. In this study, we compared the fine hepatic structures as observed by SEM and AFM. Although AFM revealed such typical hepatic structures as bile canaliculi and hepatocytes, it also showed the location of the nucleus and chromatin granules in rough relief structure, which was not visible by SEM. By contrast, SEM visualized other structures, such as microvilli, the central vein, and collagenous fibers, none of which was visualized by AFM. For better orientation and confirmation of most of the structures imaged by SEM and AFM, Congo Red-stained specimens were also examined. Amyloid deposits in the Disse's spaces were shown especially clearly in these images. The differences between the SEM and AFM images reflected the characteristics of the detection systems and methods used for sample preparation. Our results reveal that more detailed information on hepatic morphology is obtained by exploiting the advantages of both SEM and AFM.     

Controlled growth and formation of SAMs investigated by atomic force microscopy

Recently we reported a simple method for obtaining both monolayer thickness and surface patterning using self-assembled monolayers (SAMs). Here we presented a straightforward method for controlling the formation of SAMs over surfaces useful for both chemical and biological applications. Atomic force microscopy (AFM) has been used to investigate the growth mechanism and formation of octadecylsiloxane (ODS) films obtained using a less-reactive silane; octadecyltrimethoxysilane (OTMS). SAMs formation from both OTMS and octadecyltrichlorosilane (ODTS) differ in the hydrolysis step where ODTS results in hydrochloric acid formation, which may affect the delicate features on surfaces. On the other hand, OTMS does not show this behavior. In contrast to monolayer formation from chlorosilane precursors, methoxysilane SAMs have been studied less extensively. Our observations highlight the importance of controlling water content during the formation of ODS monolayers in order to get well-ordered SAMs. We have also seen that, like ODTS, OTMS exhibits monolayer growth through an island expansion process but with a comparatively slow growth rate and different island morphology. The average height of islands, surface coverage, contact angle and root-mean-square (RMS) roughness increase with OTMS adsorption time in a consecutive manner.     

Cytoskeletal response of microvessel endothelial cells to an applied stress force at the submicrometer scale studied by atomic force microscopy

Cytoskeleton fibers form an intricate three-dimensional network to provide structure and function to microvessel endothelial cells. During accommodation to blood flowing, stress fiber bundles become more prominent and align with the direction of blood flow. This network either mechanically resists the applied shear stress (lateral force) or, if deformed, is dynamically remodeled back to a preferred architecture. However, the detailed response of these stress fiber bundles to applied lateral force at submicrometer scales are as yet poorly understood. In our in vitro study, the tip, topography probe in lateral force microscopy of atomic force microscopy, acted as a tool for exerting quantitative vertical and lateral force on the filaments of the cytoskeleton. Moreover, the authors developed a formula to calculate the value of lateral force exerted on every point of the filaments. The results show that cytoskeleton fibers of healthy tight junctions in rat cerebral microvessel endothelial cells formed a cross-type network, and were reinforced and elongated in the direction of scanning under lateral force of 15-42 nN. Under peroxidation (H(2)O(2) of 300 micromol/L), the cytoskeleton remodeled at intercellular junctions, and changed over the meshwork structures into a dense bundle, that redistributed the stress. Once mechanical forces were exerted on an area, the cells shrank and lost morphologic tight junctions. It would be useful in our understanding of certain pathological processes, such as cerebral ischemia/reperfusion injury, which maybe caused by biomechanical forces and which are overlooked in current disease models.     

Diverse and conserved nano- and mesoscale structures of diatom silica revealed by atomic force microscopy

An outstanding example of biological pattern formation at the single cell level is the diversity of biomineral structures in the silica cell walls of the unicellular eukaryotic algae known as diatoms. We present a survey of cell wall silica structures of 16 diatom species, which included all major cell wall components (valves, girdle bands and setae), imaged across the nano-, meso- and microscales using atomic force microscopy. Because of atomic force microscopy's superior ability to image surface topology, this approach enabled visualization of the organization of possible underlying organic molecules involved in mineral structure formation. Diatom nanoscale silica structure varied greatly comparing the same feature in different species and different features within a single species, and frequently on different faces of the same object. These data indicate that there is not a strict relation between nanoscale silica morphology and the type of structure that contains it. On the mesoscale, there was a preponderance of linear structures regardless of the object imaged, suggesting that assembly or organization of linear organic molecules or subcellular assemblies that confine a linear space play an essential and conserved role in structure formation on that scale. Microscale structure imparted an overall influence over nano- and mesoscale structure, indicating that shaping of the silica deposition vesicle plays a key role in structure formation. These results provide insights into the design and assembly principles involved in diatom silica structure formation, facilitating an understanding of the native system and potentially aiding in development of biomimetic approaches.     

Topographic effects on adhesive force mapping of stretched DNA molecules by pulsed-force-mode atomic force microscopy

Adhesive interaction between a tip and a sample surface was examined on a microscopic scale by pulsed-force-mode atomic force microscopy (PFM-AFM). The signal measured by monitoring pull-off force is influenced by various factors such as topography, elasticity, electrostatic charges, and adsorbed water on surfaces. Here, we focus on the topographic effects on the adhesive interaction. To clarify the topographic influence, the adhesive force measurement of a stretched DNA molecule with a smaller radius of curvature than that of a tip was carried out at low relative humidity (RH) with an alkanethiol-modified tip. The experimental conditions such as low RH and the use of the alkanethiol-modified tip were required to minimise the influence of water capillary force on hydrated DNA strands. The hydrophobic modification of a substrate surface was also important to minimise the adsorbed water effect. The DNA molecules were stretched on the substrate surfaces by an immobilisation process called a dynamic molecular combing method. The two-component vapour-phase surface modification with an alkylsilane mixed with a silane derivative containing an amino end group enhanced the DNA adsorption due to the electrostatic interaction. The experimental results for the topographic effects on the adhesive force mapping were reproducible.     

Effect of aging on morphology of organo-montmorillonite modified bitumen by atomic force microscopy

The morphology of unmodified and organo-montmorillonite modified bitumens was investigated by atomic force microscopy. The influence of thin film oven test and ultraviolet aging on the morphology of the binders was also analysed. The atomic force microscopy results showed that bitumen displayed a 'bee-like' structure and the dimension of the 'bee-like' structures was decreased to some extent with the introduction of organo-montmorillonite. Organo-montmorillonite showed a better interaction with the dispersed domains in comparison with the matrix in bitumen, which led to an obvious increase in the contrast between the dispersed domains and the matrix in bitumen. Compared with the unmodified bitumen, the single-phase trend in the organo-montmorillonite modified bitumen could be effectively prevented during thin film oven test and ultraviolet aging, indicating its good aging resistance which was in accordance with changes in physical properties of the organo-montmorillonite modified bitumen before and after aging.     

Immobilization of DNA on 11-mercaptoundecanoic acid-modified gold (111) surface for atomic force microscopy imaging

Immobilized DNA on preformed 11-mercaptoundecanoic acids (MUDA) self-assembled monolayers (SAMs) on a gold (111) surface was bound by a divalent cation bridges was imaged by atomic force microscopy (AFM). The DNA immobilization was attributed to the formation of ionic bridges between the carboxylate groups of MUDA and the phosphate groups of DNA. AFM images revealed that DNA molecules could be immobilized strongly enough to permit stable and reproducible imaging. The effect of different bridge cations, such as Mg(2+), Zn(2+) and Cu(2+), and the pH of DNA assembled solution on immobilization and conformation of DNA was studied. Plasmid DNA pBR 322/Pst I molecules were straightened by using a molecular combing technique on the MUDA surface.     

Study on water‐dispersible colloids in saline–alkali soils by atomic force microscopy and spectrometric methods

Recent studies have revealed that water‐dispersible colloids play an important role in the transport of nutrients and contaminants in soils. In this study, water‐dispersible colloids extracted from saline–alkali soils have been characterized by atomic force microscopy (AFM), X‐ray diffraction (XRD), X‐ray photoelectron spectroscopy (XPS), and UV absorption spectra. AFM observation indicated that the water‐dispersible colloids contain some large plates and many small spherical particles. XRD, XPS, and UV absorption measurement revealed that the water‐dispersible colloids are composed of kaolinite, illite, calcite, quartz and humic acid. In addition, UV absorption measurement demonstrated that the humic acids are associated with clay minerals. Water‐dispersible colloids in the saline–alkali soils after hydrolyzed polymaleic anhydride treatment and an agricultural soil (nonsaline–alkali soil) were also investigated for comparison. The obtained results implied that the saline–alkali condition facilitates the formation of a large quantity of colloids. The use of AFM combined with spectrometric methods in the present study provides new knowledge on the colloid characteristics of saline–alkali soils. Microsc. Res. Tech. 79:525–531, 2016. © 2016 Wiley Periodicals, Inc.     

Surface chemistry-mechanical property relationship of low density polyethylene: an IR+visible sum frequency generation spectroscopy and atomic force microscopy study

Surface-specific IR+visible sum frequency generation (SFG) spectroscopy was used to obtain chemical composition of two polymer surfaces. The SFG surface vibrational spectrum of pure low density polyethylene and that of a commercial sample of the same kind of polymer, which contains additives, are markedly different. This correlates well with the very different surface mechanical properties, i.e., stiffness (indicative of the elastic modulus) and friction, which were measured by atomic force microscopy (AFM) on the same polymer surfaces. The surface of CLDPE is dominated by methoxy (−OCH₃) contained additives, segregated from the bulk, which explains a lower stiffness, adhesion and friction of the surface, as measured by AFM. This revised version was published online in August 2006 with corrections to the Cover Date.     

Characterization of the tip-loading force-dependent tunneling behavior in alkanethiol metal–molecule–metal junctions by conducting atomic force microscopy

We report on a tip-loading force-dependent tunneling behavior through alkanethiol self-assembled monolayers formed in metal–molecule–metal junctions, using conducting atomic force microscopy. The metal–molecule contacts were formed by placing a conductive tip in a stationary point contact on alkanethiol self-assembled monolayers under a controlled tip-loading force. Current–voltage characteristics in the alkanethiol junctions are simultaneously measured, while varying the loading forces. Tunneling current through the alkanethiol junctions increases and decay coefficient β_N decreases, respectively, with increasing tip-loading force, which results from enhanced intermolecular charge transfer in a tilted molecular configuration under the tip-loading effect.     

Study of the nanoscopic deformation of an annealed nafion film by using atomic force microscopy and a patterned substrate

We demonstrated the repetitive imaging of the same area of a nafion film before and after annealing by using atomic force microscopy (AFM). In order to find the exact same area of the same sample after changing the cantilever and reattaching the sample, a micropatterned substrate was developed. A micropattern with a 250–500 μm pitch was prepared on the backside of a transparent glass substrate. This pattern includes various signs such as colored letters and numbers at the center of each lattice of the pattern. The nanostructures fabricated by AFM nanolithography on a nafion film using this new method were successfully characterized before and after annealing (over 100 °C). The AFM images clearly showed that the nanostructures on a nafion film were dramatically changed by annealing. The data indicated an evidence to understand why the nafion fuel cell does not work well at high temperatures. Our method is probably effective for the study of nanoscopic dynamics in various surface structures.     

The observation of large magnetite (Fe3O4) crystals from magnetotactic bacteria by electron and atomic force microscopy

Magnetite crystals inside coccoid magnetotactic bacteria found in lagoons near Rio de Janeiro city were examined by electron microscopy (EM) and atomic force microscopy (AFM). For AFM, ultrathin sections of bacteria embedded in Epon resin were etched with an ethanolic NaOH solution and observed both in the height and in the force modes. Comparative electron microscope images were useful for identifying crystalline reliefs in the etched sections. Different situations representing particular arrangements of crystal chains were observed by AFM. The majority of the bacteria examined presented unusually large magnetite crystals which remained strongly attached in linear chains even after the laboratory procedures for their isolation. This behaviour is different from all other biogenic magnetite crystals isolated so far. It is suggested that this attachment is due to the strong field between individual crystals as well as to the contact areas, which are the largest observed until now. The correct identification of a particular topography by AFM as a crystal relief may be critical when crystals are not aligned in chains; in these cases the linear dimensions and the presence of well-defined edges and faces are important features to be taken into account. Characterization of the crystal faces is important for the study of magnetotactic micro-organisms since the crystalline habits seem to be species-specific. Observation of etched sections proved to be a helpful approach for crystal relief observation, especially when small amounts of bacteria were available.