Water-solid interfaces probed by high-resolution atomic force microscopy

Water-solid interfaces play important roles across a broad range of scientific and application fields. In the past decades, atomic force microscopy (AFM) has significantly deepened our understanding of water-solid interfaces at molecular scale. In this review, we describe the recent progresses on probing water-solid interfaces by noncontact AFM, highlighting the imaging of interfacial water with ultrahigh spatial resolution. In particular, the recent development of qPlus-based AFM with functionalized tips has made it possible to directly image the H-bonding skeleton of interfacial water under UHV environment. Based on high-order electrostatic forces, such a technique even enables submolecular-level imaging of weakly bonded water structures with negligible disturbance. In addition, the three-dimensional (3D) AFM using low-noise cantilever deflection sensors can achieve atomic resolution imaging at liquid/solid interfaces, which opens up the possibility of probing the hydration layer structures under realistic conditions. We then discuss the application of those AFM techniques to various interfacial water systems, including water clusters, ion hydrates, water chains, water monolayers/multilayers and bulk water/ice on different surfaces under UHV or ambient environments. Some important issues will be addressed, including the H-bonding topology, ice nucleation and growth, ion hydration and transport, dielectric properties of water, etc. In the end, we present an outlook on the directions of future AFM studies of water at interfaces and the challenges faced by this field, as well as the development of new AFM techniques.     

Observation of multicellular spinning behavior of Proteus mirabilis by atomic force microscopy and multifunctional microscopy

This study aimed to observe the multicellular spinning behavior of Proteus mirabilis by atomic force microscopy (AFM) and multifunctional microscopy in order to understand the mechanism underlying this spinning movement and its biological significance. Multifunctional microscopy with charge-coupled device (CCD) and real-time AFM showed changes in cell structure and shape of P. mirabilis during multicellular spinning movement. Specifically, the morphological characteristics of P. mirabilis, multicellular spinning dynamics, and unique movement were observed. Our findings indicate that the multicellular spinning behavior of P. mirabilis may be used to collect nutrients, perform colonization, and squeeze out competitors. The movement characteristics of P. mirabilis are vital to the organism's biological adaptability to the surrounding environment.     

Atomic force microscopy probing of cell elasticity

Atomic force microscopy (AFM) has recently provided the great progress in the study of micro- and nanostructures including living cells and cell organelles. Modern AFM techniques allow solving a number of problems of cell biomechanics due to simultaneous evaluation of the local mechanical properties and the topography of the living cells at a high spatial resolution and force sensitivity. Particularly, force spectroscopy is used for mapping mechanical properties of a single cell that provides information on cellular structures including cytoskeleton structure.

This entry is aimed to review the recent AFM applications for the study of dynamics and mechanical properties of intact cells associated with different cell events such as locomotion, differentiation and aging, physiological activation and electromotility, as well as cell pathology. Local mechanical characteristics of different cell types including muscle cells, endothelial and epithelial cells, neurons and glial cells, fibroblasts and osteoblasts, blood cells and sensory cells are analyzed in this paper.     

Atomic force microscopy and transmission electron microscopy of biocompatible magnetic fluids: A comparative analysis

The present study provides a comparative analysis of the size dispersity of magnetic nanoparticles (MNPs) within magnetic fluids as obtained from atomic force microscopy (AFM) and transmission electron microscopy (TEM). Whereas the mean particle diameter obtained from the AFM data presented a reduction of about 34% as compared to the value obtained from the TEM data, the standard deviation obtained from the AFM data is twice the value found from the TEM data. Similarities and differences in the size dispersity parameters are discussed in terms of sample preparation and tip characteristics. A two-dimensional mode for the deposition of the MNPs on top of the mica substrate is discussed as well.     

Atomic force microscopy for the investigation of molecular and cellular behavior

The present review details the methods used for the measurement of cells and their exudates using atomic force microscopy (AFM) and outlines the general conclusions drawn by the mechanical characterization of biological materials through this method. AFM is a material characterization technique that can be operated in liquid conditions, allowing its use for the investigation of the mechanical properties of biological materials in their native environments. AFM has been used for the mechanical investigation of proteins, nucleic acids, biofilms, secretions, membrane bilayers, tissues and bacterial or eukaryotic cells; however, comparison between studies is difficult due to variances between tip sizes and morphologies, sample fixation and immobilization strategies, conditions of measurement and the mechanical parameters used for the quantification of biomaterial response. Although standard protocols for the AFM investigation of biological materials are limited and minor differences in measurement conditions may create large discrepancies, the method is nonetheless highly effective for comparatively evaluating the mechanical integrity of biomaterials and can be used for the real-time acquisition of elasticity data following the introduction of a chemical or mechanical stimulus. While it is currently of limited diagnostic value, the technique is also useful for basic research in cancer biology and the characterization of disease progression and wound healing processes.     

Binding studies of costunolide and dehydrocostuslactone with HSA by spectroscopy and atomic force microscopy

Human serum albumin (HSA), a major plasma protein and plasma-derived therapeutic, interacts with a wide variety of drugs and native plasma metabolites. In this study the interactions of costunolide (CE) and dehydrocostuslactone (DE) with HSA were investigated by molecule modeling, atomic force microscopy (AFM), and different optical techniques. In the mechanism discussion, it was proved that fluorescence quenching of HSA by both of the drugs is a result of the formation of drug-HSA complexes. Binding parameters for the reactions were determined according to the Stern-Volmer equation and static quenching. The results of thermodynamic parameters ΔG⁰, ΔH⁰, and ΔS⁰ at different temperatures indicated that hydrogen bonding interactions play a major role in the drug-HSA associations process. The binding properties were further studied by quantitative analysis of CD, FTIR, and Raman spectra. Furthermore, AFM results showed that the dimension of HSA molecules became more swollen after binding with the drugs.     

Monitoring of mechanical properties of serially passaged bovine articular chondrocytes by atomic force microscopy

Atomic force microscopy (AFM) is a powerful tool in imaging cells and tissues and probing their mechanical properties. Articular chondrocytes, the cells responsible for the production and maintenance of cartilaginous extracellular matrix in the knee joint, change their morphology and dedifferentiate during in vitro expansion culture. It was unclear if the mechanical properties of chondrocytes change accompanying phenotype variation. The elasticity of in vitro serially cultured bovine articular chondrocytes was investigated using AFM. The chondrocytes changed their morphology from round to spindle-like. The freeze-dried P0 chondrocytes showed significantly higher modulus than did the serially passaged (P1–P4) chondrocytes. The change of chondrocyte morphology was accompanied with a decrease of elastic modulus.     

Eutectic alloy microstructure: atomic force microscopy analysis

The exciting microstructures found in several eutectic alloys are a result of a cooperative growth, which is connected to the atomic transfer in the melt ahead the solid/liquid interface. In a eutectic system, the growth of solid phases depends on the simultaneous rejection of constituents to the liquid phase, which causes adjustments of the melt composition and hence, mass transport by diffusion normal to the growth direction. Generally, eutectic microstructures are examined by using optical (OM) and scanning electron microscopy (SEM). While OM may not provide the necessary resolution, the eutectic microstructure may present three-dimensional features, as a result of etching, which is not always possible to be observed by SEM. As an alternative, this paper describes the use of atomic force microscopy (AFM) in understanding micro-scale feature of a eutectic microstructure. For such a purpose, directionally solidified samples of a Ni–Al–V lamellar eutectic, a Ni–Al–Mo fibrous eutectic and a Ni–Al–Nb three-phase eutectic were examined. The results obtained provided a new picture of multi-phase microstructures and allows one to understand their new characteristics.     

Calculation of the optimal imaging parameters for frequency modulation atomic force microscopy

True atomic resolution of conductors and insulators is now routinely obtained in vacuum by frequency modulation atomic force microscopy. So far, the imaging parameters (i.e., eigenfrequency, stiffness and oscillation amplitude of the cantilever, frequency shift) which result in optimal spatial resolution for a given cantilever and sample have been found empirically. Here, we calculate the optimal set of parameters from first principles as a function of the tip–sample system. The result shows that the either the acquisition rate or the signal-to-noise ratio could be increased by up to two orders of magnitude by using stiffer cantilevers and smaller amplitudes than are in use today.     

DNA adsorption and desorption on mica surface studied by atomic force microscopy

The adsorption of DNA molecules on mica surface and the following desorption of DNA molecules at ethanol-mica interface were studied using atomic force microscopy. By changing DNA concentration, different morphologies on mica surface have been observed. A very uniform and orderly monolayer of DNA molecules was constructed on the mica surface with a DNA concentration of 30 ng/μL. When the samples were immersed into ethanol for about 15 min, various desorption degree of DNA from mica (0-99%) was achieved. It was found that with the increase of DNA concentration, the desorption degree of DNA from the mica at ethanol-mica interface decreased. And when the uniform and orderly DNA monolayers were formed on the mica surface, almost no DNA molecule desorbed from the mica surface in this process. The results indicated that the uniform and orderly DNA monolayer is one of the most stable DNA structures formed on the mica surface. In addition, we have studied the structure change of DNA molecules after desorbed from the mica surface with atomic force microscopy, and found that the desorption might be ascribed to the ethanol-induced DNA condensation.     

Atomic force microscopy observation of peroxynitrite-induced erythrocyte cytoskeleton reorganization

Atomic force microscopy (AFM) was used to study surface layers of fixed intact erythrocytes. Advantages of simultaneous analysis of surface topography and lateral force maps in the investigation of cytoskeleton structure were shown. Fractal analysis was applied to the lateral force maps of erythrocyte surfaces to evaluate the complexity of the cytoskeleton. Peroxynitrite was used as an oxidant to induce changes in the cytoskeleton structure of intact erythrocytes. Peroxynitrite action on whole blood leads to local abnormalities in the erythrocyte cytoskeleton structure, as well as cytoskeleton reorganization in protruded regions of crenated erythrocytes.     

Study on the interactions between anti-cancer drug oxaliplatin and DNA by atomic force microscopy

Oxaliplatin is one of the most important anticancer drugs at present. However, the mechanism of action of oxaliplatin is still controversial. In this study, the interactions between oxaliplatin and a plasmid DNA have been studied so as to reveal the structural basis of its activity. The structural characteristic of pUC19 DNA (2 ng/μL) incubated with 100 μmol/L and 1000 μmol/L of oxaliplatin for the different time on a freshly cleaved highly ordered pyrolytic graphite (HOPG) surface was investigated by atomic force microscopy (AFM). High resolution AFM observation indicated that oxaliplatin can induce pUC19 DNA molecules change from the extended conformation to the entangled structures with many nodes, and finally to the compact particles. The present AFM results provide structural evidence about the interactions between oxaliplatin and circular duplex DNA containing multiple targets.     

Deoxyribonucleic acid and chromatin imaging of endometriosis and endometrial carcinoma using atomic force microscopy

Abstract

Introduction: Clinical differential diagnosis of endometrial carcinoma is challenging, as signs and symptoms may vary considerably and there is a lack of reliable diagnostic serum biomarkers.

Aim of the study: The aim of our work was to characterize the deoxyribonucleic acid and chromatin changes in the tissue of patients confirmed to be suffering from endometriosis and endometrial adenocarcinoma and compare it with a healthy control group.

Material and methods: All samples were collected during recommended surgical interventions, and after the DNA isolation, a sonification followed by crosslink of chromatin were done. Consequently, both DNA and chromatin were examined using atomic force microscopy.

Results: A chromatin immunoprecipitation was used for the in vivo observation of conformational chromatin changes. The width of ssDNA showed a significant difference, almost double the control value in the endometrial cancer sample versus control (by 73?±?5% wider, p?<?0.001). In contrast, the height of ssDNA was highest in the frozen pelvis patient sample (by 510?±?12% compared to control, p?<?0.01).

Conclusion: Our results suggest that the horizontal size of single-stranded deoxyribonucleic acid and nucleosomes can help to identify potential patients with endometrial adenocarcinoma, while the height of the same parameter is associated with endometriosis.     

Investigating the lateral motion of SiGe islands by selective chemical etching

SiGe islands grown by deposition of 10 monolayers of Ge on Si(0 0 1) at 740 °C were investigated by using a combination of selective wet chemical etching and atomic force microscopy. The used etchant, a solution consisting of ammonium hydroxide and hydrogen peroxide, shows a high selectivity of Ge over Si_xGe_1−x and is characterized by relatively slow etching rates for Si-rich alloys. By performing successive etching experiments on the same sample area, we are able to gain a deeper insight into the lateral displacement the islands undergo during post growth annealing.     

Ultrastructural organization of premature condensed chromosomes at S-phase as observed by atomic force microscopy

In this study, we used calyculin A to induce premature condensed chromosomes (PCC). S-phase PCC is as “pulverized” appearance when viewed by light microscopy. Then, we applied atomic force microscopy (AFM) to investigate the ultrastructual organization of S-phase PCC. S-phase PCC shows ridges and grooves as observed by AFM. After trypsin treatment, chromosome surface roughness is increased and chromosome thickness is decreased. At high magnification, the ridges are composed of densely packed 30 nm chromatin fibers which form chromosome axis. Around the ridges, many 30 nm chromatin fibers radiate from center. Some of the 30 nm chromatin fibers are free ends. The grooves are not real “gap”, but several 30 nm chromatin fibers which connect two ridges and form “grid” structure. There are four chromatin fibers detached from chromosome: two free straight 30 nm chromatin fibers, one loop chromatin fiber and one straight combining with loop chromatin fiber. These results suggested that the S-phase PCC was high-order organization of 30 nm chromatin fibers and the 30 nm chromatin fibers could exist as loops and free ends.     

New control methodology of microcantilevers in atomic force microscopy

We apply an external feedback control technique to vibrating microcantilevers in atomic force microscopy. Here we have no difficulty in getting information on periodic orbits required for application of the external feedback control unlike controlling chaos since stable orbits are used as reference ones. This approach enables us not only to control vibrations of the cantilevers but also to measure the sample surfaces (surface topographies) simultaneously. The efficiency and validity of our approach is demonstrated by numerical simulations and a theoretical analysis with the assistance of numerical computations.     

Electron microscopy and atomic force microscopy studies of chromatin and metaphase chromosome structure

The folding of the chromatin filament and, in particular, the organization of genomic DNA within metaphase chromosomes has attracted the interest of many laboratories during the last five decades. This review discusses our current understanding of chromatin higher-order structure based on results obtained with transmission electron microscopy (TEM), cryo-electron microscopy (cryo-EM), and different atomic force microscopy (AFM) techniques.Chromatin isolated from different cell types in buffers without cations form extended filaments with nucleosomes visible as separated units. In presence of low concentrations of Mg²⁺, chromatin filaments are folded into fibers having a diameter of ∼30 nm. Highly compact fibers were obtained with isolated chromatin fragments in solutions containing 1–2 mM Mg²⁺. The high density of these fibers suggested that the successive turns of the chromatin filament are interdigitated. Similar results were obtained with reconstituted nucleosome arrays under the same ionic conditions. This led to the proposal of compact interdigitated solenoid models having a helical pitch of 4–5 nm. These findings, together with the observation of columns of stacked nucleosomes in different liquid crystal phases formed by aggregation of nucleosome core particles at high concentration, and different experimental evidences obtained using other approaches, indicate that face-to-face interactions between nucleosomes are very important for the formation of dense chromatin structures.Chromatin fibers were observed in metaphase chromosome preparations in deionized water and in buffers containing EDTA, but chromosomes in presence of the Mg²⁺ concentrations found in metaphase (5–22 mM) are very compact, without visible fibers. Moreover, a recent cryo-electron microscopy analysis of vitreous sections of mitotic cells indicated that chromatin has a disordered organization, which does not support the existence of 30-nm fibers in condensed chromosomes. TEM images of partially denatured chromosomes obtained using different procedures that maintain the ionic conditions of metaphase showed that bulk chromatin in chromosomes is organized forming multilayered plate-like structures. The structure and mechanical properties of these plates were studied using cryo-EM, electron tomography, AFM imaging in aqueous media, and AFM-based nanotribology and force spectroscopy. The results obtained indicated that the chromatin filament forms a flexible two-dimensional network, in which DNA is the main component responsible for the mechanical strength observed in friction force measurements. The discovery of this unexpected structure based on a planar geometry has opened completely new possibilities for the understanding of chromatin folding in metaphase chromosomes. It was proposed that chromatids are formed by many stacked thin chromatin plates oriented perpendicular to the chromatid axis. Different experimental evidences indicated that nucleosomes in the plates are irregularly oriented, and that the successive layers are interdigitated (the apparent layer thickness is 5–6 nm), allowing face-to-face interactions between nucleosomes of adjacent layers. The high density of this structure is in agreement with the high concentration of DNA observed in metaphase chromosomes of different species, and the irregular orientation of nucleosomes within the plates make these results compatible with those obtained with mitotic cell cryo-sections. The multilaminar chromatin structure proposed for chromosomes allows an easy explanation of chromosome banding and of the band splitting observed in stretched chromosomes.     

Investigations of C60 molecules deposited on Si(111) by noncontact atomic force microscopy

We demonstrated the high resolution imaging of the organic molecules using noncontact atomic force microscopy in ultrahigh vacuum. The sample was C₆₀ molecules deposited on the Si(111)-7×7 reconstructed surface. When the thickness of the C₆₀ film was submonolayer, we could image some isolated C₆₀ molecules and the reconstructed Si surface simultaneously. However, the imaging was highly unstable not only because of the large structure but also due to the large difference between the interaction forces on the molecules and on the Si surface. On the other hand, when the thickness of the C₆₀ molecules was almost monolayer, individual molecules could be stably imaged.     

Morphology of synthetic DOPA-eumelanin deposited on glass and mica substrates: An atomic force microscopy investigation

Bright field microscopy and atomic force microscopy techniques are used to investigate morphological properties of synthetic eumelanin, obtained by oxidation of l-DOPA solution, deposited on glass and mica substrates. Deposits of eumelanin are characterized by aggregates with different shape and size. On a micrometric scale, filamentous as well as granular structures are present on glass and mica substrates, with a larger density on the former than on the latter. On a nanometric scale, filamentous aggregates, several microns long and about 100 nm wide and high, and granular aggregates, ∼50 nm high and 100 nm wide, are found on both substrates, whereas point-like deposits less than 10 nm high and less than 50 nm wide are found on mica substrate. Dynamic light scattering measurements and atomic force microscopy images support the evidence that eumelanin presents only nanometric point-like aggregates in aqueous solution, whereas such nanoaggregates organize themselves according to granular and filamentous structures when deposition occurs, as a consequence of interactions with the substrate surface.     

I-V curve oscillation observed by atomic force microscopy

Oscillation on the current-voltage curve measured by atomic force microscopy is observed when the distance between the tip and sample is large enough and beyond a critical value. The appearance of the oscillation is attributed to the excitation of electron standing waves between the tip and sample. From the first peak position and the voltage difference between the first two peaks on the current-voltage curve, the value of the work function at the detected point on silver film surface and the distance between the tip and the detected point can be calculated.