Investigating biomolecular recognition at the cell surface using atomic force microscopy

Probing the interaction forces that drive biomolecular recognition on cell surfaces is essential for understanding diverse biological processes. Force spectroscopy has been a widely used dynamic analytical technique, allowing measurement of such interactions at the molecular and cellular level. The capabilities of working under near physiological environments, combined with excellent force and lateral resolution make atomic force microscopy (AFM)-based force spectroscopy a powerful approach to measure biomolecular interaction forces not only on non-biological substrates, but also on soft, dynamic cell surfaces. Over the last few years, AFM-based force spectroscopy has provided biophysical insight into how biomolecules on cell surfaces interact with each other and induce relevant biological processes. In this review, we focus on describing the technique of force spectroscopy using the AFM, specifically in the context of probing cell surfaces. We summarize recent progress in understanding the recognition and interactions between macromolecules that may be found at cell surfaces from a force spectroscopy perspective. We further discuss the challenges and future prospects of the application of this versatile technique.     

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.     

Elastic modulus of suspended purple membrane measured by atomic force microscopy

We have probed the mechanical properties of purple membrane (PM) in a physiological environment using the atomic force microscope (AFM). By suspending PM over nano-trenches, the elastic properties of PM can be evaluated free from the interaction with the substrate. Force-displacement curves were obtained on the suspended membrane and the data was compared to that of a simple model of a thin film over a trench. By fitting the data to the model, the elastic modulus of PM was estimated to be 8 MPa. When the membrane is repeatedly indented, we observed a change in the force-distance data consistent with damage to the two-dimensional crystal of PM. In this paper we demonstrate that the AFM allows us to evaluate the mechanics of biological membranes in their native conditions.     

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.     

Growth of thin polymer films containing side-chain azo-dye analyzed by atomic force microscopy

Thin films containing both the azo-dye disperse red 1 (DR1) and the poly(methylmetacrylate) (PMMA) or the poly(phenylenevinylene) (PPV) are deposited by Langmuir-Blodgett and spin coating techniques on various substrates. The morphology, surface structure and growth pattern of the azo-dye-polymers were studied by atomic force microscopy. Nucleation and growth processes are responsible for the generation of different structures. The spin coated films were additionally oriented using the electric field poling method (corona poling). The film homogeneity is improved by this method in all cases. Due to the polar character of DR1 molecules, rod-like sub-structures are observed after the corona poling process in DR1-MMA films. The indium tin oxide surface enhances reorientation of the azo-dye-polymer molecules during corona poling and results in a significant reduction of the surface roughness.     

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.     

Noncontact atomic force microscopy: Bond imaging and beyond

It was a long-cherished dream for chemists to take a direct look at chemical bonding, a fundamental component of chemistry. This dream was finally accomplished by the state-of-the-art noncontact atomic force microscopy (NC-AFM) equipped with qPlus force sensors and carbon monoxide (CO) functionalized tips. The resolved interconnectivity between atoms and molecules in NC-AFM frequency shift images is interpreted as chemical bonding, providing essential knowledge of the bond length, bond angle and even bond order. The featured contrast of different chemical bonds can serve as fingerprints for further interpretation of chemical structures toward unknown species synthesized on surfaces. This breakthrough enriches characterization tools for surface science and brings our understanding of on-surface reactions to a new level. Beyond bond imaging, the application of NC-AFM has been extended to quantifying interatomic interactions, identifying three-dimensional nanostructures, manipulating molecules and reactions, as well as determining molecular electronic characteristics. Moreover, some recent efforts address the improvement of the usability and versatility of the bond-resolved NC-AFM technique, including high-resolution molecular investigation on bulk insulators, application-specific tip modification, stable bond imaging above liquid helium temperature and autonomous experimentation implemented by artificial intelligence.     

Atomic scale properties of interior interfaces of semiconductor heterostructures as determined by quasi-digital highly selective etching and atomic force microscopy

We report on first experiments combining quasi-digital highly selective etching and atomic force microscopy (AFM) to examine the interior interfaces of semiconductor heterostructures. Lattice matched (GaIn)As/InP heterostructures grown by metalorganic vapour-phase epitaxy (MOVPE) are taken as a model system to check the capabilities of this new method. Standard selective etchants for different material systems have been optimized in selectivity and etch rate to achieve a quasi-digital etching behaviour. In this way, the real structure of interior interfaces can be determined by AFM. We find a significant difference between the surface of the heterostructure and the interior interfaces.     

Study of nitrogen ion implantation and diffusion phenomena on thin chromium layers followed by the atomic force microscopy and secondary ion mass spectroscopy techniques characterization

This research investigates the effect of ion implantation dosage level and further thermal treatment on the physical characteristics of chromium coatings on Si(1 1 1) substrates. Chromium films had been exposed to nitrogen ion fluencies of 1 × 10¹⁷, 3 × 10¹⁷, 6 × 10¹⁷ and 10 × 10¹⁷ N⁺ cm⁻² with a 15 keV energy level. Obtained samples had been heat treated at 450 °C at a pressure of 2 × 10⁻² Torr in an argon atmosphere for 30 h. Atomic force microscopy (AFM) images showed significant increase in surface roughness as a result of nitrogen ion fluence increase. Secondary ion mass spectroscopy (SIMS) studies revealed a clear increased accumulation of Cr₂N phase near the surface as a result of higher N⁺ fluence. XRD patterns showed preferred growth of [0 0 2] and [1 1 1] planes of Cr₂N phase as a result of higher ion implantation fluence. These results had been explained based on the nucleation-growth of Cr₂N phase and nitrogen atoms diffusion history during the thermal treatment process.     

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.     

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.     

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.     

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.     

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.     

Sub-Angstrom oscillation amplitude non-contact atomic force microscopy for lateral force gradient measurement

We report the first results from novel sub-Angstrom oscillation amplitude non-contact atomic force microscopy developed for lateral force gradient measurements. Quantitative lateral force gradients between a tungsten tip and Si(1 1 1)-(7 × 7) surface can be measured using this microscope. Simultaneous lateral force gradient and scanning tunnelling microscope images of single and multi atomic steps are obtained. In our measurement, tunnel current is used as feedback. The lateral stiffness contrast has been observed to be 2.5 N/m at single atomic step, in contrast to 13 N/m at multi atomic step on Si(1 1 1) surface. We also carried out a series of lateral stiffness-distance spectroscopy. We observed lateral stiffness-distance curves exhibit sharp increase in the stiffness as the sample is approached towards the surface. We usually observed positive stiffness and sometimes going into slightly negative region.     

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.     

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.     

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.     

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.