Advances In Atomic Force Microscopy Research Articles

DNA Morphology: Global Alteration of DNA Topological States Induced by Chemotherapeutic Agents and Its Implication in Cancer.

The dynamic topological states of chromosomal DNA regulate many cellular fundamental processes universally in all three domains of life, that is, bacteria, archaea, and eukaryotes. DNA-binding proteins maintain the regional and global supercoiling of the chromosome and thereby regulate the chromatin architecture that ultimately influences the gene expression network and other DNA-centric molecular events in various microenvironments and growth phases. DNA-binding small molecules are pivotal weapons for treating a wide range of cancers. Recent advances in single-molecule biophysical tools have uncovered the fact that many DNA-binding ligands not only alter the regional DNA supercoiling but also modulate the overall morphology of DNA. Here we provide insight into recent advances in atomic force microscopy (AFM) acquired DNA structural change induced by therapeutically important mono- and bis-intercalating anticancer agents as well as DNA-adduct-forming anticancer drugs. We also emphasize the growing evidence of the mechanistic relevance of changes in DNA topology in the anticancer cellular responses of DNA-targeting chemotherapeutic agents.

Combining atomic force microscopy with complementary techniques for multidimensional single-cell analysis.

The advent of atomic force microscopy (AFM) provides an amazing instrument for characterising the structures and properties of living biological systems under aqueous conditions with unprecedented spatiotemporal resolution. In addition to its own unique capabilities for applications in life sciences, AFM is highly compatible and has been widely integrated with various complementary techniques to simultaneously sense the multidimensional (biological, chemical and physical) properties of biological systems, offering novel possibilities for comprehensively revealing the underlying mechanisms guiding life activities particularly in the studies of single cells. Herein, typical combinations of AFM and complementary techniques (including optical microscopy, ultrasound, infrared spectroscopy, Raman spectroscopy, fluidic force microscopy and traction force microscopy) and their applications in single-cell analysis are reviewed. The future perspectives are also provided.

Viscoelasticity of single folded proteins using dynamic atomic force microscopy.

The advent of atomic force microscopy, along with optical tweezers, ushered in a new field of single molecule force spectroscopy, wherein the response of a single protein or a macromolecule to external mechanical perturbations is measured. Controlled forces ranging from pN to nN are applied to measure the unfolding force distribution of a single protein domain. In a clamp type experiment, the folded protein is subjected to a constant force to measure the unfolding time distribution. Simultaneously, there were efforts to measure the elastic and viscous response of a single domain by applying sinusoidal forces and measuring the resulting deformations produced in a bid to quantify its viscoelasticity. The deformation's phase lag with respect to the applied force provides the elastic and viscous response of the protein, akin to oscillatory rheology. Despite numerous technical advances in AFM, an artefact-free measurement of a folded protein's viscoelasticity largely remains a challenge. In this perspective, we review efforts to measure the viscoelasticity of proteins using dynamic AFM, identifying pitfalls that make these measurements elusive. Finally, we discuss a new promising method, which reported viscoelasticity of a folded protein and its implications for our understanding of protein dynamics and structural flexibility.

Advances in Atomic Force Microscopy for the Electromechanical Characterization of Piezoelectric and Ferroelectric Nanomaterials

Given the social demand for self-powering wearable electronics, it is necessary to develop composite materials that exhibit both good flexibility and excellent piezoelectric performances. Intensive research on synthesis methods and devising characterization techniques for piezoelectric nanomaterials in various forms has been conducted. In particular, characterization techniques for piezoelectric nanomaterials require different approaches from those for conventional bulk materials. Atomic force microscopy (AFM)-based characterization techniques work based on the local physical interactions between the AFM tip and sample surfaces, making them an irreplaceable tool for studying the electromechanical properties of piezoelectric nanomaterials. Piezoresponse force microscopy (PFM), conductive AFM (C-AFM), and lateral force microscopy (LFM) are three representative AFM-based techniques used to characterize the piezoelectric and ferroelectric properties of nanomaterials. Coupled with the appearance of diverse novel nanomaterials such nanowires, free-standing nanorods, and electrospun nanofibers, AFM-based characterization techniques are becoming freer from artifacts and the need for quantitative measurements. PFM was initially developed to image the microstructures of piezoelectric materials, and well-calibrated techniques designed to realize quantitative measurements have been applied to nanomaterials. In contrast, C-AFM and LFM were initially used to measure the conductivity of diverse materials and the nanotribology of material surfaces. Over the last decade, they have proved their versatility and can now be used to evaluate the direct piezoelectric effect and the mechanical properties of piezoelectric nanomaterials. In these cases, systematic understanding with regard to the measurement principles is required for accurate measurements and analyses. In the present review article, we discuss earlier work in which AFM-based electromechanical characterization techniques were applied to nanomaterials to evaluate piezoelectric and ferroelectric properties. Also discussed is the importance of gaining a comprehensive understanding of the resulting signals.

Ultrastructural characterisation of young and aged dental enamel by atomic force microscopy.

Recent advances in atomic force microscopy (AFM) have allowed the characterisation of dental-associated biomaterials and biological surfaces with high resolution. In this context, the topography of dental enamel - the hardest mineralised tissue in the body - has been explored with AFM-based approaches at the microscale. With age, teeth are known to suffer changes that can impact their structural stability and function; however, changes in enamel structure because of ageing have not yet been explored with nanoscale resolution. Therefore, the aim of this exploratory work was to optimise an approach to characterise the ultrastructure of dental enamel and determine potential differences in topography, hydroxyapatite (HA) crystal size, and surface roughness at the nanoscale associated to ageing. For this, a total of six teeth were collected from human donors from which enamel specimens were prepared. By employing intermittent contact (AC mode) imaging, HA crystals were characterised in both transversal and longitudinal orientation (respect to surface plane) with high resolution in environmental conditions. The external enamel surface displayed the presence of a pellicle-like coating on its surface that was not observable on cleaned specimens. Acid-etching exposed crystals that were imaged and morphologically characterised in high resolution at the nanoscale in both the external and internal regions of enamel in older and younger specimens. Our results demonstrated important individual variations in HA crystal width and roughness parameters across the analysed specimens; however, an increase in surface roughness and decrease in HA width was observed for the pooled older external enamel group compared to younger specimens. Overall, high-resolution AFM was an effective approach for the qualitative and quantitative characterisation of human dental enamel ultrastructure. Future work should focus on exploring the ageing of dental enamel with increased sample sizes to compensate for individual differences as well as other potential confounding factors such as behavioural habits and mechanical forces.

AFM imaging and single-molecule recognition of plant cell walls.

New advances in atomic force microscopy (AFM) enable real-time imaging of live plant cell walls. Imaging is achieved by recording the atomic forces between a cell wall surface and a sharp tip mounted at the end of a flexible cantilever that is raster scanned. This allows direct characterization of the native nanostructures by height and nanomechanical properties by modulus in physiological fluids. In addition, AFM-based tip-enhanced Raman spectroscopy (AFM-TERS) can acquire the chemical composition of the cell wall, elucidating the relationship between the cell wall nanostructures, components, and functions.

Advances in Atomic Force Microscopy: Imaging of Two- and Three-Dimensional Interfacial Water.

Interfacial water is closely related to many core scientific and technological issues, covering a broad range of fields, such as material science, geochemistry, electrochemistry and biology. The understanding of the structure and dynamics of interfacial water is the basis of dealing with a series of issues in science and technology. In recent years, atomic force microscopy (AFM) with ultrahigh resolution has become a very powerful option for the understanding of the complex structural and dynamic properties of interfacial water on solid surfaces. In this perspective, we provide an overview of the application of AFM in the study of two dimensional (2D) or three dimensional (3D) interfacial water, and present the prospect and challenges of the AFM-related techniques in experiments and simulations, in order to gain a better understanding of the physicochemical properties of interfacial water.

Определение характеристик мембран на основе нанопористого оксида алюминия методом АСМ

This scientific work presents the results of a study of the structural features of membranes based on nanoporous alumina using atomic force microscopy (AFM). The capabilities of scanning probe microscopy (SPM), in particular atomic force microscopy, are widely known, but with regard to dielectric materials, the capabilities and advantages of AFM are increasing. The capabilities of AMS with respect to the surface of various nanostructured materials are primarily related to its resolving capabilities. The resolving power of AFM is primarily associated with cantilevers, which are used for surface scanning. In the case of studying the surface of membranes based on nanoporous alumina, the possibilities of AFM and the use of its various techniques are shown. Atomic force microscopy is used to study the surface of various dielectric solid and polymer samples. It is only necessary to select the required AFM technique for surface investigation. You also need to pay attention to the probes that are used for scanning.

Nanoscale Chemical Imaging by Photo‐Induced Force Microscopy: Technical Aspects and Application to the Geosciences

Photo‐induced force microscopy (PiFM) is a new‐frontier technique that combines the advantages of atomic force microscopy with infrared spectroscopy and allows for the simultaneous acquisition of 3D topographic data with molecular chemical information at high spatial (~ 5 nm) and spectral (~ 1 cm−1) resolution at the nanoscale. This non‐destructive technique is time efficient as it requires only conventional mirror‐polishing and has fast mapping rates on the order of a few minutes that allow the study of dynamic processes via time series. Here, we review the method’s historical development, working principle, data acquisition, and evaluation, and provide a comparison with traditional geochemical methods. We review PiFM studies in the areas of materials science, chemistry and biology. In addition, we provide the first applications for geochemical samples including the visualization of faint growth zonation in zircons, the identification of fluid speciation in high‐pressure experimental samples, and of nanoscale organic phases in biominerals. We demonstrate that PiFM analysis is a time‐ and cost‐efficient technique combining high‐resolution surface imaging with molecular chemical information at the nanoscale and, thus, complements and expands traditional geochemical methods.

The biophysics of bacterial infections: Adhesion events in the light of force spectroscopy

Bacterial infections are the most eminent public health challenge of the 21st century. The primary step leading to infection is bacterial adhesion to the surface of host cells or medical devices, which is mediated by a multitude of molecular interactions. At the interface of life sciences and physics, last years advances in atomic force microscopy (AFM)-based force spectroscopy techniques have made possible to measure the forces driving bacteria-cell and bacteria-materials interactions on a single molecule/cell basis (single molecule/cell force spectroscopy).Among the bacteria-(bio)materials surface interactions, the life-threatening infections associated to medical devices involving Staphylococcus aureus and Escherichia coli are the most eminent. On the other hand, Pseudomonas aeruginosa binding to the pulmonary and urinary tract or the Helicobacter pylori binding to the gastric mucosa, are classical examples of bacteria-host cell interactions that end in serious infections.As we approach the end of the antibiotic era, acquisition of a deeper knowledge of the fundamental forces involved in bacteria – host cells/(bio)materials surface adhesion is crucial for the identification of new ligand-binding events and its assessment as novel targets for alternative anti-infective therapies.This article aims to highlight the potential of AFM-based force spectroscopy for new targeted therapies development against bacterial infections in which adhesion plays a pivotal role and does not aim to be an extensive overview on the AFM technical capabilities and theory of single molecule force spectroscopy.

Multiparametric atomic force microscopy imaging of single native exosomes.

The advent of atomic force microscopy (AFM) provides a novel powerful tool for addressing biological issues in their native states. AFM uses a sharp tip mounted at the end of a microfabricated cantilever to probe the specimens immobilized on the support. Compared with other high-resolution imaging and measurement techniques (e.g. super-resolution optical microscopy, scanning electron microscopy, transmission electron microscopy, and magnetic/optical tweezers), the unique merit of AFM is that it is able to simultaneously acquire the structures and properties of living biological samples under aqueous conditions with unprecedented spatiotemporal resolution (nanometer spatial resolution and millisecond temporal resolution) [1], making AFM an invaluable platform for revealing the underlying mechanisms guiding life activities. The wide applications of AFM in molecular and cell biology provide considerable novel insights into the physiological/pathological processes [2]. Particularly, in recent years, a new AFM imaging mode, which is called peak force tapping (PFT)...

Altered N-glycan composition impacts flagella-mediated adhesion in Chlamydomonas reinhardtii.

For the unicellular alga Chlamydomonas reinhardtii, the presence of N-glycosylated proteins on the surface of two flagella is crucial for both cell-cell interaction during mating and flagellar surface adhesion. However, it is not known whether only the presence or also the composition of N-glycans attached to respective proteins is important for these processes. To this end, we tested several C. reinhardtii insertional mutants and a CRISPR/Cas9 knockout mutant of xylosyltransferase 1A, all possessing altered N-glycan compositions. Taking advantage of atomic force microscopy and micropipette force measurements, our data revealed that reduction in N-glycan complexity impedes the adhesion force required for binding the flagella to surfaces. This results in impaired polystyrene bead binding and transport but not gliding of cells on solid surfaces. Notably, assembly, intraflagellar transport, and protein import into flagella are not affected by altered N-glycosylation. Thus, we conclude that proper N-glycosylation of flagellar proteins is crucial for adhering C. reinhardtii cells onto surfaces, indicating that N-glycans mediate surface adhesion via direct surface contact.

Temporal sequence of the human RBCs' vesiculation observed in nano-scale with application of AFM and complementary techniques

Based on the multimodal characterization of human red blood cells (RBCs), the link between the storage-related sequence of the nanoscale changes in RBC membranes in the relation to their biochemical profile as well as mechanical and functional properties was presented. On the background of the accumulation of RBCs waste products, programmed cell death and impaired rheological properties, progressive alterations in the RBC membranes including changes in their height and diameter as well as the in situ characterization of RBC-derived microparticles (RMPs) on the RBCs surface were presented. The advantage of atomic force microscopy (AFM) in RMPs visualization, even at the very early stage of vesiculation, was shown based on the results revealed by other reference techniques. The nanoscale characterization of RMPs was correlated with a decrease in cholesterol and triglycerides levels in the RBC membranes, proving the link between the lipids leakage from RBCs and the process of vesiculation.

<italic>In situ</italic> imaging and analysis of the nanostructures in natural hydrogels from carnivorous plants by atomic force microscopy

Natural hydrogels have been widely applied in the field of biomedicine for their biocompatible and biodegradable characteristics. However, due to the lack of adequate observation tools, so far the detailed organizations and structures of native natural hydrogels at the nanoscale are still not fully understood. The advent of atomic force microscopy (AFM) provides a novel powerful tool for characterizing biomaterials, but studies about utilizing AFM to investigate the nanostructures of native natural hydrogels are still scarce. In this paper, AFM in situ high-resolution imaging was used to reveal the nanoscopic fine structures of the natural hydrogels secreted by four types of carnivorous plants ( Drosera capensis , Pinguicula cyclosecta , Sarracenia rubra , and Dionaea muscipula ). Mucilage secreted by Drosera capensis or Pinguicula cyclosecta was coated on the surface of mica, and the subsequent AFM imaging of the mucilage-coated mica in air clearly revealed that both the mucilage secreted by Drosera capensis and Pinguicula cyclosecta contained a large number of nanofibers which had diverse self-assembly behaviors. Nectar secreted by Sarracenia rubra or Dionaea muscipula was coated on the surface of glass slides, and AFM images of the nectar-coated glass slide recorded in deionized water showed that both the nectar secreted by Sarracenia rubra and Dionaea muscipula considerably contained nanoparticles. Statistical results showed that the size of nanoparticles in the nectar of Dionaea muscipula was significantly larger than that of nanoparticles in the nectar of Sarracenia rubra . The study improves our understanding of the natural hydrogels secreted by carnivorous plants and provides a novel approach for characterizing the nanostructures of natural biomaterials in their native states, offering new possibilities for the studies of supramolecular biomaterials.

The Clustering of mApoE Anti-Amyloidogenic Peptide on Nanoparticle Surface Does Not Alter Its Performance in Controlling Beta-Amyloid Aggregation.

The deposition of amyloid-β (Aβ) plaques in the brain is a significant pathological signature of Alzheimer’s disease, correlating with synaptic dysfunction and neurodegeneration. Several compounds, peptides, or drugs have been designed to redirect or stop Aβ aggregation. Among them, the trideca-peptide CWG-LRKLRKRLLR (mApoE), which is derived from the receptor binding sequence of apolipoprotein E, is effectively able to inhibit Aβ aggregation and to promote fibril disaggregation. Taking advantage of Atomic Force Microscopy (AFM) imaging and fluorescence techniques, we investigate if the clustering of mApoE on gold nanoparticles (AuNP) surface may affect its performance in controlling Aβ aggregation/disaggregation processes. The results showed that the ability of free mApoE to destroy preformed Aβ fibrils or to hinder the Aβ aggregation process is preserved after its clustering on AuNP. This allows the possibility to design multifunctional drug delivery systems with clustering of anti-amyloidogenic molecules on any NP surface without affecting their performance in controlling Aβ aggregation processes.

Nanoscale Organization and Functional Analysis of Carnivorous Plant Mucilage by Atomic Force Microscopy

Uncovering the underlying mechanisms guiding the behaviors of natural sticky glue is of important significance for developing novel biomimetic or bioinspired materials to regulate cellular activities. Carnivorous plants secrete adhesive mucilage to capture insects, but the nanoscale organizations of the mucilage are still not fully understood. In particular, the advent of atomic force microscopy (AFM) provides a powerful tool for investigating the structures and properties of biological samples in their native states with unprecedented spatial resolution, offering novel possibilities for the studies of characterizing biomaterials. In this work, AFM was utilized to reveal the nanostructures of mucilage secreted by carnivorous plant (Pinguicula and Sarracenia) for promoting cell growth. AFM imaging of the mucilage-coated substrates in air showed that nanostructures (nanoparticles and nanofibers) with different assembly behaviors were significantly observed in mucilage, which were confirmed by electron microscopy imaging. AFM in situ imaging in liquids remarkably revealed that nanoparticles were contained in native mucilage. The mechanical properties of individual nanofibers were visualized and quantified by AFM indenting assays. The elemental organizations of the mucilage were analyzed, and the experiments of cells grown on mucilage-coated substrates indicated that carnivorous plant mucilage could facilitate cell growth. The research provides novel insights into the nanostructures and mechanical properties as well as biological functions of mucilage secreted by carnivorous plants, which will have potential impacts on the studies of biomaterials for tuning cell behaviors.

Nano-scientific Application of Atomic Force Microscopy in Pathology: from Molecules to Tissues.

The advantages of atomic force microscopy (AFM) in biological research are its high imaging resolution, sensitivity, and ability to operate in physiological conditions. Over the past decades, rigorous studies have been performed to determine the potential applications of AFM techniques in disease diagnosis and prognosis. Many pathological conditions are accompanied by alterations in the morphology, adhesion properties, mechanical compliances, and molecular composition of cells and tissues. The accurate determination of such alterations can be utilized as a diagnostic and prognostic marker. Alteration in cell morphology represents changes in cell structure and membrane proteins induced by pathologic progression of diseases. Mechanical compliances are also modulated by the active rearrangements of cytoskeleton or extracellular matrix triggered by disease pathogenesis. In addition, adhesion is a critical step in the progression of many diseases including infectious and neurodegenerative diseases. Recent advances in AFM techniques have demonstrated their ability to obtain molecular composition as well as topographic information. The quantitative characterization of molecular alteration in biological specimens in terms of disease progression provides a new avenue to understand the underlying mechanisms of disease onset and progression. In this review, we have highlighted the application of diverse AFM techniques in pathological investigations.

Advances in Atomic Force Microscopy: Weakly Perturbative Imaging of the Interfacial Water.

The structure and dynamics of interfacial water, determined by the water-interface interactions, are important for a wide range of applied fields and natural processes, such as water diffusion (Kim et al., 2013), electrochemistry (Markovic, 2013), heterogeneous catalysis (Over et al., 2000), and lubrication (Zilibotti et al., 2013). The precise understanding of water-interface interactions largely relies on the development of atomic-scale experimental techniques (Guo et al., 2014) and computational methods (Hapala et al., 2014b). Scanning probe microscopy has been extensively applied to probe interfacial water in many interdisciplinary fields (Ichii et al., 2012; Shiotari and Sugimoto, 2017; Peng et al., 2018a). In this perspective, we review the recent progress in the noncontact atomic force microscopy (nc-AFM) imaging and AFM simulation techniques and discuss how the newly developed techniques are applied to study the properties of interfacial water. The nc-AFM with the quadrupole-like CO-terminated tip can achieve ultrahigh-resolution imaging of the interfacial water on different surfaces, trace the reconstruction of H-bonding network and determine the intrinsic structures of the weakly bonded water clusters and even their metastable states. In the end, we present an outlook on the directions of future AFM studies of interfacial water as well as the challenges faced by this field.

Use of Atomic Force Microscopy to Measure Mechanical Properties and Turgor Pressure of Plant Cells and Plant Tissues.

We present here the use of atomic force microscopy to indent plant tissues and recover its mechanical properties. Using two different microscopes in indentation mode, we show how to measure an elastic modulus and use it to evaluate cell wall mechanical properties. In addition, we also explain how to evaluate turgor pressure. The main advantages of atomic force microscopy are that it is non-invasive, relatively rapid (5~20 min), and that virtually any type of living plant tissue that is superficially flat can be analyzed without the need for treatment. The resolution can be very good, depending on the tip size and on the number of measurements per unit area. One limitation of this method is that it only gives direct access to the superficial cell layer.

Tunable Hybrid Biopolymeric Hydrogel Scaffolds Based on Atomic Force Microscopy Characterizations for Tissue Engineering.

Developing adequate biomaterials to engineer cell-scaffold interactions has become a promising way for physically regulating the biological behaviors of cells in the field of tissue engineering. Biopolymeric hydrogels have shown great merits as cellular scaffolds due to their biocompatible and biodegradable characteristics. In particular, the advent of atomic force microscopy (AFM) provides a powerful tool for characterizing native specimens at the micro/nanoscale, but utilizing AFM to investigate the detailed structures and properties of hydrogel scaffolds has been still scarce. In this paper, hybrid natural biopolymers are used to form hydrogel scaffolds which exhibit tunable structural and mechanical properties characterized by AFM peak force tapping imaging, and the applications of the formed hydrogel scaffolds in tissue engineering are studied. AFM morphological images showed that the cross-linking reactions of sodium alginate and gum arabic via calcium cations yielded the porous hydrogel scaffolds. By altering the component ratios, AFM mechanical images showed that the porous and mechanical properties (Young's modulus and adhesion force) of the hydrogel scaffolds were tunable. Next, the nanoscale structural and mechanical dynamics of the fabricated hydrogel scaffolds during the degradation process were revealed by AFM peak force tapping imaging. The experimental results on three different types of cells showed that the fabricated hydrogel scaffolds facilitate the formation of cellular spheroids. The research provides a novel idea to design tunable hydrogel scaffolds based on AFM characterizations for investigating cell-scaffold interactions, which will have potential impacts on tissue engineering.