Dynamics of Molecular Self-Assembly of Short Peptides at Liquid-Solid Interfaces - Effect of Charged Amino Acid Point Mutations

Self-organizing solid-binding peptides on atomically flat solid surfaces offer a unique bio/nano hybrid platform, useful for understanding the basic nature of biology/solid coupling and their practical applications. The surface behavior of peptides is determined by their molecular folding, which is influenced by various factors and is challenging to study. Here, the effect of charged amino acids is studied on the self-assembly behavior of a directed evolution selected graphite-binding dodecapeptide on graphite surface. Two mutations, M6 and M8, are designed to introduce negatively and positively charged moieties, respectively, at the anchoring domain of the wild-type (WT) peptide, affecting both binding and assembly. The questions addressed here are whether mutant peptides exhibit molecular crystal formation and demonstrate molecular recognition on the solid surface based on the specific mutations. Frequency-modulated atomic force microscopy is used for observations of the surface processes dynamically in water at molecular resolution over several hours at the ambient. The results indicate that while the mutants display distinct folding and surface behavior, each homogeneously nucleates and forms 2D self-organized patterns, akin to the WT peptide. However, their growth dynamics, domain formation, and crystalline lattice structures differ significantly. The results represent a significant step toward the rational design of bio/solid interfaces, potent facilitators of a variety of future implementations.

Synthesis of optically active star polymers consisting of helical poly(phenylacetylene) chains by the living polymerization of phenylacetylenes and their chiroptical properties

Star polymers consisting of three helical poly(phenylacetylene) chains with a precisely controlled molecular weight (molar mass dispersity < 1.03) were successfully synthesized by the living polymerization of phenylacetylene derivatives with a Rh-based multicomponent catalyst system comprising trifunctional initiators, which have three phenylboronates centered on a benzene ring, the Rh complex [Rh(nbd)Cl]2, diphenylacetylene, triphenylphosphine, and a base. The analysis of chiroptical properties of the optically active star polymers obtained by the living polymerization of optically active phenylacetylene derivatives revealed that the star polymers exhibited chiral amplification properties owing to their unique topology compared with the corresponding linear polymers.

Protocol for live imaging of intracellular nanoscale structures using atomic force microscopy with nanoneedle probes

Atomic force microscopy (AFM) is capable of nanoscale imaging but has so far only been used on cell surfaces when applied to a living cell. Here, we describe a step-by-step protocol for nanoendoscopy-AFM, which enables the imaging of nanoscale structures inside living cells. The protocol consists of cell staining, fabrication of the nanoneedle probes, observation inside living cells using 2D and 3D nanoendoscopy-AFM, and visualization of the 3D data. For complete details on the use and execution of this protocol, please refer to Penedo et al. (2021)1 and Penedo et al. (2021).2.

Nanopipette Fabrication Guidelines for SICM Nanoscale Imaging

Scanning ion conductance microscopy (SICM) is a promising tool for visualizing the dynamics of nanoscale cell surface topography. However, there are still no guidelines for fabricating nanopipettes with ideal shape consisting of small apertures and thin glass walls. Therefore, most of the SICM imaging has been at a standstill at the submicron scale. In this study, we established a simple and highly reproducible method for the fabrication of nanopipettes with sub-20 nm apertures. To validate the improvement in the spatial resolution, we performed time-lapse imaging of the formation and disappearance of endocytic pits as a model of nanoscale time-lapse topographic imaging. We have also successfully imaged the localization of the hot spot and the released extracellular vesicles. The nanopipette fabrication guidelines for the SICM nanoscale topographic imaging can be an essential tool for understanding cell-cell communication.

Three-dimensional ordering of water molecules reflecting hydroxyl groups on sapphire (001) and α-quartz (100) surfaces

Water molecules on oxide surfaces influence the chemical reactivity and molecular adsorption behavior of oxides. Herein, three-dimensional atomic force microscopy (3D-AFM) and molecular dynamics simulations are used to visualize the surface hydroxyl (OH) groups and their hydration structures on sapphire (001) and α-quartz (100) surfaces at the atomic-scale. The obtained results revealed that the spatial density distributions and hydrogen-bonding strengths of surface OH groups affect their local hydration structures. In particular, the force curves obtained by 3D-AFM suggest that the hydration forces of water molecules intensify at sites where water molecules strongly interact with the surface OH groups. The insights obtained in this study deepen our understanding of the affinities of Al2O3 and SiO2 for water molecules and contribute to the use of 3D-AFM in the investigation of atomic-scale hydration structures on various surfaces, thereby benefiting a wide range of research fields dealing with solid-liquid interfaces.

Morphological Changes of Polymer-Grafted Nanocellulose during a Drying Process

Nanocellulose is emerging as a sustainable building block in materials science. Surface modification via polymer grafting has proven to be effective in tuning diverse material properties of nanocellulose, including wettability of films and the reinforcement effect in polymer matrices. Despite its widespread use in various environments, the structure of a single polymer-grafted nanocellulose remains poorly understood. Here, we investigate the morphologies of polymer-grafted CNFs at water-mica and air-mica interfaces by using all-atom molecular dynamics simulation and atomic force microscopy. We show that the morphologies of the polymer-grafted CNFs undergo a marked change in response to the surrounding environment due to variations in the conformation of the surface polymer chains. Our results provide novel insights into the molecular structure of polymer-grafted CNFs and can facilitate the design and development of innovative biomass-based nanomaterials.

Size-Dependent Corrosion of Al-Fe Intermetallic Particles at Al-Mg Alloy Surfaces Investigated by In-Liquid Nanoscale Potential Measurement Technique

Corrosion of Al alloy often starts from the nanoscale corrosion around the surface-exposed Al-Fe intermetallic particles (IMPs) and leads to a serious damage limiting its application range in the automobile industry. To solve this issue, understanding of the nanoscale corrosion mechanism around the IMP is essential, yet it is impeded by the difficulties in directly visualizing nanoscale distribution of reaction activity. Here, this difficulty is overcomed by open-loop electric potential microscopy (OL-EPM) and investigate nanoscale corrosion behavior around the IMPs in H₂ SO₄ solution. The OL-EPM results reveal that the corrosion around a small IMP settles down in a short time (<30 min) after transient dissolution of the IMP surface while that around a large IMP lasts for a long time especially at its edges and results in a severe damage of the IMP and matrix. This result suggests that an Al alloy with many small IMPs gives a better corrosion resistance than that with few large IMPs if the total Fe content is the same. This difference is confirmed by corrosion weight loss test using Al alloys with different IMP sizes. This finding should give an important guideline to improve the corrosion resistance of Al alloy.

Biophysical Properties of the Fibril Structure of the Toxic Conformer of Amyloid-β42: Characterization by Atomic Force Microscopy in Liquid and Molecular Docking

Alzheimer's disease is associated with the aggregation of the misfolded neuronal peptide, amyloid-β42 (Aβ42). Evidence has suggested that several reasons are responsible for the toxicity caused by the aggregation of Aβ42, including the conformational restriction of Aβ42. In this study, one of the toxic conformers of Aβ42, which contains a Glu-to-Pro substitution (E22P-Aβ42), was explored using atomic force microscopy and molecular docking to study the aggregation dynamics. We proposed a systematic model of fibril formation to better understand the molecular basis of conformational transitions in the Aβ42 species. Our results demonstrated the formation of amorphous aggregates in E22P-Aβ42 that are stem-based, network-like structures, while the formation of mature fibrils occurred in the less toxic conformer of Aβ42, E22-Aβ42, that are sphere-like flexible structures. A comparison was made between the biophysical properties of E22P-Aβ42 and E22-Aβ42 that revealed that E22P-Aβ42 had greater stiffness, dihedral angle, number of β sheets involved, and elasticity, compared with E22-Aβ42. These findings will have considerable implications toward our understanding of the structural basis of the toxicity caused by conformational diversity in Aβ42 species.

Molecular Dynamics of Drying-Induced Structural Transformations in a Single Nanocellulose

Nanocellulose is attracting attention in the field of materials science as a sustainable building block. Nanocellulose-based materials, such as films, membranes, and foams, are fabricated by drying colloidal dispersions. However, little is known about how the structure of a single nanocellulose changes during the complex drying process. Here, all-atom molecular dynamics simulations and atomic force microscopy is used to investigate the structural dynamics of single nanocellulose during drying. It is found that the twist morphology of the nanocellulose became localized along the fibril axis during the final stage of the drying process. Moreover, it is shown that conformational changes at C6 hydroxymethyl groups and glycoside bond is accompanied by the twist localization, indicating that the increase in the crystallinity occurred in the process. It is expected that the results will provide molecular insights into nanocellulose structures in material processing, which is helpful for the design of materials with advanced functionalities.

Molecular Scale Structure and Kinetics of Layer-by-Layer Peptide Self-Organization at Atomically Flat Solid Surfaces

Understanding the mechanisms of self-organization of short peptides into two- and three-dimensional architectures are of great interest in the formation of crystalline biomolecular systems and their practical applications. Since the assembly is a dynamic process, the study of structural development is challenging at the submolecular dimensions continuously across an adequate time scale in the natural biological environment, in addition to the complexities stemming from the labile molecular structures of short peptides. Self-organization of solid binding peptides on surfaces offers prospects to overcome these challenges. Here we use a graphite binding dodecapeptide, GrBP5, and record its self-organization process of the first two layers on highly oriented pyrolytic graphite surface in an aqueous solution by using frequency modulation atomic force microscopy in situ. The observations suggest that the first layer forms homogeneously, generating self-organized crystals with a lattice structure in contact with the underlying graphite. The second layer formation is mostly heterogeneous, triggered by the crystalline defects on the first layer, growing row-by-row establishing nominally diverse biomolecular self-organized structures with transient crystalline phases. The assembly is highly dependent on the peptide concentration, with the nucleation being high in high molecular concentrations, e.g., >100 μM, while the domain size is small, with an increase in the growth rate that gradually slows down. Self-assembled peptide crystals are composed of either singlets or doublets establishing P1 and P2 oblique lattices, respectively, each commensurate with the underlying graphite lattice with chiral crystal relations. This work provides insights into the surface behavior of short peptides on solids and offers quantitative guidance toward elucidating molecular mechanisms of self-assembly helping in the scientific understanding and construction of coherent bio/nano hybrid interfaces.

Correlative Analysis of Ion-Concentration Profile and Surface Nanoscale Topography Changes Using Operando Scanning Ion Conductance Microscopy

Although various spectroscopic methods have been developed to capture ion-concentration profile changes, it is still difficult to visualize the ion-concentration profile and surface topographical changes simultaneously during the charging/discharging of lithium-ion batteries (LIBs). To tackle this issue, we have developed an operando scanning ion conductance microscopy (SICM) method that can directly visualize an ion-concentration profile and surface topography using a SICM nanopipette while controlling the sample potential or current with a potentiostat for characterizing the polarization state during charging/discharging. Using operando SICM on the negative electrode (anode) of LIBs, we have characterized ion-concentration profile changes and the reversible volume changes related to the phase transition during cyclic voltammetry (CV) and charge/discharge of the graphite anode. Operando SICM is a versatile technique that is likely to be of major value for evaluating the correlation between the electrolyte concentration profile and nanoscale surface topography changes.

Molecular Assembly and Gelating Behavior of (L)-Alanine Derivatives

In this study, we designed and synthesized a low-molecular-weight organogelator derived from (l)-amino acids. We performed gelation assays using (l)-amino acid derivatives to confirm the gelation ability, which was found to be high in several compounds. The (l)-alanine derivatives were determined to be excellent gelators, forming good gels even when smaller amounts were added. These results led to a library of amino acid-derived organogelators. In addition, the thermal properties of the (l)-alanine derivatives with high gelation performance were measured. Differential scanning calorimetry measurements revealed that the thermal stability of the gels could be controlled by changing the gelator concentration. The surface states of the obtained gels were observed by field-emission scanning electron microscopy and atomic force microscopy measurements, which confirmed the structure of the self-molecular aggregates. Self-molecular aggregates were observed to be helical or sheet-like, and the gels were constructed by forming aggregates via self-molecular recognition.

Identification of a novel type of focal adhesion remodelling via FAK/FRNK replacement, and its contribution to cancer progression

Numerous studies have investigated the various cellular responses against genotoxic stress, including those mediated by focal adhesions. We here identified a novel type of focal adhesion remodelling that occurs under genotoxic stress conditions, which involves the replacement of active focal adhesion kinase (FAK) with FAK-related non-kinase (FRNK). FRNK stabilized focal adhesions, leading to strong cell-matrix adhesion, and FRNK-depleted cells were easily detached from extracellular matrix upon genotoxic stress. This remodelling occurred in a wide variety of cells. In vivo, the stomachs of Frnk-knockout mice were severely damaged by genotoxic stress, highlighting the protective role of FRNK against genotoxic stress. FRNK was also found to play a vital role in cancer progression, because FRNK depletion significantly inhibited cancer dissemination and progression in a mouse cancer model. Furthermore, in human cancers, FRNK was predominantly expressed in metastatic tissues and not in primary tissues. We hence conclude that this novel type of focal adhesion remodelling reinforces cell adhesion and acts against genotoxic stress, which results in the protection of normal tissues, but in turn facilitates cancer progression.

Highly Stable Triangular Single-Layer 2D Assemblies: Synthesis and Their Stimuli-Responsive Elastic and Anisotropic Curling

Synthesis of highly stable single-layer two-dimensional assemblies (SLAs) is a key challenge in supramolecular science, especially those with long-range molecular order and well-defined morphology. Here, thin (thickness < 2 nm) triangular Au(I)-thiolate SLAs with high thermo-, solvato- and mechano- stability have been synthesized via a double-ligand co-assembly strategy. Furthermore, the SLAs show assembly-level elastic and anisotropic deformation responses to external stimuli as a result of the long-range anisotropic molecular packing, which provides SLAs with new application potentials in bio-mimic nanomechanics.

Formation and evolution of carbonaceous asteroid Ryugu: Direct evidence from returned samples

Samples of the carbonaceous asteroid Ryugu were brought to Earth by the Hayabusa2 spacecraft. We analyzed 17 Ryugu samples measuring 1 to 8 millimeters. Carbon dioxide-bearing water inclusions are present within a pyrrhotite crystal, indicating that Ryugu's parent asteroid formed in the outer Solar System. The samples contain low abundances of materials that formed at high temperatures, such as chondrules and calcium- and aluminum-rich inclusions. The samples are rich in phyllosilicates and carbonates, which formed through aqueous alteration reactions at low temperature, high pH, and water/rock ratios of <1 (by mass). Less altered fragments contain olivine, pyroxene, amorphous silicates, calcite, and phosphide. Numerical simulations, based on the mineralogical and physical properties of the samples, indicate that Ryugu's parent body formed ~2 million years after the beginning of Solar System formation.

Ion-specific nanoscale compaction of cysteine-modified poly(acrylic acid) brushes revealed by 3D scanning force microscopy with frequency modulation detection

Stimuli-responsive polyelectrolyte brushes adapt their physico-chemical properties according to pH and ion concentrations of the solution in contact. We synthesized a poly(acrylic acid) bearing cysteine residues at side chains and a lipid head group at the terminal, and incorporated them into a phospholipid monolayer deposited on a hydrophobic silane monolayer. The ion-specific, nanoscale response of polyelectrolyte brushes was detected by using three-dimensional scanning force microscopy (3D-SFM) combined with frequency modulation detection. The obtained topographic and mechanical landscapes indicated that the brushes were uniformly stretched, undergoing a gradual transition from the brush to the bulk electrolyte in the absence of divalent cations. When 1 mM calcium ions were added, the brushes were uniformly compacted, exhibiting a sharper brush-to-bulk transition. Remarkably, the addition of 1 mM cadmium ions made the brush surface significantly rough and the mechanical landscape highly heterogeneous. Currently, cadmium-specific nanoscale compaction of the brushes is attributed to the coordination of thiol and carboxyl side chains with cadmium ions, as suggested for naturally occurring, heavy metal binding proteins.

Actin-binding domain of Rng2 sparsely bound on F-actin strongly inhibits actin movement on myosin II

We report a case in which sub-stoichiometric binding of an actin-binding protein has profound structural and functional consequences, providing an insight into the fundamental properties of actin regulation. Rng2 is an IQGAP contained in contractile rings in the fission yeast Schizosaccharomyces pombe Here, we used high-speed atomic force microscopy and electron microscopy and found that sub-stoichiometric binding of the calponin-homology actin-binding domain of Rng2 (Rng2CHD) induces global structural changes in skeletal muscle actin filaments, including shortening of the filament helical pitch. Sub-stoichiometric binding of Rng2CHD also reduced the affinity between actin filaments and muscle myosin II carrying ADP and strongly inhibited the motility of actin filaments on myosin II in vitro. On skeletal muscle myosin II-coated surfaces, Rng2CHD stopped the actin movements at a binding ratio of 11%. Rng2CHD also inhibited actin movements on myosin II of the amoeba Dictyostelium, but in this case, by detaching actin filaments from myosin II-coated surfaces. Thus, sparsely bound Rng2CHD induces apparently cooperative structural changes in actin filaments and inhibits force generation by actomyosin II.

Molecular insights on the crystalline cellulose-water interfaces via three-dimensional atomic force microscopy

Cellulose, a renewable structural biopolymer, is ubiquitous in nature and is the basic reinforcement component of the natural hierarchical structures of living plants, bacteria, and tunicates. However, a detailed picture of the crystalline cellulose surface at the molecular level is still unavailable. Here, using atomic force microscopy (AFM) and molecular dynamics (MD) simulations, we revealed the molecular details of the cellulose chain arrangements on the surfaces of individual cellulose nanocrystals (CNCs) in water. Furthermore, we visualized the three-dimensional (3D) local arrangement of water molecules near the CNC surface using 3D AFM. AFM experiments and MD simulations showed anisotropic water structuring, as determined by the surface topologies and exposed chemical moieties. These findings provide important insights into our understanding of the interfacial interactions between CNCs and water at the molecular level. This may allow the establishment of the structure-property relationship of CNCs extracted from various biomass sources.

Visualizing Molecular-Scale Adsorption Structures of Anti-freezing Surfactants on Sapphire (0001) Surfaces at Different Concentrations by 3D Scanning Force Microscopy

Anti-freezing surfactants form an adsorption layer at the solid-water interface to inhibit the nucleation and growth of ice. However, this mechanism has not been elucidated at the molecular scale because of the difficulties in visualizing such adsorption structures. In this study, we overcome this limitation by directly visualizing the three-dimensional (3D) adsorption structures of anti-freezing surfactants, hexadecyltrimethylammonium bromide (C₁₆TABs), on sapphire (0001) surfaces through 3D scanning force microscopy. We present molecularly resolved two-dimensional/3D images of the adsorption structures in solutions of 1, 10, and 100 ppm. At 1 ppm, the molecules form a monolayer with a flat-lying configuration. At 10 ppm, the molecular orientation is closer to the upright configuration, with a relatively large tilt angle. At 100 ppm, the molecules form a bilayer with almost upright configurations, providing excellent screening of the sapphire surface from water. Owing to the steric and electrostatic repulsion between adjacent molecular head groups, the surface of the bilayer exhibits relatively large fluctuations, inhibiting the formation of stable ice-like structures. The understanding of molecular-level mechanisms provides important guidelines for improving the design of anti-freezing surfactants for practical applications such as car coolants.

Probing the Structural Details of Chitin Nanocrystal-Water Interfaces by Three-Dimensional Atomic Force Microscopy

Chitin is one of the most abundant and renewable natural biopolymers. It exists in the form of crystalline microfibrils and is the basic structural building block of many biological materials. Its surface crystalline structure is yet to be reported at the molecular level. Herein, atomic force microscopy (AFM) in combination with molecular dynamics simulations reveals the molecular-scale structural details of the chitin nanocrystal (chitin NC)-water interface. High-resolution AFM images reveal the molecular details of chitin chain arrangements at the surfaces of individual chitin NCs, showing highly ordered, stable crystalline structures almost free of structural defects or disorder. 3D-AFM measurements with submolecular spatial resolution demonstrate that chitin NC surfaces interact strongly with interfacial water molecules creating stable, well-ordered hydration layers. Inhomogeneous encapsulation of the underlying chitin substrate by these hydration layers reflects the chitin NCs' multifaceted surface character with different chain arrangements and molecular packing. These findings provide important insights into chitin NC structures at the molecular level, which is critical for developing the properties of chitin-based nanomaterials. Furthermore, these results will contribute to a better understanding of the chemical and enzymatic hydrolysis of chitin and other native polysaccharides, which is also essential for the enzymatic conversion of biomass.

Unraveling the Host-Selective Toxic Interaction of Cassiicolin with Lipid Membranes and Its Cytotoxicity

Cassiicolin (Cas), a toxin produced by Corynespora cassiicola, is responsible for Corynespora leaf fall disease in susceptible rubber trees. Currently, the molecular mechanisms of the cytotoxicity of Cas and its host selectivity have not been fully elucidated. Here, we analyzed the binding of Cas1 and Cas2 to membranes consisting of different plant lipids and their membrane disruption activities. Using high-speed atomic force microscopy and confocal microscopy, we reveal that the binding and disruption activities of Cas1 and Cas2 on lipid membranes are strongly dependent on the specific plant lipids. The negative phospholipids, glycerolipids, and sterols are more sensitive to membrane damage caused by Cas1 and Cas2 than neutral phospholipids and betaine lipids. Mature Cas1 and Cas2 play an essential role in causing membrane disruption. Cytotoxicity tests on rubber leaves of Rubber Research Institute of Vietnam (RRIV) 1, RRIV 4, and Prang Besar (PB) 255 clones suggest that the toxins cause necrosis of rubber leaves, except for the strong resistance of PB 255 against Cas2. Cryogenic scanning electron microscopy analyses of necrotic leaf tissues treated with Cas1 confirm that cytoplasmic membranes are vulnerable to the toxin. Thus, the host selectivity of Cas toxin is attained by the lipid-dependent binding activity of Cas to the membrane, and the cytotoxicity of Cas arises from its ability to form biofilm-like structures and to disrupt specific membranes.

Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality

Three-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid-liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chromosomes or proteins in cells, with the expectation of being able to resolve their three-dimensional structures. Here, we have developed a computational method to simulate 3D-AFM images of biopolymers by using the Jarzynski equality. It is found that some parts of the fiber structure of biopolymers are indeed resolved in the 3D-AFM image. The dependency of 3D-AFM images on the vertical scanning velocity is investigated, and optimum scanning velocities are found. It is also clarified that forces in nonequilibrium processes are measured in 3D-AFM measurements when the dynamics of polymers are slower than the scanning of the probe.

Chemical fixation creates nanoscale clusters on the cell surface by aggregating membrane proteins

Chemical fixations have been thought to preserve the structures of the cells or tissues. However, given that the fixatives create crosslinks or aggregate proteins, there is a possibility that these fixatives create nanoscale artefacts by aggregation of membrane proteins which move around freely to some extent on the cell surface. Despite this, little research has been conducted about this problem, probably because there has been no method for observing cell surface structures at the nanoscale. In this study, we have developed a method to observe cell surfaces stably and with high resolution using atomic force microscopy and a microporous silicon nitride membrane. We demonstrate that the size of the protrusions on the cell surface is increased after treatment with three commonly used fixatives and show that these protrusions were created by the aggregation of membrane proteins by fixatives. These results call attention when observing fixed cell surfaces at the nanoscale.

Atomic force microscopy imaging shows that cell fixation can lead to unwanted aggregation of membrane proteins.

Visualizing intracellular nanostructures of living cells by nanoendoscopy-AFM

Atomic force microscopy (AFM) is the only technique that allows label-free imaging of nanoscale biomolecular dynamics, playing a crucial role in solving biological questions that cannot be addressed by other major bioimaging tools (fluorescence or electron microscopy). However, such imaging is possible only for systems either extracted from cells or reconstructed on solid substrates. Thus, nanodynamics inside living cells largely remain inaccessible with the current nanoimaging techniques. Here, we overcome this limitation by nanoendoscopy-AFM, where a needle-like nanoprobe is inserted into a living cell, presenting actin fiber three-dimensional (3D) maps, and 2D nanodynamics of the membrane inner scaffold, resulting in undetectable changes in cell viability. Unlike previous AFM methods, the nanoprobe directly accesses the target intracellular components, exploiting all the AFM capabilities, such as high-resolution imaging, nanomechanical mapping, and molecular recognition. These features should greatly expand the range of intracellular structures observable in living cells.

Local Cross-Coupling Activity of Azide-Hexa(ethylene glycol)-Terminated Self-Assembled Monolayers Investigated by Atomic Force Microscopy

Azide-oligo(ethylene glycol)-terminated self-assembled monolayers (N₃-OEG-SAMs) are promising interfacial structures for surface functionalization. Its many potential applications include chemical/bio-sensing and construction of surface models owing to its cross-coupling activity that originates from the azide group and oligo(ethylene glycol) (OEG) units for non-specific adsorption resistance. However, there are only a few studies and limited information, particularly on the molecular-scale structures and local cross-coupling activities of N₃-OEG-SAMs, which are vital to understanding its surface properties and interfacial molecular design. In this study, molecular-scale surface structures and cross-coupling activity of azide-hexa(ethylene glycol)-terminated SAMs (N₃-EG₆-SAMs) were investigated using frequency modulation atomic force microscopy (FM-AFM) in liquid. The N₃-EG₆-SAMs were prepared on Au(111) substrates through the self-assembly of 11-azido-hexa(ethylene glycol)-undecane-1-thiol (N₃-EG₆-C₁₁-HS) molecules obtained from a liquid phase. Subnanometer-resolution surface structures were visualized in an aqueous solution using a laboratory-built FM-AFM instrument. The results show a well-ordered molecular arrangement in the N₃-EG₆-SAM and its clean surfaces originating from the adsorption resistance property of the terminal EG₆ units. Surface functionalization by the cross-coupling reaction of copper(I)-catalyzed azide-alkyne cycloaddition was observed, indicating a structural change in the form of fluctuating structures and island-shaped structures depending on the concentration of the alkyne molecules. The FM-AFM imaging enabled to provide information on the relationship between the surface structures and cross-coupling activity. These findings provide molecular-scale information on the functionalization of the N₃-EG₆-SAMs, which is helpful for the interfacial molecular design based on alkanethiol SAMs in many applications.

Macrocyclic Peptide-Conjugated Tip for Fast and Selective Molecular Recognition Imaging by High-Speed Atomic Force Microscopy

Fast and selective recognition of molecules at the nanometer scale without labeling is a much desired but still challenging goal to achieve. Here, we show the use of high-speed atomic force microscopy (HS-AFM) for real-time and real-space recognition of unlabeled membrane receptors using tips conjugated with small synthetic macrocyclic peptides. The single-molecule recognition method is validated by experiments on the human hepatocyte growth factor receptor (hMET), which selectively binds to the macrocyclic peptide aMD4. By testing and comparing aMD4 synthesized with linkers of different lengths and rigidities, we maximize the interaction between the functionalized tip and hMET added to both a mica surface and supported lipid bilayers. Phase contrast imaging by HS-AFM enables us to discriminate nonlabeled hMET against the murine MET homologue, which does not bind to aMD4. Moreover, using ligands and linkers of small size, we achieve minimal deterioration of the spatial resolution in simultaneous topographic imaging. The versatility of macrocyclic peptides in detecting unlimited types of membrane receptors with high selectivity and the fast imaging by HS-AFM broaden the range of future applications of this method for molecular recognition without labeling.

Visualisation of helical structures of poly(diphenylacetylene)s bearing chiral amide pendants by atomic force microscopy

The helical structures of poly(diphenylacetylene)s bearing optically active substituents linked through amide bonds and with a helicity memory have been visualised using atomic force microscopy. The polymers self-assembled into an ordered 2D monolayer on highly oriented pyrolytic graphite upon exposure to solvent vapour, whose helical pitch and handedness (right- and left-handed) were for the first time directly revealed at molecular resolution.

Characterization of the Depth of Discharge-Dependent Charge Transfer Resistance of a Single LiFePO4 Particle

The discharged state affects the charge transfer resistance of lithium-ion secondary batteries (LIBs), which is referred to as the depth of discharge (DOD). To understand the intrinsic charge/discharge property of LIBs, the DOD-dependent charge transfer resistance at the solid-liquid interface is required. However, in a general composite electrode, the conductive additive and organic polymeric binder are unevenly distributed, resulting in a complicated electron conduction/ion conduction path. As a result, estimating the DOD-dependent rate-determining factor of LIBs is difficult. In contrast, in micro/nanoscale electrochemical measurements, the primary or secondary particle is evaluated without using a conductive additive and providing an ideal mass transport condition. To control the DOD state of a single LiFePO₄ active material and evaluate the DOD-dependent charge transfer kinetic parameters, we use scanning electrochemical cell microscopy (SECCM), which uses a micropipette to form an electrochemical cell on a sample surface. The difference in charge transfer resistance at the solid-liquid interface depending on the DOD state and electrolyte solution could be confirmed using SECCM.

High-Speed Atomic Force Microscopy of the Structure and Dynamics of Calcite Nanoscale Etch Pits

Calcite dissolution is initiated by the formation of a nanoscale etch pit followed by step edge propagation and hence strongly influenced by the interactions between surface diffusing ions and step edges. However, such atomic-scale dynamics are mostly inaccessible with current imaging tools. Here, we overcome this limitation by using our recent development of high-speed frequency modulation atomic force microscopy. By visualizing atomic-scale structural changes of the etch pits at the calcite surface in water, we found the existence of mobile and less-mobile surface adsorption layers (SALs) in the etch pits. We also found that some etch pits maintain their size for a long time without expansion, and their step edges are often associated with less-mobile SALs, suggesting their step stabilization effect.

Nanoscale Reactivity Mapping of a Single-Crystal Boron-Doped Diamond Particle

Boron-doped diamond (BDD) is most often grown by chemical vapor deposition (CVD) in polycrystalline form, where the electrochemical response is averaged over the whole surface. Deconvoluting the impact of crystal orientation, surface termination, and boron-doped concentration on the electrochemical response is extremely challenging. To tackle this problem, we use CVD to grow isolated single-crystal microparticles of BDD with the crystal facets (100, square-shaped) and (111, triangle-shaped) exposed and combine with hopping mode scanning electrochemical cell microscopy (HM-SECCM) for electrochemical interrogation of the individual crystal faces (planar and nonplanar). Measurements are made on both hydrogen- (H-) and oxygen (O-)-terminated single-crystal facets with two different redox mediators, [Ru(NH₃)₆]^3+/2+ and Fe(CN)₆^4-/3-. Extraction of the half-wave potential from linear sweep and cyclic voltammetric experiments at all measurement (pixel) points shows unequivocally that electron transfer is faster at the H-terminated (111) surface than at the H-terminated (100) face, attributed to boron dopant differences. The most dramatic differences were seen for [Ru(NH₃)₆]^3+/2+ when comparing the O-terminated (100) surface to the H-terminated (100) face. Removal of the H-surface conductivity layer and a potential-dependent density of states were thought to be responsible for the behavior observed. Finally, a bimodal distribution in the electrochemical activity on the as-grown H-terminated polycrystalline BDD electrode is attributed to the dominance of differently doped (100) and (111) facets in the material.

Cell penetration efficiency analysis of different atomic force microscopy nanoneedles into living cells

Over the last decade, nanoneedle-based systems have demonstrated to be extremely useful in cell biology. They can be used as nanotools for drug delivery, biosensing or biomolecular recognition inside cells; or they can be employed to select and sort in parallel a large number of living cells. When using these nanoprobes, the most important requirement is to minimize the cell damage, reducing the forces and indentation lengths needed to penetrate the cell membrane. This is normally achieved by reducing the diameter of the nanoneedles. However, several studies have shown that nanoneedles with a flat tip display lower penetration forces and indentation lengths. In this work, we have tested different nanoneedle shapes and diameters to reduce the force and the indentation length needed to penetrate the cell membrane, demonstrating that ultra-thin and sharp nanoprobes can further reduce them, consequently minimizing the cell damage.

Structural and mechanical characteristics of exosomes from osteosarcoma cells explored by 3D-atomic force microscopy

Exosomes have recently gained interest as mediators of cell-to-cell communication and as potential biomarkers for cancer and other diseases. They also have potential as nanocarriers for drug delivery systems. Therefore, detailed structural, molecular, and biomechanical characterization of exosomes is of great importance for developing methods to detect and identify the changes associated with the presence of cancer and other diseases. Here, we employed three-dimensional atomic force microscopy (3D-AFM) to reveal the structural and nanomechanical properties of exosomes at high spatial resolution in physiologically relevant conditions. The substructural details of exosomes released from three different cell types were determined based on 3D-AFM force mapping. The resulting analysis revealed the presence of distinct local domains bulging out from the exosome surfaces, which were associated with the exosomal membrane proteins present on the outer surface. The nanomechanical properties of individual exosomes were determined from the 3D-force maps. We found a considerably high elastic modulus, ranging from 50 to 350 MPa, as compared to that obtained for synthetic liposomes. Moreover, malignancy-dependent changes in the exosome mechanical properties were revealed by comparing metastatic and nonmetastatic tumor cell-derived exosomes. We found a clear difference in their Young's modulus values, suggesting differences in their protein profiles and other exosomal contents. Exosomes derived from a highly aggressive and metastatic k-ras-activated human osteosarcoma (OS) cell line (143B) showed a higher Young's modulus than that derived from a nonaggressive and nonmetastatic k-ras-wildtype human OS cell line (HOS). The increased elastic modulus of the 143B cell-derived exosomes was ascribed to the presence of abundant specific proteins responsible for elastic fiber formation as determined by mass spectroscopy and confirmed by western blotting and ELISA. Therefore, we conclude that exosomes derived from metastatic tumor cells carry an exclusive protein content that differs from their nonmetastatic counterparts, and thus they exhibit different mechanical characteristics. Discrimination between metastatic and nonmetastatic malignant cell-derived exosomes would be of great importance for studying exosome biological functions and using them as diagnostic biomarkers for various tumor types. Our findings further suggest that metastatic tumor cells release exosomes that express increased levels of elastic fiber-associated proteins to preserve their softness.

Atomic-scale structures and dynamics at the growing calcite step edge investigated by high-speed frequency modulation atomic force microscopy

We have investigated the calcite growth mechanism by directly imaging atomic-scale structural changes at the growing step edges with high-speed frequency modulation atomic force microscopy (HS-FM-AFM). We compared the results...

Geometrical Characterization of Glass Nanopipettes with Sub-10 nm Pore Diameter by Transmission Electron Microscopy

Glass nanopipettes are widely used for various applications in nanosciences. In most of the applications, it is important to characterize their geometrical parameters, such as the aperture size and the inner cone angle at the tip region. For nanopipettes with sub-10 nm aperture and thin wall thickness, transmission electron microscopy (TEM) must be most instrumental in their precise geometrical measurement. However, this measurement has remained a challenge because heat generated by electron beam irradiation would largely deform sub-10 nm nanopipettes. Here, we provide methods for preparing TEM specimens that do not cause deformation of such tiny nanopipettes.

Improvements in fundamental performance of in-liquid frequency modulation atomic force microscopy

In-liquid frequency modulation atomic force microscopy (FM-AFM) has been used for visualizing subnanometer-scale surface structures of minerals, organic thin films and biological systems. In addition, three-dimensional atomic force microscopy (3D-AFM) has been developed by combining it with a three-dimensional (3D) tip scanning method. This method enabled the visualization of 3D distributions of water (i.e. hydration structures) and flexible molecular chains at subnanometer-scale resolution. While these applications highlighted the unique capabilities of FM-AFM, its force resolution, speed and stability are not necessarily at a satisfactory level for practical applications. Recently, there have been significant advancements in these fundamental performances. The force resolution was dramatically improved by using a small cantilever, which enabled the imaging of a 3D hydration structure even in pure water and made it possible to directly compare experimental results with simulated ones. In addition, the improved force resolution allowed the enhancement of imaging speed without compromising spatial resolution. To achieve this goal, efforts have been made for improving bandwidth, resonance frequency and/or latency of various components, including a high-speed phase-locked loop (PLL) circuit. With these improvements, now atomic-resolution in-liquid FM-AFM imaging can be performed at ∼1 s/frame. Furthermore, a Si-coating method was found to improve stability and reproducibility of atomic-resolution imaging owing to formation of a stable hydration structure on a tip apex. These improvements have opened up new possibilities of atomic-scale studies on solid-liquid interfacial phenomena by in-liquid FM-AFM.

Nanoscale kinetic imaging of lithium ion secondary battery materials using scanning electrochemical cell microscopy

To visualize the electrochemical reactivity and obtain the diffusion coefficient of the anode of lithium-ion batteries, we used scanning electrochemical cell microscopy (SECCM) in a glovebox. SECCM provided the facet-dependent diffusion coefficient on a Li₄Ti₅O₁₂ (LTO) thin-film electrode and detected the metastable crystal phase of Li_xFePO₄.

Tip dependence of three-dimensional scanning force microscopy images of calcite-water interfaces investigated by simulation and experiments

In this study, we have investigated the influence of the tip on the three-dimensional scanning force microscopy (3D-SFM) images of calcite-water interfaces by experiments and simulations. We calculated 3D force images by simulations with the solvent tip approximation (STA), Ca, CO3 and OH tip models. For all the 3D images, the z profiles at the surface Ca and CO3 sites alternately show oscillatory peaks corresponding to the hydration layers. However, the peak heights and spacings become larger when the mechanical stability of the tip becomes higher. For analyzing the xy slices of the 3D force images, we developed the extended STA (E-STA) model which allowed us to reveal the strong correlation between the hydration structure just under the tip and the atomic-scale force contrasts. Based on these understandings on the image features showing the strong tip dependence, we developed a method for objectively estimating the similarity between 3D force images. With this method, we compared the simulated images with the three experimentally obtained ones. Among them, two images showed a relatively high similarity with the image obtained by the simulation with the Ca or the CO3 tip model. Based on these agreements, we characterized the hydration structure and mechanical stability of the experimentally used tips. The understanding and methodology presented here should help us to derive accurate information on the tip and the interfacial structure from experimentally obtained 3D-SFM images.

Self-assembly of small molecules at hydrophobic interfaces using group effect

Although common in nature, the self-assembly of small molecules at sold-liquid interfaces is difficult to control in artificial systems. The high mobility of dissolved small molecules limits their residence at the interface, typically restricting the self-assembly to systems under confinement or with mobile tethers between the molecules and the surface. Small hydrogen-bonding molecules can overcome these issues by exploiting group-effect stabilization to achieve non-tethered self-assembly at hydrophobic interfaces. Significantly, the weak molecular interactions with the solid makes it possible to influence the interfacial hydrogen bond network, potentially creating a wide variety of supramolecular structures. Here we investigate the nanoscale details of water and alcohols mixtures self-assembling at the interface with graphite through group-effect. We explore the interplay between inter-molecular and surface interactions by adding small amounts of foreign molecules able to interfere with the hydrogen bond network and systematically varying the length of the alcohol hydrocarbon chain. The resulting supramolecular structures forming at room temperature are then examined using atomic force microscopy with insights from computer simulations. We show that the group-based self-assembly approach investigated here is general and can be reproduced on other substrates such as molybdenum disulphide and graphene oxide, potentially making it relevant for a wide variety of systems.

High-Resolution Electrochemical Mapping of the Hydrogen Evolution Reaction on Transition-Metal Dichalcogenide Nanosheets

High-resolution scanning electrochemical cell microscopy (SECCM) is used to image and quantitatively analyze the hydrogen evolution reaction (HER) catalytically active sites of 1H-MoS₂ nanosheets, MoS₂ , and WS₂ heteronanosheets. Using a 20 nm radius nanopipette and hopping mode scanning, the resolution of SECCM was beyond the optical microscopy limit and visualized a small triangular MoS₂ nanosheet with a side length of ca. 130 nm. The electrochemical cell provides local cyclic voltammograms with a nanoscale spatial resolution for visualizing HER active sites as electrochemical images. The HER activity difference of edge, terrace, and heterojunction of MoS₂ and WS₂ were revealed. The SECCM imaging directly visualized the relationship of HER activity and number of MoS₂ nanosheet layers and unveiled the heterogeneous aging state of MoS₂ nanosheets. SECCM can be used for improving local HER activities by producing sulfur vacancies using electrochemical reaction at the selected region.

High-Speed SICM for the Visualization of Nanoscale Dynamic Structural Changes in Hippocampal Neurons

Dynamic reassembly of the cytoskeleton and structural changes represented by dendritic spines, cargo transport, and synapse formation are closely related to memory. However, the visualization of the nanoscale topography is challenging because of the diffraction limit of optical microscopy. Scanning ion conductance microscopy (SICM) is an effective tool for visualizing the nanoscale topography changes of the cell surface without labeling. The temporal resolution of SICM is a critical issue of live-cell time-lapse imaging. Here, we developed a new scanning method, automation region of interest (AR)-mode SICM, to select the next imaging region by predicting the location of a cell, thus improving the scanning speed of time-lapse imaging. The newly developed algorithm reduced the scanning time by half. The time-lapse images provided not only novel information about nanoscale structural changes but also quantitative information on the dendritic spine and synaptic bouton volume changes and formation process of the neural network that are closely related to memory. Furthermore, translocation of plasmalemmal precursor vesicles (ppvs), for which fluorescent labeling has not been established, were also visualized along with the rearrangement of the cytoskeleton at the growth cone.

[Unlabeled imaging of primary cilia by scanning ion conductance microscopy]

Primary cilia are non-motile cilia consisting of a centriole-derived basal body and a microtubule-based axoneme. In recent years, the structure and function of primary cilia have been attracting attention due to the relation with the onset of ciliary disease. Scanning ion conductance microscopy (SICM) is a probe microscopy used to measure the topography and functions of living cells at nanoscale. Furthermore, the labelling procedure is not necessary for SICM measurement compare to fluorescence imaging. We compared the structures of primary cilia of human retinal pigment epithelial cell line (RPE-1 cells) and Madin-Darby canine kidney cell line (MDCK cells) at nanoscale by using SICM. In addition, high resolution SICM images have also succeeded in visualizing ciliary pockets that difficult to be fluorescently labeled.

[In situ chemical sensing by using scanning probe microscope]

Scanning electrochemical microscopy (SECM), which utilizes microelectrodes as a probe to measure the chemicals released and consumed by cells as current signal, is a promising tool for measuring the metabolites of cells. We have improved SECM resolution for single cell imaging by miniaturizing the size of the electrode and developing hybrid system of SECM and scanning ion conductance microscopy (SICM), which utilizes nanopipette as a probe to measure live cell topography. SECM-SICM provides simultaneous imaging of concentration profiles of chemical substances and cell surface topography. Using this system, we successfully measured the release of neurotransmitters from PC12 cells. In addition, the nanoscale electrodes are useful for intracellular chemical detection by inserting the electrodes into cells and measured reactive oxygen species (ROS).