Structural and functional imaging with carbon nanotube AFM probes

Atomic Force Microscopy Reveals that the Drosophila Telomere-Capping Protein Verrocchio Is a Single-Stranded DNA-Binding Protein

Atomic force microscopy (AFM) is a scanning probe technique that allows visualization of biological samples with a nanometric resolution. Determination of the physical properties of biological molecules at a single-molecule level is achieved through topographic analysis of the sample adsorbed on a flat and smooth surface. AFM has been widely used for the structural analysis of nucleic acid-protein interactions, providing insights on binding specificity and stoichiometry of proteins forming complexes with DNA substrates. Analysis of single-stranded DNA-binding proteins by AFM requires specific single-stranded/double-stranded hybrid DNA molecules as substrates for protein binding. In this chapter we describe the protocol for AFM characterization of binding properties of Drosophila telomeric protein Ver using DNA constructs that mimic the structure of chromosome ends. We provide details on the methodology used, including the procedures for the generation of DNA substrates, the preparation of samples for AFM visualization, and the data analysis of AFM images. The presented procedure can be adapted for the structural studies of any single-stranded DNA-binding protein.

Interaction of Human Telomeric i-Motif DNA with Single-Walled Carbon Nanotubes: Insights from Molecular Dynamics Simulations

This work deals with molecular dynamics simulations of human telomeric i-motif DNA interacting with functionalized single-walled carbon nanotubes. We study two kinds of i-motifs differing by the protonation state of cytosines, i.e., unprotonated ones representative to neutral pH and with half of the cytosines protonated and representative to acidic conditions. These i-motifs interact with two kinds of carbon nanotubes differing mainly in chirality (diameter), i.e., (10, 0) and (20, 0). Additionally, these nanotubes were on-tip functionalized by amino groups or by guanine- containing residues. We found that protonated i-motif adsorbs strongly, although not specifically, on the nanotube surfaces with its 3' and 5' ends directed toward the surface and that adsorption does not affect the i-motif shape and hydrogen bonds existing between C:C⁺ pairs. The functional groups on the nanotube tips have minimal effect either on position of i-motif or on its binding strength. Unprotonated i-motif, in turn, deteriorates significantly during interaction with the nanotubes and its binding strength is rather high as well. We found that (10, 0) nanotubes destroy the i-motif shape faster than (20, 0). Moreover the i-motif either tries to wrap the nanotube or migrates to its tip and becomes immobilized due to interaction with guanine residue localized on the nanotube tip and attempts to incorporate its 3' end into the nanotube interior. No hydrogen bonds exist within the unprotonated i-motif prior to and after adsorption on the nanotube. Thus, carbon nanotubes do not improve the stability of unprotonated i-motif due to simple adsorption or just physical interactions. We hypothesize that the stabilizing effect of carbon nanotubes reported in the literature is due to proton transfer from the functional group in the nanotube to cytosines and subsequent formation of C:C⁺ pairs.

Towards nanoscale electrical measurements in liquid by advanced KPFM techniques: a review

Fundamental mechanisms of energy storage, corrosion, sensing, and multiple biological functionalities are directly coupled to electrical processes and ionic dynamics at solid-liquid interfaces. In many cases, these processes are spatially inhomogeneous taking place at grain boundaries, step edges, point defects, ion channels, etc and possess complex time and voltage dependent dynamics. This necessitates time-resolved and real-space probing of these phenomena. In this review, we discuss the applications of force-sensitive voltage modulated scanning probe microscopy (SPM) for probing electrical phenomena at solid-liquid interfaces. We first describe the working principles behind electrostatic and Kelvin probe force microscopies (EFM & KPFM) at the gas-solid interface, review the state of the art in advanced KPFM methods and developments to (i) overcome limitations of classical KPFM, (ii) expand the information accessible from KPFM, and (iii) extend KPFM operation to liquid environments. We briefly discuss the theoretical framework of electrical double layer (EDL) forces and dynamics, the implications and breakdown of classical EDL models for highly charged interfaces or under high ion concentrations, and describe recent modifications of the classical EDL theory relevant for understanding nanoscale electrical measurements at the solid-liquid interface. We further review the latest achievements in mapping surface charge, dielectric constants, and electrodynamic and electrochemical processes in liquids. Finally, we outline the key challenges and opportunities that exist in the field of nanoscale electrical measurements in liquid as well as providing a roadmap for the future development of liquid KPFM.

Atomic Force Microscopy for Protein Detection and Their Physicoсhemical Characterization

This review is focused on the atomic force microscopy (AFM) capabilities to study the properties of protein biomolecules and to detect the proteins in solution. The possibilities of application of a wide range of measuring techniques and modes for visualization of proteins, determination of their stoichiometric characteristics and physicochemical properties, are analyzed. Particular attention is paid to the use of AFM as a molecular detector for detection of proteins in solutions at low concentrations, and also for determination of functional properties of single biomolecules, including the activity of individual molecules of enzymes. Prospects for the development of AFM in combination with other methods for studying biomacromolecules are discussed.

Graphene Coated Nanoprobes: A Review

Nanoprobes are one of the most important components in several fields of nanoscience to study materials, molecules and particles. In scanning probe microscopes, the nanoprobes consist on silicon tips coated with thin metallic films to provide additional properties, such as conductivity. However, if the experiments involve high currents or lateral frictions, the initial properties of the tips can wear out very fast. One possible solution is the use of hard coatings, such as diamond, or making the entire tip out of a precious material (platinum or diamond). However, this strategy is more expensive and the diamond coatings can damage the samples. In this context, the use of graphene as a protective coating for nanoprobes has attracted considerable interest. Here we review the main literature in this field, and discuss the fabrication, performance and scalability of nanoprobes.

Stabilization, Assembly, and Toxicity of Trimers Derived from Aβ

Oligomers of the β-amyloid peptide Aβ have emerged as important contributors to neurodegeneration in Alzheimer’s disease. Mounting evidence suggests that Aβ trimers and higher-order oligomers derived from trimers have special significance in the early stages of Alzheimer’s disease. Elucidating the structures of these trimers and higher-order oligomers is paramount for understanding their role in neurodegeneration. This paper describes the design, synthesis, X-ray crystallographic structures, and biophysical and biological properties of two stabilized trimers derived from the central and C-terminal regions of Aβ. These triangular trimers are stabilized through three disulfide cross-links between the monomer subunits. The X-ray crystallographic structures reveal that the stabilized trimers assemble hierarchically to form hexamers, dodecamers, and annular porelike structures. Solution-phase biophysical studies reveal that the stabilized trimers assemble in solution to form oligomers that recapitulate some of the higher-order assemblies observed crystallographically. The stabilized trimers share many of the biological characteristics of oligomers of full-length Aβ, including toxicity toward a neuronally derived human cell line, activation of caspase-3 mediated apoptosis, and reactivity with the oligomer-specific antibody A11. These studies support the biological significance of the triangular trimer assembly of Aβ β-hairpins and may offer a deeper understanding of the molecular basis of Alzheimer’s disease.

Nanotechnology, Metal Nanoparticles, and Biomedical Applications of Nanotechnology

Nanotechnology has emerged as an important field of modern scientific research due to its diverse range of applications in the area of electronics, material sciences, biomedical engineering, and medicines at nano levels such as healthcare, cosmetics, food and feed, environmental health, optics, biomedical sciences, chemical industries, drug-gene delivery, energy science, optoelectronics, catalysis, reprography, single electron transistors, light emitters, nonlinear optical devices, and photoelectrochemical applications and other applications. Due to these immense applications of nanotechnology in biomedical science, it has became possible to design the pharmaceuticals in such a way that they could directly treat diseased cells like cancer and make microscopic repairs in hard-to-operate-on areas of the body. The nanomachines have been designed to clean up toxins or oil spills, recycle all garbage, eliminate landfills, etc. The chapter summarizes the present and future applications of nanotechnology for human welfare but needs further study in catalysis, optical devices, sensor technology, cancer treatment, and drug delivery systems.

Nanostructured Tip-Shaped Biosensors: Application of Six Sigma Approach for Enhanced Manufacturing

Nanostructured tip-shaped biosensors have drawn attention for biomolecule detection as they are promising for highly sensitive and specific detection of a target analyte. Using a nanostructured tip, the sensitivity is increased to identify individual molecules because of the high aspect ratio structure. Various detection methods, such as electrochemistry, fluorescence microcopy, and Raman spectroscopy, have been attempted to enhance the sensitivity and the specificity. Due to the confined path of electrons, electrochemical measurement using a nanotip enables the detection of single molecules. When an electric field is combined with capillary action and fluid flow, target molecules can be effectively concentrated onto a nanotip surface for detection. To enhance the concentration efficacy, a dendritic nanotip rather than a single tip could be used to detect target analytes, such as nanoparticles, cells, and DNA. However, reproducible fabrication with relation to specific detection remains a challenge due to the instability of a manufacturing method, resulting in inconsistent shape. In this paper, nanostructured biosensors are reviewed with our experimental results using dendritic nanotips for sequence specific detection of DNA. By the aid of the Six Sigma approach, the fabrication yield of dendritic nanotips increases from 20.0% to 86.6%. Using the nanotips, DNA is concentrated and detected in a sequence specific way with the detection limit equivalent to 1000 CFU/mL. The pros and cons of a nanotip biosensor are evaluated in conjunction with future prospects.

Potential mechanisms and implications for the formation of tau oligomeric strains

The culmination of many years of increasing research into the toxicity of tau aggregation in neurodegenerative disease has led to the consensus that soluble, oligomeric forms of tau are likely the most toxic entities in disease. While tauopathies overlap in the presence of tau pathology, each disease has a unique combination of symptoms and pathological features; however, most study into tau has grouped tau oligomers and studied them as a homogenous population. Established evidence from the prion field combined with the most recent tau and amyloidogenic protein research suggests that tau is a prion-like protein, capable of seeding the spread of pathology throughout the brain. Thus, it is likely that tau may also form prion-like strains or diverse conformational structures that may differ by disease and underlie some of the differences in symptoms and pathology in neurodegenerative tauopathies. The development of techniques and new technology for the detection of tau oligomeric strains may, therefore, lead to more efficacious diagnostic and treatment strategies for neurodegenerative disease. [Formula: see text].

Multifunctional hydrogel nano-probes for atomic force microscopy

Since the invention of the atomic force microscope (AFM) three decades ago, there have been numerous advances in its measurement capabilities. Curiously, throughout these developments, the fundamental nature of the force-sensing probe-the key actuating element-has remained largely unchanged. It is produced by long-established microfabrication etching strategies and typically composed of silicon-based materials. Here, we report a new class of photopolymerizable hydrogel nano-probes that are produced by bottom-up fabrication with compressible replica moulding. The hydrogel probes demonstrate excellent capabilities for AFM imaging and force measurement applications while enabling programmable, multifunctional capabilities based on compositionally adjustable mechanical properties and facile encapsulation of various nanomaterials. Taken together, the simple, fast and affordable manufacturing route and multifunctional capabilities of hydrogel AFM nano-probes highlight the potential of soft matter mechanical transducers in nanotechnology applications. The fabrication scheme can also be readily utilized to prepare hydrogel cantilevers, including in parallel arrays, for nanomechanical sensor devices.

X-ray Crystallographic Structures of a Trimer, Dodecamer, and Annular Pore Formed by an Aβ17-36 β-Hairpin

High-resolution structures of oligomers formed by the β-amyloid peptide Aβ are needed to understand the molecular basis of Alzheimer’s disease and develop therapies. This paper presents the X-ray crystallographic structures of oligomers formed by a 20-residue peptide segment derived from Aβ. The development of a peptide in which Aβ_17–36 is stabilized as a β-hairpin is described, and the X-ray crystallographic structures of oligomers it forms are reported. Two covalent constraints act in tandem to stabilize the Aβ_17–36 peptide in a hairpin conformation: a δ-linked ornithine turn connecting positions 17 and 36 to create a macrocycle and an intramolecular disulfide linkage between positions 24 and 29. An N-methyl group at position 33 blocks uncontrolled aggregation. The peptide readily crystallizes as a folded β-hairpin, which assembles hierarchically in the crystal lattice. Three β-hairpin monomers assemble to form a triangular trimer, four trimers assemble in a tetrahedral arrangement to form a dodecamer, and five dodecamers pack together to form an annular pore. This hierarchical assembly provides a model, in which full-length Aβ transitions from an unfolded monomer to a folded β-hairpin, which assembles to form oligomers that further pack to form an annular pore. This model may provide a better understanding of the molecular basis of Alzheimer’s disease at atomic resolution.

Membrane-mediated amyloid formation of PrP 106-126: A kinetic study

PrP 106-126 conserves the pathogenic and physicochemical properties of the Scrapie isoform of the prion protein. PrP 106-126 and other amyloidal proteins are capable of inducing ion permeability through cell membranes, and this property may represent the common primary mechanism of pathogenesis in the amyloid-related degenerative diseases. However, for many amyloidal proteins, despite numerous phenomenological observations of their interactions with membranes, it has been difficult to determine the molecular mechanisms by which the proteins cause ion permeability. One approach that has not been undertaken is the kinetic study of protein-membrane interactions. We found that the reaction time constant of the interaction between PrP 106-126 and membranes is suitable for such studies. The kinetic experiment with giant lipid vesicles showed that the membrane area first increased by peptide binding but then decreased. The membrane area decrease was coincidental with appearance of extramembranous aggregates including lipid molecules. Sometimes, the membrane area would increase again followed by another decrease. The kinetic experiment with small vesicles was monitored by circular dichroism for peptide conformation changes. The results are consistent with a molecular simulation following a simple set of well-defined rules. We deduced that at the molecular level the formation of peptide amyloids incorporated lipid molecules as part of the aggregates. Most importantly the amyloid aggregates desorbed from the lipid bilayer, consistent with the macroscopic phenomena observed with giant vesicles. Thus we conclude that the main effect of membrane-mediated amyloid formation is extraction of lipid molecules from the membrane. We discuss the likelihood of this effect on membrane ion permeability.

Nanotube field electron emission: principles, development, and applications

There is a growing trend to apply field emission (FE) electron sources in vacuum electronic devices due to their fast response, high efficiency and low energy consumption compared to thermionic emission ones. Carbon nanotubes (CNTs) have been regarded as a promising class of electron field emitters since the 1990s and have promoted the development of FE technology greatly because of their high electrical and thermal conductivity, chemical stability, high aspect ratio and small size. Recent studies have shown that FE from CNTs has the potential to replace conventional thermionic emission in many areas and that it exhibits advanced features in practical applications. Consequently, FE from nanotubes and applications thereof have attracted much attention. This paper provides a comprehensive review of both recent advances in CNT field emitters and issues related to applications of CNT based FE. FE theories and principles are introduced, and the early development of field emitters is related. CNT emitter types and their FE performance are discussed. The current situation for applications based on nanotube FE is reviewed. Although challenges remain, the tremendous progress made in CNT FE over the past ten years indicates the field's development potential.

Fast and reliable method of conductive carbon nanotube-probe fabrication for scanning probe microscopy

We demonstrate the procedure of scanning probe microscopy (SPM) conductive probe fabrication with a single multi-walled carbon nanotube (MWNT) on a silicon cantilever pyramid. The nanotube bundle reliably attached to the metal-covered pyramid is formed using dielectrophoresis technique from the MWNT suspension. It is shown that the dimpled aluminum sample can be used both for shortening/modification of the nanotube bundle by applying pulse voltage between the probe and the sample and for controlling the probe shape via atomic force microscopy imaging the sample. Carbon nanotube attached to cantilever covered with noble metal is suitable for SPM imaging in such modulation regimes as capacitance contrast microscopy, Kelvin probe microscopy, and scanning gate microscopy. The majority of such probes are conductive with conductivity not degrading within hours of SPM imaging.

High-stroke silicon-on-insulator MEMS nanopositioner: control design for non-raster scan atomic force microscopy

A 2-degree of freedom microelectromechanical systems nanopositioner designed for on-chip atomic force microscopy (AFM) is presented. The device is fabricated using a silicon-on-insulator-based process and is designed as a parallel kinematic mechanism. It contains a central scan table and two sets of electrostatic comb actuators along each orthogonal axis, which provides displacement ranges greater than ±10 μm. The first in-plane resonance modes are located at 1274 Hz and 1286 Hz for the X and Y axes, respectively. To measure lateral displacements of the stage, electrothermal position sensors are incorporated in the design. To facilitate high-speed scans, the highly resonant dynamics of the system are controlled using damping loops in conjunction with internal model controllers that enable accurate tracking of fast sinusoidal set-points. To cancel the effect of sensor drift on controlled displacements, washout controllers are used in the damping loops. The feedback controlled nanopositioner is successfully used to perform several AFM scans in contact mode via a Lissajous scan method with a large scan area of 20 μm × 20 μm. The maximum scan rate demonstrated is 1 kHz.

Resonance frequency and mass identification of zeptogram-scale nanosensor based on the nonlocal beam theory

Free vibration and mass detection of carbon nanotube-based sensors are studied in this paper. Since the mechanical properties of carbon nanotubes possess a size effect, the nonlocal beam model is used to characterize flexural vibration of nanosensors carrying a concentrated nanoparticle, where the size effect is reflected by a nonlocal parameter. For nanocantilever or bridged sensor, frequency equations are derived when a nanoparticle is carried at the free end or the middle, respectively. Exact resonance frequencies are numerically determined for clamped-free, simply-supported, and clamped-clamped resonators. Alternative approximations of fundamental frequency are given in closed form within the relative error less than 0.4%, 0.6%, and 1.4% for cantilever, simply-supported, and bridged sensors, respectively. Mass identification formulae are derived in terms of the frequency shift. Identified masses via the present approach coincide with those using the molecular mechanics approach and reach as low as 10(-24)kg. The obtained results indicate that the nonlocal effect decreases the resonance frequency except for the fundamental frequency of nanocantilever sensor. These results are helpful to the design of micro/nanomechanical zeptogram-scale biosensor.

Material properties of viral nanocages explored by atomic force microscopy

Single-particle nanoindentation by atomic force microscopy (AFM) is an emergent technique to characterize the material properties of nano-sized proteinaceous systems. AFM uses a very small tip attached to a cantilever to scan the surface of the substrate. As a result of the sensitive feedback loop of AFM, the force applied by the tip on the substrate during scanning can be controlled and monitored. By accurately controlling this scanning force, topographical maps of fragile substrates can be acquired to study the morphology of the substrate. In addition, mechanical properties of the substrate like stiffness and breaking point can be determined by using the force spectroscopy capability of AFM. Here we discuss basics of AFM operation and how this technique is used to determine the structure and mechanical properties of protein nanocages, in particular viral particles. Knowledge of morphology as well as mechanical properties is essential for understanding viral life cycles, including genome packaging, capsid maturation, and uncoating, but also contributes to the development of diagnostics, vaccines, imaging modalities, and targeted therapeutic devices based on viruslike particles.

Single molecule technologies

Single molecule technologies provide an alternative set of approaches to conventional techniques and promise to deliver fundamentally new information about biological processes at the level of molecular movement, dynamics and function. As several of these mature and become more accessible for routine use in molecular biology laboratories, the potential impact on drug discovery research and development should be significant.:

The formation of tau pore-like structures is prevalent and cell specific: possible implications for the disease phenotypes

Pathological aggregation of the microtubule-associated protein tau and subsequent accumulation of neurofibrillary tangles (NFTs) or other tau-containing inclusions are defining histopathological features of many neurodegenerative diseases, which are collectively known as tauopathies. Due to conflicting results regarding a correlation between the presence of NFTs and disease progression, the mechanism linking pathological tau aggregation with cell death is poorly understood. An emerging view is that NFTs are not the toxic entity in tauopathies; rather, tau intermediates between monomers and NFTs are pathogenic. Several proteins associated with neurodegenerative diseases, such as β-amyloid (Aβ) and α-synuclein, have the tendency to form pore-like amyloid structures (annular protofibrils, APFs) that mimic the membrane-disrupting properties of pore-forming protein toxins. The present study examined the similarities of tau APFs with other tau amyloid species and showed for the first time the presence of tau APFs in brain tissue from patients with progressive supranuclear palsy (PSP) and dementia with Lewy bodies (DLB), as well as in the P301L mouse model, which overexpresses mutated tau. Furthermore, we found that APFs are preceded by tau oligomers and do not go on to form NFTs, evading fibrillar fate. Collectively, our results demonstrate that in vivo APF formation depends on mutations in tau, phosphorylation levels, and cell type. These findings establish the pathological significance of tau APFs in vivo and highlight their suitability as therapeutic targets for several neurodegenerative tauopathies.

Inhibition of amyloid beta-induced synaptotoxicity by a pentapeptide derived from the glycine zipper region of the neurotoxic peptide

A major characteristic of Alzheimer's disease is the presence of amyloid beta (Aβ) oligomers and aggregates in the brain. Aβ oligomers interact with the neuronal membrane inducing perforations, causing an influx of calcium ions and increasing the release of synaptic vesicles that leads to a delayed synaptic failure by vesicle depletion. Here, we identified a neuroprotective pentapeptide anti-Aβ compound having the sequence of the glycine zipper region of the C-terminal of Aβ (G33LMVG37). Docking and Förster resonance energy transfer experiments showed that G33LMVG37 interacts with Aβ at the C-terminal region, which is important for Aβ association and insertion into the lipid membrane. Furthermore, this pentapeptide interfered with Aβ aggregation, association, and perforation of the plasma membrane. The synaptotoxicity induced by Aβ after acute and chronic applications were abolished by G33LMVG37. These results provide a novel rationale for drug development against Alzheimer's disease.

Astrocytes contain amyloid-β annular protofibrils in Alzheimer's disease brains

Annular protofibrils (APFs) represent a newly described and distinct class of amyloid structures formed by disease-associated proteins. In vitro, these pore-like structures have been implicated in membrane permeabilization and ion homeostasis via pore formation. Still, their formation and relevance in vivo are poorly understood. Herein, we report that APFs are in human Alzheimer's disease brain samples and that amyloid-β APFs were associated with activated astrocytes. Moreover, we show that amyloid-β APFs in astrocytes adopt a conformation in which the N-terminal region is buried inside the wall of the pore. Our results together with previous studies suggest that the formation of amyloid-β APFs in astrocytes could be a relevant event in the pathogenesis of Alzheimer's disease and validate this amyloidogenic structure as a target for the prevention of the disease.

Triaxial AFM probes for noncontact trapping and manipulation

We show that a triaxial atomic force microscopy probe creates a noncontact trap for a single particle in a fluid via negative dielectrophoresis. A zero in the electric field profile traps the particle above the probe surface, avoiding adhesion, and the repulsive region surrounding the zero pushes other particles away, preventing clustering. Triaxial probes are promising for three-dimensional assembly and for selective imaging of a particular property of a sample using interchangeable functionalized particles.

Indirect identification and compensation of lateral scanner resonances in atomic force microscopes

Improving the imaging speed of atomic force microscopy (AFM) requires accurate nanopositioning at high speeds. However, high speed operation excites resonances in the AFM's mechanical scanner that can distort the image, and therefore typical users of commercial AFMs elect to operate microscopes at speeds below which scanner resonances are observed. Although traditional robust feedforward controllers and input shaping have proven effective at minimizing the influence of scanner distortions, the lack of direct measurement and use of model-based controllers have required disassembling the microscope to access lateral scanner motion with external sensors in order to perform a full system identification experiment, which places excessive demands on routine microscope operators. Further, since the lightly damped instrument dynamics often change from experiment to experiment, model-based controllers designed from offline system identification experiments must trade off high speed performance for robustness to modeling errors. This work represents a new way to automatically characterize the lateral scanner dynamics without addition of lateral sensors, and shape the commanded input signals in such a way that disturbing dynamics are not excited. Scanner coupling between the lateral and out-of-plane directions is exploited and used to build a minimal model of the scanner that is also sufficient to describe the nature of the distorting resonances. This model informs the design of an online input shaper used to suppress spectral components of the high speed command signals. The method presented is distinct from alternative approaches in that neither an information-complete system identification experiment nor microscope modification are required. Because the system identification is performed online immediately before imaging, no tradeoff of performance is required. This approach has enabled an increase in the scan rates of unmodified commercial AFMs from 1-4 lines s(-1) to over 40 lines s(-1).

Fabrication and buckling dynamics of nanoneedle AFM probes

A new method for the fabrication of high-aspect-ratio probes by electron beam induced deposition is described. This technique allows the fabrication of cylindrical 'nanoneedle' structures on the atomic force microscope (AFM) probe tip which can be used for accurate imaging of surfaces with high steep features. Scanning electron microscope (SEM) imaging showed that needles with diameters in the range of 18-100 nm could be obtained by this technique. The needles were shown to undergo buckling deformation under large tip-sample forces. The deformation was observed to recover elastically under vertical deformations of up to ∼ 60% of the needle length, preventing damage to the needle. A technique of stabilizing the needle against buckling by coating it with additional electron beam deposited carbon was also investigated; it was shown that coated needles of 75 nm or greater total diameter did not buckle even under tip-sample forces of ∼ 1.5 µN.

Amyloid-β annular protofibrils evade fibrillar fate in Alzheimer disease brain

Annular protofibrils (APFs) represent a new and distinct class of amyloid structures formed by disease-associated proteins. In vitro, these pore-like structures have been implicated in membrane permeabilization and ion homeostasis via pore formation. Still, evidence for their formation and relevance in vivo is lacking. Herein, we report that APFs are in a distinct pathway from fibril formation in vitro and in vivo. In human Alzheimer disease brain samples, amyloid-β APFs were associated with diffuse plaques, but not compact plaques; moreover, we show the formation of intracellular APFs. Our results together with previous studies suggest that the prevention of amyloid-β annular protofibril formation could be a relevant target for the prevention of amyloid-β toxicity in Alzheimer disease.

High throughput nanofabrication of silicon nanowire and carbon nanotube tips on AFM probes by stencil-deposited catalysts

A new and versatile technique for the wafer scale nanofabrication of silicon nanowire (SiNW) and multiwalled carbon nanotube (MWNT) tips on atomic force microscope (AFM) probes is presented. Catalyst material for the SiNW and MWNT growth was deposited on prefabricated AFM probes using aligned wafer scale nanostencil lithography. Individual vertical SiNWs were grown epitaxially by a catalytic vapor-liquid-solid (VLS) process and MWNTs were grown by a plasma-enhanced chemical vapor (PECVD) process on the AFM probes. The AFM probes were tested for imaging micrometers-deep trenches, where they demonstrated a significantly better performance than commercial high aspect ratio tips. Our method demonstrates a reliable and cost-efficient route toward wafer scale manufacturing of SiNW and MWNT AFM probes.

Nanowiring Enzymes to Carbon Nanotube Probes

The observation of spectroscopic signals in response to mechanically induced changes in biological macromolecules can be enabled at an unprecedented level of resolution by coupling single-molecule manipulation/sensing using carbon nanotubes with single-molecule fluorescence imaging. Proteins, DNA and other biomolecules can be attached to nanotubes to give highly specific single-molecule probes for the investigation of intermolecular dynamics, the assembly of hybrid biological and nanoscale materials and the development of molecular electronics. Recent advances in nanotube fabrication and Atomic Force Microscope (AFM) imaging with nanotube tips have demonstrated the potential of these tools to achieve high-resolution images of single molecules. In addition, proof-of-principle demonstrations of nanotube functionalization and attachment of single molecules to these probes have been successfully made.

Improved techniques for the growth and attachment of single wall carbon nanotubes as robust and well-characterized tools for AFM imaging are being developed. This work serves as a foundation toward development of single-molecule sensors and manipulators on nanotube AFM tips for a hybrid atomic force microscope that also has single-molecule fluorescence imaging capability. An individual single wall carbon nanotube (SWNT) attached to an AFM tip can function as a structural scaffold for nanoscale device fabrication on a scanning probe. Such a probe can have a novel role, to trigger specific biochemical reactions or conformational changes in a biological system with nanometer precision. The consequences of these perturbations can be read out in real time by single-molecule fluorescence and/or AFM sensing. For example, electrical wiring of single redox enzymes to carbon nanotube scanning probes will allow for observation and electrochemical control of single enzymatic reactions, by monitoring fluorescence from a redox-active cofactor or the formation of fluorescent products. Enzymes “nanowired” to carbon nanotube tips may enable extremely sensitive probing of biological stimulus-response with high spatial resolution, including product-induced signal transduction.

Combined atomic force microscopy and fluorescence microscopy

The atomic force microscope (AFM) is a high-resolution scanning-probe instrument which has become an important tool for cellular and molecular biophysics in recent years, but lacks the time resolution and functional specificities offered by fluorescence microscopic techniques. The advantages of both methods may be exploited by combining and synchronizing them. In this paper, the biological applications of AFM, fluorescence, and their combinations are briefly reviewed, and the assembly and utilization of a spatially and temporally synchronized AFM and total internal reflection fluorescence microscope are described. The application of the method is demonstrated on a fluorescently labeled cell culture.

Controlled functionalization of carbon nanotubes by a solvent-free multicomponent approach

The present work reports the solvent-free, one-pot functionalization of multiwall carbon nanotubes (CNTs) based on the 1,3-dipolar cycloaddition of azomethine ylides using N-benzyloxycarbonyl glycine and formaldehyde. The surface morphology of the functionalized CNTs was investigated by scanning tunneling microscopy. The effect of temperature on the reaction was studied by thermogravimetry and X-ray photoelectron spectroscopy (XPS). XPS was a key technique for the detailed chemical analysis of the CNT surface. The formation of two major reaction products was observed, namely a cyclic benzyl carbamate and a pyrrolidine. The concentration of the two products varied with reaction temperature and time. At 180 °C, the main product was the cyclic benzyl carbamate, while at 250 °C the major product was the pyrrolidine. This simple, solvent-free chemical procedure yields CNTs with fine-tuned surface functionality.

Microwave-assisted fabrication of carbon nanotube AFM tips

A new, fast, alternative approach for the fabrication of carbon nanotube (CNT) atomic force microscopy (AFM) tips is reported. Thereby, the tube material is grown on the apex of an AFM tip by utilizing microwave irradiation and selective heating of the catalyst. Reaction times as short as three minutes allowed the fabrication of CNT AFM tips in a highly efficient process. This method represents a promising approach toward a cheaper, faster, and straightforward synthesis of CNT AFM tips.

Sampling protein form and function with the atomic force microscope

To study the structure, function, and interactions of proteins, a plethora of techniques is available. Many techniques sample such parameters in non-physiological environments (e.g. in air, ice, or vacuum). Atomic force microscopy (AFM), however, is a powerful biophysical technique that can probe these parameters under physiological buffer conditions. With the atomic force microscope operating under such conditions, it is possible to obtain images of biological structures without requiring labeling and to follow dynamic processes in real time. Furthermore, by operating in force spectroscopy mode, it can probe intramolecular interactions and binding strengths. In structural biology, it has proven its ability to image proteins and protein conformational changes at submolecular resolution, and in proteomics, it is developing as a tool to map surface proteomes and to study protein function by force spectroscopy methods. The power of AFM to combine studies of protein form and protein function enables bridging various research fields to come to a comprehensive, molecular level picture of biological processes. We review the use of AFM imaging and force spectroscopy techniques and discuss the major advances of these experiments in further understanding form and function of proteins at the nanoscale in physiologically relevant environments.

Atomic force microscopy of polymer brushes: colloidal versus sharp tips

Force versus distance profiles acquired by atomic force microscopy probe the structure and interactions of polymer brushes. An interpretation utilizing the Derjaguin approximation and assuming local compression of the brush is justified when colloidal probes are utilized. The assumptions underlying this approach are not satisfied for sharp tips, and deviations from this model were reported for experiments and simulations. The sharp-tip force law proposed assumes that the free energy penalty of insertion into the brush is due to the osmotic pressure of the unperturbed brush. This static force law is in semiquantitative agreement with the simulation results of Murat and Grest (Murat, M.; Grest, G. S. Macromolecules 1996, 29, 8282).

Functionalized carbon nanotubes for potential medicinal applications

Functionalized carbon nanotubes display unique properties that enable a variety of medicinal applications, including the diagnosis and treatment of cancer, infectious diseases and central nervous system disorders, and applications in tissue engineering. These potential applications are particularly encouraged by their ability to penetrate biological membranes and relatively low toxicity. High aspect ratio, unique optical property and the likeness as small molecule make carbon nanotubes an unusual allotrope of element carbon. After functionalization, carbon nanotubes display potentials for a variety of medicinal applications, including the diagnosis and treatment of cancer, infectious diseases and central nervous system disorders, and applications in tissue engineering. These potential applications are particularly encouraged by their ability to penetrate biological membranes and relatively low toxicity.

A tripod molecular tip for single molecule ligand-receptor force spectroscopy by AFM

Tripod-shaped molecules were designed for chemical modification of the surface of probes used for atomic force microscopy (AFM). These chemically functionalized tips were used for chemical force spectroscopy (CFS) measurements of the ligand-protein receptor interaction in a biotin-NeutrAvidin model system. We demonstrate that by using this unique tripodal system, we can achieve significantly lower density of ligand on the AFM tip apex, which is optimal for true single molecule measurements. Furthermore, the molecular tripods form highly stable bonds to the AFM probes, leading to more robust and reproducible unbinding force data, thereby addressing one of the challenges in CFS studies. Histogram analysis of the hundreds of collected unbinding forces showed a specific distribution with a peak force maximum at approximately 165 pN, in good agreement with the previously reported data of single rupture events of biotin-avidin. We compared these molecular tripod tips with a molecular monopod. The results showed that the molecular tripods are more robust for repeated measurements. The distinct biotin-avidin force maximum was not observed in the control experiments. This indicated that the force distribution observed for molecular tripods corresponds to the specific rupture force between biotin and avidin. The improved robustness of molecular tripods for CFS will provide benefits in other ligand-receptor unbinding studies, including those of transmembrane receptor systems, which require high resolution, sensitivity, and reproducibility in force spectroscopy measurements.

Nanomaterials and nanoparticles: sources and toxicity

This review is presented as a common foundation for scientists interested in nanoparticles, their origin,activity, and biological toxicity. It is written with the goal of rationalizing and informing public health concerns related to this sometimes-strange new science of "nano," while raising awareness of nanomaterials' toxicity among scientists and manufacturers handling them.We show that humans have always been exposed to tiny particles via dust storms, volcanic ash, and other natural processes, and that our bodily systems are well adapted to protect us from these potentially harmful intruders. There ticuloendothelial system, in particular, actively neutralizes and eliminates foreign matter in the body,including viruses and nonbiological particles. Particles originating from human activities have existed for millennia, e.g., smoke from combustion and lint from garments, but the recent development of industry and combustion-based engine transportation has profoundly increased an thropogenic particulate pollution. Significantly, technological advancement has also changed the character of particulate pollution, increasing the proportion of nanometer-sized particles--"nanoparticles"--and expanding the variety of chemical compositions. Recent epidemiological studies have shown a strong correlation between particulate air pollution levels, respiratory and cardiovascular diseases, various cancers, and mortality. Adverse effects of nanoparticles on human health depend on individual factors such as genetics and existing disease, as well as exposure, and nanoparticle chemistry, size, shape,agglomeration state, and electromagnetic properties. Animal and human studies show that inhaled nanoparticles are less efficiently removed than larger particles by the macrophage clearance mechanisms in the lungs, causing lung damage, and that nanoparticles can translocate through the circulatory, lymphatic, and nervous systems to many tissues and organs, including the brain. The key to understanding the toxicity of nanoparticles is that their minute size, smaller than cells and cellular organelles, allows them to penetrate these basic biological structures, disrupting their normal function.Examples of toxic effects include tissue inflammation, and altered cellular redox balance toward oxidation, causing abnormal function or cell death. The manipulation of matter at the scale of atoms,"nanotechnology," is creating many new materials with characteristics not always easily predicted from current knowledge. Within the nearly limitless diversity of these materials, some happen to be toxic to biological systems, others are relatively benign, while others confer health benefits. Some of these materials have desirable characteristics for industrial applications, as nanostructured materials often exhibit beneficial properties, from UV absorbance in sunscreen to oil-less lubrication of motors.A rational science-based approach is needed to minimize harm caused by these materials, while supporting continued study and appropriate industrial development. As current knowledge of the toxicology of "bulk" materials may not suffice in reliably predicting toxic forms of nanoparticles,ongoing and expanded study of "nanotoxicity" will be necessary. For nanotechnologies with clearly associated health risks, intelligent design of materials and devices is needed to derive the benefits of these new technologies while limiting adverse health impacts. Human exposure to toxic nanoparticles can be reduced through identifying creation-exposure pathways of toxins, a study that may someday soon unravel the mysteries of diseases such as Parkinson's and Alzheimer's. Reduction in fossil fuel combustion would have a large impact on global human exposure to nanoparticles, as would limiting deforestation and desertification.While nanotoxicity is a relatively new concept to science, this review reveals the result of life's long history of evolution in the presence of nanoparticles, and how the human body, in particular, has adapted to defend itself against nanoparticulate intruders.

Growth and morphology control of carbon nanotubes at the apexes of pyramidal silicon tips

We describe the development of catalysed chemical vapour deposition (cCVD) growth schemes suitable for the production of carbon nanotube atomic force microscopy (CNT-AFM) probes. Growth and sample processing conditions are utilized that both incorporate safety in the process, e.g. the use of ethanol (EtOH) vapour as a carbon feedstock and hydrogen at only 4% (flow proportion), and simplicity, e.g. no catalyst patterning is required. Cobalt is employed as the growth catalyst and thin films of aluminium on silicon as the substrate material. Purpose-fabricated silicon substrates containing large numbers of tip structures are used as models of AFM probes. This enables growth to be carried out on many tips at once, facilitating a thorough investigation of the effect of different growth schemes on yields. cCVD growth schemes are chosen which produce stabilizing high density networks of carbon nanotubes on the sidewalls of the pyramidal tips to aid in anchoring the apex protruding carbon nanotube(s) in place. This results in long-lasting AFM imaging tips. We demonstrate that through rational tailoring of cCVD conditions it is possible to tune the growth conditions such that CNTs which protrude straight from tip apexes can be obtained at yields of greater than or equal to 78%. Application of suitable growth schemes to CNT growth on commercially available AFM probes resulted in CNT-AFM probes which were found to be extremely useful for extended lifetime metrological profiling of complex structures.

Single-photon atomic force microscopy

In the last few years, an array of novel technologies, especially the big family of scanning probe microscopy, now often integrated with other powerful imaging tools such as laser confocal microscopy and total internal reflection fluorescence microscopy, have been widely applied in the investigation of biomolecular interactions and dynamics. But it is still a great challenge to directly monitor the dynamics of biomolecular interactions with high spatial and temporal resolution in living cells. An innovative method termed "single-photon atomic force microscopy" (SP-AFM), superior to existing techniques in tracing biomolecular interactions and dynamics in vivo, was proposed on the basis of the combination of atomic force microscopy with the technologies of carbon nanotubes and single-photon detection. As a unique tool, SP-AFM, capable of simultaneous topography imaging and molecular identification at the subnanometer level by synchronous acquisitions and analyses of the surface topography and fluorescent optical signals while scanning the sample, could play a very important role in exploring biomolecular interactions and dynamics in living cells or in a complicated biomolecular background.