Evaluation of interaction between histidine binding Cu2+ ion and histidine by atomic force microscopy

This paper presents a direct interaction force measurement between histidine molecules using AFM force-distance curve measurement. AFM force-distance curves between the histidine-modified cantilever and substrate in the different conditions with or without intercalating Cu2+ ion were measured and interpreted via Gaussian curve fitting analyses. The adhesion force between histidine molecules was shown to be 110 pN under the presence of Cu2+. The result was compareable to the measured adhesion force about 0 pN, which was measured by the removal of Cu2+ ion with the addition of EDTA. The result indicated the direct histidine-histidie interaction was difficult without the role of the bridigible ionic component. From the results, the possibility of direct measurement on chemical affinities between biomolecules was suggested by using AFM force-distance curve analyses. Especially, the current approach showed the possible affinity measurement techniques that elucidate the role of bridge ions.     

Specific aptamer-protein interaction studied by atomic force microscopy

Aptamers are a new class of synthetic DNA/RNA oligonucleotides generated from in vitro selection to selectively bind with various molecules. Due to their molecular recognition capability for proteins, aptamers are becoming promising reagents in protein detection and new drug development. In this study, the specific interaction between the protein immunoglobulin E (IgE) and its 37-nt aptamer has been measured directly by atomic force microscopy. The single-molecule unbinding force between IgE and the aptamer is determined using the Poisson statistical method. The individual unbinding force between IgE and its monoclonal antibody has also been obtained and compared to that between IgE and the aptamer. The results reveal the high affinity of the aptamer to protein, which could match or even surpass that of the antibody to its antigen.     

Fabrication of metal nanostructures by atomic force microscopy nanomachining and related applications

In this work, the fabrication of metal nanostructures by a combination of atomic force microscopy nanomachining on a thin polymer resist, metal coating and lift-off is presented. Nanodots with sizes down to 20 nm and nanowires with widths ranging between 40 and 100 nm have been successfully created by nanoindenting and nanoscratching. The results exemplify the feasibility and effectiveness of the present technique as an alternative to e-beam lithography. The localized surface plasmon resonance properties of the fabricated nanostructures are characterized. The chemical sensing capability of a single nanowire based on resistance increase is also demonstrated.     

Preparation of protein nanoarray on silicon surface by atomic force microscopy nanofabrication

Atomic force microscopy (AFM) with bias control is employed to fabricate oxidized nanopatterns on a silicon surface with a feature size as low as 50 nm. Nanopatterns made by a Pt/Ir coating probes have larger feature size than these made by the probe without, but the patterning speed is fast, 0.1 s per dot. 20 nm gold nanoparticles are immobilized on oxide nanopatterns to elucidate the dimensions of the nanoparticles on an oxide nanopattern. These patterning conditions are utilized to prepare a nanoarray for the immobilization of biotins to interact with free streptavidins. The resultant height of the biotin labeled on oxidized nanopattern is 0.93 +/- 0.1 nm and the combined height of biotin-streptavidin is 5.14 +/- 0.45 nm, as determined using the imaging functions of AFM. Based on the experimental results, a nano biochip of silicon dioxide can be utilized to monitor molecular interactions on the nanometer scale under static conditions and without the labeling of fluorescence dyes.     

Direct measurement of interaction force between hydrophilic silica surfaces in triblock copolymer solutions with salt by atomic force microscopy

Triblock copolymers composed of polyethylene oxide (PEO) and polypropylene oxide (PPO) are used in various fields as nonionic surfactants. In this study, we measured interaction forces between untreated hydrophilic silica surfaces in solutions with two typical triblock copolymers, Pluronic P123 (PEO₂₀PPO₇₀PEO₂₀) and F127 (PEO₉₉PPO₆₅PEO₉₉), in the presence of 1 mM and 500 mM NaCl using atomic force microscopy (AFM). In solutions at the copolymer concentration of 1 µM, which is below the critical micelle concentration (CMC), the measured interaction forces were monotonically repulsive in the presence of 1 mM NaCl, which suggested the brush-like conformation of copolymers on the surfaces. When the concentration of NaCl was increased to 500 mM, interaction forces became attractive, which indicated the bridging of adsorbed polymers onto surfaces, the strength of which varied depending on the affinity and adsorption density of copolymers. The interactions at the copolymer concentration of 1 mM, which were above the CMC of both copolymers, were steric repulsions between adsorbed micelles on the surfaces with 1 mM of NaCl. For 500 mM of NaCl, an attractive jump after a steric repulsion was observed only in the force curve for P123, which inferred that the displacement of micelles from the surfaces was presumably due to a decrease in the strength of adsorption caused by the dehydration of EO groups. These results indicated that the length of the EO group considerably affected the interactions.     

Studying the effect of alginate overproduction on Pseudomonas aeruginosa biofilm by atomic force microscopy

Pseudomonas aeruginosa is the most important pathogen in cystic fibrosis patients and forms biofilms in the lung. P. aeruginosa strains isolated from the lungs of the patients have a mucoid phenotype overproducing alginate. The phenotype forms highly structured biofilms which are more resistant to antibiotics than biofilms formed by its nonmucoid phenotype. Conversion to the alginate-overproducing phenotype occurs through a mutation in rpoN gene in the strains. The biofilms formed by the alginate-overproducing phenotype are highly sticky, but their stickiness has not been measured. Herein, the stickiness of biofilms formed by the rpoN mutant was measured by atomic force microscopy (AFM). Confocal laser scanning microscopy showed that the biofilms formed by the slowly-growing rpoN mutant were more structured than those formed by the wild-type strain. AFM analysis indicated that the biofilms formed by the rpoN mutant were stickier than those formed by the wild type strain during the attachment and establishment stages, but the difference in stickiness was greatly reduced during the maturation stage possibly due to the cytosolic contents released from dead cells in the biofilms formed by the wild type. These results suggest that the alginate overproduction greatly affects the physical properties (topography and stickiness) of P. aeruginosa biofilms as well as the physiological properties (cell death and growth) of the bacterial cells inside the biofilms.     

Study of deuterium metal interaction by ion implantation

Dynamic and non-equilibrium effects involving interaction between deuterium and radiation produced defects were studied during deuterium implantation of Cu and Ti. The technique of neutron yield measurement during deuterium implantation was employed and theoretical analysis was made to study the dynamics. SIMS, GIXRD and SEM studies on deuterium implanted samples were employed to study the evolution of implanted deuterium profiles, structure of deuterides and surface topography respectively.     

Spin-stretching of DNA and protein molecules for detection by fluorescence and atomic force microscopy

We have developed a rapid and efficient way of stretching DNA and denatured protein molecules for detection by fluorescence microscopy and atomic force microscopy (AFM). In the described method, a viscous drag created by transient rotational flow stretches randomly coiled DNA molecules or denatured proteins. Stretching is achieved by dispensing a droplet of sample solution containing DNA or denatured protein on a MgCl2-soaked mica surface. We present fluorescent images of straightened lambdaDNA molecules and AFM images of stress-shared, reduced von Willebrand factor as well as straightened lambdaDNA. The described quick and reliable spin-stretching technique will find wide applications in the analysis of single biopolymer molecules.     

Monitoring DNA immobilization and hybridization on surfaces by atomic force microscopy force measurements

DNA immobilization and hybridization was carried out on Au substrates that were modified with mercaptopropanoic acid and then treated with aluminum(III) solution. The positively charged AI(III) film can be used to immobilize both ds-DNA and ss-DNA. Atomic force microscopy (AFM) was used to monitor the process by force measurements between a negatively charged silica tip and the substrates while immersed in dilute electrolyte. Surface hybridization of ss-DNA produces an increase in the surface charge and surface potential of the substrates, which is reflected by the increasing repulsive force as determined from AFM force-separation curves. A single-base mismatch was detectable in surface hybridization. The AFM force measuring technique was also employed to investigate the interaction of Ru(phen)3(2+) with ss-DNA and ds-DNA. The force measurement results showed that there is a small interaction between Ru(phen)3(2+) and ss-DNA, which was ascribed to the electrostatic binding of Ru(phen)3(2+) to the ss-DNA surface. For ds-DNA, there is a strong interaction which is believed to be due to the association or intercalation of Ru(phen)3(2+) with ds-DNA.     

Precise control of nanofabrication by atomic force microscopy

With an aim of the precise control of the anodic oxidation process by atomic force microscopy, the technical improvement has been carried out based on the mechanism studies. The accuracy and reliability of the nanofabrication have been improved by the combination of ambient humidity control, improvement of instrumental performance and meniscus lifetime control. In parallel, the mechanism study has been proceeded through the detection of Faradaic current. The in situ Faradaic current detection of the nano-oxidation process can actually work as a sensitive monitor for the nano-oxidation process with a high reliability. From an engineering viewpoint with an eye to practical applications, controllable physical parameters which affect on the product size are enumerated to consider what we should do to raise the precision of nano-oxidation. Then the fast fabrication in a large area by a patchwork method, Faradaic current detection during oxidation-reduction reaction, and nanofabrication by current-control are shown as examples.     

The surface structure effect on the average height in atomic force microscopy investigations

The dependences of the average height on the scan area width and surface profile structure in atomic force microscopy are analyzed. It is shown by the example of the average height that, in the analysis of the atomic force microscopy data, it is necessary to determine local and global statistical parameters. The local statistical parameters can be larger than the global ones. For the given example, the scaling function is determined, which makes it possible to relate several experimental parameters for predicting the average height.     

Study on antibacterial mechanism of copper-bearing austenitic antibacterial stainless steel by atomic force microscopy

A study was made on the antibacterial mechanism of copper-bearing austenitic antibacterial stainless steel by a series of methods such as atomic force microscopy (AFM) observation, force-distance curves and inductively coupled plasma mass spectrometer test. It was observed by AFM that the structure of the outer cell membrane responsible for the cell permeability was substantially changed for the bacteria after contacting with the antibacterial stainless steel, showing that cell walls were seriously damaged and a lot of contents in the cells leaked. It was also found that the adhesion force of bacteria to antibacterial stainless steel was considerably greater than that to the contrast steel, indicating that the electrostatic forces by Cu(2+ )being an important factor for killing bacteria.     

Surface evaluation of whey protein films by atomic force microscopy and water vapour permeability analysis

The atomic force microscopy (AFM) technique is a powerful tool for studying surfaces and has been used to provide qualitative and quantitative information about nanometer‐scale matter properties that are often inaccessible by any other experimental technique. In this work AFM was used to evaluate the surfaces of edible films produced with whey protein concentrate (WPC). The morphology and the roughness of the films were analysed. The effects of WPC and plasticizer concentration were characterized in terms of water vapour permeability (WVP) and roughness parameters. Roughness was calculated through the images captured with AFM. AFM can be useful to identify structural changes of the film resulting from sample preparation. The results showed a relation between water vapour permeability and area roughness, through different sample preparation. The analyses of topography through roughness obtained with AFM, demonstrated the correlation between the morphology of the film, obtained with nanometer resolution and WVP. Copyright © 2004 John Wiley & Sons, Ltd.     

Study of the low stress plasticity in single-crystal MgO by nanoindentation and atomic force microscopy

Berkovich nanoindentations have been performed at ambient temperature with a new apparatus on (001) cleaved surfaces of single-crystal Magnesium Oxide (MgO). Rosette slip lines pattern has been observed at a nanometric scale by Atomic Force Microscope. Moreover, the load-displacement curves present particular features such as pop-in, which has been linked to the AFM surface topography observations. Finally, we show that the combination of a new nanoindentation apparatus and an Atomic Force Microscope allows to study the very early stages of the plastic deformation during a nanoindentation in terms of individual dislocations.     

Nanodissection of single- and double-stranded DNA by atomic force microscopy

Nanodissection of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) has been investigated by atomic force microscopy (AFM). It is found that both ss- and dsDNA can be repeatedly dissected by an AFM tip. However, a comparison study indicates that ssDNA is a little bit more easily broken by the AFM tip than dsDNA. This is supported by the fact that the time requested to break ssDNA is shorter than that of dsDNA in the same dissection procedure under the same load. Our experiment also shows that dissection of the DNA strand is very sensitive to the load applied, and a small change of the load lead to different results.     

Non-contact atomic force microscopy study of atomic manipulation on an insulator surface by nanoindentation

Experimental results on vertical manipulation on an insulator surface using non-contact atomic force microscopy are presented. Cleaved ionic KCl(100) single crystal is used as an insulator surface. With the nanoindentation method used, the vertical manipulation of a single atom in an ionic crystal surface is more difficult than in a semiconductor surface. Therefore, in many cases, more than one surface atom is manipulated while, in rare cases, single-atom manipulation is successfully performed. Lateral manipulation of a vacancy has occasionally succeeded on the KCl(100) surface. We have presumed that the lateral manipulation was induced by pulling.