Imaging the substructure of antibodies with tapping-mode AFM in air: the importance of a water layer on mica

Monoclonal antibodies (immunoglobulin G; IgG) against the N-terminal domain of the A subunit of DNA gyrase have been imaged using tapping-mode atomic force microscopy under ambient conditions on hydrophilic mica surfaces. The familiar tri-nodal submolecular resolution of IgG (i.e. 50-kDa resolution) has been achieved when operating the microscope with the tip predominantly in the attractive force regime. Under common laboratory conditions of about 40% relative humidity, the resolution of this substructure was not achieved owing to motion of the antibodies on the surface and/or image distortion from tip–sample instabilities. Reproducible imaging of the tri-nodal antibody substructure was achieved by desiccating the samples for extended periods of time (1 week or more) before imaging. This effect is attributed to the presence of a humidity-dependent thin water layer (a few molecules or nanometres thick), which has been observed previously using the surface force apparatus and scanning polarization force microscopy. Desiccation of the mica surfaces allowed enough water to be removed from the mica surface to prevent this effect. Degradation in the image quality over the imaging period of an hour or two was observed, owing to re-adsorption of water under the ambient laboratory conditions.     

Mechanically engraved mica surface using the atomic force microscope tip facilitates return to a specific sample location

By controlling the interaction between the atomic force microscope tip and mica, patterns of different sizes and shape have been produced on the surface of mica. Using these operator-constructed patterns as a reliable marker, the original scanned sample location can be re-located and imaged again on the same mica surface by atomic force microscopy (AFM). This location technique can be used to find the same object again even if the sample was removed from the AFM instrument or the sample was imaged in a different mode.     

Comparison of different aminofunctionalization strategies for attachment of single antibodies to AFM cantilevers

Atomic force microscopy (AFM) has developed into a key technique for elucidation of biological systems on the single molecular level. In particular, molecular recognition force microscopy has proven to be a powerful tool for the investigation of biological interactions under near physiological conditions. For this purpose, ligands are tethered to AFM tips and the interaction forces with cognate receptors on the sample surface are measured with pico-Newton accuracy. In the first step of tip functionalization, amino groups are typically introduced on the initially inert AFM tip. Several methods have been developed to reproducibly adjust the desired low density of amino groups on the tip surface, i.e. esterification with ethanolamine, gas-phase silanization with aminopropyl-triethoxysilane (APTES), or treatment with aminophenyl-trimethoxysilane (APhS) in toluene solution. In the present study, the usefulness of these methods for attachments of antibodies to AFM tips was characterized by a standardized test system, in which biotinylated IgG was bound to the tip and a dense monolayer of avidin on mica served as test sample. All three methods of aminofunctionalization were found fully satisfactory for attachment of single antibodies to AFM tips, only in a parallel macroscopic assay on silicon nitride chips a minor difference was found in that APTES appeared to yield a slightly lower surface density of amino groups.     

Atomically resolved imaging by low-temperature frequency-modulation atomic force microscopy using a quartz length-extension resonator

Low-temperature ultrahigh vacuum frequency-modulation atomic force microscopy (AFM) was performed using a 1 MHz length-extension type of quartz resonator as a force sensor. Taking advantage of the high stiffness of the resonator, the AFM was operated with an oscillation amplitude smaller than 100 pm, which is favorable for high spatial resolution, without snapping an AFM tip onto a sample surface. Atomically resolved imaging of the adatom structure on the Si(111)-(7x7) surface was successfully obtained.     

Imaging DNA molecules on mica surface by atomic force microscopy in air and in liquid

DNA molecules immobilized on mica surface by various methods have been observed by atomic force microscopy both in air and in liquid. Divalent cations and 3-aminopropyltriethoxysilane (APTES) modified mica surface have been used to immobilize the DNA molecules. Optimal DNA and divalent cations concentration for AFM imaging are presented. Among the different methods of modifying mica surface with APTES, the water solution modifying method appears to get the best results. When using high DNA concentration for AFM imaging, DNA networks can be formed. A simple method to extend long DNA molecules is demonstrated. The optimal imaging conditions and AFM operating techniques are discussed. Different DNA immobilizing methods have been compared and evaluated.     

Assembling and imaging of his-tag green fluorescent protein on mica surfaces studied by atomic force microscopy and fluorescence microscopy

The adsorption of his-tag green fluorescent protein (GFPH(6)) onto the mica surfaces has been studied by atomic force microscopy (AFM) and laser confocal fluorescence microscopy. By controlling the adsorption conditions, separated single GFPH(6) and GFPH(6) monolayer can be adsorbed and formed on mica surfaces. In present experiments, based on the AFM measurement, we found that the adsorbed GFPH(6) was bound on the mica surface with its beta-sheets. The formed GFPH(6) monolayer on mica surfaces was flat, uniform, and stable. Some applications of the formed monolayer have been demonstrated. The formed monolayer can be used as a substrate for DNA imaging and AFM mechanical lithography.     

Improvement of DNA-visualization in dynamic mode atomic force microscopy in air

Near-contact mode atomic force microscopy (AFM) imaging leads to sharper representations of DNA double strands on mica imaged at ambient conditions compared with noncontact mode AFM. Phase shift was used for feedback control yielding height information using a simple model calculation. No contact between tip and sample occurs. Measured DNA widths were up to four times smaller than measured with the same AFM tip in noncontact mode at ambient condition.     

AFM针尖对胶原样品表面一种损伤现象的研究

用AFM对吸附于云母表面的胶原蛋白的研究过程中，观察到一种AFM针尖对样品损伤现象。在小范围的扫描过程中．胶原蛋白在AFM针尖的作用下。产生了明显的移动。改变了其原来平整、均匀分布的表面特征。此现象文献中也曾有报道，在本实验中能重复出现。本文进一步分析讨论这种现象产生的原因，对比了不同成像模式下AFM针尖对样品表面的影响。结果表明，用Tapping Mode(TM)，扫描过程对样品表面几乎不产生影响，但是Non Contact Mode(NCM)在扫描过程中对样品表面产生了损伤作用。证明了TM模式更适合于对生物样品的研究。实验还发现这种损伤的程度和扫描范围的大小、针尖扫描的方向有着很大关系。     

Jumping mode AFM imaging of biomolecules in the repulsive electrical double layer

We present a method to image single biomolecules in aqueous media by atomic force microscope (AFM) without establishing any mechanical contact between the tip and the sample. It works by placing the feedback set point in the repulsive electrical double-layer curve just before the mechanical instability occurs. We use the jumping operation mode, where the set point is controlled at every image point and a stable imaging is achieved for several hours. This is a necessary condition for this method to be operative, otherwise the tip can fall in contact in a short time. The method is applied to image single-avidin protein molecules deposited on cleaved mica. In addition, the dependence of the height of avidin molecules as a function of ion concentration, due to differences in surface charge density of mica and avidin, is tentatively used to deduce relative values of these quantities.     

运用碳纳米管原子力显微镜针尖减小长程力作用的研究

减小探针和样品表面之间的长程宏观力是原子力显微镜获得高分辨率成像的关键。首先通过理论分析得出影响长程力的主要因素是探针的几何形状和尺寸。然后分别运用几何形状和尺寸不同的原子力显微镜的传统Si针尖和碳纳米管针尖对样品进行扫描试验研究,结果显示碳纳米管针尖较传统针尖获得了高分辨率的图像。这一结果表明,碳纳米管针尖减小了成像中宏观长程作用力的影响,是理想的原子力显微镜针尖。     

Analysis of direct immobilized recombinant protein G on a gold surface

For the immobilization of IgG, various techniques such as chemical linker, thiolated protein G methods, and fragmentation of antibodies have been reported [Y.M. Bae, B.K. Oh, W. Lee, W.H. Lee, J.W. Choi, Biosensors Bioelectron. 21 (2005) 103; W. Lee, B.K. Oh, W.H. Lee, J.W. Choi, Colloids Surf. B-Biointerfaces, 40 (2005) 143; A.A. Karyakin, G.V. Presnova, M.Y. Rubtsova, A.M. Egorov, Anal. Chem. 72 (2000) 3805]. Here, we modified the immunoglobulin Fc-binding B-domain of protein G to contain two cysteine residues at its C-terminus by a genetic engineering technique. The resulting recombinant protein, RPGcys, retained IgG-binding activity in the same manner as native protein G. RPGcys was immobilized on a gold surface by strong affinity between thiol of cysteine and gold. The orientations of both IgG layers immobilized on the base recombinant protein Gs were analyzed by fluorescence microscope, atomic force microscope (AFM), and surface plasmon resonance (SPR). Our data revealed that IgG-binding activity of RPGcys on gold surface significantly increased in comparison to wild type of protein G (RPGwild), which was physically adsorbed due to absence of cysteine residue. Immobilization of highly oriented antibodies based on cysteine-modified protein G could be useful for the fabrication of immunosensor systems.     

Immobilization and condensation of DNA with 3-aminopropyltriethoxysilane studied by atomic force microscopy

We used different methods to modify a mica surface with 3-aminopropyltriethoxysilane (APTES), and then used it as substrate to immobilize DNA for atomic force microscopy (AFM) observation. The evaporation method and solution modifying method were investigated and evaluated. The solution modifying method was found to be relatively simple and effective. Using an APTES solution-modified mica surface, DNA immobilization appeared more reproducible and it could be imaged in liquid. The mixed solution of APTES and DNA was dropped directly onto the mica surface for AFM imaging. We found that DNA can condense in APTES water solutions. Toroids, rods and intermediate structures of condensation were captured by AFM.     

Atomic force microscopy imaging of actin cortical cytoskeleton of Xenopus laevis oocyte

In this study we report an atomic force microscopy (AFM) investigation of the actin cortical cytoskeleton of Xenopus laevis oocytes. Samples consisted of inside‐out orientated plasma membrane patches of X. laevis oocytes with overhanging cytoplasmic material. They were spread on a freshly cleaved mica surface, subsequently treated with Triton X‐100 detergent and chemically fixed. The presence of actin fibres in oocyte patches was proved by fluorescence microscopy imaging. Contact mode AFM imaging was performed in air in constant force conditions. Reproducible high‐resolution AFM images of a filamentous structure were obtained. The filamentous structure was identified as an actin cortical cytoskeleton, investigating its disaggregation induced by cytochalasin D treatment. The thinnest fibres showed a height of 7 nm in accordance with the diameter of a single actin microfilament. The results suggest that AFM imaging can be used for the high‐resolution study of the actin cortical cytoskeleton of the X. laevis oocyte and its modifications mediated by the action of drugs and toxins.     

Development of eddy current microscopy for high resolution electrical conductivity imaging using atomic force microscopy

We present a high resolution electrical conductivity imaging technique based on the principles of eddy current and atomic force microscopy (AFM). An electromagnetic coil is used to generate eddy currents in an electrically conducting material. The eddy currents generated in the conducting sample are detected and measured with a magnetic tip attached to a flexible cantilever of an AFM. The eddy current generation and its interaction with the magnetic tip cantilever are theoretically modeled using monopole approximation. The model is used to estimate the eddy current force between the magnetic tip and the electrically conducting sample. The theoretical model is also used to choose a magnetic tip-cantilever system with appropriate magnetic field and spring constant to facilitate the design of a high resolution electrical conductivity imaging system. The force between the tip and the sample due to eddy currents is measured as a function of the separation distance and compared to the model in a single crystal copper. Images of electrical conductivity variations in a polycrystalline dual phase titanium alloy (Ti-6Al-4V) sample are obtained by scanning the magnetic tip-cantilever held at a standoff distance from the sample surface. The contrast in the image is explained based on the electrical conductivity and eddy current force between the magnetic tip and the sample. The spatial resolution of the eddy current imaging system is determined by imaging carbon nanofibers in a polymer matrix. The advantages, limitations, and applications of the technique are discussed.     

Facilitating the pickup of individual DNA molecules by AFM nanomanipulation with tips mechanically worn on bare mica

The tip is one of the critical factors to improve the efficiency in picking up individual DNA molecules from solid substrates based on atomic force microscope (AFM) nanomanipulation. We found that wearing AFM tips on certain solid substrates in advance to nanomanipulation operation would largely improve the pickup efficiency, which was ascribed to the increasing affinity of the tip to the DNA molecules along with the increase of the tip radius after wearing. It was demonstrated that bare mica was superior to APTES-modified mica to keep the tip clean while wearing, which was crucial for DNA pickup during AFM nanomanipulation.     

The analysis of morphological distortion during AFM study of cells

Atomic force microscopy (AFM) has been widely applied in cellular morphology study. However, morphological information including volume and roughness obtained by AFM are usually affected by different kinds of factors, which include the microscopic system itself, imaging mode, or external factors such as AFM probe or tip condition. In this study, based on red blood cell model, the dependence of cellular morphology, volume, and roughness on several parameters of the imaging was evaluated and, furthermore, a general rule and resolution for trustful analysis had been suggested. In addition, the potential effects that resulted from sample itself had also been analyzed based on adhesive force analysis. The results indicated that the scanning range and the imaging mode affect cellular volume and roughness, and the distorted images should be ascribed to blunt tip, contaminated tip, and the shape of tip. The analysis of morphological distortion during AFM investigation of cells provides a reference for researchers using AFM.     

Dynamic friction measurements with an atomic force microscope on polymer surfaces

The combination of scanning friction force microscopy (SFFM) and lock‐in techniques leads to dynamic SFFM (DSFFM) and provides great advantages in friction force studies with sub‐micrometre resolution. In this paper are presented measurements on thin adsorbed organic films on polymers (polymer blend of 75% poly(allylaminehydrochloride) (PAA) and 25% poly(diallyl‐dimethylammonium chloride) (PDDAC)) and on mica (as a reference). The amplitude and phase response as a function of the excitation amplitude can be explained on hard surfaces by a simple static and dynamic friction model. This model allows us further to distinguish static friction forces and kinetic friction forces in a quantitative way. Furthermore, we demonstrate the use of these spectra to determine the correct modulation amplitude of the excitation to achieve the optimal friction contrasts directly. Polymer data suggest that the viscoelastic shear flow under the atomic force microscope (AFM) tip is responsible for the shape of the phase and amplitude spectrum. Lastly, we demonstrate that DSFFM is a useful technique for surface characterisation in situations where SFFM may not be adequate.     

Dynamic force microscopy imaging of native membranes

We employed magnetic ACmode atomic force microscopy (MACmode AFM) as a novel dynamic force microscopy method to image surfaces of biological membranes in their native environments. The lateral resolution achieved under optimized imaging conditions was in the nanometer range, even when the sample was only weakly attached to the support. Purple membranes (PM) from Halobacterium salinarum were used as a test standard for topographical imaging. The hexagonal arrangement of the bacteriorhodopsin trimers on the cytoplasmic side of PM was resolved with 1.5nm lateral accuracy, a resolution similar to images obtained in contact and tapping-mode AFM. Human rhinovirus 2 (HRV2) particles were attached to mica surfaces via nonspecific interactions. The capsid structure and 2nm sized protein loops of HRV2 were routinely obtained without any displacement of the virus. Globular and filamentous structures on living and fixed endothelial cells were observed with a resolution of 5-20nm. These examples show that MACmode AFM is a favorable method in studying the topography of soft and weakly attached biological samples with high resolution under physiological conditions.     

Carbon nanotubes: a promising standard for quantitative evaluation of AFM tip apex geometry

The direct contact between tip and sample in atomic force microscopy (AFM) leads to demand for a quantitative knowledge of the AFM tip apex geometry in high-resolution AFM imaging and many other types of AFM applications like force measurements and surface roughness measurements. Given, the AFM tip apex may change continuously during measurements due to wear or during storage due to oxidation, it is very desirable to develop an easy and quick way for quantitative evaluation of AFM tip radius when necessary. In this study, we present an efficient method based on Zenhausern model (Scanning 14 (1992) 212) by measuring single-wall carbon nanotubes deposited on a flat substrate to reach this goal. Experimental results show the method can be used for routine quantitative evaluation of AFM tip apex geometry for tips with effective radii down to the nanometer scale.     

Measuring the sizes of nanospheres on a rough surface by using atomic force microscopy and a curvature-reconstruction method

One of the advantages of atomic force microscopy (AFM) is that it can accurately measure the heights of targets on flat substrates. It is difficult, however, to determine the shape of nanoparticles on rough surfaces. We therefore propose a curvature-reconstruction method that estimates the sizes of particles by fitting sphere curvatures acquired from raw AFM data. We evaluated this fitting estimation using 15-, 30-, and 50-nm gold nanoparticles on mica and confirmed that particle sizes could be estimated within 5% from 20% of their curvature measured using a carbon nanotube (CNT) tip. We also estimated the sizes of nanoparticles on the rough surface of dried cells and found we also can estimate the size of those particles within 5%, which is difficult when we only used the height information. The results indicate the size of nanoparticles even on rough surfaces can be measured by using our method and a CNT tip.