Probing chromatin with the scanning force microscope

With the scanning force microscope (SFM), one can image the topography of biological material adsorbed at air-solid or liquid-solid interfaces with up to nanometer resolution. In principle, fixation, contrast enhancement, and labeling are not required. We have adapted specimen preparation techniques of conventional electron microscopy for visualizing chromatin ultra-structures in the SFM. A beaded substructure of the nucleoprotein filament was obtained after hypotonic lysis of chicken erythrocytes and air drying. The beads-on-astring morphology of the basic nucleosomal assembly was well delineated. The nucleosomes appeared as round protrusions with an apparent height of 4–6 nm. The histogram of center-to-center distances between adjacent nucleosome cores along the filament axis had a peak at 30 nm. Reversible changes in the three-dimensional structure were observed upon exposure of airdried samples of metaphase chromosomes to solutions of different ionic strengths.     

Quantitative membrane electrostatics with the atomic force microscope

The atomic force microscope (AFM) is sensitive to electric double layer interactions in electrolyte solutions, but provides only a qualitative view of interfacial electrostatics. We have fully characterized silicon nitride probe tips and other experimental parameters to allow a quantitative electrostatic analysis by AFM, and we have tested the validity of a simple analytical force expression through numerical simulations. As a test sample, we have measured the effective surface charge density of supported zwitterionic dioleoylphosphatidylcholine membranes with a variable fraction of anionic dioleoylphosphatidylserine. The resulting surface charge density and surface potential values are in quantitative agreement with those predicted by the Gouy-Chapman-Stern model of membrane charge regulation, but only when the numerical analysis is employed. In addition, we demonstrate that the AFM can detect double layer forces at a separation of several screening lengths, and that the probe only perturbs the membrane surface potential by <2%. Finally, we demonstrate 50-nm resolution electrostatic mapping on heterogeneous model membranes with the AFM. This novel combination of capabilities demonstrates that the AFM is a unique and powerful probe of membrane electrostatics.     

Imaging the membrane protein bacteriorhodopsin with the atomic force microscope.

The membrane protein bacteriorhodopsin was imaged in buffer solution at room temperature with the atomic force microscope. Three different substrates were used: mica, silanized glass and lipid bilayers. Single bacteriorhodopsin molecules could be imaged in purple membranes adsorbed to mica. A depression was observed between the bacteriorhodopsin molecules. The two dimensional Fourier transform showed the hexagonal lattice with a lattice constant of 6.21 +/- 0.20 nm which is in agreement with results of electron diffraction experiments. Spots at a resolution of approximately 1.1 nm could be resolved. A protein, cationic ferritin, could be imaged bound to the purple membranes on glass which was silanized with aminopropyltriethoxysilane. This opens the possibility of studying receptor/ligand binding under native conditions. In addition, purple membranes bound to a lipid bilayer were imaged. These images may help in interpreting results of functional studies done with purple membranes adsorbed to black lipid membranes.     

Measuring local surface charge densities in electrolyte solutions with a scanning force microscope

To show that local surface charge densities can be measured with a scanning force microscope purple membranes adsorbed to alumina were imaged in electrolyte solutions. Force versus distance curves were measured on purple membranes and on the bare alumina with standard silicon nitride tips. By comparing the electrostatic force measured on both substances, the surface charge density of purple membranes could be calculated from the known charge density of alumina. The charge density of purple membranes was estimated to be -0.05 C/m².     

Probing specific molecular conformations with the scanning force microscope. Complexes of plasmid DNA and anti-Z-DNA antibodies.

An anti-Z-DNA IgG antibody was used to probe for the left-handed Z-DNA conformation of a d(CG)11 insert in a negatively supercoiled plasmid DNA (pAN022). The complexes were spread on mica in the presence of a quaternary ammonium detergent benzyldimethylalkylammonium chloride and imaged with a scanning force microscope (SFM). The high affinity anti-Z-DNA antibody was retained even after restriction endonuclease cleavage of the DNA. The two arms in the product molecules had unequal lengths in conformity with the known location of the Z-DNA forming insert. Most complexes exhibited one IgG per DNA molecule. The bound antibodies were up to approximately 35 nm in diameter and extended approximately 2 nm from the mica surface. They were generally in a lateral orientation relative to the DNA, in accordance with prior chemical modification experimental data indicating a bipedal mode of binding for an anti-Z-DNA IgG. However, the SFM images also suggest that the DNA bends to accommodate the two Fab combining regions of the antibody. This study demonstrates the utility of the SFM for investigating conformation-dependent molecular recognition.     

Observing single biomolecules at work with the atomic force microscope

Progress in the application of the atomic force microscope (AFM) to imaging and manipulating biomolecules is the result of improved instrumentation, sample preparation methods and image acquisition conditions. Biological membranes can be imaged in their native state at a lateral resolution of 0.5-1 nm and a vertical resolution of 0. 1-0.2 nm. Conformational changes that are related to functions can be resolved to a similar resolution, complementing atomic structure data acquired by other methods. The unique capability of the AFM to directly observe single proteins in their native environments provides insights into the interactions of proteins that form functional assemblies. In addition, single molecule force spectroscopy combined with single molecule imaging provides unprecedented possibilities for analyzing intramolecular and intermolecular forces. This review discusses recent examples that illustrate the power of AFM.     

Hydration force in the atomic force microscope: A computational study.

Using a hard sphere model and numerical calculations, the effect of the hydration force between a conical tip and a flat surface in the atomic force microscope (AFM) is examined. The numerical results show that the hydration force remains oscillatory, even down to a tip apex of a single water molecule, but its lateral extent is limited to a size of a few water molecules. In general, the contribution of the hydration force is relatively small, but, given the small imaging force ( approximately 0.1 nN) typically used for biological specimens, a layer of water molecules is likely to remain "bound" to the specimen surface. This water layer, between the tip and specimen, could act as a "lubricant" to reduce lateral force, and thus could be one of the reasons for the remarkably high resolution achieved with contact-mode AFM. To disrupt this layer, and to have a true tip-sample contact, a probe force of several nanonewtons would be required. The numerical results also show that the ultimate apex of the tip will determine the magnitude of the hydration force, but that the averaged hydration pressure is independent of the radius of curvature. This latter conclusion suggests that there should be no penalty for the use of sharper tips if hydration force is the dominant interaction between the tip and the specimen, which might be realizable under certain conditions. Furthermore, the calculated hydration energy near the specimen surface compares well with experimentally determined values with an atomic force microscope, providing further support to the validity of these calculations.     

A scanning electron microscope study of microvascular anastomoses.

The abdominal aortas of 30 rats were sutured under an operating microscope. The results were studied under a scanning electron microscope at 8 different periods after operation, ranging from 3 minutes to one month. The observations are presented.     

High-resolution imaging using a novel atomic force microscope and confocal laser scanning microscope hybrid instrument: essential sample preparation aspects

The recent data explosion in global gene expression profiling and proteomics has resulted in a need to determine the mechanistic role of biomarker signatures in pathogenicity. Consequently, elaborate technologies are required to assess increasingly smaller sub-cellular compartments and constituents. We describe the development, evaluation and application of an efficient sample preparation methodology to facilitate coupled atomic force microscopy and confocal laser scanning microscopy (AFM–CLSM), providing a novel means of concurrent high-resolution structural and fluorescence imaging. Due to their fragile nature and nanoscale dimensions, filopodia were selected as a model to develop the procedure that maximised fluorescence response, while maintaining epithelial cell ultra-structure. Fixation with ultra-pure methanol-free formaldehyde coupled to quantum dot nanocrystal labelling proved to be vital in achieving high quality AFM–CLSM images. We demonstrated for the first time that filopodia have a “quilted” surface structure. Additionally, high ultra-structural ridges on the apical cell surface resolved by AFM corresponded to punctate moesin clusters, representing direct visualisation of moesin linkages between transmembrane proteins and the cytoskeleton. The capacity of this novel multi-modal imaging technique to probe topography, molecular composition and biophysical properties of ultra-structural features therefore provides unique information that will significantly contribute to our understanding of cellular structure–function relationships.     

Lateral diffusion measurement at high spatial resolution by scanning microphotolysis in a confocal microscope.

Fluorescence photobleaching methods have been widely used to study diffusion processes in the plasma membrane of single living cells and other membrane systems. Here we describe the application of a new photobleaching technique, scanning microphotolysis. Employing a recently developed extension module to a commercial confocal microscope, an intensive laser beam was switched on and off during scanning according to a user definable image mask. Thereby the location, geometry, and number of photolysed spots could be chosen arbitrarily, their size ranging from tens of micrometers down to the diffraction limit. Therewith we bleached circular areas on the surface of single living 3T3 cells labeled with the fluorescent lipid analog NBD-HPC. Subsequently, the fluorescence recovery process was observed using the attenuated laser beam for excitation. This yielded image stacks representing snapshots of the spatial distribution of fluorescent molecules. From these we computed the radial distribution functions of the photobleached dye molecules. The variance of these distributions is linearly related to the diffusion constant, time, and the mobile fraction of the diffusing species. Furthermore, we compared directly the theoretically expected and measured distribution functions, and could thus determine the diffusion coefficient from each single image. The results of these two new evaluation methods (D = 0.3 +/- 0.1 micron 2/s) agreed well with the outcome of conventional fluorescence recovery measurements. We show that by scanning microphotolysis information on dynamical processes such as diffusion of lipids or proteins can be acquired at the superior spatial resolution of a confocal laser scanning microscope.     

Native-DIGE: a new look at the mitochondrial membrane proteome

Respiratory chain proteins play a pivotal role in mitochondrial metabolism and thereby in the aging process. Differential display of the mitochondrial proteome reveals the abundance changes occurring in proteins as response to complex events such as senescence and aging. However, there is an absolute need to implement a detection technique that could potentially encompass the hydrophobic and very basic membrane proteins, along with the soluble ones. It is also important to assess protein-protein interactions, besides changes in abundance. Native-difference gel electrophoresis (DIGE) is an approach that facilitates sensitive quantitative assessment of changes in membrane and soluble proteins. It stretches the boundaries of detecting abundance changes to protein-protein interactions for interpretation of a proteome in a more "meaningful" way. Here we evaluate the benefits of blue-native fluorescence DIGE as a method in differential quantitative proteomics with a focus on critical issues for application and experimental design.     

Mapping interaction forces with the atomic force microscope.

Force curves were recorded as the sample was raster-scanned under the tip. This opens new opportunities for imaging with the atomic force microscope: several characteristics of the samples can be measured simultaneously, for example, topography, adhesion forces, elasticity, van der Waals, and electrostatic interactions. The new opportunities are illustrated by images of several characteristics of thin metal films, aggregates of lysozyme, and single molecules of DNA.     

A scanning electron microscope study of human cerebral arteries.

Human cerebral arteries were obtained from autopsy, fixed under pressure, cut open, and tacked onto pieces of cork. For one artery the intima was partly teased away, exposing the media, and treated with a silver nitrate process. For another artery the adventitia was exposed. Both arteries were processed through graded ethanols and coated with gold paladium for the scanning electron microscope. The collagen fibers of the adventitia were approximately 5 mum in diameter and consisted of a bundle of microfilaments, each of which had a diameter of 800-1000 A (1 A = 10(-10) m). The collagen fibers were oriented parallel to the long axis of the artery. The muscle cells of the media had a diameter of 2-5 mum and were arranged circumferentially with a pitch of approximately 20 degrees. The collagen fibers of the media travel perpendicular to the muscle cells, and parallel to the long axis of the artery. The fibrillar components of the elastin in the intima had a diameter of approximately 700-1000 A and were arranged parallel to the long axis of the artery. It was postulated that the fibrillar part of the elastin was the elastic component of the elastin.     

A scanning electron microscope study of mouse peritoneal mesothelium.

As seen in the scanning electron microscope, peritoneal mesothelial cells of the mouse diaphragm, anterior abdominal wall and intestinal serosa carry numerous microvilli. These microvilli are absent over certain areas of the cell surface and are sometimes, interlocked in meshwork patterns or coronal formation. The apical cell membranes of the mesothelium at the base of the microvilli, are invaginated by many plasmalemmal vesicles and vacuoles and carry a number of protruding spherical structures. Deep circular craters, giving the impression of stomata, are also visible.