Infrared imaging of single nanoparticles via strong field enhancement in a scanning nanogap.

We demonstrate nanoscale resolved infrared imaging of single nanoparticles employing near-field coupling in the nanoscopic gap between the metal tip of a scattering-type near-field optical microscope and the substrate supporting the particles. Experimental and theoretical evidence is provided that highly reflecting or polariton-resonant substrates strongly enhance the near-field optical particle contrast. Using Si substrates we succeeded in detecting Au particles as small as 8 nm (

Direct observation of different surface structures on high-resolution images of native halorhodopsin.

Halorhodopsin (HR) was investigated with atomic force microscopic techniques (AFM) in aqueous solution. Two-dimensional (2D) crystals of HR were obtained by purifying an HR membrane fraction with the same buoyant density as the purple membrane (HR-PM) from the overexpressing strain Halobacterium salinarum D2. The membrane patches of HR were immobilized on mica. Images with a resolution up to 14 A were recorded. Crystals showed an orthogonal structure and the orientation of the molecules showed p42(1)2 symmetry; thus, alternate tetramers are inverted in the membrane. The crystal surface was found to display different structures depending on the imaging force used, indicating that some parts of the HR molecule are more rigid but others more compressible. From samples with single tetramers missing in the crystalline patches dimensions of the unit cell could be determined. Helix-connecting loops in single molecules of halorhodopsin were assigned. The images indicate that the large extracellular BC loop covers the whole molecule and is very flexible.

From images to interactions: high-resolution phase imaging in tapping-mode atomic force microscopy.

In tapping-mode atomic force microscopy, the phase shift between excitation and response of the cantilever is used as a material-dependent signal complementary to topography. The localization of information in the phase signal is demonstrated with 1.4-nm lateral resolution on purple membrane of Halobacterium salinarum in buffer solution. In a first-order approximation, the phase signal is found to correlate with modulations of the tip oscillation amplitude, induced by topography. Extending the analysis to contributions of the tip-sample interaction area as a second-order approximation, a method is proposed to extract information about the interaction from the phase signal for surfaces with a roughness in the order of the tip radius.

AFM imaging in solution of protein-DNA complexes formed on DNA anchored to a gold surface.

A chemical procedure for anchoring DNA molecules to gold surfaces was used to facilitate the imaging of DNA and DNA-protein complexes in buffer solution by tapping mode atomic force microscopy (TMAFM). For preparing flat gold surfaces, a novel approach was employed by evaporating small amounts of gold onto freshly cleaved mica to give flat films that were stable under aqueous buffer conditions. The thickness of the investigated films ranged from 1 to 10 nm. For typical films of 4-6 nm, which were stable under aqueous buffer conditions, the root mean square (RMS) roughness ranged between 0.25 and 0.5 nm, as measured by atomic force microscopy (AFM). This roughness is comparable to that of obtained by the template stripped gold (TSG) technique, which is widely used in scanning probe microscopy but involves more preparation steps. In order to visualize DNA and DNA-protein complexes by TMAFM, the DNA was chemisorbed to the gold surface through a linker carrying a terminal thiol group at the 5'-end of each of the DNA strands. The modified DNA fragments were bound to the gold films and imaged in buffer solution, while unmodified DNA could not be visualized. Since the DNA was not dried during the process, it can be assumed that its native conformation was retained. This mode of anchoring did not prevent interaction with proteins, as confirmed by the observation that the topology of a complex formed by adding the protein to a surface-anchored DNA was the same as that obtained by anchoring a pre-formed complex to the gold surface. We attribute this observation to the fact that the DNA is anchored to the gold surfaces only through its ends, therefore the DNA-support interaction is minimized but imaging is still possible.

Changes in the surface structure of purple membrane upon illumination measured by atomic force microscopy.

Bacteriorhodopsin (BR) patches with a diameter of 1 to 3 µm were investigated in their native state by atomic force microscopy (AFM) in buffer solution. The patches were immobilized deposited and investigated on mica in 150 mM KCl and 10 mM Tris-buffer at pH 8. Under this buffer condition they adsorb preferred with their extracellular side to the solid support mica. The structure of the two-dimensional light adapted crystals was resolved with an imaging force of about 100 pN up to a resolution of 13 Å. The topography of the surface gets smoother if an imaging force of 1000 pN was applied indicating that protruding structures are compressed. Upon illumination with white light, during imaging with a force of 200 pN, the surface structure of the BR lattice changed. The force- and light-induced structural changes were reversible.

Distribution of the surfactant-associated protein C within a lung surfactant model film investigated by near-field optical microscopy.

Lung surfactant films at the air/water interface exhibit the particularity that surfactant molecules are expelled from the surface monolayer into a surface associated multilamellar phase during compression. They are able to re-enter the surface film during the following expansion. The underlying mechanism for this behavior is not fully understood yet. However, an important role is ascribed to the surfactant-associated protein C (SP-C). Here, we studied a model lung surfactant, consisting of dipalmitoylphosphatidylcholine (DPPC), dipalmitoylphosphatidylglycerol (DPPG), and SP-C, by means of scanning near-field optical microscopy (SNOM). Attaching a fluorescent dye to the protein allowed the localization of its lateral distribution at various surface pressures with high resolution. At an early stage of compression, the film appears demixed into a pure lipid phase and a protein-enriched phase. Within the latter phase, protein aggregations are revealed. They show a uniform density, having three times the fluorescence intensity of their surroundings. Across the phase boundary between the lipid phase and the protein-rich phase, there is a protein density gradient rather than an abrupt border. When the film is highly compressed, we observe the formation of multilamellar structures that are fluorescent. They are often surrounded by a slightly fluorescent monolayer. The fluorescence of the multilayer stacks (i. e., the protein content per unit area) is proportional to the height of the stacks.

Rotary and unidirectional metal shadowing of VAT: localization of the substrate-binding domain.

AAA-ATPases have important roles in manifold cellular processes. VAT (valosine-containing protein-like ATPase of Thermoplasma acidophilum), a hexameric archaeal member of this family, has the tripartite domain structure N-D1-D2 that is characteristic of many members of this family. N, the N-terminal domain of 20.5 kDa, has been implicated in substrate binding. We have applied rotary and unidirectional shadowing to VAT and an N-terminally deleted mutant, VAT(Delta N), in order to map the location of this domain. For the analysis of data derived from unidirectionally shadowed samples we used a new approach combining eigenvector analysis with surface relief reconstruction. Averages of rotary shadowed particles as well as relief reconstructions map the N-terminal domains to the periphery of the hexameric complex and reveal their bipartite structure. Thus, this method appears to be well suited to study the conformational changes that occur during the functional cycle of the protein.

Gold-tagged RNA-A probe for macromolecular assemblies.

Ribonucleic acids (RNAs) play a key role in many fundamental life processes. These polymers are often found complexed with proteins in extremely large particles whose molecular mass may reach several millions of daltons (e.g., ribosomes, spliceosomes, and viruses). Structural studies of such RNA-protein complexes should help elucidate their mode of action. For the structural analyses of many macromolecular assemblies, electron microscopy (EM) has served an instrumental role. However, localization by EM of RNA within biological complexes is not yet a straightforward undertaking. Here we describe a methodology for the covalent tagging of RNA molecules with gold clusters, thereby enabling their direct visualization by microscopical methods. Our strategy involves transcription in vitro of RNAs that carry free thiol groups, using ribonucleoside triphosphate analogs containing a substituent with a terminal thiol group on their heterocyclic ring. This synthesis is followed by coupling of gold clusters to the thiolated transcript through a maleimido group. Visualization of such gold-tagged RNAs by transmission electron microscopy showed spots of gold clusters, with a diameter of 1-2 nm, arranged at nearly regular distances on an imaginary curve that presumably corresponds to the RNA chain. This assignment was corroborated by atomic force microscopy that exhibited images of RNA chains in which knob-like structures, whose height corresponds to the diameter of the gold clusters, were clearly seen. This study demonstrates the potential use of nucleic acids that are covalently labeled with gold clusters for the structural characterization of protein-RNA complexes.

Escherichia coli RNA polymerase translocation is accompanied by periodic bending of the DNA.

RNA polymerase was halted in consecutive registers of RNA synthesis ranging from registers 11 to 68. Non-denaturing gel electrophoresis shows that the mobility of the complexes varies (up to 15%), indicating that halted complexes differ in their conformation. The electrophoretic mobility changes with an approximate 10-register periodicity. The change of the mobility can be attributed to relative changes of RNA polymerase-induced bending angle. We suggest that the periodicity of the bending angle reflects periodic changes of the conformation of the halted complexes that might have relevance for the translocation mechanism.

High-resolution AFM-imaging and mechanistic analysis of the 20 S proteasome.

As macromolecular protease complex, the 20 S proteasome is responsible for the degradation of cellular proteins and the generation of peptide epitopes for antigen presentation. Here, structural and functional aspects of the 20 S proteasome from Thermoplasma acidophilum have been investigated by atomic force microscopy (AFM) and surface plasmon resonance (SPR). Due to engineered histidine tags introduced at defined positions, the proteasome complex was pre-oriented at ultra-flat chelator lipid membranes allowing for high-resolution imaging by AFM. Within these two-dimensional protein arrays, the overall structure of the proteasome and the organization of individual subunits was resolved under native conditions without fixation or crosslinking. In addition, the substrate-proteasome interaction was monitored in real-time by SPR using a novel approach. Instead of following enzyme activity by product formation, the association and dissociation kinetics of the substrate-proteasome complex were analyzed during proteolysis of the polypeptide chain. By blocking the active sites with a specific inhibitor, the substrate binding step could be dissected from the degradation step thus resolving mechanistic details of substrate recognition and cleavage by the 20 S proteasome.

Atomic-force microscopy on the olfactory dendrites of the silkmoths antheraea polyphemus and A. pernyi

Olfactory transduction is thought to occur in the outer dendritic membrane of insect olfactory receptor neurons. Electrophysiological studies have indicated that the outer dendritic membrane has non-specific cation channels and inositol-triphosphate-dependent Ca2+ channels. The presence of such channels is further supported by the observation that pheromone-stimulated dendrites take up cobalt. However, to date, there is no structural evidence for these channels. Therefore, in order to search for putative ion channels, we have imaged the membrane of the olfactory dendrites in the scanning electron microscope (SEM) and the atomic-force microscope (AFM), after extruding the dendrites out of the olfactory hairs and fixing them on plastic coverslips. With the aid of the SEM, we could see the beaded structure of the dendrite but no fine structural details, as the membrane was sputtered with gold. With the use of the contact mode of the AFM, we could see "pores" that were deeper than 3 nm and with a diameter of about 15 nm. The density of the "pores" was approximately 20/ microm2 or 10 000 pores per thick dendrite. We believe these to be putative ion channels based on indirect evidence.

Hydration scanning tunneling microscopy of DNA and a bacterial surface protein.

Hydration scanning tunneling microscopy is based on the electrical conductivity of molecularly thin water layers which adsorb to the sample surfaces in a humid atmosphere. It allows reliable imaging of biological specimens and even insulators, provided they are hydrophilic. Here, we present results obtained with linearized plasmid DNA on mica and a bacterial surface protein layer (the HPI layer). A width of 3 nm was measured for the DNA molecules and a quasi-periodic structure along the molecules with a repeat distance of about 5 nm was observed. We show that-depending on the tunneling voltage-there are two different imaging modes for the DNA samples: at higher voltages, real tunneling or field emission is responsible for the charge transfer between tip and sample. In contrast, at lower voltages we found indications of a water meniscus between tip and surface. The HPI layer, however, seems to be imaged at most voltages without a water meniscus.

Hydration-scanning tunneling microscopy as a reliable method for imaging biological specimens and hydrophilic insulators.

The recently discovered high lateral conductivity of molecularly thin adsorbed water films enables investigation of biological specimens, and even of surfaces of hydrophilic insulators by scanning tunneling microscopy (STM). Here we demonstrate the capabilities of this method, which we call hydration-STM (HSTM), with images of various specimens taken in humid atmosphere: We obtained images of a glass coverslip, collagen molecules, tobacco mosaic virus, lipid bilayers and cryosectioned bovine achilles tendon on mica. To elucidate the physical mechanism of this conduction phenomenon we recorded current-voltage curves on hydrated mica. This revealed a basically ohmic behavior of the I-V curves without a threshold voltage to activate the current transport and indicates that electrochemistry probably does not dominate the surface conductivity. We assume that the conduction mechanism is due to structuring of water at the surface.

Lateral electrical conductivity of mica-supported lipid bilayer membranes measured by scanning tunneling microscopy.

Lateral electric conductivity of mica-supported lipid monolayers and of the corresponding lipid bilayers has been studied by means of scanning tunneling microscopy (STM). The surface of freshly cleaved mica itself was found to be conductive when exposed to humid air. Lipid monolayers were transferred onto such a surface by means of the Langmuir-Blodgett technique, which makes the mica surface hydrophobic and suppresses the electric current along the surface in the experimentally accessible humidity (5-80%) and applied voltage (0-10 V) range. This is true for dipalmitoylphosphatidylethanolamine (DPPE) as well as dipalmitoylphosphatidylcholine (DPPC) monolayers. Repeated deposition of DPPC layers by means of the Langmuir-Blodgett LB technique does not lead to the formation of a stable surface-supported bilayer because of the high hydrophilicity of the phosphatidylcholine headgroups that causes DPPC/DPPC bilayers to peel off the supporting surface during the sample preparation. In contrast to this, a DPPE or a DPPC monolayer on top of a DPPE monolayer gives rise to a rather stable mica-supported bilayer that can be studied by STM. Electric currents between 10 and 100 fA, depending on the ambient humidity, flow along the DPPE bilayer surface, in the humidity range between 35 and 60%. The DPPC surface, which is more hydrophilic, is up to 100 times more conductive under comparable conditions. Anomalous high lateral conductivity thus depends on, and probably proceeds via, the surface-adsorbed water layers. The prominence of ambient humidity and surface hydrophilicity on the measured lateral currents suggests this. The combination of our STM data and previously published water adsorption isotherms as a function of the relative humidity indicate that one layer or less of adsorbed water suffices for mediating the measurable lateral currents. The fact that similar observations are also made for other hydrophilic substrates supports the conclusion that lateral conductivity via surface-adsorbed water is a rather general phenomenon.

Atomic force microscope measurements and manipulation of Langmuir-Blodgett films with modified tips.

A simple method for rendering atomic force microscope tips and cantilevers hydrophilic or hydrophobic through glow discharge in an appropriate gas atmosphere is introduced. Force curves at different humidities of these modified cantilevers were taken on freshly cleaved mica (hydrophilic surface) and on a monolayer of dipalmitoylphosphatidylethanolamine transferred onto mica (hydrophobic surface) to characterize the behavior of the cantilevers on hydrophilic and hydrophobic surfaces. Furthermore, Langmuir-Blodgett bilayers, with a dipalmitoylphosphatidylethanolamine bottom layer and a dipalmitoylphosphatidylcholine top layer, were imaged in the constant force mode in a multimode atomic force microscope in air under controlled humidity conditions. The friction and elasticity signal were recorded parallel to the topography. By varying the force exerted by the tip on the sample, different layers of the Langmuir-Blodgett system could be removed or flattened. Removal exposed underlying layers that exhibited a different friction and elasticity behavior. Furthermore, force scans with tips rendered hydrophobic were taken on the different layers of the sample to characterize the hydrophilic/hydrophobic nature of the layers. Only by combining the results obtained by the different methods can the structure of the lipid layer systems be identified.

Hybrid scanning transmission electron/scanning tunneling microscope system for the preparation and investigation of biomolecules.

A hybrid scanning transmission electron/scanning tunneling microscope vacuum system is introduced, which allows freeze drying and metal coating of biological samples and their simultaneous observation by scanning transmission electron microscopy and scanning tunnelling microscopy (STM). Different metal coatings and STM tips were analysed to obtain the highest possible resolution for such a system. Bovine liver catalase was used as a test sample and the STM results are compared to a molecular scale model.

Scanning tunneling microscopy of insulators and biological specimens based on lateral conductivity of ultrathin water films.

Scanning tunneling microscopy is based on the flow of an electrical current and thus cannot be used to directly image insulating material. It has been found, however, that a very thin film of water (about one monolayer) adsorbed to a surface exhibits a surprisingly high conductivity that is sufficient to allow scanning tunneling microscope imaging at currents below 1 picoampere. Hydrophilic insulators, such as glass and mica, can thus be imaged in humid air. The same is true for biological specimens deposited on such surfaces, as demonstrated by the scanning tunneling microscope imaging of plasmid DNA on mica.

Atomic force microscopy of a hydrated bacterial surface protein.

The protein surface layer of the bacterium Deinococcus radiodurans (HPI layer) was examined with an atomic force microscope (AFM). The measurements on the air-dried, but still hydrated layer were performed in the attractive imaging mode in which the forces between tip and sample are much smaller than in AFM in the repulsive mode or in scanning tunnelling microscopy (STM). The results are compared with STM and transmission electron microscopy (TEM) data.

Thickness determination of biological samples with a zeta-calibrated scanning tunneling microscope.

A single-tube scanning tunneling microscope has been zeta-calibrated by using atomic steps of crystalline gold and was used for measuring the thickness of two biological samples, metal-coated as well as uncoated. The hexagonal surface layer of the bacterium Deinococcus radiodurans with an open network-type structure shows thickness values that are strongly influenced by the substrate and the preparation method. In contrast, the thickness of the purple membrane of Halobacterium halobium with its densely packed less-corrugated structure exhibits very little variation in thickness in coated preparations and the values obtained are in good agreement with x-ray data.

Scanning tunnelling microscopy of biomacromolecules.

When imaging biomacromolecules with a STM, coating of specimens with a conductive layer is a convenient preparation method which provides a good rate of success. Utilizing evaporated platinum/carbon as a coating film we have investigated two biomacromolecules of very different appearance. The first of these is the HPI-layer, a natural two-dimensional protein crystal with a period of 18 nm, which is found on the surface of the bacterium Deinococcus radiodurans. The second specimen is type IV collagen which forms long triple-helical strands approx. 1.5 nm in diameter. The resulting STM pictures compare very well with electron microscopical images.