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PubMed2004

Three-dimensional imaging of living and dying neurons with atomic force microscopy.

Atomic Force Microscopy (AFM) has been used to image the morphology of developing neurons and their processes. Additionally, AFM can physically interact with the cell under investigation in numerous ways. Here we use the AFM to both three-dimensionally image the neuron and to inflict a nano/micro-puncture to its membrane. Thus, the same instrument used as a tool to precisely penetrate/cut the membrane at the nanoscale level is employed to image the morphological responses to damage. These first high resolution AFM images of living chick dorsal root ganglion cells and cells of sympathetic ganglion and their growing processes provide confirmation of familiar morphologies. The increased resolution of the AFM revealed these structures to be significantly more complex and variable than anticipated. Moreover we describe novel, dynamic, and unreported architectures, particularly large dorsally projecting ridges, spines, and ribbons of cytoplasm that appear and disappear on the order of minutes. In addition, minute (ca. 100 nm) hair-like extensions of membrane along the walls of nerve processes that also shift in shape and density, appearing and disappearing over periods of minutes were seen. We also provide "real time" images of the death of the neuron cell body after nano/micro scale damage to its membrane. These somas excreted their degraded cytoplasm, revealed as an enlarging pool beneath and around the cell. Conversely, identical injury, even repeated perforations and nanoslices, to the neurite's membrane do not lead to demise of the process. This experimental study not only provides unreported neurobiology and neurotrauma, but also emphasizes the unique versatility of AFM as an instrument that can (1) physically manipulate cells, (2) provide precise quantitative measurements of distance, surface area and volume at the nanoscale if required, (3) derive physiologically significant data such as membrane pressure and compliance, and (4) during the same period of study--provide unexcelled imaging of living samples.

Animals↗
PubMed2003

Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy.

Atomic force microscopy (AFM) has been applied in many biological investigations in the past 15 years. This review focuses on the application of AFM for quantitatively characterizing the structural and thermodynamic properties of protein-protein and protein-nucleic acid complexes. AFM can be used to determine the stoichiometries and association constants of multiprotein assemblies and to quantify changes in conformations of proteins and protein-nucleic acid complexes. In addition, AFM in solution permits the observation of the dynamic properties of biomolecular complexes and the measurement of intermolecular forces between biomolecules. Recent advances in cryogenic AFM, AFM on two-dimensional crystals, carbon nanotube probes, solution imaging, high-speed AFM, and manipulation capabilities enhance these applications by improving AFM resolution and the dynamic and operative capabilities of the AFM. These developments make AFM a powerful tool for investigating the biomolecular assemblies and interactions that govern gene regulation.

Air↗
PubMed1995

The structure and stability of phospholipid bilayers by atomic force microscopy.

Atomic force microscopy (AFM) was used to investigate the structure, stability, and defects of the hydrophilic surfaces of Langmuir-Blodgett bilayer films of distearoylphosphatidylcholine (DSPC) and dipalmitoylphosphatidylethanolamine (DPPE) in the solid phase, and dilinoleoylphosphatidylethanolamine (DLPE) in the fluid phase. Their relative resilience to external mechanical stress by the scanning tip and by fluid exchange were also investigated. DPPE monolayers showed parallel ridges at the surface with a period of 0.49 nm, corresponding to the rows of aligned headgroups consistent with the known crystallographic structure. DSPC and DLPE monolayers did not show any periodic order. The solid DSPC and DPPE monolayers were stable to continued rastering by the AFM tip; however, the stability of DLPE monolayers depended on the pH of the aqueous environment. Structural defects in the form of monolayer gaps and holes were observed after fluid exchange, but the defects in DLPE monolayer at pH 11 were stable during consecutive scanning. At pH 9 and below, the defects induced by fluid exchange over DLPE monolayers were more extensive and were deformed easily by consecutive scanning of the AFM tip at a force of 10 nN. The pH dependence of resilience was explained by the increasing bending energy or frustration due to the high spontaneous curvature of DLPE monolayers at low pH. The tangential stress exerted by the AFM tip on the deformable monolayers eventually produced a ripple pattern, which could be described as a periodic buckling known as Shallamach waves.

Biophysical Phenomena↗
PubMed2000

Biomolecular interactions measured by atomic force microscopy.

Atomic force microscopy (AFM) is nowadays frequently applied to determine interaction forces between biological molecules. Starting with the detection of the first discrete unbinding forces between ligands and receptors by AFM only several years ago, measurements have become more and more quantitative. At the same time, theories have been developed to describe and understand the dynamics of the unbinding process and experimental techniques have been refined to verify this theory. In addition, the detection of molecular recognition forces has been exploited to map and image the location of binding sites. In this review we discuss the important contributions that have led to the development of this field. In addition, we emphasize the potential of chemically well-defined surface modification techniques to further improve reproducible measurements by AFM. This increased reproducibility will pave the way for a better understanding of molecular interactions in cell biology.

Biophysics↗
PubMed2004

Nanofabrication with atomic force microscopy.

Atomic force microscopy (AFM) was developed in 1986. It is an important and versatile surface technique, and is used in many research fields. In this review, we have summarized the methods and applications of AFM, with emphasis on nanofabrication. AFM is capable of visualizing surface properties at high spatial resolution and determining biomolecular interaction as well as fabricating nanostructures. Recently, AFM-based nanotechnologies such as nanomanipulation, force lithography, nanografting, nanooxidation and dip-pen nanolithography were developed rapidly. AFM tip (typical radius ranged from several nanometers to tens of nanometers) is used to modify the sample surface, either physically or chemically, at nanometer scale. Nanopatterns composed of semiconductors, metal, biomolecules, polymers, etc., were constructed with various AFM-based nanotechnologies, thus making AFM a promising technique for nanofabrication. AFM-based nanotechnologies have potential applications in nanoelectronics, bioanalysis, biosensors, actuators and high-density data storage devices.

Image Interpretation, Computer-Assisted↗
PubMedDate not supplied

Analysis of ligand-receptor interactions in cells by atomic force microscopy.

Atomic force microscopy (AFM) increasingly has been used to analyse "receptor" function, either by using purified proteins ("molecular recognition microscopy") or, more recently, in situ in living cells. The latter approach has been enabled by the use of a modified commercial AFM, linked to a confocal microscope, which has allowed adhesion forces between ligands and receptors in cells to be measured and mapped, and downstream cellular responses analysed. We review the application of AFM to cell biology and, in particular, to the study of ligand-receptor interactions and draw examples from our own work and that of others to show the utility of AFM, including for the exploration of cell surface functionalities. We also identify shortcomings of AFM in comparison to "standard" methods, such as receptor auto-radiography or immuno-detection, that are widely applied in cell biology and pharmacological analysis.

Animals↗
PubMed2007

Single molecule studies of protein folding using atomic force microscopy.

Atomic force microscopy (AFM) offers new insights into the ability of proteins to resist mechanical force. The technique has been opened up by the availability of easy-to-use instruments that are commercially available, so that the technique no longer relies on the need to build instruments in the lab. Indeed it may become common for AFM instruments to sit beside stopped-flow apparatus in protein folding laboratories. In this chapter, we describe the instrument set-up, the preparation of suitable protein substrate, and the collection of data. Data selection and analysis are more complex than for conventional stopped-flow ensemble studies, but offer new insights into the function of proteins in vivo.

Microscopy, Atomic Force↗
PubMed1999

A physical approach to reduce nonspecific adhesion in molecular recognition atomic force microscopy.

Atomic force microscopy is one of the few techniques that allow analysis of biological recognition processes at the single-molecule level. A major limitation of this approach is the nonspecific interaction between the force sensor and substrate. We have modeled the nonspecific interaction by looking at the interaction potential between a conical Si3N4 tip with a spherical end face and a mica surface in solution, using DLVO (Derjaguin, Landau, Verwey, Overbeek) theory and numerical calculations. Insertion of the tip-sample potential in a simulation of an approach-retract cycle of the cantilever gives the well-known force-distance curve. Simulating a force-distance curve at low salt concentration predicts a discrete hopping of the tip, caused by thermal fluctuations. This hopping behavior was observed experimentally and gave rise to a novel approach to making measurements in adhesion mode that essentially works in the repulsive regime. The distance between tip and sample will still be small enough to allow spacer-involved specific interactions, and the percentage of nonspecific interactions of the bare tip with the mica is minimized. We have validated this physical model by imaging intercellular adhesion molecule 1 (ICAM-1) antigen with a tip functionalized with anti-ICAM-1 antibody. The measurement demonstrated that a significant decrease in the number of nonspecific interactions was realized, and the topographical image quality and the specific bonding capability of the tip were not affected.

Algorithms↗
PubMed1999

Thickness and elasticity of gram-negative murein sacculi measured by atomic force microscopy.

Atomic force microscopy was used to measure the thickness of air-dried, collapsed murein sacculi from Escherichia coli K-12 and Pseudomonas aeruginosa PAO1. Air-dried sacculi from E. coli had a thickness of 3.0 nm, whereas those from P. aeruginosa were 1.5 nm thick. When rehydrated, the sacculi of both bacteria swelled to double their anhydrous thickness. Computer simulation of a section of a model single-layer peptidoglycan network in an aqueous solution with a Debye shielding length of 0.3 nm gave a mass distribution full width at half height of 2.4 nm, in essential agreement with these results. When E. coli sacculi were suspended over a narrow groove that had been etched into a silicon surface and the tip of the atomic force microscope used to depress and stretch the peptidoglycan, an elastic modulus of 2.5 x 10(7) N/m(2) was determined for hydrated sacculi; they were perfectly elastic, springing back to their original position when the tip was removed. Dried sacculi were more rigid with a modulus of 3 x 10(8) to 4 x 10(8) N/m(2) and at times could be broken by the atomic force microscope tip. Sacculi aligned over the groove with their long axis at right angles to the channel axis were more deformable than those with their long axis parallel to the groove axis, as would be expected if the peptidoglycan strands in the sacculus were oriented at right angles to the long cell axis of this gram-negative rod. Polar caps were not found to be more rigid structures but collapsed to the same thickness as the cylindrical portions of the sacculi. The elasticity of intact E. coli sacculi is such that, if the peptidoglycan strands are aligned in unison, the interstrand spacing should increase by 12% with every 1 atm increase in (turgor) pressure. Assuming an unstressed hydrated interstrand spacing of 1.3 nm (R. E. Burge, A. G. Fowler, and D. A. Reaveley, J. Mol. Biol. 117:927-953, 1977) and an internal turgor pressure of 3 to 5 atm (or 304 to 507 kPa) (A. L. Koch, Adv. Microbial Physiol. 24:301-366, 1983), the natural interstrand spacing in cells would be 1.6 to 2.0 nm. Clearly, if large macromolecules of a diameter greater than these spacings are secreted through this layer, the local ordering of the peptidoglycan must somehow be disrupted.

Cell Wall↗
PubMed2001

Effect of Gravity on Colloidal Deposition Studied by Atomic Force Microscopy.

Atomic force microscopy (AFM) was used to study the effect of gravitational forces on the deposition of submicrometer colloidal particles onto solid surfaces to test the usual assumption that the contribution of gravity to the behavior of particles with diameters <1 &mgr;m is negligible. The effects of both particle size and density were examined using polystyrene sulfate latex, silica, and colloidal gold particles of several sizes ranging from 10 nm to 1 &mgr;m. The results show that significant differences are observed in the deposition of colloidal particles onto horizontal and vertical surfaces, under identical suspension conditions and exposure times, showing that gravitational forces can have a considerable effect. This effect was quantified by analysis of the AFM images. The experimental results are compared to calculations of the expected coverage and particle surface concentration assuming diffusion-limited adsorption and deposition by sedimentation. Gravity can be negligible for low-density particles with diameters considerably smaller than 1 &mgr;m. However, if the density of the colloidal particles is high, as in the case of colloidal gold, gravity can become a significant driving force for particle transport to the surface, even for particles with diameters much smaller than 100 nm. Copyright 2001 Academic Press.

Journal Article↗
PubMed1994

New internal structure of spider dragline silk revealed by atomic force microscopy.

Atomic force microscopy was used to study the three-dimensional nanometer-scale structure of the dragline silk of Nephila clavipes from microtomed sections of the silk. Contrary to a previously proposed model of randomly distributed protein crystallites interspersed in amorphous regions, a highly organized skin-core structure of the fiber was observed. The skin appeared to be thin with no discernible distinct features. The core consists of pleated fibril-like structures, which are arranged in two concentric cylinders. Upon stretching, the pleats were smoothed out substantially. The mechanical properties of spider silk can quite straightforwardly be related to the newly observed structures.

Animals↗
PubMed2003

The dynamic nature of contact angles as measured by atomic force microscopy.

Atomic force microscopy appears to be a useful tool for determining the contact angle for small particles. It is shown in this paper that the contact angle of a spherical polyethylene particle changes with the speed of the AFM piezoelectric translator. Such dynamic behavior of the contact angle and other uncertainties such as the position of the three-phase contact on the particle surface during bubble-particle interaction make it difficult to decide whether or not the AFM single-particle contact angle can be used to describe the hydrophobic state of the particle surface.

Letter↗
PubMed2004

Direct visualisation of heavy ion induced DNA fragmentation using atomic force microscopy.

Atomic Force Microscopy of phiX174 plasmids irradiated in vitro was used to visualise the DNA fragmentation induced by heavy ions and to compare it to the fragmentation pattern obtained after X-irradiation. Fragment distributions induced by low ion fuences were found to be much more shifted towards small fragment sizes than the distributions obtained after corresponding doses of X-rays. The average fragment length was found to be significantly smaller than the full plasmid length even for single ion traversals.

DNA↗
PubMed2001

Nanotribology of Si oxide layers on Si by atomic force microscopy.

Atomic force microscopy (AFM) has been used for tribological studies of Si surfaces covered by oxide layers of various kinds: chemical oxides prepared by the SC1 (NH4OH/H2O2/H2O) and the SC2 (HCl/H2O2/H2O) treatments and a thermal oxide. In the case of the SC1 chemical oxide, the oxide layer was scratched and the underlying Si substrate was ploughed by the Si3N4 AFM tip. On the other hand, no wear of the sample was noted on the other surfaces: the AFM often produced elevated patterns in the shape of the scanned area, which were no longer visible after HF etching. By annealing the SC1-treated surface in N2 gas at above 200 degrees C for 30 min, the oxide layer could not be scratched any more. By soaking the thermal oxide in KOH, the oxide layer was then scratched. It is concluded that the presence of OH bases is the necessary condition for the nano-scratching of the oxide layers.

Journal Article↗
PubMed2002

Developments for inverted atomic force microscopy.

Atomic force microscopy (AFM) has been used to study a wide range of systems. Chemically and biologically modified probes have extended AFM by coupling chemical and biological information with the physical measurements. In an effort to further expand the capabilities of modified AFM probes, previous studies investigated the use of an inverted AFM design (i-AFM), wherein a microfabricated tip array is used to image a cantilever-supported sample. This report details developments in cantilever and tip array fabrication which are aimed at improving the applicability and performance of this i-AFM design. Using an epoxy-based procedure, commercial cantilevers were modified with a series of standard substrates, including template-stripped gold, highly oriented pyrolytic graphite, and mica. The samples on these cantilevers were imaged with i-AFM, and lateral force images are obtained. This paper demonstrates the first use of i-AFM for measuring friction.

Journal Article↗
PubMed2000

Microphase separation at the surface of block copolymers, as studied with atomic force microscopy.

Atomic force microscopy (AFM) is used to study the phase separation process occurring in block copolymers in the solid state. The simultaneous measurement of the amplitude and the phase of the oscillating cantilever in the tapping mode operation provides the surface topography along with the cartography of the microdomains of different mechanical properties. This technique thus allows to characterize the size and shape of those microdomains and their organization at the surface (e.g. cubic lattice spheres, hexagonal lattice of cylinders, or lamellae). In this study, a series of symmetric triblock copolymers made of a inner elastomeric sequence (poly(butadiene) or poly(alkylacrylate)) and two outer thermoplastic sequences (poly(methylmethacrylate)) is analyzed by AFM in the tapping mode. The microphase separation and their morphology are essential factors for the potential of these materials as a new class of thermoplastic elastomers. Special attention is paid to the control of the surface morphology, as observed by AFM, by the molecular structure of the copolymers (volume ratio of the sequences, molecular weight, length of the alkyl side group) and the experimental conditions used for the sample preparation. The molecular structure of the chains is completely controlled by the synthesis, which relies on the sequential living anionic polymerization of the comonomers. The copolymers are analyzed as solvent-cast films, whose characteristics depend on the solvent used and the annealing conditions. The surface arrangement of the phase-separated elastomeric and thermoplastic microdomains observed on the AFM phase images is discussed on the basis of quantitative information provided by the statistical analysis by Fourier transform and grain size distribution calculations.

Journal Article↗
PubMed2006

Partial validation of cross flow ultrafiltration by atomic force microscopy.

Atomic force microscopy was used to evaluate a cross flow ultrafiltration (CFUF) system. The CFUF system was used for the size fractionation of natural colloidal material from freshwaters. Analysis of the images of bulk water, permeates, and retentates shows the primary materials observed were near-spherical structures with height dimensions up to approximately 12 nm. The number of colloidal particles (per unit area) on the mica surfaces derived from the retentates increased by a factor of 2 between a concentration factor (cf) of 1 and of 20. Colloidal densities of nanoparticles were approximately 2 orders of magnitude lower in the permeate compared to the retentate, indicating a good size fractionation. As the cf value increased from 1 to 20, the percentage of <1-nm material decreased substantially and the percentage of >1-nm material increased substantially in the retentates. Line transects along a surface and surface roughness values show good agreement with the above results. Results suggest the size fractionation is good but not perfect and high cf values produce a better size fractionation, although some retention of small material is always observed. High cf values are recommended.

Journal Article↗
PubMed2003

Silicalite crystal growth investigated by atomic force microscopy.

Atomic force microscopy has been used to image the various facets of two morphologically distinct samples of silicalite. The smaller (20 microm) sample A crystals show 1 nm high radial growth terraces. The larger (240 microm) sample B crystals show growth terraces 1 to 2 orders of magnitude higher than the terraces on sample A with growth edges parallel to the crystallographic axes. Moreover, the terraces on the (010) face are significantly higher than the terraces on the (100) face - inconsistent with the previously proposed 90 degrees intergrowth structure. Sample A highlights that under certain synthetic conditions, silicalite grows in a manner akin to zeolites Y and A, via the deposition of layers comprising, in the case of silicalite, pentasil chains. It is probable that the rate of terrace advance is identical on the (010) and (100) faces, and it is the rate of terrace nucleation that dictates the overall growth rate of each facet and hence the relative size expressed in the final crystal morphology. Analysis of the growth terraces of sample B and detailed consideration of the structures of both MFI, and a closely related material MEL, lead to the proposal of a generalized growth mechanism for silicalite including the incorporation of defects within the structure. These defects are thought to be responsible for both the relative and the absolute terrace heights observed and may also explain the hourglass phenomenon observed by optical microscopy. The implications of this growth mechanism, supported by results of infrared microscopy, generate a new dimension to the continuing debate on the existence of intergrowths within one of the most important structures relevant to zeolite catalysis.

Journal Article↗