Atomic force microscopy and other scanning probe microscopies

Atomic Force Microscopy: A three-dimensional reconstructive tool of oral microbiota in gingivitis and periodontitis

Aim:

This study aims to ascertain the advantages of Atomic Force Microscopy (AFM) in the morphologic study of microorganisms and their interactions within the subgingival biofilm in patients with gingivitis and periodontitis.

Settings and Design:

Conducted a study on twenty patients, ten patients with severe periodontitis with probing the pocket depth of ≥8 mm, with a clinical attachment loss (CAL) of ≥6 mm CAL and ten patients with gingivitis: ≥5 mm pocket depth, and no attachment loss, was selected for the study.

Materials and Methods:

Bacterial biofilms were collected and slide preparation done. Morphological study was done using AFM. AFM consists of a cantilever-mounted tip, a piezoelectric scanner, a photodetector diode, a laser diode, and a feedback control. The laser beam is reflected from back of the cantilever into the quadrant of the photodetector. AFM works on the principle of interaction between the tip and the sample which causes the cantilever to deflect, thereby changing the position of laser onto the photodetector. Methodology used for studying the bacteria through AFM includes the following: (1) Probe type: Platinum coated silicon nitrate tip. (2) Probe force: 0.11 N/m. (3) Probe geometry: Triangular shaped tip. (4) Probe frequency: 22 KHz. (5) Probe immobilization: Used in Contact mode. AFM Solver Pro-M (NT-MDT) equipped with ETALON probe was used to take images in Nova software.

Results:

The investigation showed various morphological features, such as shape, size, and secretory product-like vesicles of the bacterial species involved in gingivitis and periodontitis. More bacterial surface details were studied by reproducing a three-dimensional reconstruction using AFM.

Conclusions:

The morphological variations of bacteria of different sizes, and shapes, cell wall structures, secretory product-like vesicles flagellated and filamentous microorganisms, polymorphonuclear leukocytes, and bacterial coaggregation analysis were done by AFM. Results of the present study conclude that AFM is a quite a reliable method for studying morphology of bacterial species involving periodontal diseases and is also used to study microbial interactions in biofilm.

Quantifying Drug-Induced Nanomechanics and Mechanical Effects to Single Cardiomyocytes for Optimal Drug Administration To Minimize Cardiotoxicity

Contrary to the well-studied dynamics and mechanics at organ and tissue levels, there is still a lack of good understanding for single cell dynamics and mechanics. Single cell dynamics and mechanics may act as an interface to provide unique information reflecting activities at the organ and tissue levels. This research was aimed at quantifying doxorubicin- and dexrazoxane-induced nanomechanics and mechanical effects to single cardiomyocytes, to reveal the therapeutic effectiveness of drugs at the single cell level and to optimize drug administration for reducing cardiotoxicity. This work employed a nanoinstrumentation platform, including a digital holographic microscope combined with an atomic force microscope, which can characterize cell stiffness and beating dynamics in response to drug exposures in real time and obtain time-dose-dependent effects of cardiotoxicity and protection. Through this research, an acute increase and a delayed decrease of surface beating force induced by doxorubicin was characterized. Dexrazoxane treated cells maintained better beating force and mechanical functions than cells without any treatment, which demonstrated cardioprotective effects of dexrazoxane. In addition, combined drug effects were quantitatively evaluated following various drug administration protocols. Preadministration of dexrazoxane was demonstrated to have protective effects against doxorubicin, which could lead to better strategies for cardiotoxicity prevention and anticancer drug administration. This study concluded that quantification of nanomechanics and mechanical effects at the single cell level could offer unique insights of molecular mechanisms involved in cellular activities influencing organ and tissue level responses to drug exposure, providing a new opportunity for the development of effective and time-dose-dependent strategies of drug administration.

PeakForce Tapping resolves individual microvilli on living cells

Microvilli are a common structure found on epithelial cells that increase the apical surface thus enhancing the transmembrane transport capacity and also serve as one of the cell's mechanosensors. These structures are composed of microfilaments and cytoplasm, covered by plasma membrane. Epithelial cell function is usually coupled to the density of microvilli and its individual size illustrated by diseases, in which microvilli degradation causes malabsorption and diarrhea. Atomic force microscopy (AFM) has been widely used to study the topography and morphology of living cells. Visualizing soft and flexible structures such as microvilli on the apical surface of a live cell has been very challenging because the native microvilli structures are displaced and deformed by the interaction with the probe. PeakForce Tapping® is an AFM imaging mode, which allows reducing tip-sample interactions in time (microseconds) and controlling force in the low pico-Newton range. Data acquisition of this mode was optimized by using a newly developed PeakForce QNM-Live Cell probe, having a short cantilever with a 17-µm-long tip that minimizes hydrodynamic effects between the cantilever and the sample surface. In this paper, we have demonstrated for the first time the visualization of the microvilli on living kidney cells with AFM using PeakForce Tapping. The structures observed display a force dependence representing either the whole microvilli or just the tips of the microvilli layer. Together, PeakForce Tapping allows force control in the low pico-Newton range and enables the visualization of very soft and flexible structures on living cells under physiological conditions.

AFM characterization of chemically treated corneal cells

We present a characterization of chemically treated cells using atomic force microscopy (AFM) which can observe changes in morphology and elasticity of cells. Since AFM has the significant advantage that it does not require fixation of samples, the method is simple and can capture various properties of living cells. In this study, corneal epithelial and endothelial cells were examined. The topography images of the corneal cells without glutaraldehyde (GA) fixation were successfully obtained. The images showed a natural three-dimensional shape of these cells, which scanning electron microscope (SEM) images could not provide. The AFM images of GA-fixed cells were taken and compared with a SEM image reported in the literature. Our results show that longer time for GA fixation makes the surface of the corneal endothelial tissue stiffer. Also, longer treatment results in relatively large structural variation in samples. Combined with conventional histochemical methods, this approach helps us gain an overall understanding of the influence of such chemical treatment.

Atomic force microscopy of bacteria from periodontal subgingival biofilm: Preliminary study results

Objective:

Atomic force microscope (AFM) is a technology that allows analysis of the nanoscale morphology of bacteria within biofilm and provides details that may be better useful for understanding the role of bacterial interactions in the periodontal disease.

Material and Methods:

Five patients with periodontal ≥5 mm pockets diagnosed as generalized periodontitis and five patients with slight gingivitis were selected for the investigation. Bacteria biofilms were collected and morphologically investigated by AFM application.

Results:

The investigation revealed how periodontitis bacteria are characterized by specific morphologic features of the cell wall. The major representative species of bacteria causing periodontal diseases have been reproduced by a three-dimensional reconstruction showing the bacteria surface details.

Conclusions:

The presence of complex glycocalyx structures, bacteriophage-like vesicles, spirochetes (classic and cystic morphology) and bacterial co-aggregation has been identified by the AFM analysis. The results suggest that AFM is a reliable technique for studying bacterial morphology and for examining microbial interactions in dental plaque.

Morphogenesis of mimivirus and its viral factories: an atomic force microscopy study of infected cells

Amoebas infected with mimivirus were disrupted at sequential stages of virus production and were visualized by atomic force microscopy. The development of virus factories proceeded over 3 to 4 h postinfection and resulted from the coalescence of 0.5- to 2-μm vesicles, possibly bearing nucleic acid, derived from either the nuclear membrane or the closely associated rough endoplasmic reticulum. Virus factories actively producing virus capsids on their surfaces were imaged, and this allowed the morphogenesis of the capsids to be delineated. The first feature to appear on a virus factory surface when a new capsid is born is the center of a stargate, which is a pentameric protein oligomer. As the arms of the stargate grow from the pentamer, a rough disk the diameter of a capsid thickens around it. This marks the initial emergence of a protein-coated membrane vesicle. The capsid self-assembles on the vesicle. Hillocks capped by different pentameric proteins spontaneously appear on the emerging vesicle at positions that are ultimately occupied by 5-fold icosahedral vertices. A lattice of coat protein nucleates at each of the 5-fold vertices, but not at the stargate, and then spreads outward from the vertices over the surface, merging seamlessly to complete the icosahedral capsid. Filling with DNA and associated proteins occurs by the transfer of nucleic acid from the interior of the virus factory into the nearly completed capsids. The portal, through which the DNA enters, is sealed by a plug of protein having a diameter of about 40 nm. A layer of integument protein that anchors the surface fibers is acquired by the passage of capsids through a membrane enriched in the protein. The coating of surface fibers is similarly acquired when the integument protein-coated capsids pass through a second membrane that has a forest of surface fibers embedded on one side.

Nanostructure-induced DNA condensation

The control of the DNA condensation process is essential for compaction of DNA in chromatin, as well as for biological applications such as nonviral gene therapy. This review endeavours to reflect the progress of investigations on DNA condensation effects of nanostructure-based condensing agents (such as nanoparticles, nanotubes, cationic polymer and peptide agents) observed by using atomic force microscopy (AFM) and other techniques. The environmental effects on structural characteristics of nanostructure-induced DNA condensates are also discussed.

Characterizing ultrathin and thick organic layers by surface plasmon resonance three-wavelength and waveguide mode analysis

A three-wavelength angular-scanning surface plasmon resonance based analysis has been utilized for characterizing optical properties of organic nanometer-thick layers with a wide range of thicknesses. The thickness and refractive index were determined for sample layers with thicknesses ranging from subnanometer to hundreds of nanometers. The analysis approach allows for simultaneous determination of both the refractive index and thickness without prior knowledge of either the refractive index or the thickness of the sample layers and without the help of other instruments, as opposed to current methods and approaches for characterizing optical properties of organic nanometer-thick layers. The applicability of the three-wavelength angular-scanning surface plasmon resonance approach for characterizing thin and thick organic layers was demonstrated by ex situ deposited mono- and multilayers of stearic acid and hydrogenated soy phosphatidylcholine and in situ layer-by-layer deposition of two different polyelectrolyte multilayer systems. In addition to the three-wavelength angular-scanning surface plasmon resonance approach, another surface plasmon resonance optical phenomenon, i.e., the surface plasmon resonance waveguide mode, was utilized to characterize organic sample layers whose thicknesses border the micrometer scale. This was demonstrated by characterizing both in situ layer-by-layer deposited polyelectrolyte multilayer systems and an ex situ deposited spin-coated polymer layer.

Atomic force microscopy of viruses

Atomic force microscopy (AFM) is a helpful tool to acquire nanometric-resolution images, and also to perform a certain physical characterization of specimens, including their stiffness and mechanical resilience. Besides of the wide range of applications, from materials science to biology, this technique works in a variety of conditions as long as the sample is supported on a solid surface, in air, ultra high vacuum or, most importantly for virus research, in liquids. The adaptability of this technique is also fostered by the variety of sizes of the specimens that it can dealt with, such as atoms, molecules, molecular complexes including viruses and cells, and the possibility to observe dynamic processes in real time. Indeed, AFM facilitates single molecule experiments enabling not only to see but also to touch the material under study (i.e., to undertake mechanical manipulations), and constitutes a fundamental source of information for material characterization. In particular, the study of the mechanical properties at the nanoscale of viruses and other biomolecular aggregates, is providing an important set of data which help to elaborate mechano-chemical structure/function models of molecular biomachines, expanding and complementing the information obtained by other structural techniques.

Protein particulate detection issues in biotherapeutics development--current status

Formation of aggregates and particulates in biopharmaceutical formulation continues to be one of the major quality concerns in biotherapeutics development. The presence of large quantities of aggregates is believed to be one of the causes of unwanted immunogenic responses. Protein particulates can form in a wide range of sizes and shapes. Therefore, a comprehensive characterization of particulates in biologics formulation continues to be challenging. The quantity of small size aggregates (e.g., dimer) in a stable biologics formulation is well controlled using precision analytical techniques (e.g., high-performance liquid chromatography). Particulate in clinical and commercial formulations is monitored using visual inspection and subvisible particulate counting assays. While visual inspection (by human eye or automated systems) is intended to detect particulates (intrinsic and extrinsic) of ~100 μm or larger, the subvisible counting methods cover smaller size ranges down to 10 μm. It is well recognized that research of particulates in the submicron (<1 μm) and low-micron (1-10 μm) ranges may provide important clues to understand the mechanism of particulate formation. The recent years have seen a significant increase in the development of newer technologies for more comprehensive characterization of particulates. This is attributed to increased awareness in this field of research over the past 5 years, stimulated by scholarly articles, commentaries, and robust discussions in various forums. This article provides an overview of emerging detection technologies that provide complementary characterization data encompassing a wider size range of particulates. It also discusses their advantages and limitations in the context of applications in biotherapeutics development.

Advanced microscopy techniques to assess solid-state properties of inhalation medicines

Efficient control and characterisation of the physico-chemical properties of active pharmaceutical ingredients (APIs) and excipients for orally inhaled drug products (OIDPs) are critical to successful product development. Control and reduction of risk require the introduction of a material science based approach to product development and the use of advanced analytical tools in understanding how the solid-state properties of the input materials influence structure and product functionality. The key issues to be addressed, at a microscopic scale, are understanding how the critical quality attributes of input materials influence surface, interfacial and particulate interactions within OIDPs. This review offers an in-depth discussion on the use of advanced microscopy techniques in characterising of the solid-state properties of particulate materials for OIDPs. The review covers the fundamental principles of the techniques, instrumentation types, data interpretation and specific applications in relation to the product development of OIDPs.

An atomic force microscopy investigation of cyanophage structure

Marine viruses have only relatively recently come to the attention of molecular biologists, and the extraordinary diversity of potential host organisms suggests a new wealth of genetic and structural forms. A promising technology for characterizing and describing the viruses structurally is atomic force microscopy (AFM). We provide examples here of some of the different architectures and novel structural features that emerge from even a very limited investigation, one focused on cyanophages, viruses that infect cyanobacteria (blue-green algae). These were isolated by phage selection of viruses collected from California coastal waters. We present AFM images of tailed, spherical, filamentous, rod shaped viruses, and others of eccentric form. Among the tailed phages numerous myoviruses were observed, some having long tail fibers, some other none, and some having no visible baseplate. Syphoviruses and a podovirus were also seen. We also describe a unique structural features found on some tailed marine phages that appear to have no terrestrial homolog. These are long, 450 nm, complex helical tail fibers terminating in a unique pattern of 3+1 globular units made up of about 20 small proteins.

Investigation of bacteriophage T4 by atomic force microscopy

Bacteriophage T4 was visualized using atomic force microscopy (AFM). The images were consistent with, and complementary to electron microscopy images. Head heights of dried particles containing DNA were about 75 nm in length and 60 nm in width, or about 100 nm and 85 nm respectively when scanned in fluid. The diameter of hydrated tail assemblies was 28 nm and their lengths about 130 nm. Seven to eight pronounced, right-handed helical turns with a pitch of 15 nm were evident on the tail assemblies. At the distal end of the tail was a knob shaped mass, presumably the baseplate. The opposite end, where the tail assembly joins the head, was tapered and connected to the portal complex, which was also visible. Phage that had ejected their DNA revealed the internal injection tube of the tail assembly. Heads disrupted by osmotic shock yielded boluses of closely packed DNA that unraveled slowly to expose threads composed of multiple twisted strands of nucleic acid. Assembly errors resulted in the appearance of several percent of the phage exhibiting two rather than one tail assemblies that were consistently oriented at about 72° to one another. No pattern of capsomeres was visible on native T4 heads. A mutant that is negative for the surface proteins hoc and soc, however, clearly revealed the icosahedral arrangement of ring shaped capsomeres on the surface. The hexameric rings have an outside diameter of about 14 nm, a pronounced central depression, and a center-to-center distance of 15 nm. Phage collapsed on cell surfaces appeared to be dissolving, possibly into the cell membrane.

Atom scale characterization of the near apex region of an atomic force microscope tip

Three-dimensional atom probe tomography (APT) is successfully used to analyze the near-apex regions of an atomic force microscope (AFM) tip. Atom scale material structure and chemistry from APT analysis for standard silicon AFM tips and silicon AFM tips coated with a thin film of Cu is presented. Comparison of the thin film data with that observed using transmission electron microscopy indicates that APT can be reliably used to investigate the material structure and chemistry of the apex of an AFM tip at near atomic scales.

Structural analysis of a Synechococcus myovirus S-CAM4 and infected cells by atomic force microscopy

A tailed cyanophage, S-CAM4 (family Myoviridae) from California coastal waters that infects Synechococcus, was characterized by atomic force microscopy. Capsomeric clusters of protein composing the 85 nm diameter icosahedral head were resolved and indicated a triangulation number of T=16. The 140 nm tail assembly, exhibiting a helical appearance with a 13 nm pitch, was seen in both extended and contracted states, the latter exposing the injection tube within. Attached below the base plate were six 50 nm long fibres, and six fibres 275-300 nm in length protruded from the periphery of the base plate. Protein-free DNA was abundant from ruptured heads. Virus attached en masse, in clusters and individually to cells, and cell fragments were recorded, as were perforated cells lysed by the phages. The capsid structure appears most closely related to that of the cyanophage Syn9 and the Bacillus subtilis phage SPO1, which may, in turn, be evolutionarily related to herpesvirus.

Biophysical and atomic force microscopy characterization of the RNA from satellite tobacco mosaic virus

Agarose gel electrophoresis, circular dichroism and differential scanning calorimetry showed that single-stranded RNA from satellite tobacco mosaic virus transforms from a conformationally ‘closed state’ at 4°C to a more conformationally ‘open state’ at 65°C. The transition is reversible and shows no hysteresis. Atomic force microscopy (AFM) allowed visualization of the two states and indicated that the conformationally ‘closed state’ probably corresponds to the native encapsidated conformation, and that the ‘open state’ represents a conformation, characterized as short, thick chains of domains, as a consequence of the loss of tertiary interactions. Heating from 75°C to 85°C in the presence of EDTA was necessary to further unravel the ‘open’ conformation RNA into extended chains of lengths >280 nm. Virus exposed to low concentrations of phenol at 65°C, extruded RNA as distinctive ‘pigtails’ in a synchronous fashion, and these ‘pigtails’ then elongated, as the RNA was further discharged by the particles. Moderate concentrations of phenol at 65°C produced complete disruption of virions and only remains of decomposed particles and disordered RNA were evident. AFM images of RNA emerging from disrupted virions appear most consistent with linear arrangements of structural domains.

An alternative method to determining optical lever sensitivity in atomic force microscopy without tip-sample contact

Force studies using atomic force microscopy generally require knowledge of the cantilever spring constants and the optical lever sensitivity. The traditional method of evaluating the optical lever sensitivity by pressing the tip against a hard surface can damage the tip, especially sharp ones. Here a method is shown to calculate the sensitivity without having to bring the tip into contact. Instead a sharpened tungsten wire is used to cause a point contact directly onto the cantilever and cause cantilever bending. Using beam theory, the sensitivity thus found can be converted to the equivalent sensitivity that would be obtained using the tip location. A comparison is presented between sensitivity values obtained from the conventional tip contact method and those derived from the wire-based technique for a range of cantilevers in air. It was found that the difference between the calculated sensitivity from the wire-based technique and the sensitivity obtained conventionally was less than 12%. These measurements indicate the presented method offers a simple alternative approach to obtain optical lever sensitivity without compromising the tip shape.

Atomic force microscopy investigation of vaccinia virus structure

Vaccinia virus was treated in a controlled manner with various combinations of nonionic detergents, reducing agents, and proteolytic enzymes, and successive products of the reactions were visualized using atomic force microscopy (AFM). Following removal of the outer lipid/protein membrane, a layer 20 to 40 nm in thickness was encountered that was composed of fibrous elements which, under reducing conditions, rapidly decomposed into individual monomers on the substrate. Beneath this layer was the virus core and its prominent lateral bodies, which could be dissociated or degraded with proteases. The core, in addition to the lateral bodies, was composed of a thick, multilayered shell of proteins of diverse sizes and shapes. The shell, which was readily etched with proteases, was thoroughly permeated with pores, or channels. Prolonged exposure to proteases and reductants produced disgorgement of the viral DNA from the remainders of the cores and also left residual, flattened, protease-resistant sacs on the imaging substrate. The DNA was readily visualized by AFM, which revealed some regions to be "soldered" by proteins, others to be heavily complexed with protein, and yet other parts to apparently exist as bundled, naked DNA. Prolonged exposure to proteases deproteinized the DNA, leaving masses of extended, free DNA. Estimates of the interior core volume suggest moderate but not extreme compaction of the genome.

Correlation between Enterococcus faecalis biofilms development stage and quantitative surface roughness using atomic force microscopy

Biofilms are assemblages of microorganisms and their associated extracellular products at an interface and typically with an abiotic or biotic surface. The study of the morphology of biofilms is important because they are associated with processes of biofouling, corrosion, catalysis, pollutant transformation, dental caries, drug resistance, and so forth. In the literature, biofilms have been examined by atomic force microscopy (AFM), which has proven to be a potent tool to study different aspects of the biofilm development on solid surfaces. In this work, we used AFM to investigate topographical changes during the development process of Enterococcus faecalis biofilms, which were generated on sterile cellulose nitrate membrane (CNM) filters in brain heart infusion (BHI) broth agar blood plates after 24, 36, 72, 192, and 360 h. AFM height images showed topographical changes due to biofilm development, which were used to characterize several aspects of the bacterial surface, such as the presence of extracellular polymeric substance, and the biofilm development stage. Changes in the development stage of the biofilm were shown to correlate with changes in the surface roughness as quantified through the mean roughness.

A mechanical spike accompanies the action potential in Mammalian nerve terminals

Large and rapid changes in light scattering accompany secretion from nerve terminals of the mammalian neurohypophysis (posterior pituitary). In the mouse, these intrinsic optical signals are intimately related to the arrival of the action potential E-wave and the release of arginine vasopressin and oxytocin (S-wave). Here we have used a high bandwidth atomic force microscope to demonstrate that these light-scattering signals are associated with changes in terminal volume that are detected as nanometer-scale movements of a cantilever positioned on top of the neurohypophysis. The most rapid mechanical response ("spike"), having a duration shorter than the action potential but comparable to that of the E-wave, represents a transient increase in terminal volume due to water movement associated with Na(+)-influx. The slower mechanical event ("dip"), on the other hand, depends upon Ca(2+)-entry as well as on intraterminal Ca(2+)-transients and, analogously to the S-wave, seems to monitor events associated with secretion.

Dynamic adhesion of T lymphocytes to endothelial cells revealed by atomic force microscopy

The recruitment of T lymphocytes to lymphoid organs or sites of inflammation is a crucial step in adaptive immunity. These processes require endothelial activation and expression of adhesion molecules, including E- and P-selectins, intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1). However, the complete characterization of the adhesion strength and dynamics between lymphocytes and endothelial cells has been hampered by the lack of sensitive quantitative techniques. Here we report on the application of atomic force microscopy to characterize the interaction between individual pairs of living T lymphocytes (i.e., Jurkat cells) and human umbilical vein endothelial cells (HUVECs). The detachment of individual cell-cell conjugates was a complex process involving several step-like rupture events and the viscoelastic deformation of cells on the scale of several microns. Adhesion between Jurkat cells and activated endothelial cells increased with compression force and contact time, with the most dramatic changes occurring within the first half second of contact. After 0.25 sec of contact, E-selectin, ICAM-1, and VCAM-1 contributed to 18%, 39%, and 41% of total adhesion strength, respectively, suggesting that ICAM-1 and VCAM-1 contributed more than the selectins in supporting cell attachment.

Topography of the free-energy landscape probed via mechanical unfolding of proteins

Single-molecule experiments in which proteins are unfolded by applying mechanical stretching forces generally force unfolding to proceed along a reaction coordinate that is different from that in chemical or thermal denaturation. Here we simulate the mechanical unfolding and refolding of a minimalist off-lattice model of the protein ubiquitin to explore in detail the slice of the multidimensional free-energy landscape that is accessible via mechanical pulling experiments. We find that while the free-energy profile along typical "chemical" reaction coordinates may exhibit two minima, corresponding to the native and denatured states, the free energy G(z) is typically a monotonic function of the mechanical coordinate z equal to the protein extension. Application of a stretching force along z tilts the free-energy landscape resulting in a bistable (or multistable) free energy G(z)-fz probed in mechanical unfolding experiments. We construct a two-dimensional free-energy surface as a function of both chemical and mechanical reaction coordinates and examine the coupling between the two. We further study the refolding trajectories after the protein has been prestretched by a large force, as well as the mechanical unfolding trajectories in the presence of a large stretching force. We demonstrate that the stretching forces required to destabilize the native state thermodynamically are larger than those expected on the basis of previous experimental estimates of G(z). This finding is consistent with the recent experimental studies, indicating that proteins may refold even in the presence of a substantial stretching force. Finally, we show that for certain temperatures the free energy of a polyprotein chain consisting of multiple domains is a linear function of the chain extension. We propose that the recently observed "slow phase" in the refolding of proteins under mechanical tension may be viewed as downhill diffusion in such a linear potential.

Radial compression elasticity of single DNA molecules studied by vibrating scanning polarization force microscopy

The radial compression properties of single DNA molecules have been studied using vibrating scanning polarization force microscopy. By imaging DNA molecules at different vibration amplitude set-point values, we obtain the correlations between radially applied force and DNA compression, from which the radial compressive elasticity can be deduced. The estimated elastic modulus is approximately 20-70 MPa under small external forces (<0.4 nN) and increases to approximately 100-200 MPa for large loads.

Physical properties of Escherichia coli P pili measured by optical tweezers

The mechanical behavior of individual P pili of uropathogenic Escherichia coli has been investigated using optical tweezers. P pili, whose main part constitutes the PapA rod, composed of approximately 10(3) PapA subunits in a helical arrangement, are distributed over the bacterial surface and mediate adhesion to host cells. They are particularly important in the pathogenesis of E. coli colonizing the upper urinary tract and kidneys. A biological model system has been established for in situ measurements of the forces that occur during mechanical stretching of pili. A mathematical model of the force-versus-elongation behavior of an individual pilus has been developed. Three elongation regions of pili were identified. In region I, P pili stretch elastically, up to a relative elongation of 16 +/- 3%. The product of elasticity modulus and area of a P pilus, EA, was assessed to 154 +/- 20 pN (n=6). In region II, the quaternary structure of the PapA rod unfolds under a constant force of 27 +/- 2 pN (n approximately 100) by a sequential breaking of the interactions between adjacent layers of PapA subunits. This unfolding can elongate the pilus up to 7 +/- 2 times. In region III, pili elongate in a nonlinear manner as a result of stretching until the bond ruptures.

Atomic force microscopy of BHK-21 cells: an investigation of cell fixation techniques

The atomic force microscope (AFM) has been used to image a wide variety of biological samples, including cultured cells, in air. Whilst cultured cells have been prepared for AFM analysis using a variety of matrices and fixatives, a definitive study of sample preparation and its effects on cell morphology has not, as far as the authors are aware, previously been reported. Although a considerable number of cell fixatives exist, no single fixative is ideal for all investigations. Prior to the performance of specialised techniques, such as atomic force microscopy of cultured cells in air, the cell fixation method must be investigated and optimised. The fixative abilities of 2% paraformaldehyde-lysine-periodate, 0.25% glutaraldehyde, paraformaldehyde-glutaraldehyde, 4% phosphate-buffered formal saline, 1% formaldehyde, methanol:acetone, formal saline, 4% paraformaldehyde and ethanol:acetic acid were assessed in this study. A qualitative assessment system was used to evaluate the efficacy of the above fixatives using conventional fixation criteria (i.e. the presence of fibroblastic morphology consistent with optical microscopy and the absence of fixation artifacts). The optimal fixative was identified as 4% paraformaldehyde, which was capable of providing optically consistent images of BHK-21 (fibroblastic) cells, whose heights remained within the measurement capability of the AFM instrument used in this study.

Selectins-an emerging target for drug delivery

Selectins are multifunctional adhesion molecules that mediate the initial interactions between circulating leukocytes and cells of the endothelium. First identified over a decade ago, selectins have provided insight into areas as diverse as normal lymphocyte homing, leukocyte recruitment during inflammatory responses, carbohydrate ligand biosynthesis and adhesion-mediated signalling. Of late, selectins were introduced as targets for drug delivery in the development of new anti-inflammatory therapeutics and in anti-cancer therapy. This review will examine the selectins and their ligands with a focus on recent findings on their role in physiology and pathophysiology as well as the emerging role of selectins as targets in controlled drug delivery.

An overview of the biophysical applications of atomic force microscopy

The potentialities of the atomic force microscopy (AFM) make it a tool of undeniable value for the study of biologically relevant samples. AFM is progressively becoming a usual benchtop technique. In average, more than one paper is published every day on AFM biological applications. This figure overcomes materials science applications, showing that 17 years after its invention, AFM has completely crossed the limits of its traditional areas of application. Its potential to image the structure of biomolecules or bio-surfaces with molecular or even sub-molecular resolution, study samples under physiological conditions (which allows to follow in situ the real time dynamics of some biological events), measure local chemical, physical and mechanical properties of a sample and manipulate single molecules should be emphasized.

Silatrane-based surface chemistry for immobilization of DNA, protein-DNA complexes and other biological materials

The procedure of surface functionalization based on the use of 1-(3-Aminopropyl)silatrane (APS) instead of our early procedure utilizing aminopropyl triethoxy silane (APTES) is described. Unlike APTES, APS is less reactive and extremely resistant to hydrolysis and polymerization at neutral pH. The kinetics of DNA adsorption to APS-mica was studied. The results are consistent with a diffusion controlled mechanism suggesting that DNA molecules bind irreversibly with the surface upon immobilization. This conclusion is supported by the data on imaging of supercoiled DNA, the labile conformations of which are very sensitive to the conditions at the surface-liquid interface. In addition, we demonstrated directly that the segments of DNA molecules could move along the surface if the sample is imaged in aqueous solution without drying of the sample. Using the time-lapse mode of AFM imaging we visualized the transition of purine-pyrimidine sequence in supercoiled DNA from intramolecular triple-helical conformation (H-form) into the B-helix upon the change of pH from acidic (pH 5) to neutral. The mechanisms of the H-to-B transitions and the correlation of the local structural transitions with a global DNA conformation are discussed.

Nanoscale tripodal 1,3,5,7-tetrasubstituted adamantanes for AFM applications

The synthesis of four novel nanoscale 1,3,5,7-tetrasubstituted adamantanes 22 and 25-27 designed for atomic force microscopy (AFM) applications is described. Each tetrahedrally shaped molecule incorporates a broad tripodal base made up of three identical legs that terminate with a sulfur-containing moiety, which is either a 4-acetylsulfanylmethylphenyl unit or else a (1,2,5-dithiazepan-1-yl)phenyl unit. The sulfur atoms are intended for eventual binding of the molecule multivalently to the apex of a gold-coated commercial AFM tip through formation of multiple S-Au bonds. In each molecule, the fourth terminus is a para-substituted benzoic acid methyl ester that is designed to scan the sample. We demonstrate that 27 is sufficiently large and rigid to be imaged by a conventional AFM tip. Adamantanes 22 and 25-27 may also find application as chemically well-defined nanoscale objects for calibration of AFM tips.

Structure of intracellular mature vaccinia virus visualized by in situ atomic force microscopy

Vaccinia virus, the basis of the smallpox vaccine, is one of the largest viruses to replicate in humans. We have used in situ atomic force microscopy (AFM) to directly visualize fully hydrated, intact intracellular mature vaccinia virus (IMV) virions and chemical and enzymatic treatment products thereof. The latter included virion cores, core-enveloping coats, and core substructures. The isolated coats appeared to be composed of a highly cross-linked protein array. AFM imaging of core substructures indicated association of the linear viral DNA genome with a segmented protein sheath forming an extended approximately 16-nm-diameter filament with helical surface topography; enclosure of this filament within a 30- to 40-nm-diameter tubule which also shows helical topography; and enclosure of the folded, condensed 30- to 40-nm-diameter tubule within the core by a wall covered with peg-like projections. Proteins observed attached to the 30- to 40-nm-diameter tubules may mediate folding and/or compaction of the tubules and/or represent vestiges of the core wall and/or pegs. An accessory "satellite domain" was observed protruding from the intact core. This corresponded in size to isolated 70- to 100-nm-diameter particles that were imaged independently and might represent detached accessory domains. AFM imaging of intact virions indicated that IMV underwent a reversible shrinkage upon dehydration (as much as 2.2- to 2.5-fold in the height dimension), accompanied by topological and topographical changes, including protrusion of the satellite domain. As shown here, the chemical and enzymatic dissection of large, asymmetrical virus particles in combination with in situ AFM provides an informative complement to other structure determination techniques.

Surface biology of DNA by atomic force microscopy

The atomic force microscope operates on surfaces. Since surfaces occupy much of the space in living organisms, surface biology is a valid and valuable form of biology that has been difficult to investigate in the past owing to a lack of good technology. Atomic force microscopy (AFM) of DNA has been used to investigate DNA condensation for gene therapy, DNA mapping and sizing, and a few applications to cancer research and to nanotechnology. Some of the most exciting new applications for atomic force microscopy of DNA involve pulling on single DNA molecules to obtain measurements of single-molecule mechanics and thermodynamics.

Structural evidence for a possible role of reversible disulphide bridge formation in the elasticity of the muscle protein titin

BACKGROUND

The giant muscle protein titin contributes to the filament system in skeletal and cardiac muscle cells by connecting the Z disk and the central M line of the sarcomere. One of the physiological functions of titin is to act as a passive spring in the sarcomere, which is achieved by the elastic properties of its central I band region. Titin contains about 300 domains of which more than half are folded as immunoglobulin-like (Ig) domains. Ig domain segments of the I band of titin have been extensively used as templates to investigate the molecular basis of protein elasticity.

RESULTS

The structure of the Ig domain I1 from the I band of titin has been determined to 2.1 A resolution. It reveals a novel, reversible disulphide bridge, which is neither required for correct folding nor changes the chemical stability of I1, but it is predicted to contribute mechanically to the elastic properties of titin in active sarcomeres. From the 92 Ig domains in the longest isoform of titin, at least 40 domains have a potential for disulphide bridge formation.

CONCLUSIONS

We propose a model where the formation of disulphide bridges under oxidative stress conditions could regulate the elasticity of the I band in titin by increasing sarcomeric resistance. In this model, the formation of the disulphide bridge could refrain a possible directed motion of the two beta sheets or other mechanically stable entities of the I1 Ig domain with respect to each other when exposed to mechanical forces.

Probing biopolymers with the atomic force microscope: a review

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Physical morphology and surface properties of unsaturated Pseudomonas putida biofilms

Unsaturated biofilms of Pseudomonas putida, i.e., biofilms grown in humid air, were analyzed by atomic force microscopy to determine surface morphology, roughness, and adhesion forces in the outer and basal cell layers of fresh and desiccated biofilms. Desiccated biofilms were equilibrated with a 75.5% relative humidity atmosphere, which is far below the relative humidity of 98 to 99% at which these biofilms were cultured. In sharp contrast to the effects of drying on biofilms grown in fluid, we observed that drying caused little change in morphology, roughness, or adhesion forces in these unsaturated biofilms. Surface roughness for moist and dry biofilms increased approximately linearly with increasing scan sizes. This indicated that the divides between bacteria contributed more to overall roughness than did extracellular polymeric substances (EPS) on individual bacteria. The EPS formed higher-order structures we termed mesostructures. These mesostructures are much larger than the discrete polymers of glycolipids and proteins that have been previously characterized on the outer surface of these gram-negative bacteria.