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Results for “Microscopy, Atomic Force”

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PubMed2006

Observation of single-stranded DNA on mica and highly oriented pyrolytic graphite by atomic force microscopy.

Atomic force microscopy was used to image single-stranded DNA (ssDNA) adsorbed on mica modified by Mg(2+), by 3-aminopropyltriethoxysilane or on modified highly oriented pyrolytic graphite (HOPG). ssDNA molecules on mica have compact structures with lumps, loops and super twisting, while on modified HOPG graphite ssDNA molecules adopt a conformation without secondary structures. We have shown that the immobilization of ssDNA under standard conditions on modified HOPG eliminates intramolecular base-pairing, thus this method could be important for studying certain processes involving ssDNA in more details.

Aluminum Silicates↗

PubMed2006

Ultrastructural appearance of embedded and polished wood cell walls as revealed by Atomic Force Microscopy.

Atomic Force Microscopy (AFM) was used to investigate the ultrastructural appearance of transverse wood cell wall surfaces in embedded and polished Norway spruce wood blocks. The prepared surfaces showed only little height differences, suitable for high resolution AFM phase contrast imaging. Our results revealed randomly arranged wood cell wall components in the thick secondary 2 (S2) layers of the tracheid cell walls. It is concluded that the observed distribution pattern of the cellulose fibril/matrix structure is close to the original cell wall structure. In this context, the plasticity of wood cell wall components to re-arrange and adjust to different conditions resulting in diverse structural pattern is discussed.

Cell Wall↗

PubMed1999

Heptameric structures of two alpha-hemolysin mutants imaged with in situ atomic force microscopy.

Atomic force microscopy has been used to study self-assembled structures of two alpha-hemolysin mutants. For a mutant (alphaHL-H5) that was locked into the prepore state on fluid phase egg-PC membranes, we visualized, for the first time, heptameric prepores and showed that the 7-fold axis in the prepore lies perpendicular to the membrane surface. For another mutant (TCM) with the transmembrane domain, the self-assembled oligomer that assumes the conformation of the fully assembled pore is also a heptamer. These results show that heptamers are the preferred oligomerization state of alpha-hemolysin.

Bacterial Toxins↗

PubMed1998

Observation of geometric structure of collagen molecules by atomic force microscopy.

Atomic force microscopy was used to study the geometric structure of collagen fibrils and molecules of rat calcanean tendon tissues. The authors found that the diameter of the fibrils ranged from 124 to 170 nm, and their geometric form suggested a helical winding with spectral period from 59.4 to 61.7 nm, close to the band dimensions reported by electron microscopy. At high magnification, the surface of these bands revealed images that probably correspond to the almost crystalline array of collagen molecules, with the triple helix structure almost visible. The typical helix width is 1.43 nm, with main periods of 1.15 and 8.03 nm, very close to the dimensions reported by X-ray diffraction.

Achilles Tendon↗

PubMed1996

Visualization of plant cell walls by atomic force microscopy.

Atomic force microscopy has been used to visualize the ultrastructure of hydrated plant cell wall material from prepared apple (Malus pumila MILL; Cox orange pippin), water chestnut (Eleocharis dulcis L.), potato (Solanum tuberosum L.; Bintje), and carrot (Daucus carota L.; Amsterdamse bak) parenchyma. Samples of cell wall material in aqueous suspension were deposited onto freshly cleaved mica. Excess water was blotted away and the moist samples were imaged in air at ambient temperature and humidity. The three-dimensional images obtained highlighted the layered structure of the plant cell walls and revealed features interpreted as individual cellulose microfibrils and plasmodesmata.

Biophysical Phenomena↗

PubMed1997

Imaging Plasmodium falciparum-infected ghost and parasite by atomic force microscopy.

Atomic force microscopy was used to image the membrane cytoskeleton network of normal and P. falciparum-infected ghosts. The membrane cytoskeleton network was examined in air-dried ghost preparations from normal and infected cells. We found that the spectrin network was changed in infected ghosts. The thickness of the normal red cell membrane was about 15.05 +/- 2.27 nm, while the thickness of the P. falciparum-infected membrane was found to be 22.97 +/- 3.84 nm. The ghost containing ring stage parasites exhibited areas of particle-like protrusions ranging in size from 0.2 to 0.7 micron. The surface of the P. falciparum parasite was also imaged in air-dried samples, showing the existence of a large protrusion extending from the parasite surface.

Animals↗

PubMedDate not supplied

Site-specific binding of the 9.5 kilodalton DNA-binding protein ORF80 visualized by atomic force microscopy.

Atomic force microscopy (AFM) has been used to examine the binding properties of the DNA-binding protein ORF80 to DNA. ORF80 is a 9.5 kDa protein that binds site-specifically to double-stranded DNA of the sequence TTAA-N(7)-TTAA. Direct sizing of the protein complexes on DNA fragments from the plasmid pRN1 with AFM shows that the protein ORF80 binds preferentially to two positions. These positions agree well with the ORF80 binding sites determined by footprinting analysis. The measurements allow an estimate of the stoichiometry of the DNA-protein complexes. In contrast to previous results, the single-molecule experiments suggest that only a low number of ORF80 molecules bind to a DNA-binding site.

Archaeal Proteins↗

PubMedDate not supplied

Interferon alpha-2a interactions on glass vial surfaces measured by atomic force microscopy.

Atomic force microscopy was used to study adsorption and adhesion peculiarities of interferon alpha-2a on glass and mica surfaces. The specific protein adsorption behavior as a function of the pH value was illustrated on mica by single molecule imaging, while adhesion forces between interferon molecules and inner surfaces of borosilicate glass vials were measured directly under aqueous buffer conditions by force microscopy. We found that the adhesion force on Schott FIOLAX Type I plus was reduced by 40% of the total adhesion force measured on Schott FIOLAX, a standard type I borosilicate glass quality. These results reflect the anticipated superiority of the special "Type I plus" coating over undesired protein adsorption to glass. In addition, this study gives insight into a new method to predict unintended protein adsorption to glass container walls and to characterize the adsorption process by force measurement.

Adsorption↗

PubMed2005

Unraveling the architecture of viruses by high-resolution atomic force microscopy.

Atomic force microscopy (AFM) has recently emerged as an effective complement to other structure determination techniques for studying virus structure and function. AFM allows the direct visualization of viruses in a hydrated state and can probe surface topography in unrivaled detail. Moreover, AFM can be used to elucidate dynamic processes associated with the life cycle of viruses in vitro. It can readily produce high-resolution, nonaveraged, single-particle images of both polymorphic and pleiomorphic viruses. Although AFM does not yield images of internal structures within an intact virion as do penetrating techniques such as electron microscopy and X-ray crystallography, nonetheless, by visualizing the surfaces of internal structures upon treatment with chemical and enzymatic agents, as we demonstrated recently with vaccinia virus, modeling of the complex architecture of a large virus is possible.

Cryoelectron Microscopy↗

PubMed2006

Extremely high dose neutron dosimetry using CR-39 and atomic force microscopy.

Atomic force microscopy (AFM) has been applied to the analysis of CR-39 nuclear track detectors for high dose neutron dosimetry. As a feasible study to extract the neutron dose, we have employed a (239)Pu-Be neutron source with the traditional track density measurement of recoil proton etch pits from a high density polyethylene (CH(2)) radiator. After very short etching ( approximately 1 microm), etch pit densities were measured as a function of neutron fluence (neutron dose) up to 1.4 x 10(10) cm(-2) (6.6 Sv). Neutron sensitivity was also measured to be 6.6 x 10(-4). Maximum measurable neutron dose was estimated to be approximately 200 Sv by measuring the fraction of the total image area occupied by the etch pits.

Dose-Response Relationship, Radiation↗

PubMed1997

Molecular resolution imaging of macromolecular crystals by atomic force microscopy.

Atomic force microscopy (AFM) images at the molecular level have been obtained for a number of different protein and virus crystals. They can be utilized in some special cases to obtain information useful to crystal structure analyses by x-ray diffraction. In particular, questions of space group enantiomer, the packing of molecules within a unit cell, the number of molecules per asymmetric unit, and the dispositions of multiple molecules within the asymmetric unit may be resolved. In addition, because of the increasing sensitivity and resolution of the AFM technique, some molecular features of very large asymmetric units may be within reach. We describe here high-resolution studies, using AFM, to visualize individual molecules and viruses in their crystal lattices. These investigations included fungal lipase, lysozyme, thaumatin, canavalin, and satellite tobacco mosaic virus (STMV).

Computer Simulation↗

PubMedDate not supplied

Determination of a translocation chromosome by atomic force microscopy.

Atomic force microscopy (AFM) has been used to study the translocation involving chromosomes 11 and 13. An amniocentesis procedure was performed at 18 weeks of pregnancy on a familial balanced translocation carrier mother whose karyotype was 46,XX,t(11;13) (q23;q34). After harvesting the tissue cultures, light microscopy studies (LM) have indicated that the fetus had the same translocation. A 0.3 microm gap region on the derivative chromosome 13 was determined by AFM; it was equivalent to a mid-sized G-band. The enhanced resolution of AFM with respect to its line measure analysis and three-dimensional image capture capability has allowed an extension and reconsideration of conclusions about chromosomal aberrations based on the study of LM preparations. In this manner, chromosomal disorders will be studied at nanoscale to help in the planning of new therapy strategies.

Adult↗

PubMed2002

Influence of metal ion sorption on colloidal surface forces measured by atomic force microscopy.

Atomic force microscopy (AFM) is employed to directly measure colloidal surface forces between a silica particle and a smooth glass plate in an aqueous solution with or without the presence of copper ions. Without the presence of copper ions, results show that the force between these two surfaces is repulsive and that its magnitude decreases with increasing ionic strength and decreasing pH. The surface forces are calculated based on the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory for constant surface charge and are then compared with AFM force measurements. A good agreement between theory and experimental data is reported except at very small separation distances (<3 nm) between the silica particle and the glass plate. This behavior may be attributed to non-DLVO forces, such as the hydration effect that results from the bounded water molecules on the surface of the silica particle, or to surface roughness. When copper ions are present in acidic aqueous solutions, the magnitude of the force is found to be the same as that without the presence of copper ions, which indicates that no sorption of copper ions by the silica particle occurs under these conditions. Near neutral pH, sorption of copper ions causes charge reversal for the silica particle from negative to positive. Therefore, the force between the silica particle and the glass plate changes from repulsive to attractive. The transient zeta-potential of the silica particle during sorption of copper ions is determined by representing the experimental data with the DLVO theory. In alkaline solutions, where removal of copper ions is known to occur mainly by bulk precipitation, the measured force is similar to that without the presence of copper ions, which suggests that sorption does not occur under such conditions.

Colloids↗

PubMed2002

Characterization of the adhesive mucilages secreted by live diatom cells using atomic force microscopy.

Atomic Force Microscopy (AFM) resolved the topography and mechanical properties of two distinct adhesive mucilages secreted by the marine, fouling diatom Craspedostauros australis. Tapping mode images of live cells revealed a soft and cohesive outer mucilage layer that encased most of the diatom's siliceous wall, and force curves revealed an adhesive force of 3.58 nN. High loading force, contact mode imaging resulted in cantilever 'cleaned' cell walls, which enabled the first direct observation of the active secretion of soft mucilage via pore openings. A second adhesive mucilage consisted of strands secreted at the raphe, a distinct slit in the silica wall involved in cell-substratum attachment and motility. Force measurements revealed a raphe adhesive strand(s) resistant to breaking forces up to 60 nN, and these strands could only be detached from the AFM cantilever probe using the manual stepper motor.

Adhesiveness↗

PubMed2005

Surface ultrastructure of SARS coronavirus revealed by atomic force microscopy.

Atomic force microscopy has been used to probe the surface nanostructures of severe acute respiratory syndrome coronavirus (SARS-CoV). Single crown-like virion was directly visualized and quantitative measurements of the dimensions for the structural proteins were provided. A corona of large, distinctive spikes in the envelope was measured after treatment with hydroxyoctanoic acid. High-resolution images revealed that the surface of each single SARS-CoV was surrounded with at least 15 spherical spikes having a diameter of 7.29 +/- 0.73 nm, which is in close agreement with that of S glycoproteins earlier predicted through the genomes of SARS-CoV. This study represents the first direct characterization of the surface ultrastructures of SARS-CoV particles at the nanometre scale and offers new prospects for mapping viral surface properties.

Hemagglutinins, Viral↗

PubMed2002

Direct observation of polyhydroxyalkanoate chains by atomic force microscopy.

Atomic force microscopy in the tapping mode was used to investigate aqueous acetone-treated polyhydroxyalkanoate (PHA) inclusions freshly isolated from a recombinant bacterium. The PHA is a copolymer containing about 95 mol% 3-hydroxybutyrate units while the rests are units of 3-hydroxyhexanoate, 3-hydroxyoctanoate, 3-hydroxydecanoate, and 3-hydroxydodecanoate. Polymer chains extending to several micrometers in length were observed on glass cover slips upon the evaporation of the aqueous acetone. The polymer chains seem to exist in the form of fibrillar aggregates. The height of the microfibrils was about 1 nm. Upon prolonged standing at ambient conditions, the microfibrils dissociated into finer strands of about 0.5 nm in height. The results suggest that biosynthesized PHA are stored in the inclusions in an amorphous state but with minimal chain entanglement. This is possible because the PHA chains exist in the form of fibrillar aggregates that may be the product of a special biosynthesis mechanism.

Cupriavidus necator↗

PubMed2003

Real-time imaging of the surface topography of living yeast cells by atomic force microscopy.

Atomic force microscopy (AFM) was used to image the surface topography of living Saccharomyces cerevisiae cells at high resolution and to monitor enzyme digestion of the cell wall in real time. Apart from the presence of bud scars, the surface of native cells imaged in aqueous solution was homogeneous and smooth. Topographic images of the surface were recorded to a lateral resolution of 2 nm without significant modification of the surface morphology. Successive images of single cells were collected at fixed time intervals following addition of protease and amyloglucosidase solutions. Protease caused a progressive increase of surface roughness. Large depressions surrounded by protruding edges, approximately 50 nm in height, were formed and attributed to the erosion of the mannoprotein outer layer. By contrast, no modification of the cell surface was noted upon addition of amyloglucosidase, which was consistent with the cell wall biochemical composition. These results indicate that AFM is a complementary tool to electron microscopy in that it allows the surface of living cells to be explored directly in real time.

Cell Wall↗

PubMed1997

Topography of ribosomes and initiation complexes from rat liver as revealed by atomic force microscopy.

Atomic force microscopy (AFM) was used to image ribosomes and ribosomal subunits (60S, 40S and native 40S ribosomal subunits) isolated from rat liver. A variety of topographic images were obtained directly and found to be consistent with models established by other biophysical methods. In addition, the ternary complex of eIF-2 x GTP x Met-tRNA(i) and the 43S preinitiation complex have been discerned by AFM directly. Detailed information about the binding sites for eIF-1A, eIF-2, eIF-3, and Met-tRNA(i) on the 40S ribosomal subunit was derived from the AFM images. Finally, factors which may give rise to artifactual images, namely, convolution of the AFM tip on ribosomes, surface tension collapse effect and dehydration, are discussed. This work demonstrates that AFM is useful for imaging ribosomes and translational complexes and provides valuable information that can be used to complement other well-established techniques.

Animals↗