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At least 829 records · Page 46Linked to original sources
PubMed1999

Surface-dependent conformations of human fibrinogen observed by atomic force microscopy under aqueous conditions.

Conformational differences in human fibrinogen under aqueous conditions on hydrophobic, positively charged and negatively charged surfaces, were examined by atomic force microscopy (AFM). Hydrophobic and positively charged surfaces were prepared by depositing octadecyltrichlorosilane (OTS) and 3-aminopropyltriethoxysilane (APTES) respectively on cleaned glass coverslips forming self-assembled monolayers. The negatively charged surface was prepared by freshly cleaving muscovite mica. AFM operated in fluid tapping mode with an ultrasharp carbon spike probe was used to obtain the molecular scale images. Fibrinogen displayed a characteristic trinodular structure on all three surfaces. although additional U-shaped conformations were observed on mica. In its native hydrated state, fibrinogen is well represented by three connected ellipsoids in close proximity. Quantitative dimensional analysis, which yielded structural information in three dimensions, indicates that surface-dependent structural deformation or spreading of fibrinogen increases according to the order: mica < APTES < OTS. Molecular length, and D and E domain widths of fibrinogen are increased, while the corresponding heights are decreased. The results provide direct evidence that material surface properties affect the conformational state of interacting fibrinogen.

Computer Simulation↗
PubMed1999

Atomic force microscopy to study the degranulation in rat peritoneal mast cells after activation.

We have studied the degranulation in rat peritoneal mast cells by atomic force microscopy (AFM). Although AFM has advantages close to electron microscopy (EM) in spatial resolution, visualization of surface topography in peritoneal mast cells has not been reported yet. In the present paper we have succeeded in visualizing the degranulation process of rat peritoneal mast cells by AFM. AFM images showed that secretory granules were about 1 microm in diameter and that they were densely packed in the cytoplasm surrounding the nucleus. After stimulation with compound 48/80 (5 microg/ml), the packed granules began to loosen through formation of irregular cracks, as if polymerization of actin filaments was changed; 3 min after stimulation with compound 48/80 at 37 degrees C, the packed granules were completely loosened and the nucleus was no longer covered by the granules. In addition, AFM images showed clear fringes at the edges of the spreading cells. The fringes were 30-50 nm in height and there existed many small matrixes which were secreted to the outside of the cell. The matrixes were about 80 nm in diameter and 40 nm in height. These kinds of secretory matrixes were observed here first by AFM.

Animals↗
PubMed2003

2-D array formation of genetically engineered viral cages on au surfaces and imaging by atomic force microscopy.

The preparation and subsequent imaging of a two-dimensional array of a genetically and chemically modified cowpea chlorotic mottle virus (CCMV) is described. The genetic mutation provides symmetrically dispersed exposed thiol groups on the outer surface of the virus capsid. These functional groups can be used to covalently bind the capsid to smooth Au substrate. AFM imaging suggests that the genetic mutation by itself does not promote array formation but, rather, aggregation through disulfide linkages. However, breaking the symmetry of the capsid using a solid-phase approach and chemically passivating the exposed thiol groups with iodoacetic acid results in a capsid with exposed thiols only on one side of the particle. These symmetry-broken capsids were able to form self-assembled monolayers (SAM) on a Au surface.

Alanine↗
PubMed2006

Double minute chromosomes in mouse methotrexate-resistant cells studied by atomic force microscopy.

Double minute chromosomes (DMs) are acentric, autonomously replicating extra-chromosomes and frequently mediate gene amplification in tumor and drug resistant cells. Atomic force microscopy (AFM) is a powerful tool in microbiology. We used AFM to explore the ultrastructure of DMs in mouse fibroblasts 3T3R500. DMs in various phases of cell cycle were also studied in order to elucidate the mechanisms of their duplication and separation. Metaphase spread and induced premature condensed chromosomes (PCCs) were observed under the AFM. DMs were detected to be composed of two compact spheres linked by fibers. The fibers of DMs directly connected with metaphase chromosomes were observed. Many single-minutes and few DMs were detected in G1 PCCs, while more DMs were detected in S PCCs than in G1 PCCs. Besides, all of the DMs in G2 PCCs were coupled. Our present results suggested that DMs might divide into single-minutes during or before G1-phase, followed by duplication of the single-minutes in S-phase. Moreover, we introduced a new powerful tool to study DMs and got some ideal results.

Animals↗
PubMed2002

What can atomic force microscopy tell us about protein folding?

Force spectroscopy has emerged as a new tool to study protein folding, in which force replaces the chemical denaturant used in traditional folding experiments. This new technique complements older methods and allows a range of new questions to be investigated. What sort of protein is able to resist mechanical unfolding, and to what extent is mechanical stability dictated by fold or function? What is the effect of force on the unfolding energy surface? Do proteins unfold by the same pathway in mechanical and chemical denaturation experiments? Answers to these are starting to emerge based on a combination of experimental and computational approaches. We present some of the forced unfolding experiments to date and simple methods for characterizing the unfolding potential from the results. Several studies have also begun a more fine-grained description of mechanical unfolding, for example by invoking intermediates to explain features seen in unfolding traces and by using mutagenesis to try to localize the origin of mechanical stability. We propose further experimental approaches to this goal using the protein engineering method to characterize transition states, similar to those used in conventional folding experiments. However, it is likely that a high-resolution picture of mechanical unfolding will only emerge through a combined interpretation of careful experimental work and computer simulation.

Microscopy, Atomic Force↗
PubMed2004

Neuronal tau induces DNA conformational changes observed by atomic force microscopy.

Neuronal tau associates with chromosome scaffold and localizes in the nuclear and the nucleolar organization regions in neuronal and some non-neuronal cells. Observing the interaction of neuronal tau with DNA under AFM shows that tau binds to DNA as a monomer, and tau-DNA complex forms a beads-on-a-string structure when the mass ratio is 1:10 (molar ratio of tau/DNA approximately 1:700 bp). A beads-on-a-coil structure, in which tau is as polymers, will appear when the mass ratio is up to 1:5 (molar ratio of tau/DNA approximately 1:350 bp). The present observation that neuronal tau bends the DNA double strands indicates that the appearance of the tau-DNA complex is dependent upon the mass (or molar) ratio of tau and DNA.

DNA↗
PubMed2001

Atomic force microscopy studies of ganglioside GM1 domains in phosphatidylcholine and phosphatidylcholine/cholesterol bilayers.

The distribution of ganglioside in supported lipid bilayers has been studied by atomic force microscopy. Hybrid dipalmitoylphosphatidylcholine (DPPC)/dipalmitoylphosphatidylethanolamine (DPPE) and (2:1 DPPC/cholesterol)/DPPE bilayers were prepared using the Langmuir Blodgett technique. Egg PC and DPPC bilayers were prepared by vesicle fusion. Addition of ganglioside GM1 to each of the lipid bilayers resulted in the formation of heterogeneous surfaces that had numerous small raised domains (30--200 nm in diameter). Incubation of these bilayers with cholera toxin B subunit resulted in the detection of small protein aggregates, indicating specific binding of the protein to the GM1-rich microdomains. Similar results were obtained for DPPC, DPPC/cholesterol, and egg PC, demonstrating that the overall bilayer morphology was not dependent on the method of bilayer preparation or the fluidity of the lipid mixture. However, bilayers produced by vesicle fusion provided evidence for asymmetrically distributed GM1 domains that probably reflect the presence of ganglioside in both inner and outer monolayers of the initial vesicle. The results are discussed in relation to recent inconsistencies in the estimation of sizes of lipid rafts in model and natural membranes. It is hypothesized that small ganglioside-rich microdomains may exist within larger ordered domains in both natural and model membranes.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2006

Energy-dependent disassembly of self-assembled SNARE complex: observation at nanometer resolution using atomic force microscopy.

Full-length v-SNARE protein reconstituted in lipid vesicles, when exposed to t-SNARE-reconstituted lipid membrane, results in the self-assembly of a t-/v-SNARE complex in a ring pattern, forming pores and the establishment of continuity between the opposing bilayers. In contrast, when v-SNARE protein alone (without liposomes) is exposed to t-SNARE-reconstituted lipid membrane, they also self-assemble to form t-/v-SNARE complexes, although such complexes fail to possess the characteristic ring pattern, nor do they help in the establishment of continuity between the opposing bilayers. Hence, t-SNAREs and v-SNARE need to be membrane-associated to interact in a circular array to form conducting pores in the presence of calcium. This study demonstrates that, irrespective of their arrangement, both forms of the SNARE complex can be disassembled in the presence of NSF-ATP.

Adenosine Triphosphate↗
PubMed2001

Imaging and mapping protein-binding sites on DNA regulatory regions with atomic force microscopy.

Regulation of gene expression is fundamental in biological systems. A systematic search for protein binding sites in gene promoters has been done in recent years. Biochemical techniques are easy and reliable when analysing protein interactions with short pieces of DNA, but are difficult and tedious when long pieces of DNA have to be analysed. Here we propose AFM as a reliable and easy technique for identifying protein interaction sites in long DNA molecules like gene promoters. We support this idea using a well-known model: the interaction of the Pho4 protein with the PHO5 gene promoter. We have also applied the technique to demonstrate that Mig1 protein binds to two motifs in the promoter of HXK2 gene. Our results allow us to define Mig1p as a new factor probably contributing to the carbon source-dependent transcription regulation of HXK2 gene.

Amino Acid Sequence↗
PubMedDate not supplied

Atomic force microscopy of nanometric liposome adsorption and nanoscopic membrane domain formation.

Scanning probe microscopy studies of membrane fusion and nanoscopic structures were performed using hydrated single lipids and lipid mixtures. Extruded vesicles of DMPC and mixtures at various concentrations of DLPC, DPPC and cholesterol were deposited on freshly cleaved mica and studied in a fluid environment by AFM. The nanostructures formed by these extruded liposomes ranged from isolated unilamellar vesicles to flat sheet membranes and were marked influenced by thermodynamic phase behavior. For DMPC membrane, intact bilayers exhibited a phase transition process in agreement with large bilayer patches. In the DLPC, DPPC and cholesterol mixtures, nanoscopic domain diameters ranged from approximately 25 to 48nm with height differences of approximately 1.4nm; all values were lipid composition-dependent. Our data support and extend previous studies of microscopic domains and phase boundaries of the same mixtures in giant unilamellar vesicles determined by confocal light microscopy. Our approach for preparing and utilizing supported membrane structures is potentially relevant to studies of native cell membranes.

Adsorption↗
PubMed1995

Imaging of the cytoplasmic leaflet of the plasma membrane by atomic force microscopy.

The cytoplasmic face of ventral cell membranes of Madin-Darby canine kidney (MDCK) cells grown on glass coverslips was imaged by atomic force microscopy (AFM) in air and under aqueous medium, in "contact" mode. Micrometer range scans on air-dried samples revealed a heterogeneous structure with some filaments, likely corresponding to actin filaments that abut the inner leaflet of the membrane, and a few semi-organized lattice structures that might correspond to clathrin lattices. Experiments in phosphate-buffered saline confirmed the heterogeneity of the inner membrane surface with the presence of large (> 100 nm) globular structures emerging from the surface. Using sub-micrometer scan ranges, protruding particles, that occupy most of the membrane surface, were imaged in liquid medium and in air. These particles, 8 to 40 nm x-y size, were still present following ethanol dehydration which extracts a large fraction of membrane lipids, indicating their proteic nature. Due, at least partly, to the presence of some peripheral proteins, high magnification images of the inner membrane surface were heterogeneous with regard to particle distribution. These data compare with those previously reported for the external membrane leaflet at the surface of living MDCK cells. They show that details of the cytosolic membrane surface can be resolved by AFM. Finally, the images support the view of a plasma membrane organization where proteins come into close proximity.

Air↗
PubMed1996

Detection and localization of individual antibody-antigen recognition events by atomic force microscopy.

A methodology has been developed for the study of molecular recognition at the level of single events and for the localization of sites on biosurfaces, in combining force microscopy with molecular recognition by specific ligands. For this goal, a sensor was designed by covalently linking an antibody (anti-human serum albumin, polyclonal) via a flexible spacer to the tip of a force microscope. This sensor permitted detection of single antibody-antigen recognition events by force signals of unique shape with an unbinding force of 244 +/- 22 pN. Analysis revealed that observed unbinding forces originate from the dissociation of individual Fab fragments from a human serum albumin molecule. The two Fab fragments of the antibody were found to bind independently and with equal probability. The flexible linkage provided the antibody with a 6-nm dynamical reach for binding, rendering binding probability high, 0.5 for encounter times of 60 ms. This permitted fast and reliable detection of antigenic sites during lateral scans with a positional accuracy of 1.5 nm. It is indicated that this methodology has promise for characterizing rate constants and kinetics of molecular recognition complexes and for molecular mapping of biosurfaces such as membranes.

Animals↗
PubMed2000

Atomic force microscopy of parallel DNA branched junction arrays.

BACKGROUND: The four arms of the Holliday junction are known to stack in pairs forming two helical domains whose orientations are antiparallel, but twisted positively by about 60 degrees, based on electrophoretic, FRET and AFM measurements. Recent gel retardation studies suggest that a bowtie junction (containing 5',5' and 3',3' linkages in its crossover strands) may adopt a parallel conformation. RESULTS: An AFM study of two-dimensional arrays produced by parallelograms of bowtie junctions shows that the angle between helical domains is in the range of -68+/-2 degrees. We demonstrate by AFM that the domains are parallel by constructing V-shaped structures whose arms are separated by approximately 68 degrees and approximately 112 degrees. CONCLUSIONS: The arms of the bowtie junction are parallel rather than antiparallel. The parallel or antiparallel nature of the junction apparently is determined by the local structure of the junction, but the sign of the angle appears to be a consequence of interarm electrostatic interactions.

DNA↗
PubMed2004

DNA condensation monitoring after interaction with hoechst 33258 by atomic force microscopy and fluorescence spectroscopy.

DNA condensation was only observed after the addition of Hoechst 33258 (H33258) among various types of DNA binding molecules. The morphological structural change of DNA was found to depend on the H33258 concentration. On comparison of fluorescence spectrum measurements with AFM observation, it was found that fluorescence quenching of DNA-H33258 complexes occurred after DNA condensation. Additionally, we showed that DNA condensation by H33258 was independent of sequence selectivity or binding style using two types of polynucleotides, i.e. poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC). Moreover, it was concluded that the condensation was caused by a strong hydrophobic interaction, because the dissolution of condensed DNA into its native form on dimethyl sulfoxide (DMSO) treatment was observed. This study is the first report, which defines the DNA condensation mechanism of H33258, showing the correlation between the single molecule scale morphology seen on AFM observation and the bulky scale morphology observed on fluorescence spectroscopy.

Bisbenzimidazole↗
PubMed2005

Atomic force microscopy tips (cantilevers) as molecular nucleic acid sensors.

A model single strand DNA (ssDNA) was covalently immobilized onto AFM tips (cantilevers) as specific ligand. These tips were interacted with the buffer solutions with or without free ssDNA molecules as the target strands to be detected. Immobilization and hybridization onto the cantilever surfaces were observed by optical and fluorescence microscopies. Interactions between the AFM tip (cantilever) and the aqueous medium (therefore with the target ssDNAs) were quantified by obtaining the "percent separation distance" ("PSD") as the main variable. The PSD values obtained for the buffer solutions were between -2.07 and +4.91%. There were slight increases in the negative values when non-complementary ssDNA molecules were introduced into the buffer. However, after hybridization with its complementary ssDNA, the PSD values were significantly increased (between -32.24 and -43.47%). There was a correlation between the concentration of the complementary target ssDNA in the medium and the PSD value. As a result of these promising results it was concluded that this approach may be further developed to create AFM-based molecular sensors for diverse applications.

Biosensing Techniques↗
PubMed1998

Atomic force microscopy used for the surface characterization of microcapsule immunoisolation devices.

The surface morphology of the microcapsule used as a bioartificial pancreas was examined by atomic force microscopy (AFM) under ambient conditions in a liquid environment. The standard contact mode was used for imaging. The capsules exhibited different morphologies and surface roughness depending on the composition of the cation solution: namely, the mole ratio of antigelling and gelling cations [Na+]/[Ca2+]. Surface roughness parameters obtained by AFM measurements provide quantitative information on the surface properties of the capsular membrane. In this respect, AFM can be considered a valuable technique complementary to optical microscopy in providing feedback for capsule optimization.

Artificial Organs↗
PubMed2005

Formation of aminosilane-functionalized mica for atomic force microscopy imaging of DNA.

Factors affecting the functionalization of mica with aminosilanes, in particular, aminopropyltriethoxysilane (APTES-mica), formed from the vapor phase have been systematically studied. The relative humidity (RH) during vapor deposition has been varied, and postdeposition treatment through baking has been used, as well as the comparison of mono and trifunctionality, to investigate how optimal surfaces for AFM imaging of DNA are formed. It is found that the stability of the APTES layers is a consequence of lateral polymerization and not covalent attachment to the mica substrate. At low RH (<25%), DNA adopts an open, well-resolved conformation, whereas at >25% RH, DNA surface-induced condensation occurs. Contact mode AFM scratching experiments show that two main structures of the silane layer exist at different humidity: a monolayer exists at RH < 25%, and a bilayer structure exists at RH > 25%. Finally, structural changes that these two layer types undergo after baking at 150 degrees C were investigated by AFM and X-ray photoelectron spectroscopy (XPS), and these now prevented DNA from binding to the APTES-mica, except in the presence of Mg(II) ions.

Aluminum Silicates↗
PubMed2002

Atomic force microscopy identification of transcription factor NFkappaB bound to streptavidin-pin-holding DNA probe.

A novel method for identifying DNA-binding proteins from image analysis using AFM was developed. Here, transcription factor NFkappaB, which a well-studied example of transcription activator proteins, was used as a target protein. 5'-biotinlynated double-stranded DNA probe was labeled site specifically through high affinity with streptavidin. When the biotinylated DNA fragments were incubated with the streptavidin at a 1:2 molar ratio of DNA:streptavidin, the overall efficiency of labeling was over 90%. The double-stranded DNA probes were immobilized on a mica surface by the adsorption of streptavidin that attached to the 5'-end of DNA and applied for selection of the target protein NFkappaB in solution and then AFM was used to image the DNA probe-NFkappaB complexes. The length of the distance between 5'-labeled streptavidin and NFkappaB bound on DNA probes from AFM images is 0.64, the normalized position of the NFkappaB binding site, and this result is in close agreement with the expected 299 and 167bp values.

Base Sequence↗