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PubMed2000

Plasma membrane plasticity of Xenopus laevis oocyte imaged with atomic force microscopy.

Proteins are known to form functional clusters in plasma membranes. In order to identify individual proteins within clusters we developed a method to visualize by atomic force microscopy (AFM) the cytoplasmic surface of native plasma membrane, excised from Xenopus laevis oocyte and spread on poly-L-lysine coated glass. After removal of the vitelline membrane intact oocytes were brought in contact with coated glass and then rolled off. Inside-out oriented plasma membrane patches left at the glass surface were first identified with the lipid fluorescent marker FM1-43 and then scanned by AFM. Membrane patches exhibiting the typical phospholipid bilayer height of 5 nm showed multiple proteins, protruding from the inner surface of the membrane, with heights of 5 to 20 nm. Modelling plasma membrane proteins as spherical structures embedded in the lipid bilayer and protruding into the cytoplasm allowed an estimation of the respective molecular masses. Proteins ranged from 35 to 2,000 kDa with a peak value of 280 kDa. The most frequently found membrane protein structure (40/microm2) had a total height of 10 nm and an estimated molecular mass of 280 kDa. Membrane proteins were found firmly attached to the poly-L-lysine coated glass surface while the lipid bilayer was found highly mobile. We detected protein structures with distinguishable subunits of still unknown identity. Since X. laevis oocyte is a generally accepted expression system for foreign proteins, this method could turn out to be useful to structurally identify specific proteins in their native environment at the molecular level.

Animals↗
PubMed1997

Investigation of the image contrast of tapping-mode atomic force microscopy using protein-modified cantilever tips.

In this work we have designed a simple system to investigate empirically the image contrast of tapping-mode atomic force microscopy (TMAFM). We modified the cantilever tips with protein molecules (bovine serum albumin or goat anti-biotin antibody) and used these protein-modified cantilevers to scan poly-L-lysine films and antibody layers deposited on mica in air under ambient conditions. We also investigated the effects of manipulating the setpoint voltage in this system. It was found that extra topographic features with a patchlike appearance were introduced into the TMAFM images of both the poly-L-lysine and antibody films when scanned with the protein-modified tips, even at initial preset setpoints, and were superimposed on the topography of the samples. The surface coverage of the patchlike features in the TMAFM images changes significantly with the setpoint voltage in a reversible and nonlinear manner. These are believed to arise from the surface indentation of the sample or from the structural deformation of the proteins at the tip induced in TMAFM imaging. Interestingly, it was observed in the experiment that no structural alteration or damage was discernible on the sample surface, even after continuous scanning with the protein-modified tips for a long period of time, with varying setpoint voltage. This study provides experimental evidence that cantilever tips modified with protein molecules or, under certain circumstances, even unmodified tips introduce extra topographical features (i.e., artifacts) and enhance the image contrast of TMAFM imaging of soft materials, which is dependent on their mechanical properties.

Aluminum Silicates↗
PubMed1995

High-resolution atomic-force microscopy of DNA: the pitch of the double helix.

Using a cationic lipid bilayer, we show that DNA can be reliably adsorbed to the bilayer surface for atomic force microscopy (AFM) in aqueous buffers at high resolution. The measured width of the dsDNA is close to 2 nm, and a periodic modulation on dsDNA is reproducibly detected by the AFM. The measured period is 3.4 +/- 0.4 nm, in excellent agreement with the known pitch of the double helix. The right-handedness of the double helix is directly discernible in high resolution AFM images. Thus, this approach can be readily applied to the study of DNA-protein interactions, as well as sequence mapping at high resolution.

DNA↗
PubMed2006

Atomic force microscopy of native human metaphase chromosomes in a liquid.

The present study introduces a method for obtaining three-dimensional images of native (i.e., unfixed) chromosomes by atomic force microscopy (AFM) in a liquid. Human metaphase chromosomes were isolated from a human lymphoblast-like cell line, K562, by the hexylene glycol procedure according to Wray and Stubble- field (1970), adsorbed on a silane-coated glass slide, and observed in a dynamic force mode (i.e., intermittent contact mode) of AFM in a hexylene buffer solution. In adequate operating conditions, the shape of chromosomes with paired chromatids was clearly and three-dimensionally observed by AFM. At high magnification, globular or fibrous structures about 50 nm thick could be found on the surface of each chromaid, implying that chromatin fibers were strongly wound or twisted in the chromatid. Thus, AFM imaging enabled the direct visualization of native chromosomes in a liquid at high resolution--which is comparable with that of scanning electron microscopy--and can serve to analyze the mechanism of chromosome condensation and separation in relation to the structure of chromosomes.

Cell Line, Tumor↗
PubMed1999

Probing the Saccharomyces cerevisiae centromeric DNA (CEN DNA)-binding factor 3 (CBF3) kinetochore complex by using atomic force microscopy.

Yeast centromeric DNA (CEN DNA) binding factor 3 (CBF3) is a multisubunit protein complex that binds to the essential CDEIII element in CEN DNA. The four CBF3 proteins are required for accurate chromosome segregation and are considered to be core components of the yeast kinetochore. We have examined the structure of the CBF3-CEN DNA complex by atomic force microscopy. Assembly of CBF3-CEN DNA complexes was performed by combining purified CBF3 proteins with a DNA fragment that includes the CEN region from yeast chromosome III. Atomic force microscopy images showed DNA molecules with attached globular bodies. The contour length of the DNA containing the complex is approximately 9% shorter than the DNA alone, suggesting some winding of DNA within the complex. The measured location of the single binding site indicates that the complex is located asymmetrically to the right of CDEIII extending away from CDEI and CDEII, which is consistent with previous data. The CEN DNA is bent approximately 55 degrees at the site of complex formation. A significant fraction of the complexes are linked in pairs, showing three to four DNA arms, with molecular volumes approximately three times the mean volumes of two-armed complexes. These multi-armed complexes indicate that CBF3 can bind two DNA molecules together in vitro and, thus, may be involved in holding together chromatid pairs during mitosis.

Centromere↗
PubMed1997

Visualization of supercoiled DNA with atomic force microscopy in situ.

Tertiary structure of supercoiled DNA is a significant factor in a number of genetic functions and is apparently affected by environmental conditions. We applied atomic force microscopy (AFM) for imaging the supercoiled DNA deposited at different ionic conditions. We have employed a technique for the sample preparation that permits high-resolution AFM imaging of DNA bound to the surface in buffer solutions without drying the sample (AFM in situ). The AFM data show that at low ionic strength, DNA molecules are loosely interwound supercoils with an irregular shape. Plectonemic superhelices are formed in high-concentration, near-physiological salt solutions. At such ionic conditions, superhelical loops are typically separated by regions of close helix-helix contacts. The data obtained show directly and unambiguously that overall geometry of supercoiled DNA depends dramatically on ionic conditions. This fact and the formation of close contacts between DNA helices are important features of supercoiled DNA related to its biological functions.

Aluminum Silicates↗
PubMed2006

Elastic modulus measurements from individual lactose particles using atomic force microscopy.

The elastic modulus of pharmaceutical materials affects a number of pharmaceutical processes and subsequently formulation performance and is currently assessed by bulk methods, such as beam bending of compacts. Here we demonstrate the accurate measurement of the elastic modulus of alpha monohydrate lactose from the dominant (011) face of single crystals using atomic force microscopy (AFM) as 3.45+/-0.90GPa. The criteria to ensure this data is recorded within the elastic limit and can be modelled using Hertzian theory are established. We compare and contrast this AFM method to a permanent indentation technique based upon a much larger Berkovich pyramidal indenter on a lactose compact and the wider literature. Finally the AFM was utilized to study the elastic response of amorphous lactose, demonstrating that the physical state of the amorphous material changes under repeated loading and behaves in a more crystalline manner under repeated force measurements, suggesting a pressure induced phase transition. The AFM based approach demonstrated has the significant advantages of requiring minimal sample, no need for producing a compact, being non-destructive in that no permanent indent is required and providing a technique capable of detecting variations in material properties across a single particle or a number of particles.

Chemistry, Pharmaceutical↗
PubMed2002

UV light-damaged DNA and its interaction with human replication protein A: an atomic force microscopy study.

We have imaged a non-damaged and UV-damaged DNA fragment and its complexes with human replication protein A (RPA) using tapping mode atomic force microscopy (AFM). For imaging, molecules were immobilized under nearly physiological conditions on mica surfaces. Quantitative sizing of the 538 bp DNA before and after UV light treatment shows a reduction in the contour and persistence lengths and mean square end-to-end distance as a consequence of UV irradiation. Complexes of the UV-damaged DNA with RPA, an essential component of the initial steps of nucleotide excision repair, can be detected at high resolution with AFM and reveal conformational changes of the DNA related to complex formation. By phase image analysis we are able to discriminate between protein and DNA in the complexes. The DNA molecules are found to 'wrap' around the RPA, which in turn results in a considerable reduction in its apparent contour length.

DNA↗
PubMed2005

Oligomerization states of Bowman-Birk inhibitor by atomic force microscopy and computational approaches.

Several methods have been applied to study protein-protein interaction from structural and thermodynamic point of view. The present study reveals that atomic force microscopy (AFM), molecular modeling, and docking approaches represent alternative methods offering new strategy to investigate structural aspects in oligomerization process of proteinase inhibitors. The topography of the black-eyed pea trypsin/chymotrypsin inhibitor (BTCI) was recorded by AFM and compared with computational rigid-bodies docking approaches. Multimeric states of BTCI identified from AFM analysis showed globular-ellipsoidal shapes. Monomers, dimers, trimers, and hexamers were the most prominent molecular arrays observed in AFM images as evaluated by molecular volume calculations and corroborated by in silico docking and theoretical approaches. We therefore propose that BTCI adopts stable and well-packed self-assembled states in monomer-dimer-trimer-hexamer equilibrium. Although there are no correlation between specificity and packing efficiency among proteinases and proteinase inhibitors, the AFM and docked BTCI analyses suggest that these assemblies may exist in situ to play their potential function in oligomerization process.

Computational Biology↗
PubMed2000

Atomic force microscopy of intact and digested collagen molecules.

The present study was performed to analyse the structure of non-digested and digested collagen type I molecules by atomic force microscopy (AFM). Collagen type I molecules from the bovine skin were diluted with 0.05 N acetic acid, spread on a mica plate, air-dried and observed by non-contact mode AFM in air. Collagen molecules digested with Clostridium histolyticum collagenase were also examined by AFM. Intact collagen type I molecules were observed as twisted threads ranging mainly between 280 and 310 nm in length. The surface of the molecules was uneven and both ends usually slightly bulged like a globule. Depressions on the molecules were found throughout the length, and were most prominent approximately 70 nm from one end of the molecules. The collagenase-treated collagen molecules were degraded into fragments with various lengths, which corresponded to the data from sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. The end of these fragments often appeared like a tuft, suggesting that the triple-helix unraveled at these regions.

Animals↗
PubMed2005

Assessment of elasticity and topography of Aspergillus nidulans spores via atomic force microscopy.

Previous studies have described both surface morphology and adhesive properties of fungal spores, but little information is currently available on their mechanical properties. In this study, atomic force microscopy (AFM) was used to investigate both surface topography and micromechanical properties of Aspergillus nidulans spores. To assess the influence of proteins covering the spore surface, wild-type spores were compared with spores from isogenic rodA(+) and rodA(-) strains. Tapping-mode AFM images of wild-type and rodA(+) spores in air showed characteristic "rodlet" protein structures covering a granular spore surface. In comparison, rodA(-) spores were rodlet free but showed a granular surface structure similar to that of the wild-type and rodA(+) spores. Rodlets were removed from rodA(+) spores by sonication, uncovering the underlying granular layer. Both rodlet-covered and rodlet-free spores were subjected to nanoindentation measurements, conducted in air, which showed the stiffnesses to be 110 +/- 10, 120 +/- 10, and 300 +/- 20 N/m and the elastic moduli to be 6.6 +/- 0.4, 7.0 +/- 0.7, and 22 +/- 2 GPa for wild-type, rodA(+) and rodA(-) spores, respectively. These results imply the rodlet layer is significantly softer than the underlying portion of the cell wall.

Aspergillus nidulans↗
PubMedDate not supplied

Studies of tip wear processes in tapping mode atomic force microscopy.

Tip integrity is crucial to atomic force microscope image quality. Tip wear not only compromises image resolution but also introduces artifacts. However, the factors that govern wearing have not been systematically studied. The results presented here of tip wearing on a rough titanium surface were determined by monitoring changes in tip shape and the evolution of histograms of complex surface curvatures under different control parameters. In contrast with the common assumption that operating at a low set point (the ratio of tapping amplitude to free oscillation amplitude) wears the tip quickly, we observed that a low set point actually minimizes tip wear on a hard surface regardless of the free amplitude. The results can be interpreted qualitatively with theoretical calculations based on momentum exchange at tapping impact. Operating at a low set point allows more robust scanning than with a high set point (tapping near free amplitude), providing a method to slow down tip wear. Another advantage of a low set point is that amplitude error grows faster than with a high set point by nearly an order of magnitude, permitting an increase in scanning speed.

Journal Article↗
PubMed2005

Surface structure and nanomechanical properties of Shewanella putrefaciens bacteria at two pH values (4 and 10) determined by atomic force microscopy.

The nanomechanical properties of gram-negative bacteria (Shewanella putrefaciens) were investigated in situ in aqueous solutions at two pH values, specifically, 4 and 10, by atomic force microscopy (AFM). For both pH values, the approach force curves exhibited subsequent nonlinear and linear regimens that were related to the progressive indentation of the AFM tip in the bacterial cell wall, including a priori polymeric fringe (nonlinear part), while the linear part was ascribed to compression of the plasma membrane. These results indicate the dynamic of surface ultrastructure in response to changes in pH, leading to variations in nanomechanical properties, such as the Young's modulus and the bacterial spring constant.

Bacterial Outer Membrane Proteins↗
PubMed2003

Atomic force microscopy and scanning near-field optical microscopy studies on the characterization of human metaphase chromosomes.

A better knowledge of biochemical and structural properties of human chromosomes is important for cytogenetic investigations and diagnostics. Fluorescence in situ hybridization (FISH) is a commonly used technique for the visualization of chromosomal details. Localizing specific gene probes by FISH combined with conventional fluorescence microscopy has reached its limit. Also, microdissecting DNA from G-banded human metaphase chromosomes by either a glass tip or by laser capture needs further improvement. By both atomic force microscopy (AFM) and scanning near-field optical microscopy (SNOM), local information from G-bands and chromosomal probes can be obtained. The final resolution allows a more precise localization compared to standard techniques, and the extraction of very small amounts of chromosomal DNA by the scanning probe is possible. Besides new strategies towards a better G-band and fluorescent probe detection, this study is focused on the combination of biochemical and nanomanipulation techniques which enable both nanodissection and nanoextraction of chromosomal DNA.

Cell Separation↗
PubMed2001

Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy.

The Escherichia coli protein DbpA is unique in its subclass of DEAD box RNA helicases, because it possesses ATPase-specific activity toward the peptidyl transferase center in 23S rRNA. Although its remarkable ATPase activity had been well defined toward various substrates, its RNA helicase activity remained to be characterized. Herein, we show by using biochemical assays and atomic force microscopy that DbpA exhibits ATP-stimulated unwinding activity of RNA duplex regardless of its primary sequence. This work presents an attempt to investigate the action of DEAD box proteins by a single-molecule visualization methodology. Our atomic force microscopy images enabled us to observe directly the unwinding reaction of a DEAD box helicase on long stretches of double-stranded RNA. Specifically, we could differentiate between the binding of DbpA to RNA in the absence of ATP and the formation of a Y-shaped intermediate after its progression through double-stranded RNA in the presence of ATP. Recent studies have questioned the designation of DbpA, in particular, and DEAD box proteins in general as RNA helicases. However, accumulated evidence and the results reported herein suggest that these proteins are indeed helicases that resemble in many aspects the DNA helicases.

Adenosine Triphosphatases↗
PubMed2004

Swelling and morphology of the skin layer of polyamide composite membranes: an atomic force microscopy study.

The paper introduces a new methodology for studying polyamide composite membranes for reverse osmosis (RO) and nanofiltration (NF) in liquid environments. The methodology is based on atomic force microscopy of the active layer, which had been separated from the support and placed on a solid substrate. The approach was employed to determine the thickness, interfacial morphology, and dimensional changes in solution (swelling) of polyamide films. The face (active) and back (facing the support) surfaces of the RO films appeared morphologically similar, in agreement with the recently proposed model of skin formation. Measured thickness and swelling data in conjunction with the intrinsic permeability of the membranes suggest that the selective barrier in RO membrane constitutes only a fraction of the polyamide skin, whereas NF membranes behave as nearly uniform films. For NF membranes, there was reasonable correlation between the changes in the swelling and in the permeability of the membrane and the salinity and pH of the feed.

Filtration↗
PubMed2004

Covalent immobilization of DNA onto functionalized mica for atomic force microscopy.

The immobilization of DNA on the self-assembled monolayer of 3-aminopropyltrimethoxysilane (APTES) on mica wafer functionalized with glutaraldehyde (GA) by chemical bonding was studied by atomic force microscopy (AFM). The DNA used for our investigation was amplified by polymerase chain reaction, and primers were labeled with a -NH2 group at their 5' terminus. The surfaces were analyzed by X-ray photoelectron spectroscopy (XPS) and AFM. Results from XPS and AFM showed that the mica with the APTES and activated with GA can be formed, and the flatness of the mica can be adapted for AFM images. We found that the modified surface was capable of binding DNA molecules so that it withstood a thorough rinsing with a solution of sodium dodecylsulfate. Covalent binding between the aldehyde-terminated membrane and -NH2 groups at both ends of double-stranded DNA resulted in immobilization and straightening of the DNA.

Aluminum Silicates↗
PubMed2001

Macromolecular triplex zipping observed in derivatives of fungal (1 --> 3)-beta-D-glucan by electron and atomic force microscopy.

Scleroglucan, a comb-like branched (1 --> 3)-beta-D-glucan, dissolves in water as a stiff, triple-helical structure with the single glucose branches extending from the surface. The aim of this study is to investigate structural changes in the triple-helical structure associated with selective chemical modification of the side chains. Electron and atomic force microscopy, respectively, were used to investigate the macromolecular structures of aldehyde and carboxylated derivatives of scleroglucan-namely, scleraldehyde and sclerox-with different degrees of substitution. Scleraldehyde was observed to have structures resembling the triplex of the unmodified scleroglucan for all degrees of substitution up to 1.0. Additionally, an increasing tendency to aggregate for the higher degrees of substitution was observed. Fully carboxylated scleroglucan, sclerox(1.0), prepared from solutions at ionic strengths below 1.0M, revealed dispersed, flexible, coil-like structures. This indicates an electrostatic-driven strand separation of the scleroglucan triple-helical structure occurring concomitant with an increasing fraction of the side chains bearing carboxylate groups. Annealed sclerox(1.0) samples in aqueous 1.0 and 1.5M NaCl exhibited partly, or completely, reassociated triplex ensembles, with species ranging from apparently fully zipped linear and circular topologies, partly zipped structures with triplex strand separation occurring at the ends, to dispersed single-strands with random coil-like appearance. This study shows that periodate oxidation of the scleroglucan side chains is not a sufficient modification of the side chains to induce dissociation of the triple-helical structure, whereas further oxidation of the side chains to carboxylic groups dissociates the triple-helical structure when the degree of substitution is above 0.6.

Carbohydrate Conformation↗