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PubMed1993

Atomic force microscopy study of human tooth enamel surfaces.

Human enamel features from individual crystals up to prisms were observed by atomic force microscopy (AFM). Low magnification images of vestibular tooth surfaces show the existence of enamel prisms appearing as deep holes. Individual, parallel enamel crystals show lateral faces elongated and formed by the (100) planes of hydroxyapatite (HA). Height differences between (001) faces create the roughness of enamel surface. Individual (001) crystal faces can be observed clearly at higher magnification and show the characteristic hexagonal shape with 60 degree angles between (100) faces. This study confirms the applicability of AFM for studying biological hydroxyapatite crystals.

Adolescent↗
PubMed2002

High-resolution three-dimensional imaging of the lateral plasma membrane of cochlear outer hair cells by atomic force microscopy.

The outer hair cells (OHCs) from the mammalian organ of Corti are assumed to enhance the sensitivity and the selectivity of the cochlea via an electromotile response to sound stimulation. These OHC mechanical changes feed energy back into the cochlea before completion of the transduction process by inner hair cells. OHC electromotility is thought to depend on specific transmembrane motor proteins. Electron microscopy has been used previously to image the OHC lateral plasma membrane, where voltage sensors and motors are located. A very specific and regular organization of membrane particles has been described, together with an equally specific submembraneous meshwork of cytoskeleton anchored to the plasma membrane. To confirm and extend these observations, we have used, for the first time on the OHC lateral wall, atomic force microscopy (AFM). As a result of an improved tapping mode technique as well as the unique ultrastructural organization of the OHC plasma membrane, we have obtained high-resolution three-dimensional (3D) images of a markedly enhanced quality, allowing high-resolution 3D imaging. Tapping-mode AFM confirmed the presence of regularly aligned particles (presumably transmembrane proteins) on both faces of the OHC plasma membrane. It also revealed the presence of markedly different membrane domains, smooth and undulating. The differences between these zones probably are due to local differences in cytoskeleton-membrane interactions. Moreover, 3D reconstructions allowed us to distinguish between globular and pore-like particles, a distinction that may be of great functional significance.

Animals↗
PubMed2004

Atomic force microscopy demonstrates a critical role of DNA superhelicity in nucleosome dynamics.

Nucleosome is the most basic structural unit of eukaryotic chromosome, forming an 11 nm "beads-on-a-string" fiber. The molecular mechanism of chromatin folding toward higher-order structures (30 nm and thicker fibers) is speculative; however, it is thought to be critical for the regulation of transcription, replication, and chromosome propagation. We examined the relationship between the efficiency of the nucleosome formation and the physical properties of the template DNA. A series of plasmid DNA with different lengths (3, 5, 31, 56, or 106 kb) were prepared and, together with purified histones, used for the reconstitution of chromatin fibers by a salt-dialysis method. The reconstituted chromatin fibers were visualized and analyzed by atomic force microscopy (AFM). Based on the AFM images, the efficiency of the reconstitution was dependent on the length and the negative superhelical strain of the DNA used (i.e., the longer DNA had a higher efficiency in the reconstitution, because the longer plasmids retain much higher superhelical density than the shorter ones). These results suggest that the nucleosome dynamics are tightly coupled with the DNA superhelicity. This was further supported by the fact that the linearized or topoisomerase I-treated plasmids (relaxed circular) showed very low efficiency. Namely, the negative supercoiling promoted the efficient formation of the nucleosome but the positive supercoiling strongly inhibited it.

Centromere↗
PubMed2005

Preliminary analysis of crystals of panicum mosaic virus (PMV) by X-ray diffraction and atomic force microscopy.

Panicum mosaic virus (PMV), a spherical virus of diameter about 300 A, has been crystallized in a form suitable for high-resolution structural analysis. The crystals were grown from 15% PEG 400 at room temperature and could be flash-frozen directly from their mother liquor. The crystals diffracted to beyond 2.7 A resolution. A data set was collected at 100 K to an effective resolution of 3.2 A [Weiss (2001), J. Appl. Cryst. 34, 130-135]. The crystals belonged to space group P2(1), with unit-cell parameters a=411.7, b=403.9, c=412.5 A, beta=89.7 degrees . Self-rotation functions and molecular replacement with tobacco necrosis virus as the probe model yielded tentative positions and orientations for the two entire virus particles comprising the asymmetric unit and implied a pseudo-face-centered cubic packing arrangement. Investigation of lightly glutaraldehyde-fixed crystals in water using atomic force microscopy confirms the packing arrangement given by the molecular-replacement result. The images also show that contaminating virions of the satellite virus to PMV, known as satellite panicum mosaic virus (SPMV), can be incorporated into the PMV crystals by insertion into the interstices between PMV virions in the lattice. This is the first observation of such a phenomenon in macromolecular crystals.

Crystallography, X-Ray↗
PubMed2005

Investigation by atomic force microscopy of the structure of Ty3 retrotransposon particles.

Ty3, a member of the Metaviridiae family of long-terminal-repeat retrotransposons found in Saccharomyces cerevisiae, encodes homologs of retroviral Gag and Gag-Pol proteins, which, together with genomic RNA, assemble into virus-like particles (VLPs) that undergo processing and reverse transcription. The Ty3 structural proteins, capsid and nucleocapsid, contain major homology and nucleocapsid motifs similar to retrovirus capsid and nucleocapsid proteins, but Ty3 lacks a matrix-like structural domain amino terminal to capsid. Mass spectrometry analysis of Ty3 Gag3 processing products defined an acetylated Ser residue as the amino terminus of Gag3/p34, p27, and CA/p24 species and supported a model where p34 and p27 occur in phosphorylated forms. Using atomic force microscopy, VLPs were imaged from cells producing wild-type and protease and reverse transcriptase mutant Ty3. Wild-type VLPs were found to have a broad range of diameters, but the majority, if not all of the particles, exhibited arrangements of capsomeres on their surfaces which were consistent with icosahedral symmetry. Wild-type particles were in the range of 25 to 52 nm in diameter, with particles in the 42- to 52-nm diameter range consistent with T=7 symmetry. Both classes of mutant VLPs fell into a narrower range of 44 to 53 nm in diameter and appeared to be consistent with T=7 icosahedral symmetry. The smaller particles in the wild-type population likely correspond to VLPs that have progressed to reverse transcription or later stages, which do not occur in the protease and reverse transcriptase mutants. Ty3 VLPs did not undergo major external rearrangements during proteolytic maturation.

Mass Spectrometry↗
PubMed2002

Sequential atomic force microscopy imaging of a spontaneous nanoencapsulation process.

Since hydrophilic matrices were proposed for controlled drug delivery, many polymeric excipients have been studied in order to make drug release fit the desired profiles. It has been pointed out that lambda-carrageenan, a sulphated polymer from algae, can suitably control the release rate of basic drugs from hydrophilic matrices with no need for complex technological processes. In this work, we propose a method to monitor morphologically the interaction between lambda-carrageenan and dexchlorpheniramine maleate (D-CPM), in order to find out how the release profiles can be so easily controlled. To this end, solutions of both polymer and drug were prepared at very low concentration. Solutions were mixed and samples were taken every hour over a period of 20 h. The characterization technique employed, atomic force microscopy (AFM), provides a high resolution, allowing to show the three-dimensional morphology of the samples within the nanometric scale. The results demonstrate that lambda-carrageenan is able to nanoencapsulate spontaneously D-CPM molecules, which offers the possibility to easily control the release rate of the drug. This work has moreover demonstrated the suitability of AFM for the specific case of the on-time monitoring of interaction processes that happen in pharmaceutical systems.

Carrageenan↗
PubMed2005

Fine mapping of inherent flexibility variation along DNA molecules: validation by atomic force microscopy (AFM) in buffer.

Curvature and flexibility are structural properties of central importance to genome function. However, due to the difficulties in finding suitable experimental conditions, methods for studying one without the interference of the other have proven to be difficult. We propose a new approach that provides a measure of inherent flexibility of DNA by taking advantage of two powerful techniques, X-ray crystallography and nuclear magnetic resonance. Both techniques are able to detect local curvature on DNA fragments but, while the first analyzes DNA in the solid state, the second works on DNA in solution. Comparison of the two data sets allowed us to calculate the relative contribution to flexibility of the three rotations and three translations, which relate successive base pair planes for the ten different dinucleotide steps. These values were then used to compute the variation of flexibility along a given nucleotide sequence. This allowed us to validate the method experimentally through comparisons with maps of local fluctuations in DNA molecule trajectory constructed from atomic force microscopy imaging in solution. We conclude that the six dinucleotide-step parameters defined here provide a powerful tool for the exploration of DNA structure and, consequently will make an important contribution to our understanding of DNA-sequence-dependent biological processes.

Base Sequence↗
PubMed2004

Interaction of the Zalpha domain of human ADAR1 with a negatively supercoiled plasmid visualized by atomic force microscopy.

Interest to the left-handed DNA conformation has been recently boosted by the findings that a number of proteins contain the Zalpha domain, which has been shown to specifically recognize Z-DNA. The biological function of Zalpha is presently unknown, but it has been suggested that it may specifically direct protein regions of Z-DNA induced by negative supercoiling in actively transcribing genes. Many studies, including a crystal structure in complex with Z-DNA, have focused on the human ADAR1 Zalpha domain in isolation. We have hypothesized that the recognition of a Z-DNA sequence by the Zalpha(ADAR1) domain is context specific, occurring under energetic conditions, which favor Z-DNA formation. To test this hypothesis, we have applied atomic force microscopy to image Zalpha(ADAR1) complexed with supercoiled plasmid DNAs. We have demonstrated that the Zalpha(ADAR1) binds specifically to Z-DNA and preferentially to d(CG)(n) inserts, which require less energy for Z-DNA induction compared to other sequences. A notable finding is that site-specific Zalpha binding to d(GC)(13) or d(GC)(2)C(GC)(10) inserts is observed when DNA supercoiling is insufficient to induce Z-DNA formation. These results indicate that Zalpha(ADAR1) binding facilities the B-to-Z transition and provides additional support to the model that Z-DNA binding proteins may regulate biological processes through structure-specific recognition.

Adenosine Deaminase↗
PubMed2006

Ex situ atomic force microscopy analysis of beta-amyloid self-assembly and deposition on a synthetic template.

The beta-amyloid (Abeta) deposition, which is the conversion of soluble Abeta peptides to insoluble plaques on a surface, is an essential pathological process in Alzheimer's disease (AD). The identification and characterization of possible environmental factors that may influence amyloid deposition in vivo are important to unveil the underlying etiology of AD. According to the amyloid cascade hypothesis, diffuse plaques are initial and visual deposits in the early event of AD, leading to amyloid plaques. To study amyloid deposition and growth in vitro, we prepared a synthetic template by immobilizing Abeta seeds on an N-hydroxysuccinimide ester-activated solid surface. According to our analysis with an ex situ atomic force microscope, the formation of amyloid plaque-like aggregates was mediated by the interaction between Abeta in a solution and on a synthetic template, suggesting that Abeta oligomers function well as seeds for amyloid deposition. It was observed that insoluble amyloid aggregates formed on the template surface serve as a sink of soluble Abeta in a solution as well as mediate the formation of intermediates in the pathway of amyloid fibrillization in a solution. Relative seeding efficiencies of fresh monomers, oligomers, and fully grown fibrils were analyzed by measuring the deposited plaque volume and its height distribution through atomic force microscopy. The result revealed that oligomeric forms of Abeta act more efficiently as seeds than monomers or fibrils do. Fluorescence spectroscopy with thioflavin T confirmed that amyloid aggregate formation proceeds in a concentration-dependent manner. Analysis with Fourier transform infrared spectroscopy indicated a progressive transition of soluble Abeta42 monomer to amyloid fibrils having antiparallel beta-sheet structure on the template. Furthermore, studies on the interaction between Abeta40 and 42, two major variants of Abeta derived from the amyloid precursor protein, showed that amyloid aggregate formation on the surface was accelerated further by the homogeneous association of soluble Abeta42 onto Abeta42 seeds than by other combinations. A slightly acidic condition was found to be unfavorable for amyloid formation. This study gives insight into understanding the effects of environmental factors on amyloid formation via the use of a synthetic template system.

Alzheimer Disease↗
PubMed2001

Microstructure determination of AOT + phenol organogels utilizing small-angle X-ray scattering and atomic force microscopy.

Dry reverse micelles of the anionic twin-tailed surfactant bis(2-ethylhexyl) sulfosuccinate (AOT) dissolved in nonpolar solvents spontaneously form an organogel when p-chlorophenol is added in a 1:1 AOT:phenol molar ratio. The solvents used were benzene, toluene, m-xylene, 2,2,4-trimethylpentane (isooctane), decane, dodecane, tetradecane, hexadecane, and 2,6,10,14-tetramethylpentadecane (TMPD). The proposed microstructure of the gel is based on strands of stacked phenols linked to AOT through hydrogen bonding. Small-angle X-ray scattering (SAXS) spectra of the organogels suggest a characteristic length scale for these phenol-AOT strands that is independent of concentration but dependent on the chemical nature of the nonpolar solvent used. Correlation lengths determined from the SAXS spectra indicate that the strands self-assemble into fibers. Direct visualization of the gel in its native state is accomplished by using tapping mode atomic force microscopy (AFM). It is shown that these organogels consist of fiber bundle assemblies. The SAXS and AFM data reinforce the theory of a molecular architecture consisting of three length scales-AOT/phenolic strands (ca. 2 nm in diameter) that self-assemble into fibers (ca. 10 nm in diameter), which then aggregate into fiber bundles (ca. 20-100 nm in diameter) and form the organogel.

Chlorophenols↗
PubMed2003

"Antiparallel" DNA loop in gal repressosome visualized by atomic force microscopy.

DNA looping is often involved in positive and negative regulation of gene transcription in both prokaryotes and eukaryotes. The transcription of the gal operon of Escherichia coli from two overlapping promoters P1 and P2 is negatively regulated via Gal repressosome assembly. It involves binding of two dimeric Gal repressor proteins (GalR) to two operators, O(E) and O(I), flanking the two promoters, and formation of 113 bp DNA loop due to tetramerization of the two bound GalR dimers. The process requires negatively supercoiled DNA and the presence of the histone-like protein HU. Previous modeling of the repressosome based on evaluation of DNA elastic energy suggested a mutual antiparallel, rather than parallel, orientation of the two gal operators in an under-twisted DNA loop. To visualize the Gal loop by atomic force microscopy (AFM), plasmid DNA molecules were constructed with increased distance between the two operators. The AFM results demonstrated the formation of an antiparallel DNA loop in the Gal repressosome consistent with our earlier hypothesis. Importantly, the overall shape of the GalR mediated loop proved to be indistinguishable from that in the chimerical loop of the same size containing two lac operators (instead of two gal operators) and formed by LacI. In addition, a possibility of the gal operon repression mediated by GalR in the absence of HU was shown in the new DNA constructs. Implications of these findings for the DNA structural organization in bacterial nucleoid are discussed.

Bacterial Proteins↗
PubMed2001

Imaging molecular structure and physiological function of gap junctions and hemijunctions by multimodal atomic force microscopy.

Gap junctions are specialized plasma membrane structures that join neighboring cells via specialized intercellular ion channels (hemichannels) and provide a direct pathway for cell-cell communication. They presumably mediate regulation of growth, transmission of developmental signals, coordination of muscle contraction, and maintenance of metabolic homeostasis. Hemichannels are also present in the non-junctional regions of the cell plasma membrane and they provide a direct pathway for communication between the cytoplasm and the extracellular region. Recent studies suggest that gap junctional communication is much more complex than previously anticipated, in terms of both its structure as well as its activity. While the mechanism of gap junction activity is being studied extensively, their quaternary structure, assembly, and conformational changes underlying gating of their activity as well as their physiological role are poorly understood because, due to their complex structure, these junctions are less amenable to existing techniques for high-resolution three-dimensional structure-function analyses. Atomic Force Microscopy (AFM) images molecular structure of biological specimens in an aqueous environment, allows on-line perturbations, and can be coupled with electrophysiological, biochemical, and other microscopic techniques. The present review examines the potential of AFM application for the study of the molecular structure of hydrated, native gap junctions and hemijunctions as well as their physiological functions. Special attention is paid to new, complementary, or provocative findings from AFM studies of both vertebrate and invertebrate gap junctions and hemijunctions.

Animals↗
PubMed2001

Design of functionalized lipids and evidence for their binding to photosystem II core complex by oxygen evolution measurements, atomic force microscopy, and scanning near-field optical microscopy.

Photosystem II core complex (PSII CC) absorbs light energy and triggers a series of electron transfer reactions by oxidizing water while producing molecular oxygen. Synthetic lipids with different alkyl chains and spacer lengths bearing functionalized headgroups were specifically designed to bind the Q(B) site and to anchor this large photosynthetic complex (240 kDa) in order to attempt two-dimensional crystallization. Among the series of different compounds that have been tested, oxygen evolution measurements have shown that dichlorophenyl urea (DCPU) binds very efficiently to the Q(B) site of PSII CC, and therefore, that moiety has been linked covalently to the headgroup of synthetic lipids. The analysis of the monolayer behavior of these DCPU-lipids has allowed us to select ones bearing long spacers for the anchoring of PSII CC. Oxygen evolution measurements demonstrated that these long-spacer DCPU-lipids specifically bind to PSII CC and inhibit electron transfer. With the use of atomic force microscopy (AFM) and scanning near-field optical microscopy (SNOM), it was possible to visualize domains of PSII CC bound to DCPU-lipid monolayers. SNOM imaging has enabled us to confirm that domains observed by AFM were composed of PSII CC. Indeed, the SNOM topography images presented similar domains as those observed by AFM, but in addition, it allowed us to determine that these domains are fluorescent. Electron microscopy of these domains, however, has shown that the bound PSII CC was not crystalline.

Diuron↗
PubMed2003

Atomic force microscopy of microfibrils in primary cell walls.

Examination of angiosperm primary cell walls by transmission electron microscopy shows that they contain microfibrils that probably consist of cellulose microfibrils surrounded by associated non-cellulosic polysaccharides. Previous studies using solid-state (13)C NMR spectroscopy have shown that the cellulose is all crystalline with crystallites of cross-sectional dimensions of 2-3 nm. However, it is not known if each microfibril contains only one, or more than one crystallite because there is no agreement about the dimensions of the microfibrils. Partially hydrated primary cell walls isolated from onion ( Allium cepa L.) and Arabidopsis thaliana (L.) Heynh. were examined by atomic force microscopy and the microfibril diameters determined. The cell walls of both species contained tightly interwoven microfibrils of uniform diameter: 4.4+/-0.13 nm in the onion and 5.8+/-0.17 nm in A. thaliana. The effect was also examined of extracting the A. thaliana cell walls to remove pectic polysaccharides. The microfibrils in the extracted cell walls of A. thaliana were significantly narrower (3.2+/-0.13 nm) than those in untreated walls. The results are consistent with the microfibrils containing only one cellulose crystallite.

Arabidopsis↗
PubMed1999

Atomic force microscopy imaging of DNA covalently immobilized on a functionalized mica substrate.

A procedure for covalent binding of DNA to a functionalized mica substrate is described. The approach is based on photochemical cross-linking of DNA to immobilized psoralen derivatives. A tetrafluorphenyl (TFP) ester of trimethyl psoralen (trioxalen) was synthesized, and the procedure to immobilize it onto a functionalized aminopropyl mica surface (AP-mica) was developed. DNA molecules were cross-linked to trioxalen moieties by UV irradiation of complexes. The steps of the sample preparation procedure were analyzed with x-ray photoelectron spectroscopy (XPS). Results from XPS show that an AP-mica surface can be formed by vapor phase deposition of silane and that this surface can be derivatized with trioxalen. The derivatized surface is capable of binding of DNA molecules such that, after UV cross-linking, they withstand a thorough rinsing with SDS. Observations with atomic force microscopy showed that derivatized surfaces remain smooth, so DNA molecules are easily visualized. Linear and circular DNA molecules were photochemically immobilized on the surface. The molecules are distributed over the surface uniformly, indicating rather even modification of AP-mica with trioxalen. Generally, the shapes of supercoiled molecules electrostatically immobilized on AP-mica and those photocross-linked on trioxalen-functionalized surfaces remain quite similar. This suggests that UV cross-linking does not induce formation of a noticeable number of single-stranded breaks in DNA molecules.

Aluminum Silicates↗
PubMed2004

Velocity dependent friction laws in contact mode atomic force microscopy.

Friction forces in the tip-sample contact govern the dynamics of contact mode atomic force microscopy. In ambient conditions typical contact radii between tip and sample are in the order of a few nanometers. In order to account for the large interaction area the dynamics of contact mode atomic force microscope (AFM) is investigated under the assumption of a multi-asperity contact interface between tip and sample. Thus, the kinetic friction force between tip and sample is the product of the real contact area between both solids and the interfacial shear strength. The velocity strengthening of the lateral force is modeled assuming a logarithmic relationship between shear-strength and velocity. Numerical simulations of the system dynamics with this empirical model show the existence of two different regimes in contact mode AFM: steady sliding and stick-slip where the tip undergoes periodically stiction and kinetic friction. The state of the system depends on the scan velocity as well as on the velocity dependence of the interfacial friction force between tip and sample. Already small viscous damping contributions in the tip-sample contact are sufficient to suppress stick-slip oscillations.

Journal Article↗
PubMed2005

The elasticity of individual titin PEVK exons measured by single molecule atomic force microscopy.

The I-band region of the giant muscle protein titin contains a large domain enriched for the amino acids proline, glutamate, valine, and lysine and is denoted the PEVK domain. The PEVK domain of titin encodes a random coil shown to be an important factor in the passive elasticity of titin. Muscle-specific splicing of 116 PEVK exons encodes this domain. It has been proposed that proline contents determine the elasticity of the PEVK polypeptide, where the individual exons code for "flexibility cassettes." To test this hypothesis, we have measured the elasticity of three distinct polypeptides encoded by individual PEVK exons (161, 120 and 184) that varied greatly in their proline contents (7, 14, and 37% respectively) and total PEVK contents (55, 70, and 87%). We used single molecule atomic force microscopy techniques to measure the persistence length, p, of the engineered PEVK proteins. Surprisingly, all three exons 161, 120, and 184 coded for proteins with similar values of persistence length, p = 0.92 +/- 0.38, 0.89 +/- 0.42, and 0.98 +/- 0.4 nm, respectively. We conclude that the PEVK exons encode polypeptides of similar elastic properties, unrelated to their total PEVK contents. Hence, alternative splicing solely adjusts the length of the PEVK domain of titin.

Alternative Splicing↗
PubMed2006

Origin of p(2 x 1) phase on Si(001) by noncontact atomic force microscopy at 5 k.

The controversial issue of the origin of the p(2 x 1) reconstruction of the Si(001) surface observed in recent low temperature scanning tunneling microscopy experiments is clarified here using 5 K noncontact atomic force microscopy. The c(4 x 2) phase is observed at separations corresponding to weak tip-surface interactions, confirming that it is the ground state of the surface. At larger frequency shifts the p(2 x 1) phase of symmetric dimers is observed. By studying the interaction of a reactive Si tip with the c(4 x 2) Si(001) surface using an ab initio method, we find that the observed change in the surface reconstruction is an apparent effect caused by tip induced dimer flipping resulting in a modification of the surface structure and appearance of the p(2 x 1) phase in the image. Using an appropriate scanning protocol, one can manipulate the surface reconstruction at will, which has significance in nanotechnology.

Journal Article↗