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We investigated the relationship between electrophoretic behaviors and higher order structures of triplet repeat DNA fragments by means of capillary electrophoresis and atomic force microscopy (AFM). It was suggested that the mobility difference between triplet repeat DNA and random sequence DNA should be correlated to differences in their dynamic conformation.
The microscopic surface molecular structures and macroscopic electrochemical impedance properties of the epoxysilane monolayer and anti-Escherichia coli antibody layer on an indium-tin oxide (ITO) electrode surface were studied in this paper. Characterization of stepwise changes in microscopic features of the surfaces and electrochemical properties upon the formation of each layer were carried out using both atomic force microscopy (AFM) and electrochemical impedance spectroscopy in the presence of [Fe(CN)6](3-/4-) as a redox couple. AFM images of the self-assembled monolayer (SAM) evidenced the dense, complete, and homogeneous morphology of the epoxysilane monolayer on the ITO surface. The uniformity of the epoxysilane SAM allowed antibodies to attach to the epoxy surface groups of the silanes in a similarly uniform fashion. The effects of epoxysilane monolayer and the antibody layer on the electrochemical properties of the electrode were quantitatively analyzed in terms of double layer capacitance, electron transfer resistance, Warburg impedance and solution resistance using Randles model as the equivalent circuit. It was demonstrated that the epoxysilane monolayer and the antibody layer act as barriers for the electron transfer between the electrode surface and the redox species in the solution, resulting in most significant increases in the electron transfer resistance compared to all the electric elements. Immunoreaction with E. coli O157:H7 cells demonstrated specific recognition of the immobilized anti-E. coli antibodies as evidenced by AFM imaging and impedance spectroscopy. It was found that the binding of E. coli cells mainly affected the electron transfer resistance and Warburg impedance.
Venous malformations (VM) are common vascular abnormality, and their management remains difficult. Pingyangmycin hydrochloride (PYM) is a useful sclerosant to treat venous malformations. This study was aimed to evaluate the effect of a new drug delivery system, PYM-loaded Zein/Zein-sucrose acetate isobutyrate (SAIB) in situ gels, in gelling and extending the local release of PYM. It was demonstrated that in vitro and in vivo release of PYM from the in situ gels could be extended up to 7 and 4 days, respectively. SAIB could significantly cut down the initial burst of PYM from the in situ gels (P<0.05). The possible gel forming and drug release mechanisms were described according to the morphology analysis by atomic force microscopy (AFM), optical microscopy and SEM. The gel forming efficacy and the viscosity of in situ gel solutions were satisfying.
The enzymatic activity of glucosylceramidase depends on the presence of saposin C (Sap C) and acidic phospholipid-containing membranes. In order to delineate the mechanism underlying Sap C stimulation of the enzyme activity, it is important to understand how Sap C interacts with phospholipid membranes. We studied the dynamic process of Sap C interaction with planar phospholipid membranes, in real time, using atomic force microscopy (AFM). The phospholipid membrane underwent restructuring upon addition of Sap C. The topographic characteristics of the membrane restructuring include the appearance of patch-like new features, initially emerged at the edge of phospholipid membranes and extended laterally with time. Changes in the image contrast of the phospholipid membrane observed after the Sap C addition indicate that a new phase of lipid-protein structure has formed during membrane restructuring. The process of membrane restructuring is dynamic, commencing shortly after Sap C addition, and continuing throughout the duration of AFM imaging (about 30 min, sometimes over 1 h). This study demonstrated the potential of AFM real-time imaging in studying protein-membrane interactions.
We have developed a procedure for partially relaxing the barley metaphase chromosomes and exposing fibrous structures from the chromosomes. The observation by atomic force microscopy (AFM) showed that the fibrous structures are typically 0.5 to 1 microm long and 40 to 50 nm in diameter. In higher magnification imaging, we found the fibrous structures were composed of aligned granules and looked like "knobby fiber." These observations are consistent with previously reported features of chromatin fiber observed by AFM and scanning electron microscopy, suggesting that the structures correspond to 30 nm chromatin fibers. We observed the chromatin fiber extending straight from the periphery of the chromosomes in most cases, but fibers with different shapes, such as loop and spiral, were also observed. The procedure reported here will provide a new approach for observing the organization of chromatin fiber to higher-order structures by AFM and other high-resolution microscopy.
The surface topography of human hair, as defined by the outer layer of cellular sheets, termed cuticles, largely determines the cosmetic properties of the hair. The condition of the cuticles is of great cosmetic importance, but also has the potential to aid diagnosis in the medical and forensic sciences. Atomic force microscopy (AFM) has been demonstrated to offer unique advantages for analysis of the hair surface, mainly due to the high image resolution and the ease of sample preparation. This article presents an algorithm for the automatic analysis of AFM images of human hair. The cuticular structure is characterized using a series of descriptors, such as step height, tilt angle and cuticle density, allowing quantitative analysis and comparison of different images. The usefulness of this approach is demonstrated by a classification study. Thirty-eight AFM images were measured, consisting of hair samples from (a) untreated and bleached hair samples, and (b) the root and distal ends of the hair fibre. The multivariate classification technique partial least squares discriminant analysis is used to test the ability of the algorithm to characterize the images according to the properties of the hair samples. Most of the images (86%) were found to be classified correctly.
The molecular processes that occur at the interface of an implanted biomaterial determines the host response, including phenomena such as protein adsorption, conformational changes, and subsequent interactions with cellular components. Until recently, such processes could not be observed directly. Over the past decade, atomic force microscopy (AFM) has provided mechanistic insights into the molecular level interactions that occur at the biomaterial interface. Several unique operational modes have been developed which utilize intermittent contact with the sample and decrease applied shear forces. These dynamic modes also can be used to study the role of different structural components on biomaterial micromechanical properties. Force detection techniques allow molecular level studies of individual receptor-ligand binding events, and force mapping for determining structure/function relationships. Advancements in tip manufacturing, image processing techniques, the use of model surfaces and labeling all have contributed to the advancement of the AFM as a state-of-the-art research instrument. In this report, we examine the applicability of the AFM to the study of biomaterials and cell/molecular interactions.
The Asr gene family is present in Spermatophyta. Its members are generally activated under water stress. We present evidence that tomato ASR1, one of the proteins of the family, accumulates in seed during late stages of embryogenesis, a physiological process characterized by water loss. In vitro, electrophoretic assays show a homo-dimeric structure for ASR1 and highlight strong non-covalent interactions between monomers prone to self-assemble. Direct visualization of single molecules by atomic force microscopy (AFM) confirms that ASR1 forms homodimers and that uncovers both monomers and dimers bind double stranded DNA.
RNA molecules have been much less studied by atomic force microscopy (AFM) than have DNA molecules. In this paper, AFM imaging is presented for two different RNA molecules able to self-assemble into complex supramolecular architectures. The first one is a molecular dimer of a 230-nt RNA fragment coming from the RNA genome of a murine leukaemia virus. The monomeric RNA fragment, which appears by AFM as an elongated structure with a mean aspect ratio of 1.4, assembles into a dimer of elongated structures through the formation of a 'kissing-loop' RNA interaction. The second one is a large supramolecular fibre formed of artificial self-assembling RNA molecular units called tectoRNA. The fibre lengths by AFM suggest that there are 50-70 tectoRNA units per fibre. Some methods and limitations are presented for measuring molecular volumes from AFM images.
The effect of surface modification of NiTi shape memory alloy on its corrosion behavior in Hanks' solution was determined. The near-equi-atomic super elastic NiTi (Ni 55.8 wt %) alloy used for this study was provided by Memry USA. The surfaces of heat-treated samples were modified by mechanical polishing (MP), electropolishing (EP), and electropolishing followed by chemical passivation (CP). As-heat-treated samples with straw-colored oxide finishes (SCO) and blue-colored oxide finishes (BO) also were included in the study. Surface analysis was performed using auger electron spectroscopy (AES), atomic force microscopy (AFM), and contact angle measurements (CAM). It was shown that surface roughness increased in the order CP < EP < SCO < BO < MP. The nickel release within the five groups of NiTi samples, as determined by atomic absorption spectrophotometry, reduced in time over the measured period. The level of Ni ions released over a 25-day immersion period was highest in the SCO sample (0.002 microg/day). This Ni level is negligible compared with the daily intake of Ni in an ordinary diet. The auger electron spectroscopy (AES) analyses indicated that before immersion in Hanks' physiologic solution, the main surface composition of all the samples was titanium and nickel, with a small amount of oxygen, carbon, and sulphur as contaminants. And the surface oxide thickness of the different samples increased in the order CP < EP < MP < BO < SCO. On the other hand, for the electrodes treated under the same conditions, the mean breakdown potential value decreased in the order BO > MP > CP > EP > SCO while the corrosion current density and rate increased in the order CP < SCO < EP < BO < MP.
As the application of high-resolution atomic force microscopy (AFM) has led us recently to the discovery of a unique pressure-induced circular amyloid, we used the same approach to examine morphological events accompanying insulin aggregation under ambient conditions. This study presents the multistage, hierarchical character of the spontaneous fibrillation of insulin at low pH and at 60 and 70 degrees C, and-due to the marked enhancement of image resolution achieved-brings new clues as to the fibrils' ultrastructure and mechanisms of its assembly. Specifically, focusing on the prefibrillar amorphous aggregates occurring 30 s after elevating temperature to the nucleation-enhancing 60 degrees C, revealed the tendency of the globule-shaped oligomers to queue and assembly into elongated forms. This suggests that the shape of the nuclei itself predetermines-in part-the fibrillar architecture of the amyloid. Among first fibrillar features, short but relatively thick (8-nm) seedlike forms appeared on a very short timescale within the first minute of incubation. It has been shown that such fibrils are likely to act as lateral scaffolds for the growth of amyloid. By using phase-image AFM as a nanometer-resolved probe of visco-elastic surface properties, we were able to show that bundles of early protofilaments associated into parallel fibrils are capable of a cooperative transformation into twisted, highly ordered superhelices of the mature amyloid. Independently from producing evidence for the step-resolved character of the process, intermediate and morphologically heterogeneous forms were trapped and characterized, which yields direct evidence for the multipathway character of the amyloidogenesis of insulin. Apart from the faster kinetics, the increased temperature of 70 degrees C leads to a higher degree of morphological variability: along straight rods, twisted ribbonlike structures, rod bundles, and ropelike structures become prominent in the corresponding AFM data.
A chemical procedure for anchoring DNA molecules to gold surfaces was used to facilitate the imaging of DNA and DNA-protein complexes in buffer solution by tapping mode atomic force microscopy (TMAFM). For preparing flat gold surfaces, a novel approach was employed by evaporating small amounts of gold onto freshly cleaved mica to give flat films that were stable under aqueous buffer conditions. The thickness of the investigated films ranged from 1 to 10 nm. For typical films of 4-6 nm, which were stable under aqueous buffer conditions, the root mean square (RMS) roughness ranged between 0.25 and 0.5 nm, as measured by atomic force microscopy (AFM). This roughness is comparable to that of obtained by the template stripped gold (TSG) technique, which is widely used in scanning probe microscopy but involves more preparation steps. In order to visualize DNA and DNA-protein complexes by TMAFM, the DNA was chemisorbed to the gold surface through a linker carrying a terminal thiol group at the 5'-end of each of the DNA strands. The modified DNA fragments were bound to the gold films and imaged in buffer solution, while unmodified DNA could not be visualized. Since the DNA was not dried during the process, it can be assumed that its native conformation was retained. This mode of anchoring did not prevent interaction with proteins, as confirmed by the observation that the topology of a complex formed by adding the protein to a surface-anchored DNA was the same as that obtained by anchoring a pre-formed complex to the gold surface. We attribute this observation to the fact that the DNA is anchored to the gold surfaces only through its ends, therefore the DNA-support interaction is minimized but imaging is still possible.
We have used atomic force microscopy (AFM) to study the conformation of three-way DNA junctions, intermediates of DNA replication and recombination. Immobile three-way junctions with one hairpin arm (50, 27, 18 and 7 bp long) and two relatively long linear arms were obtained by annealing two partially homologous restriction fragments. Fragments containing inverted repeats of specific length formed hairpins after denaturation. Three-way junctions were obtained by annealing one strand of a fragment from a parental plasmid with one strand of an inverted repeat-containing fragment, purified from gels, and examined by AFM. The molecules are clearly seen as three-armed molecules with one short arm and two flexible long arms. The AFM analysis revealed two important features of three-way DNA junctions. First, three-way junctions are very dynamic structures. This conclusion is supported by a high variability of the inter-arm angle detected on dried samples. The mobility of the junctions was observed directly by imaging the samples in liquid (AFM in situ). Second, measurements of the angle between the arms led to the conclusion that three-way junctions are not flat, but rather pyramid-like. Non-flatness of the junction should be taken into account in analysis of the AFM data.
Influence of molecular weight heterogeneity and drug solubility, drug loading and hydrodynamic conditions on drug release kinetics from gelatin nanoparticles were investigated. Also to assess the ability of gelatin nanoparticles as a potential intravascular probe for diagnostic purposes and in improving the biodelivery of cycloheximide (CHX), which is being used as a representative drug. Comparative characterization of 75 Bloom (type B, bovine), 175 and 300 Bloom (type A, porcine) gelatin nanoparticles was done to understand the phase behavior and hydrodynamic properties of gelatin chains and its nanoparticles. Gelatin nanoparticles were prepared by two-step desolvation method. Dynamic light scattering studies were performed to estimate hydrodynamic radii as well as intermolecular interaction. Effects of parameters like pH, temperature and molecular weight on the size and stability of the nanoparticles were studied. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) measurements were done for size and stability analysis. Enhanced visco-elastic properties of nanoparticles were observed as compared to normal solutions of gelatin.
Biomedical collagen preparations are mainly based on liquid aqueous preparations either used directly as injectables or transferred for example into solid implants or porous devices. In all cases the viscosity of the dispersion or solution has to be controlled or adjusted by pH, temperature, collagen concentration or crosslinking. We tested these effects on the rheological and structural properties of collagen fiber dispersions focusing on oscillatory rheometry. With increasing difference between pH and pI viscosity increased and went through a maximum with less rigidity of the fibers. The dispersions acted like a predominantly permanently linked network. This character changed to only partially linked at low collagen concentration due to isolation of the individual fibers. Up to 40 degrees C, temperature is a tool suitable for adjusting viscosity without changes in the network structure. At 50 degrees C, fourier transform - infrared spectroscopy (FT-IR) spectroscopy indicated the transition of the helical into random coil structure. Renaturation of the helices was found upon cooling but atomic force microscopy (AFM) indicated severe temperature induced damages of the fibers. Crosslinking with glutaraldehyde (GTA) leads to an increase in viscosity and the effect on the network structure depends on the processing conditions.
A facile, self-assembly approach to the fabrication of a robust, mesoporous, biocompatible polymeric network for the spatial organization of proteins is described. Surface-deposited poly(styrene) (PS) beads that assemble into a two-dimensional (2-D) hexagonal array are used to template cross-linked poly(vinyl alcohol) (PVA), yielding an inverse opal structure. The porous, water insoluble network is used to entrain a model, soluble protein, green fluorescent protein (GFP). The polymeric network is characterized by atomic force microscopy (AFM) and optical microscopy, and the spatial localization of the incorporated GFP is determined by fluorescence microscopy. The results demonstrate that this system may constitute a versatile platform for the lateral organization of biomolecules.
As macromolecular protease complex, the 20 S proteasome is responsible for the degradation of cellular proteins and the generation of peptide epitopes for antigen presentation. Here, structural and functional aspects of the 20 S proteasome from Thermoplasma acidophilum have been investigated by atomic force microscopy (AFM) and surface plasmon resonance (SPR). Due to engineered histidine tags introduced at defined positions, the proteasome complex was pre-oriented at ultra-flat chelator lipid membranes allowing for high-resolution imaging by AFM. Within these two-dimensional protein arrays, the overall structure of the proteasome and the organization of individual subunits was resolved under native conditions without fixation or crosslinking. In addition, the substrate-proteasome interaction was monitored in real-time by SPR using a novel approach. Instead of following enzyme activity by product formation, the association and dissociation kinetics of the substrate-proteasome complex were analyzed during proteolysis of the polypeptide chain. By blocking the active sites with a specific inhibitor, the substrate binding step could be dissected from the degradation step thus resolving mechanistic details of substrate recognition and cleavage by the 20 S proteasome.
Monolayer films of metal phosphate were prepared by sequential adsorption of phosphoric acid (PA) and metal ions (Zr4+ or Ca2+). The monolayer formation was confirmed and characterized by ellipsometry and atomic force microscopy (AFM). Nanometer-scale patterning on the self-assembled metal phosphate films has been achieved using AFM. The difference in AFM lithography on positively charged surfaces in the case of Zr4+ and Ca2+ ions was investigated and summarized. Since the presence of the positive charges allows electrons to move from a tip to a layer easily, the lithographic process initiates at a lower voltage in the layer of Zr2+ phosphate than in the layer of Ca phosphate or PA. Other lithographic results on metal phosphate layers were compared with those on a monolayer of PA.