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PubMed2004

Atomic force microscopy contact, tapping, and jumping modes for imaging biological samples in liquids.

The capabilities of the atomic force microscope for imaging biomolecules under physiological conditions has been systematically investigated. Contact, dynamic, and jumping modes have been applied to four different biological systems: DNA, purple membrane, Alzheimer paired helical filaments, and the bacteriophage phi29. These samples have been selected to cover a wide variety of biological systems in terms of sizes and substrate contact area, which make them very appropriate for the type of comparative studies carried out in the present work. Although dynamic mode atomic force microscopy is clearly the best choice for imaging soft samples in air, in liquids there is not a leading technique. In liquids, the most appropriate imaging mode depends on the sample characteristics and preparation methods. Contact or dynamic modes are the best choices for imaging molecular assemblies arranged as crystals such as the purple membrane. In this case, the advantage of image acquisition speed predominates over the disadvantage of high lateral or normal force. For imaging individual macromolecules, which are weakly bonded to the substrate, lateral and normal forces are the relevant factors, and hence the jumping mode, an imaging mode which minimizes lateral and normal forces, is preferable to other imaging modes.

Bacillus Phages↗
PubMed1999

Identification of microphases in mixed alpha- and omega-gliadin protein films investigated by atomic force microscopy.

Pure and mixed films of alpha- and omega-gliadins were studied by tapping mode atomic force microscopy (AFM). The technique was sensitive to the chemistry of the surface properties of the films, allowing imaging of the mixed gliadin phases at different ratios. In addition to the study of the phases at the micrometer level, higher resolution images allowed visualization of the protein films at the molecular level. These studies may have relevance to the formation of phases in developing protein bodies in grain, where gliadins and glutenins are deposited together. It has been assumed that the protein bodies consist of a random network of proteins; these studies indicate that microphases could be present in protein bodies. The technique provides novel methods for studying mixed biopolymer systems.

Gliadin↗
PubMed2002

Atomic force microscopy study of the interaction of Fusarium solani pisi cutinase with lipid surfaces.

We present an atomic force microscopy (AFM) study of a supported triacylglyceride multilayer phase and its interaction with lipolytic enzyme cutinase from Fusarium solani pisi. The multilayer triacylglyceride phase of coconut oil showed a rippled surface structure in the AFM images. Upon enzymatic degradation of the triacylglyceride phase, the ripple structure vanished rapidly. The apparent catalytic rate constants could be estimated based on the AFM image information. Interestingly, in one sample we observed what we interpret as a recurrent structural collapse of the cavity dug out by the protein. We interpret the cavities seen in the AFM images as molten surfaces or surface holes filled with liquidified phase containing product molecules, which appear transparent during the image recording.

Binding Sites↗
PubMed2006

MAC mode atomic force microscopy studies of living samples, ranging from cells to fresh tissue.

Magnetic AC mode (MAC mode) atomic force microscopy (AFM), a novel type of tapping mode AFM in which the cantilever is driven directly by a magnetic field, is a powerful tool for imaging with high spatial resolution and better signal-to-noise in liquid environment. It may largely extend the application of AFM to living samples, especially those are sensitive to cantilever forces, even to multilayer tissue samples. However, there are few reports on the imaging of living cells by MAC mode AFM previously. In our present study, we explore the optimal imaging conditions of MAC mode AFM on living astrocytes and fresh arterial intima surface. We also used nude tips for PicoTREC panel (i.e., Aux in BNC, a new data collecting channel) to image living samples and discussed its difference with phase imaging. We show that living biological samples can be imaged by MAC mode AFM at details of comparable resolution as those by high resolution scanning electron microscopy. Furthermore, the combination of height, amplitude, phase and TREC panel signals provide abundant informations for the characteristics of living samples, such as topography, profile, stiffness and adhesion.

Animals↗
PubMed2001

Imaging domains in model membranes with atomic force microscopy.

Lateral segregation in biomembranes can lead to the formation of biologically functional domains. This paper reviews atomic force microscopy studies on domain formation in model membranes, with special emphasis on transbilayer asymmetry, and on lateral domains induced by lipid-lipid interactions or by peptide-lipid interactions.

Animals↗
PubMed2006

Fast-scanning atomic force microscopy reveals the molecular mechanism of DNA cleavage by ApaI endonuclease.

Newly developed fast-scanning atomic force microscopy (AFM) allows the dissection of molecular events such as DNA-enzyme reactions at the single-molecule level. With this novel technology, a model is proposed of the DNA cleavage reaction by a type IIP restriction endonuclease ApaI. Detailed analyses revealed that ApaI bound to DNA as a dimer and slid along DNA in a one-dimensional diffusion manner. When it encountered a specific DNA sequence, the enzyme halted for a moment to digest the DNA. Immediately after digestion, the ApaI dimer separated into two monomers, each of which remained on the DNA end and then dissociated from the DNA end. Thus, fast-scanning AFM is a powerful tool to aid the understanding of protein structures and dynamics in biological reactions at the single-molecule level in sub-seconds.

Binding Sites↗
PubMedDate not supplied

Quantitative analysis of EcoR1 methylase-DNA complex by atomic force microscopy.

The EcoR1 methylase specifically recognize 5'-GA* ATTC-3' in DNA duplex. We directly applied atomic force microscopy (AFM) to investigate linear pBR322-EcoR1 methylase complexes and quantitatively analyzed the bend angles of linear pBR322-EcoR1 methylase complexes and the bound protein widths. In this study, we made a novel observation that DNA-EcoR1 methylase complexes exhibited two populations of conformation at recognition site: DNA bent an acute angle at the recognition site in the presence of one EcoR1 methylase monomeric molecule, while DNA bent an unacute angle at the recognition site and the complementary site on duplex DNAs in the presence of EcoR1 methylase dimer. The data indicated that the unacute angle state was the result of unique interactions between EcoR1 methylase and the recognition site and the complementary site on duplex DNAs, and suggested that the acute angle conformation could be an intermediate in the formation of the unacute angle state. Our works provide a detail insight into the DNA structural variations involved in EcoR1 methylase-binding processes and demonstrate further the versatility of AFM as an imaging technique for studying the interaction between large DNA fragment and protein.

Binding Sites↗
PubMed2004

[New measurement technics in biology and medicine: atomic force microscopy (part II)].

At present, there are a lot of biological and medical research fields, where atomic force microscopy (AFM) is being successfully used. AFM has contributed to research in the investigation of DNA, RNA structure, nucleic acid--protein complexes, chromosomes, ligand-receptor binding, cell membranes, proteins, lipids, carbohydrates, living cells (yeasts, bacteria, neurons, erythrocytes, endothelial cells); it enables to monitor drug interactions with cells and tissues, to visualize changes in protein molecular structure and crystal growth. Unlike electron microscopes, samples do not need to be stained, coated or frozen. Recent work indicates that, in the near future, AFM may be employed in ultra-sensitive immunoassay detection without any kind of labeling for both qualitative and quantitative work. AFM is more than a surface--imaging tool in that force measurements can be used to probe the physical properties of the specimen, such as molecular interactions, surface hydrophobicity, surface charges, and mechanical properties.

Biomedical Technology↗
PubMed2004

Correlated atomic force microscopy and fluorescence lifetime imaging of live bacterial cells.

We report on imaging living bacterial cells by using a correlated tapping-mode atomic force microscopy (AFM) and confocal fluorescence lifetime imaging microscopy (FLIM). For optimal imaging of Gram-negative Shewanella oneidensis MR-1 cells, we explored different methods of bacterial sample preparation, such as spreading the cells on poly-L-lysine coated surfaces or agarose gel coated surfaces. We have found that the agarose gel containing 99% ammonium acetate buffer can provide sufficient local aqueous environment for single bacterial cells. Furthermore, the cell surface topography can be characterized by tapping-mode in-air AFM imaging for the single bacterial cells that are partially embedded. Using in-air rather than under-water AFM imaging of the living cells significantly enhanced the contrast and signal-to-noise ratio of the AFM images. Near-field AFM-tip-enhanced fluorescence lifetime imaging (AFM-FLIM) holds high promise on obtaining fluorescence images beyond optical diffraction limited spatial resolution. We have previously demonstrated near-field AFM-FLIM imaging of polymer beads beyond diffraction limited spatial resolution. Here, as the first step of applying AFM-FLIM on imaging bacterial living cells, we demonstrated a correlated and consecutive AFM topographic imaging, fluorescence intensity imaging, and FLIM imaging of living bacterial cells to characterize cell polarity.

Bacteria↗
PubMed2002

Glutaraldehyde modified mica: a new surface for atomic force microscopy of chromatin.

We have found that mica surfaces functionalized with aminopropyltriethoxysilane and aldehydes bind chromatin strongly enough to permit stable and reliable solution imaging by atomic force microscopy. The method is highly reproducible, uses very small amounts of material, and is successful even with very light degrees of surface modification. This surface is far superior to the widely used aminopropyltriethoxysilane-derivatized mica surface and permits resolution of structure on the nanometer-scale in an aqueous environment, conditions that are particularly important for chromatin studies. For example, bound nucleosomal arrays demonstrate major structural changes in response to changes in solution conditions, despite their prior fixation (to maintain nucleosome loading) and tethering to the surface with glutaraldehyde. By following individual molecules through a salt titration in a flow-through cell, one can observe significant changes in apparent nucleosome size at lower [salt] and complete loss of DNA from the polynucleosomal array at high salt. The latter result demonstrates that the DNA component in these arrays is not constrained by the tethering. The former result is consistent with the salt-induced loss of histones observed in bulk solution studies of chromatin and demonstrates that even histone components of the nucleosome are somewhat labile in these fixed and tethered arrays. We foresee many important applications for this surface in future atomic force microscopy studies of chromatin.

Aluminum Silicates↗
PubMed2002

Local mechanical properties of guinea pig outer hair cells measured by atomic force microscopy.

In this study, mechanical properties of guinea pig outer hair cells (OHCs) were measured by atomic force microscopy (AFM). First, in order to confirm the availability of AFM for measurement of the mechanical properties of the OHC, Young's moduli of the OHCs measured in this study were converted into stiffnesses using a one-dimensional model of the cell and then compared with the values reported in the literature. Next, the difference in local mechanical properties of the OHC along the cell axis was measured. Finally, the relationship between Young's modulus in the middle region of the OHC and the cell length was evaluated. The results were as follows. (1) AFM is an adequate tool for the measurement of mechanical properties of the OHC. (2) Mechanical properties in the apical region of the OHC are a maximum of three times larger than those in the basal and middle regions of the cell. (3) Young's modulus in the middle region of a long OHC obtained from the apical turn of the cochlea and that of a short OHC obtained from the basal turn or the second turn are 2.0+/-0.81 kPa (n=10) and 3.7+/-0.96 kPa (n=10), respectively. In addition, it was found that Young's modulus decreases with an increase in the cell length.

Animals↗
PubMed2002

In situ atomic force microscopy of partially demineralized human dentin collagen fibrils.

Dentin collagen fibrils were studied in situ by atomic force microscopy (AFM). New data on size distribution and the axial repeat distance of hydrated and dehydrated collagen type I fibrils are presented. Polished dentin disks from third molars were partially demineralized with citric acid, leaving proteins and the collagen matrix. At this stage collagen fibrils were not resolved by AFM, but after exposure to NaOCl(aq) for 100-240 s, and presumably due to the removal of noncollagenous proteins, individual collagen fibrils and the fibril network of dentin connected to the mineralized substrate were revealed. High-aspect-ratio silicon tips in tapping mode were used to image the soft fibril network. Hydrated fibrils showed three distinct groups of diameters: 100, 91, and 83 nm and a narrow distribution of the axial repeat distance at 67 nm. Dehydration resulted in a broad distribution of the fibril diameters between 75 and 105 nm and a division of the axial repeat distance into three groups at 67, 62, and 57 nm. Subfibrillar features (4 nm) were observed on hydrated and dehydrated fibrils. The gap depth between the thick and thin repeating segments of the fibrils varied from 3 to 7 nm. Phase mode revealed mineral particles on the transition from the gap to the overlap zone of the fibrils. This method appears to be a powerful tool for the analysis of fibrillar collagen structures in calcified tissues and may aid in understanding the differences in collagen affected by chemical treatments or by diseases.

Adult↗
PubMed1999

Transverse elasticity of myofibrils of rabbit skeletal muscle studied by atomic force microscopy.

Surface structure of myofibrils of rabbit skeletal muscle and their transverse elasticity were studied by atomic force microscopy. Images of myofibrils had a periodic structure characteristic of sarcomeres of skeletal muscle fibers. The transverse elasticity distribution in the sarcomere was determined based on force-distance curves measured at various loci of single myofibrils. The Z-line in rigor myofibrils was the most rigid in all the loci of myofibrils studied under various physiological conditions. The overall transverse elasticity of myofibrils decreased in the order in rigor solution > +AMPPNP solution > relaxing solution. The "apparent" transverse Young's modulus of myofibrils estimated at the overlap region between thin and thick filaments was 84.0 +/- 18.1, 37.5 +/- 14.0, and 11.5 +/- 3.5 kPa in rigor, +AMPPNP, and relaxing solution respectively.

Adenylyl Imidodiphosphate↗