Electron microscopy and atomic force microscopy studies of chromatin and metaphase chromosome structure

The folding of the chromatin filament and, in particular, the organization of genomic DNA within metaphase chromosomes has attracted the interest of many laboratories during the last five decades. This review discusses our current understanding of chromatin higher-order structure based on results obtained with transmission electron microscopy (TEM), cryo-electron microscopy (cryo-EM), and different atomic force microscopy (AFM) techniques.Chromatin isolated from different cell types in buffers without cations form extended filaments with nucleosomes visible as separated units. In presence of low concentrations of Mg²⁺, chromatin filaments are folded into fibers having a diameter of ∼30 nm. Highly compact fibers were obtained with isolated chromatin fragments in solutions containing 1–2 mM Mg²⁺. The high density of these fibers suggested that the successive turns of the chromatin filament are interdigitated. Similar results were obtained with reconstituted nucleosome arrays under the same ionic conditions. This led to the proposal of compact interdigitated solenoid models having a helical pitch of 4–5 nm. These findings, together with the observation of columns of stacked nucleosomes in different liquid crystal phases formed by aggregation of nucleosome core particles at high concentration, and different experimental evidences obtained using other approaches, indicate that face-to-face interactions between nucleosomes are very important for the formation of dense chromatin structures.Chromatin fibers were observed in metaphase chromosome preparations in deionized water and in buffers containing EDTA, but chromosomes in presence of the Mg²⁺ concentrations found in metaphase (5–22 mM) are very compact, without visible fibers. Moreover, a recent cryo-electron microscopy analysis of vitreous sections of mitotic cells indicated that chromatin has a disordered organization, which does not support the existence of 30-nm fibers in condensed chromosomes. TEM images of partially denatured chromosomes obtained using different procedures that maintain the ionic conditions of metaphase showed that bulk chromatin in chromosomes is organized forming multilayered plate-like structures. The structure and mechanical properties of these plates were studied using cryo-EM, electron tomography, AFM imaging in aqueous media, and AFM-based nanotribology and force spectroscopy. The results obtained indicated that the chromatin filament forms a flexible two-dimensional network, in which DNA is the main component responsible for the mechanical strength observed in friction force measurements. The discovery of this unexpected structure based on a planar geometry has opened completely new possibilities for the understanding of chromatin folding in metaphase chromosomes. It was proposed that chromatids are formed by many stacked thin chromatin plates oriented perpendicular to the chromatid axis. Different experimental evidences indicated that nucleosomes in the plates are irregularly oriented, and that the successive layers are interdigitated (the apparent layer thickness is 5–6 nm), allowing face-to-face interactions between nucleosomes of adjacent layers. The high density of this structure is in agreement with the high concentration of DNA observed in metaphase chromosomes of different species, and the irregular orientation of nucleosomes within the plates make these results compatible with those obtained with mitotic cell cryo-sections. The multilaminar chromatin structure proposed for chromosomes allows an easy explanation of chromosome banding and of the band splitting observed in stretched chromosomes.     

Electron microscopy of phase transitions

The possibilities of electron microscopy for the study of phase transitions are briefly outlined and illustrated by some particular aspects of phase transitions in Pb₃V₂O₈, Ba₂NaNb₅O₁₅ and Au3+xZn. Lead orthovanadate is used as an example for the application of a procedure to distinguish between the static or dynamic nature of diffuse intensity in diffraction patterns occurring near the transition temperature. For Ba₂NaNb₅O₁₅ the behaviour of the discommensurations in the vicinity of the ferroelastic transition has been studied and the low-temperature transition around 105 K is proven to be due to a doubling of the baxis and not to a restoration of the fourfold symmetry. The decomposition mechanism of the metastable <2³3> type long period super-lattices in the binary Au_3+xZn alloys is described in terms of the withdrawal of nodes of four <3> domains.     

Electron transport through asymmetric DNA molecules

We investigate quantum mechanical electron transport along the long axis of the DNA molecule using an effective tight-binding model. The overall contour plot of transmission, the current-voltage characteristics, and the differential conductance are examined for the variation of backbone onsite energy, the energy-dependent hopping strength, and the contact coupling between the leads and the DNA molecule. It is shown that as backbone asymmetry increases, the merging and collapse of the two mini-bands take place and an extra resonance peak in the transmission appears. In addition, we present the modulation of voltage threshold in the current-voltage curves and a double-peak structure in the differential conductance due to the disappearance of the merged mini-band. Finally, in the Coulomb blockade regime of asymmetric contact coupling, a distinct and under-unity resonance in the transmission appears due to the interference effects between the DNA molecular bands and the electronic structure of the leads at the DNA-lead interface.     

Electron microscopy study of aggregation of microclusters of sulphur

A study of aggregation of sulphur particles in colloidal suspension of sulphur in water-methanol mixture using TEM and electron diffraction is reported. From the micrographs the aggregates formed have been found to be random and tenuous indicating a fractal structure. The electron diffraction patterns of the aggregates are used to study the mechanism of diffusion and reaction limited aggregation.     

Electron optics for high throughput low energy electron microscopy

Novel electron-optical components and concepts aiming at improving the throughput and extending the applications of a low energy electron microscope (LEEM) have been developed. An immersion magnetic objective lens can substantially reduce e-e interactions and the associated blur, as electrons do not form a sharp crossover in the back-focal plane. The resulting limited field of view of the immersion objective lens in mirror mode can be eliminated by immersing the cathode of the electron gun in a magnetic field. A dual illumination beam approach is used to mitigate the charging effects when the LEEM is used to image insulating surfaces. The negative charging effect, created by a partially absorbed mirror beam, is compensated by the positive charging effect of the secondary beam with an electron yield exceeding 1. On substrates illuminated with a tilted beam near glancing incidence, large shadows are formed on even the smallest topographic features, easing their detection. On magnetic substrates, the magnetic flux leaking above the surface can be detected with tilted illumination and used to image domain walls with high contrast.     

Electron microscopy observations of pretransition effects in alloys

A number of alloy systems show structural modifications upon approaching a phase transition. This can be an ordering (or disordering) effect or a deformation modulation. High-resolution electron microscopy allows one to deduce significant information on the transformation process. Examples considered are Co-Pt and Cu₃Pd for the ordering alloys and Ni—Al where ‘tweed’ shows a prefiguration of the martensite product.     

DNA adsorption and desorption on mica surface studied by atomic force microscopy

The adsorption of DNA molecules on mica surface and the following desorption of DNA molecules at ethanol-mica interface were studied using atomic force microscopy. By changing DNA concentration, different morphologies on mica surface have been observed. A very uniform and orderly monolayer of DNA molecules was constructed on the mica surface with a DNA concentration of 30 ng/μL. When the samples were immersed into ethanol for about 15 min, various desorption degree of DNA from mica (0-99%) was achieved. It was found that with the increase of DNA concentration, the desorption degree of DNA from the mica at ethanol-mica interface decreased. And when the uniform and orderly DNA monolayers were formed on the mica surface, almost no DNA molecule desorbed from the mica surface in this process. The results indicated that the uniform and orderly DNA monolayer is one of the most stable DNA structures formed on the mica surface. In addition, we have studied the structure change of DNA molecules after desorbed from the mica surface with atomic force microscopy, and found that the desorption might be ascribed to the ethanol-induced DNA condensation.     

Study on the interactions between anti-cancer drug oxaliplatin and DNA by atomic force microscopy

Oxaliplatin is one of the most important anticancer drugs at present. However, the mechanism of action of oxaliplatin is still controversial. In this study, the interactions between oxaliplatin and a plasmid DNA have been studied so as to reveal the structural basis of its activity. The structural characteristic of pUC19 DNA (2 ng/μL) incubated with 100 μmol/L and 1000 μmol/L of oxaliplatin for the different time on a freshly cleaved highly ordered pyrolytic graphite (HOPG) surface was investigated by atomic force microscopy (AFM). High resolution AFM observation indicated that oxaliplatin can induce pUC19 DNA molecules change from the extended conformation to the entangled structures with many nodes, and finally to the compact particles. The present AFM results provide structural evidence about the interactions between oxaliplatin and circular duplex DNA containing multiple targets.     

原子力显微镜扫描成像DNA分子

采用Mg2+处理DNA、APTES或戊二醛修饰云母表面、DNA拉直方法制备了λ-DNA及DNA-组蛋白复合物样品.室温下原子力显微镜以轻敲模式在空气中扫描样品成像.实验结果表明:AFM扫描成像的效果与样品的制备方法有关,同时也受操作因素影响.     

Electron microscopy studies on luteovirid transmission by aphids

Transmission electron microscopy (TEM) observations have been extensively applied to follow the route of luteovirids in their vectors. Luteovirids are icosahedral plant viruses which are phloem-limited and strictly transmitted in a circulative manner by aphids. Virus particles, acquired by aphids while feeding on an infected plant, circulate in the aphid's body without replication and are internalized during this process in two different cell types (intestinal and accessory salivary gland cells). The endocytosis mechanism at the gut level seems to rely on a clathrin-mediated entry process and virions are observed in the aphid's gut cells in various vesicular structures. After exocytosis from intestinal cells, virions are released in the aphid's body cavity where they are thought to bind to symbionin, an endosymbiotic protein. Transcytosis of the accessory salivary gland cells occurs similarly as at the gut level but in the reverse direction. Using engineered virus mutants, viral proteins required for transmission and involved in virus retention in the hemocoel have been identified. Virus mutants poorly or non aphid-transmitted have also been localized in the aphid's body by TEM. These observations reveal the crucial role of the minor capsid protein in gut internalization. While not strictly required, this protein seems to play an important role in the efficiency of this process by interacting with putative virus receptors localized on the gut apical membrane. More recently, some aphid proteins have also been shown to exhibit in vitro virus binding capacity and could potentially be components of the endocytotic apparatus.     

Observation of single- and double-stranded DNA using non-contact atomic force microscopy

Non-contact atomic force microscopy (NC-AFM) has been applied to observe single- and double-stranded DNA. For the wet processes used to prepare the sample, a strong adhesion force at the surface is observed even in vacuum conditions. Despite the presence of this adhesion force, single- and double-stranded DNA images can be obtained by NC-AFM. Because of the high sensitivity of the tip-sample interaction, NC-AFM images provide stronger contrast than tapping mode (TM)-AFM images. NC-AFM images reveal detailed structures of single- and double-stranded DNA which are not revealed by TM-AFM. In addition, several NC-AFM images show contrast artifacts, which might provide information on the detailed structure of DNA.     

The ferroelectric phase transition in tridymite type BaAL2O4 studied by electron microscopy

The paraelectric-ferroelectric (PE-FE) phase transition in stuffed tridymite BaAl₂O₄ was studied in situ by transmission electron microscopy. Electron diffraction revealed that the PE and FE phases have hexagonal symmetry. The PE-FE phase transition is accompanied by a doubling of the cell dimensions in the a-b plane. The transition is reversible, takes place over a wide temperature range (400–670 K.) and the interfaces related to the transition have a fluctuating character. The crystal structure of the high temperature PE phase was determined by high resolution electron microscopy. The structures of the PE phase (space group P6₃22, a≈ 5.22 Å, c ≈ 8.8 Å) and of the FE phase (space group P6₃, a= 10.4469(1)Å, c = 8.7927(1)Å) differ mainly by the configuration of the Al-O strings oriented along the c-axis. In the PE phase all the strings are equivalent whereas straight and corrugated strings alternate in an ordered manner in the FE phase resulting in doubling of the a and b cell parameters. Translation and orientation domains due to the decrease of the translation and point symmetry were frequently observed.     

Electron diffraction and microscopy of single-wall carbon nanotube bundles produced by different methods

The atomic structure of single-wall carbon nanotube bundles produced by three different techniques (laser ablation, electric arc discharge and catalytic chemical vapor deposition (CCVD)) has been characterized by electron diffraction and microscopy. Information on the helicity and the lattice packing has been obtained. Concerning the helicity, small bundles produced by CCVD exhibit only one or two tube helicities within a single bundle. The diffraction patterns of laser-ablation produced bundles also present well-defined but more diversified chiralities within a single bundle. By contrast the data acquired on bundles formed by arc discharge show a more diffuse pattern, characteristic of a random chirality dispersion within a single bundle. Concerning the lattice packing, informations are obtained via a detailed study of the equatorial line of the diffraction pattern for bundles produced by the three techniques. This electron diffraction study is completed by high-resolution electron microscopy. Received 8 August 2001 and Received in final form 14 March 2002     

Determination of transition curves of high-Tc superconductors by phase contrast microscopy

A new method which allows the detection of the superconducting phase transition of high-T_c superconductors (HTSC) on a microscopic scale is reported. Micro-size holes in thin foils of superconducting material are examined in a transmission electron microscope at varying temperatures. The superconducting transition induces small changes in the image intensity within the holes, which can be detected by using electronic image analysis. Superconducting transition curves are then obtained for various types of high-T_c superconductors and for given values of the applied magnetic field.     

DNA温度效应的Raman光谱研究

测定了不同温度下DNA纤维和溶液的拉曼光谱。结果表明: 当温度变化时, 碱基、磷酸根等特征振动都不同程度的受到影响, 谱线强度、频率随温度呈非线性变化。在所有的振动模式中, 腺嘌呤A的特征振动受到温度的影响最大。除了磷酸根的谱线1 101 cm-1以外, 其余谱线的波数变化均随温度的升高向低波数移动, 而且波数的移动主要集中在变性峰的起始点70 ℃左右。另外还讨论了拉曼谱线强度随温度的变化关系, 得到了38,82 ℃(纤维为85 ℃)2个峰, 其中38 ℃与DNA的功能活跃区有关, 82 ℃(和85 ℃)为DNA的变性点, 与DSC(差示扫描量热法)的测量结果一致。     

Understanding tapping-mode atomic force microscopy data on the surface of soft block copolymers

In this paper, we focus on better understanding tapping-mode atomic force microscopy (AFM) data of soft block copolymer materials with regard to: (1) phase attribution; (2) the relationship between topography and inside structure; (3) contrast-reversal artifacts; (4) the influence of annealing treatment on topography. The experiments were performed on the surface of poly(styrene–ethylene/butylene–styrene) (SEBS) triblock copolymer acting as a model system. First, by coupling AFM with transmission electron microscopy (TEM) measurements, the phase attribution for AFM images was determined. Secondly, by imaging an atomically flat SEBS surface as well as an AFM tip-scratched SEBS surface, it was confirmed that the contrast in AFM height images of soft block copolymers is not necessarily the result of surface topography but the result of lateral differences in tip-indentation depth between soft and hard microdomains. It was also found that there is an enlarging effect in AFM images on the domain size of block copolymers due to the tip-indention mechanism. Thirdly, based on the tip-indention mechanism, tentative explanations in some detail for the observed AFM artifacts (a reversal in phase image followed by another reversal in height image) as function of imaging parameters were given. Last, it was demonstrated that the commonly used annealing treatments in AFM sample preparation of block copolymers may in some cases lead to a dramatic topography change due to the unexpected order-to-order structure transition.     

Electron microscopy and EXAFS studies on oxide-supported gold-silver nanoparticles prepared by flame spray pyrolysis

Gold and gold-silver nanoparticles prepared by flame spray pyrolysis (FSP) were characterized by electron microscopy, in situ X-ray absorption spectroscopy (XANES and EXAFS), X-ray diffraction (XRD) and their catalytic activity in CO oxidation. Within this one-step flame-synthesis procedure, precursor solutions of dimethyl gold(III) acetylacetonate and silver(I) benzoate together with the corresponding precursor of the silica, iron oxide or titania support, were sprayed and combusted. In order to prepare small metal particles, a low noble metal loading was required. A loading of 0.1-1 wt.% of Au and Ag resulted in 1-6 nm particles. The size of the noble metal particles increased with higher loadings of gold and particularly silver. Both scanning transmission electron microscopy (STEM) combined with energy dispersive X-ray spectroscopy (EDXS) and X-ray absorption spectroscopy (XAS) studies proved the formation of mixed Au-Ag particles. In case of 1% Au-1% Ag/SiO₂, TEM combined with electron spectroscopic imaging (ESI) using an imaging filter could be used in addition to prove the presence of silver and gold in the same noble metal particle. CO oxidation in the presence of hydrogen was chosen as a test reaction sensitive to small gold particles. Both the influence of the particle size and the alloying of gold and silver were reflected in the CO oxidation activity.     

原子力显微镜观测生物大分子图像的一种处理方法

针对具有复杂结构的生物大分子图像,本文改进了已有的半自动化方法,设计了一种新的算法去消除背景噪声,目的在于能够从生物大分子图像高效准确地提取量化信息.通过利用这种新的处理程序对生物大分子DNA原子力显微镜图像进行了研究,不仅可以对线性构像的DNA图像进行了处理,而且对于具有分支构像复杂DNA图像也能够处理.本文所提出的数字图像处理方法具有普适性,它也可以被应用到其他成像领域. 关键词： 原子力显微镜 数字图像处理 DNA     

基于解码技术的全息显微术研究

提出了一种利用解码技术对全息显微畸变图像进行校正的方法。把全息记录中的显微镜预放大过程作为物光波产生畸变的编码过程;在波前再现过程中,用全息记录中的预放大显微镜对再现的赝实像再次放大进行解码,从而获得清晰的全息显微图像。实验验证了该方法的有效性。     

I-V curve oscillation observed by atomic force microscopy

Oscillation on the current-voltage curve measured by atomic force microscopy is observed when the distance between the tip and sample is large enough and beyond a critical value. The appearance of the oscillation is attributed to the excitation of electron standing waves between the tip and sample. From the first peak position and the voltage difference between the first two peaks on the current-voltage curve, the value of the work function at the detected point on silver film surface and the distance between the tip and the detected point can be calculated.