Measuring the viscoelastic properties of human platelets with the atomic force microscope

We have measured force curves as a function of the lateral position on top of human platelets with the atomic force microscope. These force curves show the indentation of the cell as the tip loads the sample. By analyzing these force curves we were able to determine the elastic modulus of the platelet with a lateral resolution of approximately 100 nm. The elastic moduli were in a range of 1-50 kPa measured in the frequency range of 1-50 Hz. Loading forces could be controlled with a resolution of 80 pN and indentations of the platelet could be determined with a resolution of 20 nm.     

Fabrication of a new substrate for atomic force microscopic observation of DNA molecules from an ultrasmooth sapphire plate

A new stable substrate applicable to the observation of DNA molecules by atomic force microscopy (AFM) was fabricated from a ultrasmooth sapphire (alpha-Al2O3 single crystal) plate. The atomically ultrasmooth sapphire as obtained by high-temperature annealing has hydrophobic surfaces and could not be used for the AFM observation of DNA. However, sapphire treated with Na3PO4 aqueous solution exhibited a hydrophilic character while maintaining a smooth surface structure. The surface of the wet-treated sapphire was found by x-ray photoelectron spectroscopy and AFM to be approximately 0.3 nm. The hydrophilic surface character of the ultrasmooth sapphire plate made it easy for DNA molecules to adhere to the plate. Circular molecules of the plasmid DNA could be imaged by AFM on the hydrophilic ultrasmooth sapphire plate.     

Electrostatically balanced subnanometer imaging of biological specimens by atomic force microscope

To achieve high-resolution topographs of native biological macromolecules in aqueous solution with the atomic force microscope (AFM) interactions between AFM tip and sample need to be considered. Short-range forces produce the submolecular information of high-resolution topographs. In contrast, no significant high-resolution information is provided by the long-range electrostatic double-layer force. However, this force can be adjusted by pH and electrolytes to distribute the force applied to the AFM tip over a large sample area. As demonstrated on fragile biological samples, adjustment of the electrolyte solution results in a local reduction of both vertical and lateral forces between the AFM tip and proteinous substructures. Under such electrostatically balanced conditions, the deformation of the native protein is minimized and the sample surface can be reproducibly contoured at a lateral resolution of 0.6 nm.     

贝氏体铁素体高分辨像

用TEM和HRTEM观察分析了贝氏体钢中贝氏体铁素体组织的精细结构和高分辨像。确定了多元微合金空冷贝氏体钢中贝氏体铁素体组织为细小弥散分布,且形状多样。其超亚单元尺度仅几个纳米。贝氏体铁素体条束由多个亚片条组成。HRTEM像显示最小亚片条宽度仅几个纳米,多个亚片条宽度平均值约为7.0 nm。观察结果显示,贝氏体铁素体亚片条间呈现小角度晶界排列,两亚片条间的界面并不光滑,存在台阶,其高度仅几个纳米,亚片条间界面有断续排列的原子无序区,宽度1~2 nm,长度2~3 nm。贝氏体铁素体α与残余奥氏体γ'HRTEM像显示,两者存在K-S取向关系。FFT图像变换显示出的原子图像更为清晰。α区有刃型位错存在,α/γ'界面有几个至十几个无序区原子层,尺寸为2~3 nm,在γ'区也发现有原子排列不规则区。     

Tissue localization of stable and radioactive nuclides by secondary-ion microscopy

Images of the distribution of a given nuclide in a section of biological tissue can be obtained at the microscopic level by "secondary-ion mass analysis." In this method, the images are formed by an ion-emission microscope wherein the specimen's atoms are progressively sputtered from the surface and the ions are selectively visualized by mass spectrometry according to their mass-to-charge ratios. Such images are obtained at the cost of the destruction of the specimen, which is progressively eroded at the rate of 1-10 atomic layers per second. The spatial resolution is better than 1 micrometer for an imaged area 250 micrometer in diameter and a section thickness of 1-2000 nm; thus, the analytical images are element distributions representative of 3-6000 atomic layers. Distributional images can be obtained for many nuclides, whether stable or radioactive, natural or artificially administered.     

Stabilization of biological specimens by the use of plasma polymerized hydrocarbon film for imaging with an atomic force microscope

An atomic force microscope makes imaging of biological molecules possible at high resolution. To this end all samples have to be fixed securely to a flat solid support so that they cannot be displaced by the scanning tip. We herein describe a new method to fix the biological samples to glass surfaces by depositing a thin layer of plasma polymerized methane gas in a high vacuum chamber. Such samples can thus be imaged repeatedly by an atomic force microscope without any loss of image quality.     

The Zalpha domain from human ADAR1 binds to the Z-DNA conformer of many different sequences

Z-DNA, the left-handed conformer of DNA, is stabilized by the negative supercoiling generated during the movement of an RNA polymerase through a gene. Recently, we have shown that the editing enzyme ADAR1 (double-stranded RNA adenosine deaminase, type 1) has two Z-DNA binding motifs, Zalpha and Zbeta, the function of which is currently unknown. Here we show that a peptide containing the Zalpha motif binds with high affinity to Z-DNA as a dimer, that the binding site is no larger than 6 bp and that the Zalpha domain can flip a range of sequences, including d(TA)3, into the Z-DNAconformation. Evidence is also presented to show that Zalpha and Zbeta interact to form a functional DNA binding site. Studies with atomic force microscopy reveal that binding of Zalpha to supercoiled plasmids is associated with relaxation of the plasmid. Pronounced kinking of DNA is observed, and appears to be induced by binding of Zalpha. The results reported here support a model where the Z-DNA binding motifs target ADAR1 to regions of negative supercoiling in actively transcribing genes. In this situation, binding by Zalpha would be dependent upon the local level of negative superhelicity rather than the presence of any particular sequence.     

The chromatin structure of well-spread demembranated human sperm nuclei revealed by atomic force microscopy

The fundamental structure formed when genomic DNA is packaged by protamine in the human sperm nucleus still remains essentially unresolved. It is known that the binding of protamine, a small arginine-rich protein, to DNA generates a large dense, hydrophobic complex making the sperm chromatin structure difficult to study microscopically. To visualize the internal nuclear structures, isolated human sperm nuclei were swollen extensively in saline buffer using only a reducing agent. The nuclei were swollen during deposition onto coverglass and then imaged in the atomic force microscope (AFM). The two main results obtained from imaging individual well-spread nuclei indicate that native human sperm chromatin is: (1) particulate, consisting primarily of large nodular structures averaging 98 nm in diameter, and (2) also composed of smaller, nucleosome-like particles observed to form linear chains near the nuclear periphery. These two types of chromatin particles imaged by AFM are remarkably similar to other AFM measurements made on native and reconstituted sperm and somatic chromatin.     

Effects of gravity on the electrodeposition and characterization of nickel foils

The effects of gravity on nickel electrodeposifion,the morphology and mechanical properties of deposits were studied in a super gravity field.Predictions in a microgravity field were also presented based on the obtained experimental tendency.Linear sweep voltamrnetry reveals that the nickel electrodeposition process is enhanced by increasing the gravity coefficient (G).The limiting current density changes from 10.2 to 293.0 mA.cm-2 with the increase of the G value from 10-4 to 354.The morphology of deposits was analyzed by scanning electron microscopy (SEM)and atomic force microscopy (AFM).The images show that the morphology deposited in the super gravity field has freer grain sizes and denser and smoother surfaces,The roughness reduces from 48.3 to 4.9 nm with the increase of the G value from 10-4 to 354.Meanwhile,mechanical tests indicate that the mechanical properties of nickel foils are greatly improved due to introducing a super gravity field during electrodeposition.     

Template-directed photoligation of oligodeoxyribonucleotides via 4-thiothymidine

Non-enzymatic, template-directed ligation of oligonucleotides in aqueous solution has been of great interest because of its potential synthetic and biomedical utility and implications for the origin of life. Though there are many methods for template-directed chemical ligation of oligonucleotides, there are only three reported photochemical methods. In the first report, template-directed photoligation was effected by cyclobutane dimer formation between the 5'- and 3'-terminal thymidines of two oligonucleotides with >290 nm light, which also damages DNA itself. To make the photochemistry of native DNA more selective, we have replaced the thymidine at the 5'-end of one oligonucleotide with 4-thiothymidine (s4T) and show that it photoreacts at 366 nm with a T at the 3'-endof another oligonucleotide in the presence of a complementary template. When a single mismatch is introduced opposite either the s4T or its adjoining T, the ligation efficiency drops by a factor of five or more. We also show that by linking the two ends of the oligonucleotides together, photoligation can be used to form circular DNA molecules and to 'photopadlock' circular DNA templates. Thus, s4T-mediated photo-ligation may have applications to phototriggered antisense-based or antigene-based genetic tools, diagnostic agents and drugs, especially for those situations in which chemical or enzyme-mediated ligation isundesirable or impossible, for example inside a cell.     

Atomic force microscopy study of fine structures of the entire surface of red blood cells

Glutaraldehyde-fixed red blood cells were imaged by tapping mode atomic force microscopy (TMAFM) in air at room temperature. The results show that TMAFM can visualize the morphology of the red blood cell at both cellular and nanometer scales. The scan size covers the range from several hundred nanometers to more than one hundred micrometers. TMAFM not only has a higher resolution than the optical microscope, but also can observe biological samples without precoating as required for scanning electron microscopy (SEM). The AFM images of the entire surface of an uncoated red blood cell with nanometer resolution are successfully reconstructed by 28 AFM images of the preselected subareas on the surface of the red blood cell. These images reveal directly the fine structures of the external surface of uncoated red blood cells in air. The surface exhibits a characteristic structure composed of a large number of closely-packed nanometer particles with a size ranging from a few nanometers to tens of nanometers. These "particulate" components are evenly distributed, and no jumping protrusion or depression structures were found. These particles give rise to a very smooth surface of the red blood cell as shown in a large-scan AFM image. In addition, the 28 AFM images obtained by the continuous scanning over 3 hours indicate that TMAFM can image soft biological samples such as red blood cells stably and reproducibly.     

Hydration force in the atomic force microscope: A computational study

Using a hard sphere model and numerical calculations, the effect of the hydration force between a conical tip and a flat surface in the atomic force microscope (AFM) is examined. The numerical results show that the hydration force remains oscillatory, even down to a tip apex of a single water molecule, but its lateral extent is limited to a size of a few water molecules. In general, the contribution of the hydration force is relatively small, but, given the small imaging force ( approximately 0.1 nN) typically used for biological specimens, a layer of water molecules is likely to remain "bound" to the specimen surface. This water layer, between the tip and specimen, could act as a "lubricant" to reduce lateral force, and thus could be one of the reasons for the remarkably high resolution achieved with contact-mode AFM. To disrupt this layer, and to have a true tip-sample contact, a probe force of several nanonewtons would be required. The numerical results also show that the ultimate apex of the tip will determine the magnitude of the hydration force, but that the averaged hydration pressure is independent of the radius of curvature. This latter conclusion suggests that there should be no penalty for the use of sharper tips if hydration force is the dominant interaction between the tip and the specimen, which might be realizable under certain conditions. Furthermore, the calculated hydration energy near the specimen surface compares well with experimentally determined values with an atomic force microscope, providing further support to the validity of these calculations.     

Atomic force microscopy detects changes in the interaction forces between GroEL and substrate proteins

The structure of the Escherichia coli chaperonin GroEL has been investigated by tapping-mode atomic force microscopy (AFM) under liquid. High-resolution images can be obtained, which show the up-right position of GroEL adsorbed on mica with the substrate-binding site on top. Because of this orientation, the interaction between GroEL and two substrate proteins, citrate synthase from Saccharomyces cerevisiae with a destabilizing Gly-->Ala mutation and RTEM beta-lactamase from Escherichia coli with two Cys-->Ala mutations, could be studied by force spectroscopy under different conditions. The results show that the interaction force decreases in the presence of ATP (but not of ATPgammaS) and that the force is smaller for native-like proteins than for the fully denatured ones. It also demonstrates that the interaction energy with GroEL increases with increasing molecular weight. By measuring the interaction force changes between the chaperonin and the two different substrate proteins, we could specifically detect GroEL conformational changes upon nucleotide binding.     

Cryo X-ray microscopy with high spatial resolution in amplitude and phase contrast

The resolution of transmission X-ray microscopes (TXMs) using zone plate optics is presently about 30 nm. Theory and experiments presented here show that this resolution can be obtained in radiation sensitive hydrated biological material by using shock frozen samples. For this purpose the interaction of X-rays with matter and the image formation with zone plates is described. For the first time the influence of the limited apertures of the condenser and the zone plate objective are in included in calculations of the image contrast, the photon density and radiation dose required for the object illumination. Model considerations show that lowest radiation dose and high image contrast are obtained in optimized phase contrast which exploits absorption as well as phase shift. The damaging effect of the absorbed X-rays is quantitatively evaluated by radiation-induced kinetics showing that cryogenic samples are structurally stable. To verify these theoretical models the TXM was modified to allow imaging of frozen-hydrated samples at atmospheric pressure. Details inside cells and algae as small as 35 nm are visible at 2.4 nm wavelength in amplitude contrast mode. At this resolution the cryogenic samples show no structural changes. As predicted, optimized phase contrast shows structures inside the frozen-hydrated objects with high contrast. Stereo-pair images of algae reveal the 3D organization of the organelles. Element analysis and micro-tomography of whole cryogenic cells are possible.     

Atomic force microscopy in histology and cytology

This review briefly introduces the principles of the atomic force microscope (AFM) and shows our own results of AFM application to biological samples. The AFM, invented in 1986, is an instrument that traces the surface topography of the sample with a sharp probe while monitoring the interaction forces working between the probe and sample surface. Thus, the AFM provides three-dimensional surface images of the sample with high resolution. The advantage of the AFM for biologists is that AFM can visualize non-conductive materials in a non-vacuous (i.e., air or liquid) environment. AFM images of the plasmid DNA are comparable to those by transmission electron microscopy using a rotary shadowing technique, and have the advantage of examining directly the molecule without staining nor coating. The surface structure of human metaphase chromosomes and mouse collagen fibrils demonstrated in air by the non-contact mode AFM is comparable to that obtained by scanning electron microscopy. Quantitative information on the heights of structures is further obtainable from the AFM images. Embedment-free thin tissue-sections are useful for observing intracellular structures by AFM. The present review also shows AFM images of living cultured cells which have been collected in a contact mode in liquid. This technique afforded us three-dimensional observation of the cellular movement with high resolution. Although there are some innate limitations for AFM imaging, the AFM has great potential for providing valuable new information in histology and cytology.     

Viscoelasticity of living cells allows high resolution imaging by tapping mode atomic force microscopy

Application of atomic force microscopy (AFM) to biological objects and processes under physiological conditions has been hampered so far by the deformation and destruction of the soft biological materials invoked. Here we describe a new mode of operation in which the standard V-shaped silicon nitride cantilever is oscillated under liquid and damped by the interaction between AFM tip and sample surface. Because of the viscoelastic behavior of the cellular surface, cells effectively "harden" under such a tapping motion at high frequencies and become less susceptible to deformation. Images obtained in this way primarily reveal the surface structure of the cell. It is now possible to study physiological processes, such as cell growth, with a minimal level of perturbation and high spatial resolution (approximately 20 nm).     

Can energy transfer be an indicator for DNA intercalation?

Contact energy transfer from DNA bases to various ligands, which can be represented by the ratio of the fluorescence intensity Q(lambda)/Q310nm, is measured by conventional fluorometer. 4',6-Diamidino-2-phenylindole and 2'-(4-hydroxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5'-bi-1H-benzimidazole can accept energy from DNA bases and exhibit the ratio Q(lambda)/Q310nm, similar to that of intercalators, although these molecules are known to bind preferentially to the minor groove of the adenine-thymine rich region of DNA. When porphyrin is intercalated in DNA or poly[d(G-C)2], the shape of the ratio Q(lambda)/Q310nm is distinct from that of the ethidium-DNA complex with two maxima at 250 nm and 280 nm. The ratio Q(lambda)/Q310nm of the porphyrin-poly[d(A-T)2] complex, in which porphyrin is known to bind 'outside' of the DNA stem, is similar to that of intercalators. Therefore, energy from excited DNA bases can be transferred not only to an intercalated ligand through direct contact but also to that bound in the minor groove. It follows from this observation that using energy transfer as a criterion for DNA intercalation requires extreme caution.     

Atomic force microscopy investigation of radiation-induced DNA double strand breaks

We have used atomic force microscopy (AFM) to study radiation-induced DNA double strand breaks. Double-stranded plasmid DNA was irradiated with 18-MeV electrons in aqueous buffer, using a medical linear accelerator. Doses of 50, 100, 150, and 200 Gy were delivered to DNA samples, and atomic force microscopy was used to measure the length of each DNA fragment. From these measurements, we obtained the average length of the irradiated DNA for each sample and found a linear-quadratic relationship between the average length and radiation dose.     

Near-field optical and shear-force microscopy of single fluorophores and DNA molecules

Photodynamics of individual fluorescence molecules has been studied using an aperture-type near-field scanning optical microscope with two channel fluorescence polarisation detection and tuning fork shear-force feedback. The position of maximum fluorescence from individual molecules could be localised with an accuracy of 1 nm. Dynamic processes such as translational and rotational diffusion were observed for molecules adsorbed to a glass surface or embedded in a polymer host. The in-plane molecular dipole orientation could be determined by monitoring the relative contribution of the fluorescence signal in the two perpendicular polarised directions. Rotational dynamics was investigated on 10 ms-1000 s timescale. Shear-force phase feedback was used to obtain topographic imaging of DNA fragments, with a lateral and vertical resolution comparable to scanning force microscopy. A DNA height of 1.4 nm has been measured, an indication of the non-disturbing character of the shear force mechanism.     

Crystals of a 1:1 complex between human interleukin-4 and the extracellular domain of its receptor alpha chain

The specific high-affinity binding of interleukin-4 (IL-4) to its receptor alpha chain is the crucial primary event during IL-4 signalling. Single crystals, suitable for high resolution diffraction studies, have been obtained from a complex between IL-4 and the ectodomain of the receptor alpha chain, also called IL-4-binding protein (IL-4BP). The orthorhombic crystals are in spacegroup P2(1)2(1)2(1) with cell constants a = 5.038 nm, b = 6.841 nm, c = 10.95 nm and diffract to a resolution of at least 0.25 nm when exposed to synchrotron radiation. The volume of the unit cell suggests the presence of a 1:1 IL-4/IL-4BP complex and HPLC analysis of the crystals confirmed that IL-4 and IL-4BP were present in equimolar amounts. An IL-4 variant comprising a total of four methionine residues was generated, labelled with selenomethionine and crystallised in complex with IL-4BP. The crystals are isomorphous to that of the complex with normal IL-4 and therefore can be used to solve the crystallographic phase problem by the method of multiple anomalous diffraction (MAD). The crystal structure of the IL-4/IL-4BP complex will help to understand how IL-4 and other helical cytokines bind and activate their cognate receptor.