Direct measurement of hydrogen bonding in DNA nucleotide bases by atomic force microscopy

We have used self-assembled purines and pyrimidines on planar gold surfaces and on gold-coated atomic force microscope (AFM) tips to directly probe intermolecular hydrogen bonds. Electron spectroscopy for chemical analysis (ESCA) and thermal programmed desorption (TPD) measurements of the molecular layers suggested monolayer coverage and a desorption energy of about 25 kcal/mol. Experiments were performed under water, with all four DNA bases immobilized on AFM tips and flat surfaces. Directional hydrogen-bonding interaction between the tip molecules and the surface molecules could be measured only when opposite base-pair coatings were used. The directional interactions were inhibited by excess nucleotide base in solution. Nondirectional van der Waals forces were present in all other cases. Forces as low as two interacting base pairs have been measured. With coated AFM tips, surface chemistry-sensitive recognition atomic force microscopy can be performed.     

Efficacy of novel antimicrobials against clinical isolates of opportunistic amebas

Using atomic force microscopy (AFM), we have investigated neutron-induced DNA double-strand breaks in plasmids in aqueous solution. AFM permits direct measurement of individual DNA molecules with an accuracy of a few nanometers. Furthermore, the analysis of the DNA fragment size distribution is non-parametric, whereas other methods are dependent on the model. Neutron irradiation of DNA results in the generation of many short fragments, an observation not made for damage induced by low-LET radiation. These data provide clear experimental evidence for the existence of clustered DNA double-strand breaks and demonstrate that short DNA fragments may be produced by such radiations in the absence of a nucleosomal DNA structure.     

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.     

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.     

A convenient method of aligning large DNA molecules on bare mica surfaces for atomic force microscopy

Large DNA molecules remain difficult to be imaged by atomic force microscopy (AFM) because of the tendency of aggregation. A method is described to align long DNA fibers in a single direction on unmodified mica to facilitate AFM studies. The clear background, minimal overstretching, high reproducibility and convenience of this aligning procedure make it useful for physical mapping of genome regions and the studies of DNA-protein complexes.     

Processing Ti-25Ta-5Zr Bioalloy via Anodic Oxidation Procedure at High Voltage

The current paper reports the processing of Ti-25Ta-5Zr bioalloy via anodic oxidation in NH4BF4 solution under constant potentiostatic conditions at high voltage to obtain more suitable properties for biomedical application. The maximum efficiency of the procedure is reached at highest applied voltage, when the corrosion rate in Hank’s solution is decreased approxomately six times. The topography of the anodic layer has been studied using atomic force microscopy (AFM), and the results indicated that the anodic oxidation process increases the surface roughness. The AFM images indicated a different porosity for the anodized surfaces as well. After anodizing, the hydrophilic character of Ti-25Ta-5Zr samples has increased. A good correlation between corrosion rate obtained from potentiodynamic curves and corrosion rate from ions release analysis was obtained.     

Biological water and its role in the effects of alcohol

Alcohol and water compete with each other on target membrane molecules, specifically, lipids and proteins near the membrane surface. The basis for this competition is the hydrogen bonding capability of both compounds. But alcohol's amphiphilic properties give it the capability to be attracted simultaneously to both hydrophobic and hydrophilic targets. Thus, alcohol could bind certain targets preferentially and displace water, leading to conformational consequences. This article reviews the clustering and organized character of biological water, which modulates the conformation of membrane surface molecules, particularly receptor protein. Any alcohol-induced displacement of biological water on or inside of membrane proteins creates the opportunity for allosteric change in membrane receptors. This interaction may also prevail in organelles, such as the Golgi apparatus, which have relatively low concentrations of bulk water. Target molecules of particular interest in neuronal membrane are zwitteronic phospholipids, gangliosides, and membrane proteins, including glycoproteins. FTIR and NMR spectroscopic evidence from model membrane systems shows that alcohol has a nonstereospecific binding capability for membrane surface molecules and that such binding occurs at sites that are otherwise occupied by hydrogen-bonded water. The significance of these effects seems to lie in the need to learn more about biological water as an active participant in biochemical actions. Proposed herein is a new working hypothesis that the molecular targets of ethanol action most deserving of study are those where water is trapped and there is little bulk water. Proteins (enzymes and receptors) certainly differ in this regard, as do organelles.     

The atomic force microscope detects ATP-sensitive protein clusters in the plasma membrane of transformed MDCK cells

Plasma membrane proteins are supposed to form clusters that allow 'functional cross-talk' between individual molecules within nanometre distance. However, such hypothetical protein clusters have not yet been shown directly in native plasma membranes. Therefore, we developed a technique to get access to the inner face of the plasma membrane of cultured transformed kidney (MDCK) cells. The authors applied atomic force microscopy (AFM) to visualize clusters of native proteins protruding from the cytoplasmic membrane surface. We used the K+ channel blocker iberiotoxin (IBTX), a positively charged toxin molecule, that binds with high affinity to plasma membrane potassium channels and to atomically flat mica. Thus, apical plasma membranes could be 'glued' with IBTX to the mica surface with the cytosolic side of the membrane accessible to the scanning AFM tip. The topography of these native inside-out membrane patches was imaged with AFM in electrolyte solution mimicking the cytosol. The plasma membrane could be clearly identified as a lipid bilayer with the characteristic height of 4.9 +/- 0.02 nm. Multiple proteins protruded from the lipid bilayer into the cytosolic space with molecule heights between 1 and 20 nm. Large protrusions were most likely protein clusters. Addition of the proteolytic enzyme pronase to the bath solution led to the disappearance of the proteins within minutes. The metabolic substrate ATP induced a shape-change of the protein clusters and smaller subunits became visible. ADP or the non-hydrolysable ATP analogue, ATP-gamma-S, could not exert similar effects. It is concluded that plasma membrane proteins (and/or membrane associated proteins) form 'functional clusters' in their native environment. The 'physiological' arrangement of the protein molecules within a cluster requires ATP.     

The observation of the local ordering characteristics of spermidine-condensed DNA: atomic force microscopy and polarizing microscopy studies

Condensation of DNA by multivalent cations can provide useful insights into the physical factors governing the folding and packaging of DNA in vivo. In this work, local ordered structures of spermidine-DNA complexes prepared from different DNA concentrations have been examined by using atomic force microscopy (AFM) and polarizing microscopy (PM). Two types (I and II) of DNA condensates, significantly different in sizes, were observed. It was found that for extremely dilute solutions (DNA concentrations around 1 ng/microl or below), the DNA molecules would collapse into toroidal structures with a volume equivalent to a single lambda-DNA (type I). In relatively dilute solutions (DNA concentrations between 1 and 10 ng/microll), a significantly larger structure of multimolecular toroids (circular and elliptical, type II) were formed, which were constructed by many fine particles. Measurements show that the average diameter of these fine particles was similar to the outer diameter of the monomolecular toroids observed in extremely dilute solutions, and the thickness of the multimolecular toroids had a distribution of multi-layers with height increments of 11 nm, indicating that the multimolecular toroidal structures have lamellar characteristics. Moreover, by enriching the DNA-spermidine complexes in very diluted solution, branch-like structures constructed by subunits were observed by using AFM. The analysis of the pellets in polarizing microscopy reveals a liquid-crystal-like pattern. These observations suggest that DNA-spermidine condensation could have multiple stages, which are very sensitive to the DNA and spermidine concentrations.     

Structural activity of a cloned potassium channel (ROMK1) monitored with the atomic force microscope: the "molecular-sandwich" technique

The atomic force microscope (AFM) was used to continuously follow height changes of individual protein molecules exposed to physiological stimuli. A AFM tip was coated with ROMK1 (a cloned renal epithelial potassium channel known to be highly pH sensitive) and lowered onto atomically flat mica surface until the protein was sandwiched between AFM tip and mica. Because the AFM tip was an integral part of a highly flexible cantilever, any structural alterations of the sandwiched molecule were transmitted to the cantilever. This resulted in a distortion of the cantilever that was monitored by means of a laser beam. With this system it was possible to resolve vertical height changes in the ROMK1 protein of >/=0.2 nm (approximately 5% of the molecule's height) with a time resolution of >/=1 msec. When bathed in electrolyte solution that contained the catalytic subunit of protein kinase A and 0.1 mM ATP (conditions that activate the native ion channel), we found stochastically occurring height fluctuations in the ROMK1 molecule. These changes in height were pH-dependent, being greatest at pH 7.6, and lowering the pH (either by titration or by the application of CO2) reduced their magnitude. The data show that overall changes in shape of proteins occur stochastically and increase in size and frequency when the proteins are active. This AFM "molecular-sandwich" technique, called MOST, measures structural activity of proteins in real time and could prove useful for studies on the relationship between structure and function of proteins at the molecular level.     

The use of atomic-force microscopy for the analysis of microbiological objects

Atomic force microscopy (AFM) was used for the analysis of rickettsiae and viruses. The specificity of interaction was evaluated on the basis of the adsorption of the analyzed antigen on the polymer-antibody film. The film was formed and transferred onto highly oriented pyrolytic graphite (HOPG) by the method of Langmuir-Schaefer with the use of amphiphilic polymers, alkylated polyethyleneimines. According to the data of AFM, polymer-antibody film was 10-30 nm thick and had ruptures, uneven surface. AFM images of Coxiella burnetii, rotavirus and Venezuelan equine encephalitis virus, immunoadsorbed on the antibody film, were obtained. C.burnetii, due to their size equal to (700-900) x (300-500) x Z = 200 nm, were clearly visible on the underlying surface and could be directly counted. Individual virus particles (60-80 nm) cold not be identified on such surface. To analyze such preparations, the program of image analysis was developed. The program classified the registered image with a certain standard. This program determined the presence of virus antigen on the underlying affinity surface with a high degree of precision.     

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.     

二苯卡巴肼光度法测定镀铬板表面铬氧化物含量

测定镀铬板表面镀层中铬氧化物及金属铬意义重大,但以往测定的大都是镀铬板表面铬氧化物量(以铬计,下同)和金属铬量的总和。实验在A657/A657M-03标准附录中测定镀铬板表面铬氧化物方法的基础上,通过采用辉光光谱法对氢氧化钠溶液浸泡镀铬板前后的表面进行对比分析,证实了氢氧化钠溶液仅对镀铬板表面的铬氧化物有溶解作用,而不能溶解金属铬,同时优化了铬氧化物的溶解条件和光度法测定条件。实验表明:将镀铬板浸泡到300 g/L 90 ℃的NaOH溶液中20 min可将镀铬板表面铬氧化物溶解完全;在样品溶液中加入H₂SO₄(1+1)中和至pH为7,再加入5.0 mL硫磷混酸(3+3+4)、2.0 mL AgNO₃溶液以及5.0 mL(NH₄)₂S₂O₈溶液,加热至沸腾并保持约10 min以破坏过氧化物,冷却至室温后加入3.0 mL二苯卡巴肼溶液并稀释至100 mL,在542 nm处于2 cm比色皿中测定,Cr质量在0.24～100 μg之间有较好的线性关系,其线性方程为A=0.002 1+0.013 m_Cr(μg),相关系数为0.999 7。方法检出限为0.24 μg,测定下限为1.2 μg。将最终所测得镀铬板表面铬氧化物的量除以镀铬板试样面积,最终可计算出单位面积内镀铬板表面铬氧化物的含量。采用实验方法对两类镀铬板表面铬氧化物进行测定,所得平均含量分别为12.8 mg/m²和11.1 mg/m²,其相对标准偏差分别为3.1%(n=5)和3.6%(n=5)。对镀铬板试样进行加标回收,测得铬氧化物的加标回收率在92%～101%之间。     

Characterization of Tn917 insertion mutants of Staphylococcus epidermidis affected in biofilm formation

Biofilm formation is thought to result from the concerted action of primary attachment to a specific surface and accumulation in multilayered cell clusters. Here we describe the isolation and characterization of transposon (Tn917) mutants of Staphylococcus epidermidis O-47 which were biofilm negative in the polystyrene microtiter plate assay. Among 5,000 Tn917 insertion mutants, 4 biofilm-negative mutants were isolated. Each mutant carried one copy of Tn917. The mutants were divided into two phenotypic classes: class A (mut1 and mut1a) and class B (mut2 and mut2a). Mutants of phenotypic class A lacked four cell surface proteins, were less hydrophobic, and were affected in primary attachment to polystyrene, but were still able to form multilayered cell clusters. They were able to form a biofilm on a glass surface, a trait that was even more pronounced than in the wild-type stain O-47. Loss of several surface proteins might have led to the reduced surface hydrophilic structures, thus favoring primary attachment to a glass surface and leading to subsequent biofilm formation. Mutants of phenotype class B were able to attach to polystyrene but were unable to form multilayered cell clusters, had unchanged cell surface proteins and hydrophobicity, and were unable to form a biofilm on a glass surface, mut1 and mut2 could be complemented by wild-type DNA fragments containing the Tn917 insertion sites of mut1 and mut2, respectively. The complemented biofilm-positive clone mut1 (pRC20) produced a 60-kDa protein which is postulated to function as the adhesin for binding to plastic. The traits of binding to polystyrene and the ability to form multilayered cell clusters are phenotypically and genetically distinct.     

A simplified PCR-based method for the detection of Renibacterium salmoninarum utilizing preparations of rainbow trout (Oncorhynchus mykiss, Walbaum) lymphocytes

A method for the detection of Renibacterium salmoninarum by PCR is described. A rapid, reliable procedure was developed for the extraction of DNA, which could be applied to infected kidney homogenates and head kidney lymphocyte preparations. The target for DNA amplification was a 376-bp region of the gene encoding the 57-kDa major surface antigen (MSA). The PCR was specific for R. salmoninarum and allowed the detection of 10 to 100 cells of the pathogen. Use of the PCR for the examination of experimentally infected rainbow trout showed it to be as reliable as plate culture methods for the detection of R. salmoninarum in infected kidneys.     

Behavior of supercoiled DNA

We study DNA supercoiling in a quantitative fashion by micromanipulating single linear DNA molecules with a magnetic field gradient. By anchoring one end of the DNA to multiple sites on a magnetic bead and the other end to multiple sites on a glass surface, we were able to exert torsional control on the DNA. A rotating magnetic field was used to induce rotation of the magnetic bead, and reversibly over- and underwind the molecule. The magnetic field was also used to increase or decrease the stretching force exerted by the magnetic bead on the DNA. The molecule's degree of supercoiling could therefore be quantitatively controlled and monitored, and tethered-particle motion analysis allowed us to measure the stretching force acting on the DNA. Experimental results indicate that this is a very powerful technique for measuring forces at the picoscale. We studied the effect of stretching forces ranging from 0.01 pN to 100 pN on supercoiled DNA (-0.1 < sigma < 0.2) in a variety of ionic conditions. Other effects, such as stretching-relaxing hysteresis and the braiding of two DNA molecules, are discussed.     

Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator

The structure and hydration of the DNA duplex d-(AGCGTACTAGTACGCT)2 corresponding to the trp operator fragment used in the crystal structure of the half site complex (PDB entry 1TRR) was studied by a 1.4 ns molecular dynamics simulation in water. The simulation, starting from a B-DNA conformation, used a non-bonded cutoff of 1.4 nm with a reaction field correction and resulted in a stable trajectory. The average DNA conformation obtained was closer to the ones found in the crystal structures of the complexes (PDB entries 1TRO and 1TRR) than to the crystal structure of unbound trp operator (Nucleic Acid Database entry BDJ061). The DNA hydration was characterized in terms of hydrogen bond percentages and corresponding residence times. The residence times of water molecules within 0.35 nm of the DNA non-exchangeable protons were calculated for comparison with NMR measurements of intermolecular water-DNA NOEs and nuclear magnetic relaxation dispersion measurements. No significant difference was found between major and minor groove hydration. The DNA donors and acceptors were hydrogen bonded to water molecules for 77(+/-19)% of the time on average. The average residence time of the hydrogen bonded water molecules was 11(+/-11) ps with a maximum of 223 ps. When all water molecules within NOE distance (0.35 nm) of non-exchangeable protons were considered, the average residence times increased to an average of 100(+/-4) ps and a maximum of 608 ps. These results agree with the experimental NMR results of Sunnerhagen et al. which did not show any evidence for water molecules bound with more than 1 ns residence time on the DNA surface. The exchange of hydration water from the DNA occurred in the major groove primarily through direct exchange with the bulk solvent, while access to and from the minor groove frequently proceeded via pathways involving ribose O3' and O4' and phosphate O2P oxygen atoms. The most common water diffusion pathways in the minor groove were perpendicular to the groove direction. In general, water molecules visited only a limited number of sites in the DNA grooves before exiting. The hydrogen bonding sites, where hydrogen bonds could be formed with donor and acceptor groups of the DNA, were filled with water molecules with an average B-factor value of 0.58 mn2. No special values were observed at any of the sites, where water molecules were observed both in the trp repressor/operator co-crystals and in the crystal structure of unbound DNA.