Detection of abasic sites on individual DNA molecules using atomic force microscopy

We have developed an atomic force microscopy-based method for detecting abasic sites (AP sites) on individual DNA molecules. By using uracil and uracil DNA glycosylase, we first prepared a 250-bp DNA template consisting of two AP sites at specific locations. We then detected the AP sites by marking them with biotinylated aldehyde-reactive probes and monomeric avidin. We demonstrate here that (i) the location of monomeric avidin bound on a single DNA molecule was detectable by atomic force microscopy; (ii) the observed location of avidin was in good agreement to the predicted AP sites at a few nanometer resolution; and (iii) by end-labeling the 5'-terminus of one DNA strand, the AP sites were determined without directional ambiguity. The technique described here will provide a sensitive way of locating AP sites and contribute to screen DNA damages from individual molecules.     

Improved design of a polarization converter based on semiconductor optical waveguide bends

By using an efficient vector finite-element-based beam-propagation method, we present an improved design of a polarization converter. This design relies on the use of a single-section deeply etched bent semiconductor waveguide with slanted sidewalls. By careful adjustment of the bend radius, the waveguide width, and the sidewall angle we obtained a nearly 100% polarization conversion ratio with no appreciable radiation loss and a bending angle of less than 180 degrees .     

Xenon as a probe for minority sites on solid surfaces

Atomic-level microscopies have proved useful to map solid-surface sites directly, but, because of their lack of chemical specificity, they are less adept at identifying unique chemical activity on those sites. Here we present a dual-titration approach developed to probe minority sites on solid surfaces with unique chemical properties of potential relevance to heterogeneous catalysis. Our methodology involves the initial dosing of a chemical probe such as carbon monoxide or ammonia to drive its selective adsorption onto specific sites with particular chemical activity, and the subsequent adsorption of xenon to help identify the nature of those sites. A combination of photoelectron and temperature-programmed desorption spectroscopies are used to characterize the Xe adsorption. The chemistry of oxygen-modified Ni(110) single crystals was probed to test this technique. It was observed that whereas CO does not discriminate among the various sites present on those surfaces, ammonia binds preferentially to the end of -Ni-O rows and modifies their local electrostatic potential. In addition, it was determined that adsorbed CO aids in a reversible surface reconstruction involving the coalescence of fragmented surface -Ni-O rows at high (>350 K) temperatures.     

Embedding of nanoparticles as flux pinning sites in superconducting samples

Crystallographic orientations of thin films and bulk, melt-textured YBa₂Cu₃O_x high-T_c superconductors with embedded Y₂Ba₄CuMO_x (M = Nb, Zr, Ag) nanoparticles are studied by electron backscatter diffraction. The Y₂BaCuO₅ particles exhibit no preferred orientation but have a strong negative influence on the matrix orientation. In contrast, the nanoparticles are not disturbing the texture of the YBCO matrix. For the bulk samples, depending on the preparation route, a different particle orientation with respect to the matrix is obtained. Untextured M-2411 nanoparticles are formed by solid state reaction during the melt process by adding oxides (Nb₂O₅ or Y₂O₃) to the precursor powder. Pre-formed Y₂Ba₄CuMO_x particles added to the precursor in the form of pre-reacted nanopowder, exhibit a dominant single orientation related to the surrounding YBCO matrix. In the case of thin films prepared using laser ablation with a bulk YBCO sample with embedded nanoparticles as a target, the nanoparticles are transferred into the thin film, but the transferred M-2411 particles are found to be randomly oriented. Nevertheless, these films exhibit increased flux pinning properties.     

尖棱状两组分颗粒堆积密度的研究

为了探讨耐火材料制品的密堆积结构特性,从而获得较好的颗粒堆积密度,研究了圆锥破碎机制得的粗、细两种离散颗粒体系的自由堆积密度变化．研究结果表明：当粗、细两种颗粒组分的拉径比大于5、且粗颗粒的质量分数在60%～70%之间时,体系的自由堆积密度较大；当粗、细两种颗粒的粒径比小于5、且无细粉存在时,离散颗粒体系的自由堆积密度变化不大。     

Evaluating the binding affinities of NF-kappaB protein to the single-nucleotide mismatch DNA binding sites by using double-stranded DNA microarray

Protein-DNA sequence-specific interaction plays an essential role in many biological processes. Here we immobilized a series of double-stranded DNA probes on an agarose coated slide to investigate the binding affinity of NF-kappaB p50 homodimer to the single-nucleotide mismatches (G<-->A or T<-->C) of the 10 base pair (bp) protein binding sites. The results demonstrated that the nucleotides at different positions contribute differently to the p50p50/DNA binding interaction. Within the 10 bp binding sites, the 5tG or 6cA mismatch has less effect on the protein-DNA binding affinity. Even the 5tG mismatch may have the ability to enhance the protein-DNA interaction (5t/w = 1.07). On the other hand, the 7cA or 10tG mismatch blocked the protein-DNA interaction more significantly than other six single-nucleotide mismatches. (7c/W = 0.37, 10t/W = 0.35). It also indicated that the duplex DNA probes immobilized on the agarose-coated surface were apt to be recognized by DNA-binding proteins, and this method would provide a reliable method for exploring the binding affinities of DNA-binding proteins with a larger number of DNA targets.     

Influence of initial ovality on creep life of P92 pipe bends subjected to in-plane bending

Initial ovality is an inevitable problem in the process of pipe bends manufacturing which results in the stress redistribution of the pipe bends working at high temperature. In order to study the influence of ovality on creep life of pipe bends, full-size creep experiment of P92 pipe bend subjected to in-plane bending has been conducted. The creep strains and outside diameters of dangerous positions have been measured. The microstructures of three different positions of the pipe bend were compared through SEM and the results showed the number and size of the carbide precipitation were the largest at the flank of the pipe bend, which indicated that the creep damage developed fastest at the flank. The modified Kachanov–Robatnov constitutive equations were used to stimulate the creep of P92 pipe bends with FEA software. The representative stress, damage and multiaxiality distributions of the pipe bends have been discussed. The FEA results were consistent with the experimental results and the influence of initial ovality on creep life of P92 pipe bends were analyzed. The results showed that creep life of pipe bends reduced by the increase of ovality and their relationship coincided with the parabolic law.     

水稻基因组MSAP指纹图谱构建及DNA甲基化修饰位点分离与鉴定

采用EcoR I和Hpa II/Msp I双酶切建立了适合于水稻基因组的甲基化敏感扩增多态性(MSAP)分析体系,在全基因组水平检测了水稻DNA甲基化修饰位点.以12对MSAP引物进行选择性扩增,共检测到甲基化修饰位点120个,"CCGG/GGCC"位点甲基化修饰比例为20.17%.对部分水稻基因组甲基化修饰位点进行回收,最终分离了55条存在甲基化位点变异的DNA序列,通过BLAST比对分析将其联配到水稻基因组序列上.分析表明,这些甲基化修饰位点主要集中于基因启动子区(47%)和第一外显子区(22%),在其侧翼序列中存在类似"CpG island" 典型序列特征的"CpG"二核苷酸成簇富集区.在此基础上,对应用MSAP技术分离水稻基因组DNA甲基化修饰位点的有效性以及水稻基因组序列中"CpG island"类似序列分布特征和生物意义进行了讨论.     

DNA sensing on a DNA probe-modified electrode using ferrocenylnaphthalene diimide as the electrochemically active ligand

Naphthalene diimide derivative 1 carrying ferrocenyl moieties at the termini of imide substituents binds intact calf thymus DNA 4 times more strongly than the denatured DNA, and its complex with the intact DNA dissociates 80 times more slowly than that with the denatured DNA. On the basis of these observations, ligand 1 was applied to a probe of electrochemical DNA sensing. A thiol-linked single-stranded DNA probe was immobilized through the S-Au bonding to 20-30 pmol/mm2 on a gold electrode. Following hybridization with the complementary DNA, the electrode was soaked in a solution containing 1 (intercalation step) and then washed with buffer for 5 s. The cyclic voltammogram and differential pulse voltammogram for this electrode gave an electrochemical signal due to the redox reaction of 1 that was bound to the double-stranded DNA on the electrode. Thus, dA20 and the yeast choline transport gene were quantitated at the subpicomole level. The sensitivity of DNA detection was improved to 10 zmol by reducing the amount of immobilized DNA probe and protecting the uncovered surface of the electrode with 2-mercaptoethanol.     

飞机大坡度转弯对航空相机成像的影响

飞机姿态变化是影响航空相机成像质量的关键因素,尤其是飞机进行大坡度转弯将影响航空相机照相分辨率和重叠率。采用公式推理、坐标旋转变换等方法详细分析了飞机大坡度转弯对相机照相分辨率和重叠率的影响,并以摆扫型全景相机为例,给出了飞机大坡度转弯时相机的像移模型,分析结果表明:飞机大坡度转弯过程中相机产生的最大前向像移量接近4个像素,需要进行像移补偿;而垂直飞行方向上的最大像移量小于1/8像元,对成像分辨率影响不大。依据分析结果对像移模型进行了简化,为像移补偿提供了理论依据。针对飞机大坡度转弯对照相重叠率的影响,提出了依据转弯半径和转弯角速率调整曝光时间的方法加以解决。上述分析为摆扫相机在大坡度转弯时获取高质量图像提供了理论依据。     

Vibrational coupling as a probe of adsorption at different structural sites on a stepped single-crystal electrode

Adsorption of carbon monoxide at step and terrace sites on a Pt(557) ≡ Pt(s)-[6(111) × (100)] electrode was detected with infrared spectroscopy. Vibrational coupling between adsorbates provided insights into the assembly of molecules at the different structural sites. The intermolecular coupling was weak at low coverages as CO ordered along the steps. For coverages between 40 and 70% of saturation, separate bands assignable to CO on steps and CO on terraces appeared. Coupling across this coverage range was markedly weaker on Pt(557) than on the structurally related Pt(335) ≡ Pt(s)-[4(111) × (100)] electrode surface. The results indicate that, after the steps fill, CO populates the terraces on Pt(557) at random rather than by ordering in alignment with the steps. At coverages below saturation, vibrational bands assignable to CO molecules at step and terrace sites are affected differently by changes in electrode potential. The potential-induced spectral changes for the terrace CO bands are similar to those of Pt(111)/CO, but the step CO bands show deviations from this trend at hydrogen adsorption potentials.     

Fabrication and characterization of Ag nanoparticles based on plasmid DNA as templates

Ag nanoparticles have been synthesized successfully by using plasmid DNA as templates based on photoinduced method at room temperature. The plasmid DNA with an average size of 3980 base pairs was separated from Bacillus by using molecular biology methods. The morphology and composition of the samples were characterized by Transmission electron microscopy (TEM) and Energy dispersive spectroscopy (EDS). The UV-vis spectrum was applied to study the different stages of the synthesis processes. The results showed that the Ag was successfully deposited on the surface of plasmid DNA and formed the Ag nanoparticles with average sizes of ~ 30 nm. It was suggested that this high efficiency approach has promising application for the synthesis of other metal or alloy nanoparticles.     

Preparation of bilayer graphene utilizing CuO as nucleation sites by CVD method

Graphene is an attractive 2D material for optoelectronics applications. However, due to the spontaneous nucleation characteristics of graphene growth on the metal substrates using chemical vapor deposition method, the polycrystalline graphene exhibited many crystal defects, leading to poor crystal quality. Properly controlling the density of nucleation sites is an important and necessary mean to increase the quality of graphene material. In this work, a new method to synthesize high-quality graphene on Cu substrate was reported by utilizing the CuO nanoparticles as nucleation sites. It was found that when annealing the copper substrate at 300 °C for 30 min with Ar:O₂ flow ratio of 64:1, the copper substrate showed the lowest roughness and the density of CuO nucleation sites after hydrogen etching (H₂ 21 sccm at 1035 °C). Bilayer graphene with diagonal length of ~?3 µm was successfully prepared centering on the CuO nucleation sites. This work supplied a new clue for high quality and monocrystalline graphene preparation.     

Carbon nanotubes as electrodes for dielectrophoresis of DNA

Dielectrophoresis can potentially be used as an efficient trapping tool in the fabrication of molecular devices. For nanoscale objects, however, the Brownian motion poses a challenge. We show that the use of carbon nanotube electrodes makes it possible to apply relatively low trapping voltages and still achieve high enough field gradients for trapping nanoscale objects, e.g., single molecules. We compare the efficiency and other characteristics of dielectrophoresis between carbon nanotube electrodes and lithographically fabricated metallic electrodes, in the case of trapping nanoscale DNA molecules. The results are analyzed using finite element method simulations and reveal information about the frequency-dependent polarizability of DNA.     

Single DNA molecules as probes of chromatographic surfaces

YOYO-I-labeled lambda-DNA was employed as a nanoprobe for different functionalized surfaces to elucidate adsorption in chromatography. While the negatively charged backbone is not adsorbed, the 12-base unpaired ends of this DNA provide exposed purine and pyrimidine groups for adsorption. Self-assembled monolayers (SAMs) formed on gold substrate provide a wide range of choices of surface with well-defined and well-organized functional groups. Patterns of amino-terminated, carboxylic acid-terminated, and hydroxyl-terminated SAMs are generated by lithography. Patterns of metal oxides are generated spontaneously after deposition of metals. By recording the real-time dynamic motion of DNA molecules at the SAMs/aqueous interface, one can study the various parameters governing the retentivity of an analyte during chromatographic separation. Even subtle differences among adsorptive forces can be revealed.     

钛合金锥形压痕约束因子和代表应变的确定

目的 研究钛合金性能参数与约束因子和代表应变的关系。方法 对不同性能参数条件下压痕变形过程进行有限元仿真,根据模拟结果建立约束因子和代表应变与材料性能间的定量关系。结果 发现钛合金屈服强度与压痕硬度之间存在线性关系。约束因子随着弹性模量的增加而增加,代表应变随着弹性模量的增加而减小。当弹性模量固定不变时,约束因子随屈服强度线性减小,代表应变固定不变。在材料性能范围内,使用代表应变求解的代表应力,与通过压痕硬度和约束因子求解的代表应力两者误差小于±3%。结论 材料性能不同,约束因子和代表应变的值也会变化,这两个参数并不存在统一的值。     

Titration of active acid sites on zeolites by selective poisoning of stronger acid sites

The number and minimum strength of active acid sites on CeNaY, HY and HZSM-5, have been determined by studying model reactions (isomerization of o-xylene and cracking of cumene or isooctane) and indicator reactions (cracking of tert-, sec- and n-butylbenzenes) on the zeolites by selectively poisoning the stronger acid sites, in order of strength, with pyridine. The active sites on HM in isooctane cracking have been measured by pulse poisoning with 2,6-dimethylpyridine.     

Synthesis of 99m Tc-erythromycin complex as a model for infection sites imaging

Labeling of erythromycin with ^99m Tc using SnCl₂·2H₂O as a reducing agent was investigated. Dependence of the yield of ^99m Tc-erythromycin complex on the concentrations of erythromycin and reducing agent, on pH, and on the reaction time was studied. 97% labeling yield of ^99m Tc-erythromycin complex was achieved by performing the reaction with 1.5 mg of erythromycin and 15 μg of SnCl₂·2H₂O at pH 4 for 15 min. ^99m Tc-erythromycin complex was stable for 6 h. Biodistribution studies in Albino mice bearing septic and aseptic inflammation models showed that ^99m Tc-erythromycin does not allow differentiation between septic (Staphylococcus aureus) and aseptic inflammation. The maximum accumulation of ^99m Tc-erythromycin at the infection site was observed in 30 min after administration and was followed by gradual decline. The abscess-tomuscle ratio for ^99m Tc-erythromycin was 5 ± 0.6, whereas that for the commercially available ^99m Tc ciprofloxacin was 3.8 ± 0.8.     

DNA Molecules as Standard Reference Materials I: Development of DNA Identification Sequences and Human Mitochondrial DNA Reference Sequences

This paper describes the design, construction and characterization of two DNA molecules that function as prototype Standard Reference Materials for use in the determination of DNA sequences. The first prototype reference DNA molecule was constructed to function as a true reference DNA sequence encoding the human mitochondrial hypervariable region 1. The second DNA molecule was designed to be a molecular DNA “tag” for use in the identification of DNA Standard Reference Materials. DNA molecules were chemically and enzymatically synthesized, cloned in molecular cloning vectors and sequenced using manual and automated fluorescent DNA sequencing methods. The sequence of the cloned human mitochondrial HV1 DNA shows six base pair differences from the original published DNA sequence. The molecular DNA tag sequence uses the universal genetic code with one letter amino acid abbreviations to spell the words “NIST DNA STANDARD REFERENCE MATERIAL.” The need and utility of an expanded molecular code to uniquely identify DNA molecules is discussed. The use of these DNA molecules in the development of DNA Standard Reference Materials is also described.