Stretching and imaging studies of single DNA molecules

DNA molecules were stretched on silanized mica surface with the molecular combing technique, and detected with fluorescence microscopy and atomic force microscopy. Meantime, DNA molecules were stretched with a modified dynamic molecular combing technique and studied with atomic force microscopy. The results indicate that, compared with the dynamic molecular combing technique, the modified dynamic molecular combing technique has advantages of less-sample demand and less contamination to sample; as compared with the molecular combing technique, it has better aligning effect and reproducibility. Combination of this kind of DNA molecular manipulating technique with the single DNA molecule detecting technique by atomic force microscopy and fluorescence microscopy will play an important role in the basic research of molecular dynamics and the application of gene research.     

Study of the interaction of DNA and histones by spin-stretching and droplet evaporation

Molecular combing is a powerful and simple method for aligning DNA molecules onto a surface. Using this technique combined with fluorescence microscopy, DNA-histone complexes are stretched on a hydrophobic polymethyl methacrylate (PMMA) surface and observed directly. We have developed a new method to stretch single DNA-histone complexes, termed spin-stretching. The results show that the histones markedly enhance DNA binding to the PMMA surface. DNA winds around the histones and therefore decreases in length. The number of histones that bind to each DNA molecule is found to correlate with the histone concentration. The combed DNA-histone complexes are found to depend on two factors: the binding force on the surface and the centrifugal force at its local position. Na+ ions should compete with histones for binding to DNA; however, the observed competitive binding effect of Na+ ions at low concentrations was negligible.     

Real time observation of the photocleavage of single DNA molecules

A method for real time observation of photo-cleavage of stratched λDNA at single molecular level by a fluorescent microscope coupled with CCD is developed.DNA molecules stained with YOYO-1 are stretched by the mo-lecular combing technique and fixed on a modified slide.Then the Process of Photocleavage and relaxation of DNA under radiation of blue light is observed.We speculate that the conformation change of stretched DNA and the effect of water are likely to facilitate the effect of YOYO photocleav-age DNA molecules.The photocleavage effect of YOYO for stretched DNA may be useful to study DNA elasticity,cancer research as well as the interaction between DNA and dyes.     

Optical mapping of a rice BAC clone using restriction endonuclease and imaging with fluorescent microscopy at single molecule level

A method of constructing restriction map by optical mapping and single molecule fluorescent microscopy is described. DNA molecules were aligned and adsorbed on a glass coverslip surface by a modified “molecular combing” technique, and then the surface-immobilized DNAs were cleaved in situ with a restriction endonuclease. Individual DNA molecules digested by the endonuclease EcoRⅠ were observable with fluorescent microscopy. Using optical mapping, a physical map of a rice bacterial artificial chromosome clone was constructed. This method will facilitate genomic mapping and tracing the dynamic process in real time at a single molecule level with fluorescence microscopy.     

Study the effects of metallic ions on the combination of DNA and histones with molecular combing technique

The effects of monovalent (Na^ , K^ ) and divalent (Mg^2 , Ca^2 , Mn^2 ) ions on the interaction between DNA and histone are studied using the molecular combing technique. λ-DNA molecules and DNA-histone complexes incubated with metal cations (Na^ , K^ , Mg^2 , Ca^2 , Mn^2 ) are stretched on hydrophobic surfaces, and directly observed by fluorescence microscopy. The results indicate that when these cations are added into the DNA solution, the fluorescence intensities of the stained DNA are reduced differently. The monovalent cations (Na^ , K^ ) inhibit binding of histone to DNA. The divalent cations (Mg^2 , Ca^2 , Mn^2 ) enhance significantly the binding of histone to DNA and the binding of the DNA-histone complex to the hydrophobic surface. Mn^2 also induces condensation and aggregation of the DNA- histone complex.     

银纳米线的制备及梳直

以DNA为模板在溶液中制备出了韧性好、颗粒吸附均匀且粗细可调的银纳米线.通过葡萄糖封装,观察到大量相互缠绕的银纳米线.在云母衬底表面经过梳直得到的银纳米线呈直线、长度约10-15μm、排列整齐有序且有统一取向.     

超临界二氧化碳萃取深层稠油组分的分子动力学模拟

为了从微观层面探究超临界CO_2对稠油组分的萃取机制,采用分子动力学模拟方法分析了稠油组分在砂岩表面的密度分布和吸附特征,研究了超临界CO_2对岩石表面稠油组分的萃取特点和扩散规律。研究结果表明,稠油四组分在稠油聚集体中呈现不均衡分布状态,沥青质自缔合能力强,胶质紧密包裹在沥青质周围,构成复杂的空间网状结构;芳香烃和饱和烃分布在沥青质、胶质周围,显示出稠油分子结构的层次性。沥青质与岩石表面相互作用能较大,超临界CO_2难以在沥青质中运移,扩散系数低,萃取难度大,萃取率接近于0;而芳香烃、饱和烃与岩石表面的相互作用能较小,超临界CO_2容易在芳香烃、饱和烃中溶解、运移,扩散系数大,容易被超临界CO_2萃取,萃取率可分别达到53%和28%。运用分子动力学方法揭示的微观动力学机制对于宏观认识超临界CO_2萃取稠油轻质组分具有重要意义。     

DNA分子在云母表面拉直技术的研究

对DNA分子的生物、物理和化学性质的很多研究,都要求对单个DNA分子的性质进行深入探索,实现DNA分子在基底表面上的拉直是对其深入研究的物理基础。文章在APS溶液处理过的云母片表面,通过不同的方法完成了对DNA分子的拉直操作,利用原予力显微镜对拉直后的DNA分子进行了表征,获得了DNA分子拉直后的形貌,并对每种拉直方法进行了比较和讨论。     

Direct measurement of compression spring constant of single DNA molecule with AFM

The understanding of mechanical responses of individ-ual macromolecules under a small external load (usually F<0.5 nN) is of profound importance because the induced conformational transition can result in the change of bio-logical functions[1?3]. The advent of new instrumentations, especially the development of Pico-Newton force tech-nology, has made it possible to investigate the dynamic behavior of single biomolecule and manipulate it to make direct measurements of its elastic properties[4?…     

Electrically driven directional motion of a four-wheeled molecule on a metal surface

Propelling single molecules in a controlled manner along an unmodified surface remains extremely challenging because it requires molecules that can use light, chemical or electrical energy to modulate their interaction with the surface in a way that generates motion. Nature's motor proteins have mastered the art of converting conformational changes into directed motion, and have inspired the design of artificial systems such as DNA walkers and light- and redox-driven molecular motors. But although controlled movement of single molecules along a surface has been reported, the molecules in these examples act as passive elements that either diffuse along a preferential direction with equal probability for forward and backward movement or are dragged by an STM tip. Here we present a molecule with four functional units--our previously reported rotary motors--that undergo continuous and defined conformational changes upon sequential electronic and vibrational excitation. Scanning tunnelling microscopy confirms that activation of the conformational changes of the rotors through inelastic electron tunnelling propels the molecule unidirectionally across a Cu(111) surface. The system can be adapted to follow either linear or random surface trajectories or to remain stationary, by tuning the chirality of the individual motor units. Our design provides a starting point for the exploration of more sophisticated molecular mechanical systems with directionally controlled motion.     

Molecular control over Au/GaAs diodes

The use of molecules to control electron transport is an interesting possibility, not least because of the anticipated role of molecules in future electronic devices. But physical implementations using discrete molecules are neither conceptually simple nor technically straightforward (difficulties arise in connecting the molecules to the macroscopic environment). But the use of molecules in electronic devices is not limited to single molecules, molecular wires or bulk material. Here we demonstrate that molecules can control the electrical characteristics of conventional metal-semiconductor junctions, apparently without the need for electrons to be transferred onto and through the molecules. We modify diodes by adsorbing small molecules onto single crystals of n-type GaAs semiconductor. Gold contacts were deposited onto the modified surface, using a 'soft' method to avoid damaging the molecules. By using a series of multifunctional molecules whose dipole is varied systematically, we produce diodes with an effective barrier height that is tuned by the molecule's dipole moment. These barrier heights correlate well with the change in work function of the GaAs surface after molecular modification. This behaviour is consistent with that of unmodified metal-semiconductor diodes, in which the barrier height can depend on the metal's work function.     

多原子分子势能面的李代数方法

势能面是分子反应动力学的基础,研究势能面的意义非常深远。近年来李代数方法成为研究分子势能面的强有力的工具。本文主要介绍了用动力学李代数方法构造多原子分子势能面的理论方法,及其在不同分子体系中的应用。     

Immobilization and Hybridization of cDNA Arrays on the Glass Surface

IntroductionMicroarray technology uses microscopic arrays ofDNA molecules immobilized on solid supports forbiomedical analysis,such as gene expressionanalysis,polymorphism and mutation detection,drug screening,and gene discovery[1 3] .　 Several approaches can be used to preparemicroarrays. DNA can be synthesized in situ onglass using combinatorial chemistry approach.This method typically produces microarraysconsisting of groups of oligonucleotides ranging insize from 1 0 to 2 5 bases wherea…     

Images of single-stranded nucleic acids by scanning tunnelling microscopy

The scanning tunnelling microscope has the potential to resolve the structure of biological molecules with atomic detail. Progress has been made in the imaging of dried, unshadowed double helices of DNA4-7 and in recording images of DNA under water. Also, images of unshadowed complexes of DNA with the RecA protein from Escherichia coli indicate that this technique may not be restricted to thin biological samples. Here we present images of polydeoxyadenylate molecules aligned in parallel, with their bases lying flat on a surface of highly oriented pyrolytic graphite and with their charged phosphodiester backbones protruding upwards. Based on these images, a molecular model has been built which suggests the presence of a hydrogen bond that could stabilize the parallel alignment. Our micrographs demonstrate the potential application of scanning tunnelling microscopy in structural studies of nucleic acids and provide evidence that it could be used to sequence DNA.     

表面分子印迹技术研究进展

分子印迹技术是制备对目标分子具有特异识别性能的高分子聚合物的技术,表面分子印迹是目前分子印迹技术领域的研究重点之一.本文概述了表面分子印迹材料的制备方法,主要包括牺牲载体法、聚合加膜法和化学接技法,以及近年来表面分子印迹技术的研究进展.     

苎麻纯落麻转杯纺分梳元件的研究——第一报:分梳辊型式和规格的模糊决策

本文应用模糊决策和模糊聚类分析相结合的处理模式。对苎麻纯落麻转杯纺适用的分梳辊型式和规格进行了研究。结果表明:此种处理模式有利于提高所得结论的可靠性与客观性,可应用于其它类似研究;纺制纯落麻转杯纱时,大工作角、大齿距、小齿高、细小齿形、光结度及耐磨性好的锯齿辊有利于改善纺纱性能和成纱质量;针辊是纯落麻转杯纺用分梳辊的发展方向。     

Folding DNA to create nanoscale shapes and patterns

'Bottom-up fabrication', which exploits the intrinsic properties of atoms and molecules to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by 'top-down' methods. The self-assembly of DNA molecules provides an attractive route towards this goal. Here I describe a simple method for folding long, single-stranded DNA molecules into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100 nm in diameter and approximate desired shapes such as squares, disks and five-pointed stars with a spatial resolution of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton molecular complex).     

DNA 分子中热变现象的简化动力学模型探索

在用非平衡态输运理论对ＤＮＡ分子的热变现象进行描述与研究的基础上,力图寻求一个能较全面考虑ＤＮＡ分子结构及其动力学行为的较为合理的简化动力学模型,并期望此模型不但能描述ＤＮＡ分子的整体热变性质,而且还能描述ＤＮＡ局部热变,以便能进一步探索热变的动力学机制,是用理论物理方法探讨生物学现象的初步尝试。