Neutravidin coated surfaces for single DNA molecule analysis

We present a novel approach for single DNA molecule analysis using neutravidin coated surfaces. DNA molecules are elongated and reversibly immobilized on neutravidin coated surfaces with pH and salt controls. We demonstrate restriction enzyme reactions for optical mapping and ligation for tethered DNA molecules.     

Quantitative investigations of atomic processes on metal surfaces at atomic resolution

Using the atomic resolution of the field-ion microscope (FIM) and the single-atom identification capability of the time-of-flight atom-probe field-ion microscope, fundamental properties of solid surfaces can be investigated at atomic level. Atomic structures of many surface planes are fully resolved. The chemical composition of a surface can be determined with a single atomic layer spatial resolution. Several interactions of single surface atoms, which are basic to the understanding of many surface phenomena, such as the atom to substrate surface interaction, the adatom-adatom interaction, the adatom-impurity atom interaction, the adatom-plane edge interaction, etc. can all be studied in atomic details. The charge distribution of a single atom, as manifest in its dipole moment and polarizability, can also be studied. Great advantages of FIM investigations include the availability of atomically perfect surface planes, which can be prepared by field evaporation process, and the capability of a direct observation of the atomic images. Although some electronegative atoms cannot be imaged, the surface conditions and the state of the atoms can be characterized by the atom-probe. Basic principles and results of these single-atom FIM studies are presented and discussed.     

Single molecule atomic force microscopy and force spectroscopy of chitosan

Atomic force microscopy (AFM) and AFM-based force spectroscopy was used to study the desorption of individual chitosan polymer chains from substrates with varying chemical composition. AFM images of chitosan adsorbed onto a flat mica substrate show elongated single strands or aggregated bundles. The aggregated state of the polymer is consistent with the high level of flexibility and mobility expected for a highly positively charged polymer strand. Conversely, the visualization of elongated strands indicated the presence of stabilizing interactions with the substrate. Surfaces with varying chemical composition (glass, self-assembled monolayer of mercaptoundecanoic acid/decanethiol and polytetrafluoroethylene (PTFE)) were probed with chitosan modified AFM tips and the corresponding desorption energies, calculated from plateau-like features, were attributed to the desorption of individual polymer strands. Desorption energies of 2.0±0.3×10(-20)J, 1.8±0.3×10(-20)J and 3.5±0.3×10(-20)J were obtained for glass, SAM of mercaptoundecanoic/dodecanethiol and PTFE, respectively. These single molecule level results can be used as a basis for investigating chitosan and chitosan-based materials for biomaterial applications.     

High resolution imaging of functional group distributions on carbon surfaces by tapping mode atomic force microscopy

Here we report, for the first time, the high resolution imaging of hydrophilic, polar functional group distributions on flat carbon surfaces by phase contrast in noncontact tapping mode AFM.     

Chirped coherent anti-stokes Raman scattering for high spectral resolution spectroscopy and chemically selective imaging

We describe a simple multiplex vibrational spectroscopic imaging technique based on employing chirped femtosecond pulses in a coherent anti-Stokes Raman scattering (CARS) scheme. Overlap of a femtosecond Stokes pulse with chirped pump/probe pulses introduces a temporal gate that defines the spectral resolution of the technique, allowing single-shot acquisition of high spectral resolution CARS spectra over a several hundred wavenumber bandwidth. Simulated chirped (c-) CARS spectra match the experimental results, quantifying the dependence of the high spectral resolution on the properties of the chirped pulse. c-CARS spectromicroscopy offers promise as a simple and generally applicable high spatial resolution, chemically specific imaging technique for studying complex biological and materials samples.     

Chemical strategies and characterization tools for the organization of single molecule magnets on surfaces

Addressing individual bistable magnetic molecules, known as Single Molecule Magnets (SMMs), is a fascinating goal at the borderline between molecular magnetism and spin electronics. This tutorial review focuses on the first step towards single-molecule experiments, namely the organization of SMMs on surfaces. Both preparation and characterization of surface-supported SMMs prove to be quite demanding and a multidisciplinary approach is necessary, which is described here using selected examples. We first illustrate the chemical strategies devised to assemble SMMs and to control their orientation on surfaces. Then, we present characterization tools, which have been selected on the basis of their relevance to address specific points, i.e. the chemical composition of the deposited SMM films, the organization of the molecules on the surface, the intramolecular arrangement of the spins, the magnetic anisotropy of SMMs, and eventually the dynamics of their magnetization on surfaces. Particular attention is devoted to techniques exploiting synchrotron light.     

有机分析研究进展——单原子、单分子、单细胞的分析进展

简要地对单原子、单分子、单细胞的分析方法和研究进展情况进行了评述 ,共引用文献 193篇     

DNA curtains and nanoscale curtain rods: high-throughput tools for single molecule imaging

Single molecule visualization of protein-DNA complexes can reveal details of reaction mechanisms and macromolecular dynamics inaccessible to traditional biochemical assays. However, these techniques are often limited by the inherent difficulty of collecting statistically relevant information from experiments explicitly designed to look at single events. New approaches that increase throughput capacity of single molecule methods have the potential for making these techniques more readily applicable to a variety of biological questions involving different types of DNA transactions. Here we show that nanofabricated chromium barriers, which are located at strategic positions on a fused silica slide otherwise coated with a supported lipid bilayer, can be used to organize DNA molecules into molecular curtains. The DNA that makes up the curtains is visualized by total internal reflection fluorescence microscopy (TIRFM) allowing simultaneous imaging of hundreds or thousands of aligned molecules. These DNA curtains present a robust experimental platform portending massively parallel data acquisition of individual protein-DNA interactions in real time.     

The use of atomic force microscopy for imaging the surfaces of polyamide, 6

The surface morphologies of PA 6 resulting from the use of various processing methods were studied by tapping mode atomic force microscopy. Three PA 6 samples: (1) a thin film, spin coated on a silicon wafer, (2) a freestanding film, i.e. a foil and (3) a monofilament, show definite morphological differences revealing typical supramolecular structures. The thin film having thickness of app. 35 nm is a good example of the initial step of spherulite formation where the sheaf development is still prominent. In an area of 100 μm² 1-4 spherulites can be detected which are typical of crystallization from the solution. The annealing (vacuum, 195°C, 3.5h) causes additional crystallization, which leads to a radial coordination and enlargement of spherulites to app. 50% in diameter and up to 40% in height. The morphology of foil (thickness of 100 μm) can be interpreted as a system of spherulites formed from the melt, and a typical fibrillar structure is observed on the surface of monofilament.     

Higher sensitivity secondary ion mass spectrometry of biological molecules for high resolution, chemically specific imaging

To expand the role of high spatial resolution secondary ion mass spectrometry (SIMS) in biological studies, numerous developments have been reported in recent years for enhancing the molecular ion yield of high mass molecules. These include both surface modification, including matrix-enhanced SIMS and metal-assisted SIMS, and polyatomic primary ions. Using rat brain tissue sections and a bismuth primary ion gun able to produce atomic and polyatomic primary ions, we report here how the sensitivity enhancements provided by these developments are additive. Combined surface modification and polyatomic primary ions provided approximately 15.8 times more signal than using atomic primary ions on the raw sample, whereas surface modification and polyatomic primary ions yield approximately 3.8 and approximately 8.4 times more signal. This higher sensitivity is used to generate chemically specific images of higher mass biomolecules using a single molecular ion peak.     

Use of high resolution continuum source atomic absorption spectrometry as a detector for chemically generated noble and transition metal vapors

Vapor generation and atomization conditions in a heated quartz tube to detect Ag, Cd, Co, Cu, Ni and Zn using High Resolution Continuum Source AAS (HRCSAAS), were optimized. Vapors were generated after mixing acidified solutions containing 8-hydroxiquinoline (oxine) with sodium tetrahydroborate. Afterwards, they were swept to the heated quartz cell by an argon flow.Reaction loop size and temperature of the quartz cell were optimized for each element. A temperature of 960 °C was selected as a compromise value to detect most of the metals. Afterwards, a Plackett–Burmann design was proposed to select which parameters were most important. Type of acid and its concentration were the most statistical significant variables. Optimum conditions for sequential detection of Cd, Cu, Ni and Zn were: 1 mg L^− 1 Co as catalyst, 250 mg L^− 1 oxine, 0.6 M nitric acid, 1.75% (w/w) sodium tetrahydroborate (prepared in 0.4 (w/v)% NaOH), a reaction loop of 250 µL, and a 25 L h^− 1 carrier Ar flow. Ag and Co were each detected in their own optimized conditions. Analytical performance of the system was evaluated in connection with a selected pixel number, and spectral correction was used to eliminate NO absorption bands interference in Zn detection. Detection limits were in the range of 1.5–18 μg L^− 1 for Ag, Cu, Cd and Zn, whereas sensitivity was worst for Co (169 μg L^− 1) and Ni (586 μg L^− 1). Atomization in a quartz cell of Co and Ni volatile species, generated by an addition of sodium tetrahydroborate to an acidified solution of the analytes, was reported for the first time in this paper. Precision expressed as RSD(%) had values lower than 10% except for Ni.     

Evaluation of the performance of sensors based on optical imaging of a chemically sensitive layer

Interest in the use of the optical properties of chemical indicators is growing steadily. Among the optical methods that can be used to capture changes in sensing layers, those producing images of large-area devices are particularly interesting for chemical sensor array development. Until now, few studies addressed the characterization of image sensors from the point of view of their chemical sensor application. In this paper, a method to evaluate such performance is proposed. It is based on the simultaneous measurement of absorption events in a metalloporphyrin layer with an image sensor and a quartz microbalance (QMB). Exploiting the well-known behaviour of QMB, comparison of signals enables estimation of the minimum amount of absorbed molecules that the image sensor can detect. Results indicate that at the single pixel level a standard image sensor (for example a webcam) can easily detect femtomoles of absorbed molecules. It should therefore be possible to design sensor arrays in which the pixels of images of large-area sensing layers are regarded as individual chemical sensors providing a ready and simple method for large sensor array development.     

Dynamic imaging of single DNA-protein interactions using atomic force microscopy

Atomic force microscopy (AFM) imaging of static DNA-protein complexes, in air and in liquid, can be used to directly obtain quantitative and qualitative information on the structure of different complexes. For example, DNA length, the location of preferential binding sites for proteins and bending of DNA as a result of the complexation can all be measured. Recording consecutive AFM images of DNA and protein molecules under conditions that they are still able to move and interact, or dynamic AFM imaging, however, can reveal information on the dynamic aspects of the interactions between these molecules. Here, an overview is given of the technical challenges that need to be considered for successful dynamic AFM imaging studies of individual DNA-protein interactions. Necessary technical improvements to the AFM set-up and the development of new sample preparation methods are described in this paper.     

利用探针分子红外光谱识别和表征铂族金属基单原子催化剂

单原子催化是提高贵金属利用率的有效手段,而表征单原子催化剂是理解单原子催化的基础.探针分子红外光谱可用于识别和定量催化剂样品中孤立的Pt族金属物种的浓度,从而得到负载的孤立的Pt族金属物种的局部几何形状、稳定性、活性及其分散性.本文讨论了该技术用于识别和表征含负载型孤立的Pt族金属原子催化剂的效能、应用、以及未来的发展方向.     

Structure of the amodiaquine-FPIX mu oxo dimer solution complex at atomic resolution

Using NMR inversion recovery experiments and XPLOR distance restraint calculations, we recently deduced the structure of ferriprotoporphyrin IX (FPIX) heme mu oxo dimer-antimalarial drug complexes for chloroquine (CQ), quinine (QN), and quinidine (QD) at atomic resolution [A. Leed et al., Biochemistry 2002, 41, 10245-55]. Using similar methods, we now report an unexpected structure for the complex formed between FPIX and the related drug amodiaquine (AQ). The deduced structure is further supported by comparing AQ chemical-shift data to restricted Hartree-Fock calculations. The structure further highlights the critical nature of quinoline drug side-chain composition in stabilizing noncovalent association to FPIX. Heme Fe-AQ proton distances are longer, relative to those of the CQ complex, and the AQ aromatic side chain seems to have a significant role in stabilizing the complex. Relative to the FPIX-CQ complex, a similar 2:1 stoichiometry was determined for the AQ complex, in contrast to a 4:1 stoichiometry previously suggested from calorimetry data. These solution structures add to our rapidly growing understanding of the mechanism of quinoline antimalarial drug action and will help elucidate the mechanism(s) of quinoline antimalarial drug resistance phenomena.     

High resolution electronic spectra of 7-azaindole and its Ar atom van der Waals complex

Rotationally resolved fluorescence excitation spectra of the S(1)<--S(0) origin band of 7-azaindole [1H-pyrrolo(2,3-b)pyridine] and its argon atom van der Waals complex have been recorded and assigned. The derived rotational constants give information about the geometries of the two molecules in both electronic states. The equilibrium position of the argon atom in the azaindole complex is considerably different from its position in the corresponding indole complex. Furthermore, the argon atom moves when the UV photon is absorbed. There are significant differences in the intermolecular potential energy surfaces in the two electronic states. A large, vibration-state-dependent rotation of the S(1)<--S(0) electronic transition moment vector of 7-azaindole relative to that of indole suggests that these differences have their origin in S(1)/S(2) electronic state mixing in the isolated molecule, a mixing that is enhanced by nitrogen substitution in the six-membered ring.     

Functionalized self-assembled monolayers on ultraflat gold as platforms for single molecule force spectroscopy and imaging

Single molecule force spectroscopy is a valuable tool for studying unfolding and nanomechanical properties of proteins. The common practice is to stretch proteins from a surface that was dosed to give a reasonable hit rate and to analyze the curves that exhibit the expected characteristics of a single polymer. Whether the surface-bound proteins are indeed single and isolated remains unclear, and the undesirable protein/surface interactions that obscure informative features of the force curves are implicitly assumed to be absent. In this study, mixed self-assembled monolayers (SAMs) consisting of N-hydroxysuccinimide (NHS) and oligoethylene glycol (OEG) terminated thiols on an ultraflat gold surface were used to covalently immobilize proteins via lysine residues. By the optimization of attachment sites via lysine-NHS linkages amidst a protein-resistant layer of the OEG SAM, it was possible to isolate single proteins for study in a controlled fashion. The single protein distribution on the surface is clearly demonstrated by atomic force microscopy (AFM) imaging. The OEG also significantly reduces nonspecific tip-surface interactions between the cantilever and surface. Stretching covalently attached single proteins produces high-quality and reproducible force-extension curves. This experimental strategy is an attractive platform with which to study protein structure, interactions, and nanomechanical properties of single proteins.     

热稳定单原子催化剂的理性构筑:从原子级结构到实际应用

80%以上的工业生产过程涉及催化,如化工生产、能源转换、制药和废物处理等等.催化剂的使用显著提高了生产效率,降低了生产成本,为国民经济、地球环境和人类文明的可持续发展做出了很大贡献.为了满足日益增长的生产需求和最大的经济效益,开发高效、稳定、低成本的新型催化剂已成为当务之急.金属中心负载在载体上的负载型金属催化剂因其较好的催化活性和相对较低的金属用量而受到广泛关注.研究发现,负载型结构可增强传热和传质并增加活性金属中心的分散度,从而影响催化性能.此外,负载金属的颗粒尺寸对催化剂的性能有很大影响.迄今为止,科学家们一直在通过减小金属颗粒尺寸和提高原子利用效率来提高催化剂的活性.原子级尺寸的颗粒通常表现出与大尺寸颗粒显着不同的物理和化学性质,而当活性位点的尺寸缩小到单个原子时,单原子催化剂的概念应运而生.对于单原子催化剂,金属原子中心通过配位被载体中的缺陷锚定,从而调整金属原子的电子云分布.这种配位调整使得单原子催化剂拥有与传统催化剂不同的性能.作为催化领域的新前沿,单原子催化剂已经在许多催化反应中表现出前所未有的活性和选择性.然而,许多报道的单原子催化剂在高温环境或长期催化应用中容易受到奥斯特瓦尔德熟化过程的影响,从而导致催化剂烧结和失活.而烧结的原因在于金属原子和载体之间较弱的相互作用.失活催化剂的再生和回收将大大增加工业生产的时间和经济成本.因此,开发具有优异热稳定性的单原子催化剂以满足工业需求是十分必要的.本综述首先总结了近年来关于热稳定型单原子催化剂合成方法的基础研究,并从原子尺度上分析了这些方法所构建的金属中心的结构形态和配位环境.此外,结合近些年的研究中新的表征技术与理论计算手段解释了热稳定性的来源.重点讨论了热稳定单原子催化剂的实际催化应用.分析了热稳定单原子催化剂在热催化应用中的独特作用机理、并尝试为确定催化过程中真正的活性中心以及通过原子级调控手段进行高活性热稳定单原子催化剂的合成提供理论指导.最后总结了热稳定单原子催化剂发展的主要问题,并简要分析了单原子催化领域的研究挑战和发展前景.     

Single biomolecule imaging with frequency and force modulation in tapping-mode atomic force microscopy

A new intermittent-contact atomic force microscopy (AFM) mode (frequency and force modulation AFM, FFM-AFM) has been recently proposed to characterize soft samples. This method uses excitation force frequency and amplitude modulation to eliminate bistability and reduce the tip-sample forces. This letter describes theoretical modeling of FFM-AFM applied to a single bacteriorhodopsin molecule on a substrate, showing that its cross section can be measured without damage, in contrast to conventional tapping-mode AFM. Speculations are made regarding nonideal conditions and the ability of FFM-AFM to perform quantitative nanoelasticity measurements.