基于原子力显微镜的单分子力谱在生物研究中的应用

原子力显微镜被广泛应用于生物研究领域,基于原子力显微镜的单分子力谱可以在单分子、单细胞水平上研究生物分子内和分子间的相互作用。 本文介绍了原子力显微镜单分子力谱在生物分子间相互作用、蛋白质去折叠、细胞表面生物分子、细胞力学性质和基于单分子力谱成像等研究中的最新进展。     

液体环境单分子免疫球蛋白G的原子力显微镜高分辨成像

原子力显微镜技术( AFM)具有纳米级高分辨成像能力,是研究生物大分子结构和功能的重要工具之一。制备合适的样品是获取高分辨成像的关键要素。本研究结合DNA折纸技术,将抗原分子修饰在DNA折纸上,通过分子识别作用,抗体分子与抗原分子特异性结合,形成由DNA折纸和抗原抗体复合物构成的纳米结构。利用DNA折纸在云母表面上的吸附特点,使得抗体分子选择性地吸附在衬底表面上,由此获得了液体环境中的单个地高辛抗体免疫球蛋白G( IgG)分子的“Y”超微结构形貌。本方法简单、方便,为AFM在单分子水平上检测和表征生物分子结构和功能提供帮助。     

Nucleobases modified azo‐polysiloxanes,materials with potential application in biomolecules nanomanipulation

Here we show the possibility to obtain azopolysiloxanes modified with nucleobases (adenine and thymine) with potential application in immobilization and nanomanipulation of biomolecules. We propose a photofluidization mechanism based on the concept of the conformational instability, which can explain the presence of the fluid state below the glass transition. The azopolymers were characterized by ¹H NMR, GPC, DSC, DTG, UV spectroscopy, AFM analysis, and molecular simulations. Depending on the type of nucleobase used, the surface of the azopolysiloxane film can be structured in different ways under UV irradiation. Photoisomerization studies in solid state were carried out to demonstrate the influence of the operational conditions (presence or absence of natural visible light) on the polymeric film UV response. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4240–4248, 2007     

Qualitative and quantitative topographical surface investigation and solvent effects on internal surface of polypropylene tubes

An alternative way for plastic tubes surface analysis was presented, and the time course of the effects of solvent exposure was evaluated. Atomic force microscopy was used to qualitatively and quantitatively analyze internal tubes topography. Differences in nanoroughness parameters were shown as potential markers for quality control check to detect differences among brands and areas along each tube. Mass spectrometry analysis was carried out to evaluate the effects of some solvents after the intrinsic contact with the polymer. The obtained spectra did not allow the visualization of any leaching component, suggesting a low rate of some possible reaction or dissociative interaction caused by polymer and tested solvent interactions that were in concordance with principal component analysis. The use of these techniques as tools for quality control evaluation, or search for new support to biomolecules immobilization can be seen as important innovations and can be applied in several other investigative and developmental approaches. Copyright © 2011 John Wiley & Sons, Ltd.     

Single-molecule analysis using DNA origami

During the last two decades, scientists have developed various methods that allow the detection and manipulation of single molecules, which have also been called "in singulo" approaches. Fundamental understanding of biochemical reactions, folding of biomolecules, and the screening of drugs were achieved by using these methods. Single-molecule analysis was also performed in the field of DNA nanotechnology, mainly by using atomic force microscopy. However, until recently, the approaches used commonly in nanotechnology adopted structures with a dimension of 10-20 nm, which is not suitable for many applications. The recent development of scaffolded DNA origami by Rothemund made it possible for the construction of larger defined assemblies. One of the most salient features of the origami method is the precise addressability of the structures formed: Each staple can serve as an attachment point for different kinds of nanoobjects. Thus, the method is suitable for the precise positioning of various functionalities and for the single-molecule analysis of many chemical and biochemical processes. Here we summarize recent progress in the area of single-molecule analysis using DNA origami and discuss the future directions of this research.     

Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching

Novel single-molecule fluorescence experimental techniques have prompted a growing need to develop refined computational models of dye-tagged biomolecules. As a necessary first step towards useful molecular simulations of fluorescence-labeled biomolecules, we have derived a force field for the commonly used dye, rhodamine 6G (R6G). A novel automated method is used that includes fitting the molecular mechanics potential to both vibrational frequencies and eigenvector projections derived from quantum chemical calculations. The method is benchmarked on a series of aromatic molecules then applied to derive new parameters for R6G. The force field derived reproduces well the crystal structure of R6G.     

Friction force microscopy of self-assembled monolayers: probing molecular organisation at the nanometre scale

The basic principles behind friction force microscopy are described. Applications of friction force microscopy to self-assembled monolayers are reviewed. Work in the author’s laboratory on the frictional properties of self-assembled monolayers is described, and the findings applied in the characterisation of a much more complex material, plasma-treated polyester. Friction force microscopy is found to be a powerful tool for the analysis of the chemical composition and molecular organisation of molecular materials at the nanometre scale.     

Characterization of Ultrathin Films of Cellulose Esters

The adsorption of cellulose acetate (CA), cellulose acetate propionate (CAP) and cellulose acetate butyrate (CAB) from solutions prepared in acetone onto silicon wafers led to ultrathin films, which were characterized by ellipsometry, atomic force microscopy (AFM) and contact angle measurements. The polysaccharides films were characterized in the air just after their formation and after annealing at temperatures higher than their glass transition temperature or melt temperature. The films thickness close to 2 nm and surface roughness did not vary significantly upon annealing. AFM images revealed the presence of small clumps dispersed on a homogeneous layer, which covered completely the Si wafers. Such topographic details were also observed after annealing. However, upon annealing the films surfaces changed from hydrophilic to hydrophobic, evidencing molecular re-orientation at the solid–air interface. The adhesion of bovine serum albumin (BSA) and lipase onto the cellulose esters films was quantified in order to evaluate the possibility of applying such films as selective support for biomolecules.     

A quantitative method for dual‐pass electrostatic force microscopy phase measurements

Electrostatic force microscopy (EFM) has become a powerful tool for investigating charges on surfaces. The use of phase measurement in EFM is a direct and fast way to detect electrostatic force gradients, but only qualitatively. With the dual‐pass scheme, the phase signal at lifted height is often assumed to exclude any influences from the topography, but it does not. We report the collection of both topography and phase data by EFM on charged, micron‐sized metal wires. In order to quantify the electrostatic force, a cone model and finite element analysis are provided to integrate the force gradient from the phase signal. Copyright © 2007 John Wiley & Sons, Ltd.     

Rapid Perturbation of Free‐Energy Landscapes: From In Vitro to In Vivo

Biological systems are often studied under the most “physiological” conditions possible. However, purposeful perturbation of biological systems can provide much information about their dynamics, robustness, and function. Such perturbations are particularly easy to apply at the interface of molecular biophysics and cellular biology, at which complex and highly regulated networks emerge from the behavior of individual biomolecules. Due to the size of diffusion coefficients and the length scale of biomolecules, the fastest timescales at this interface extend to below a microsecond. Thus perturbations must be induced and detected rapidly. We focus on examples of proteins and RNAs interacting with themselves (folding) or one another (binding, signaling). Beginning with general principles that have been learned from simple models and perturbation experiments in vitro, we progress to more complex environments that mimic aspects of the living cell, and finally rapid perturbation experiments in living cells. On the experimental side we highlight in particular two classes of rapid perturbation methods (nanoseconds to seconds) that have been traditionally employed in biophysical chemistry, but that will become increasingly important in cell biology and in vivo: fast relaxation techniques and phase‐sensitive modulation techniques. These techniques are now increasingly married with imaging to produce a spatiotemporal map of biomolecular stability, dynamics and, in the near future, interaction networks inside cells. Many important chemical processes occur on biologically fast timescales, and yet have important ramifications for slower biological networks.     

冷冻电镜技术应用于生物分子高分辨结构解析——2017年诺贝尔化学奖浅谈

The 2017 Nobel Prize in chemistry was awarded to Jacques Dubochet, Joachim Frank and Richard Henderson for their contribution to developing the cryo-electron microscopy (cryo-EM) method for high-resolution structure determination of biomolecules in solution. In recent years, cryo-EM is leading a revolution in structural biology, and becoming a major tool in studying the structure and function of biomolecular machines. Here, we briefly describe the method development of cryo-EM and the personal contributions of the three Nobel Laureates.     

基于核酸和蛋白的生物大分子热致液晶研究进展

生物固体大分子诸如核酸、蛋白和病毒颗粒,因其尺寸超出了分子间作用力的范围,升温之后会导致它们降解而无法形成生物大分子的液体形态。 因此,发展新型的合成和制备策略,实现无溶剂包覆的生物大分子的流体态及其应用,是一个崭新的研究领域。 结合我们前期工作,简要介绍了核酸、蛋白流体(液晶态和液体态)材料的制备及性质。 借助静电力自组装,上述生物大分子能够与带有相反电荷的表面活性剂结合,形成热致液晶材料,其热致液晶性质使得生物分子具有长程有序性和流动性,在此基础上,可以探索生物大分子在无水环境下的技术应用。     

Microscopic features of methacrylate polymers with zwitterionic pendant groups determined by various techniques

The objective of this work was to determine microscopic structural features of three methacrylate polymers with different numbers of diethylene glycol residues and zwitterionic pendant groups. X‐ray diffraction, electron microscopy, and scanning probe microscopy techniques were employed. X‐ray data led to the adoption of a model made up of molecular aggregates forming lamellar domains, establishing in this way ordered characteristics of these kinds of polymers. Scanning electron microscopy images provided evidence of the occurrence of a lamellar structure forming the morphology of the polymers. This was corroborated by atomic force microscopy experiments. Transmission electron microscopy revealed that the lamellar aggregates conformed into clusters immersed in a polymeric matrix. From phase‐contrast images, information on the homogeneity of the composition at a molecular surface level was obtained. Then, the techniques provided evidence of the lamellar domain characteristics of the studied sulfobetaines. The crystallinity was a function of the number of ethoxy groups because as this number increased, the crystallinity became lower © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1152–1160, 2005     

Adsorption of bovine serum albumin on polyelectrolyte-coated glass substrates: applications to colloidal lithography

The adsorption of bovine serum albumin (BSA) labeled with fluorescein isothiocyanate (FITC) on polyelectrolyte-coated glass substrates was investigated using fluorescence microscopy. Glass substrates may inhibit adsorption of proteins due to electrostatic repulsion. However, when the substrate is modified with a thin film of positively charged polyelectrolytes, proteins can be adsorbed due to the attractive electrostatic interactions. In this study, poly(allylamine-hydrochloride) (PAH) molecules, which have positively charged amino groups at pH 7, were used to generate a positively charged layer on the glass substrate. A surfactant, sodium dodecyl sulphate (SDS), was used to alter the glass-protein interaction and subsequently modulate the coverage of adsorbed protein. We applied this technique to control the heterogeneously charged microscopic patterns of biomolecules created when the adsorption of protein is done in conjunction with colloidal lithography.     

Determination of solid surface tension from particle-substrate pull-off forces measured with the atomic force microscope

Atomic force microscopy (AFM) is capable of solid surface characterization at the microscopic and submicroscopic scales. It can also be used for the determination of surface tension of solids (gamma) from pull-off force (F) measurements, followed by analysis of the measured F values using contact mechanics theoretical models. Although a majority of the literature gamma results was obtained using either Johnson-Kendall-Roberts (JKR) or Derjaguin-Muller-Toporov (DMT) models, re-analysis of the published experimental data presented in this paper indicates that these models are regularly misused. Additional complication in determination of gamma values using the AFM technique is that the measured pull-off forces have poor reproducibility. Reproducible and meaningful F values can be obtained with strict control over AFM experimental conditions during the pull-off force measurements (low humidity level, controlled and known loads) for high quality substrates and probes (surfaces should be free of heterogeneity, roughness, and contamination). Any probe or substrate imperfections complicate the interpretation of experimental results and often reduce the quality of the generated data. In this review, surface imperfection in terms of roughness and heterogeneity that influence the pull-off force are analyzed based upon the contact mechanics models. Simple correlations are proposed that could guide in selection and preparation of AFM probes and substrates for gamma determination and selection of loading conditions during the pull-off force measurements. Finally, the possibility of AFM measurements of solid surface tension using materials with rough surfaces is discussed.     

Structures and electrical properties of ferroelectric copolymer ultrathin films

Ultrathin films of ferroelectric copolymer vinylidenefluoride and trifluoroethylene, P(VDF-TrFE), were successfully obtained by spin-coating and their nanoscale structures and electrical properties were studied utilizing atomic force microscopy (AFM). We succeeded in obtaining ultrathin copolymer films on graphite whose thickness ranged from 1 nm to several tens of nanometers by controlling concentration of copolymer solutions in methylethylketone. We found that ultrathin films thinner than 4 nm showed layered structures whose layer thickness was about 0.5 nm. On the other hand, films thicker than 4 nm formed typical edge-on lamellar crystal structures. Furthermore, we investigated surface potential distribution and piezoelectric property by AFM-based techniques and discussed interaction between electrical dipoles in the molecular chains and graphite substrate.     

非传统晶体生长的早期观察

晶体早期生长的研究揭示,在某些体系中,晶体生长可能并不遵循传统路径.借由某些聚合物或生物分子的帮助,无机晶体的前驱体或纳米晶体在生长初期有可能聚集为无序的大块颗粒.这些聚集体表面晶化形成高结晶度高密度的外壳,随后完成从表面到核心的晶化过程.此逆向晶体生长机理在一些诸如沸石、钙钛矿、金属和金属氧化物等无机化合物体系中均已被发现,在其他材料体系里也将得到验证.认识这一新的晶体生长路径将给予我们更多的自由度来实现晶体形态控制,也有助于我们对于许多天然矿物形成机制的理解.本文简要回顾了最近本领域研究中一些典型逆向晶体生长的例子.     

Optical‐Resolution Photoacoustic Microscopy for Volumetric and Spectral Analysis of Histological and Immunochemical Samples

Optical‐resolution photoacoustic microscopy (OR‐PAM) is an imaging modality with superb penetration depth and excellent absorption contrast. Here we demonstrate, for the first time, that this technique can advance quantitative analysis of conventional chromogenic histochemistry. Because OR‐PAM can quantify the absorption contrast at different wavelengths, it is feasible to spectrally resolve the specific biomolecules involved in a staining color. Furthermore, the tomographic capability of OR‐PAM allows for noninvasive volumetric imaging of a thick sample without microtoming it. By immunostaining the sample with different chromogenic agents, we further demonstrated the ability of OR‐PAM to resolve different types of cells in a coculture sample with imaging depths up to 1 mm. Taken together, the integration of OR‐PAM with (immuno)histochemistry offers a simple and versatile technique with broad applications in cell biology, pathology, tissue engineering, and related biomedical studies.