Biochemical and anisotropical properties of tendons

Tendons are formed by dense connective tissue composed of an abundant extracellular matrix (ECM) that is constituted mainly of collagen molecules, which are organized into fibrils, fibers, fiber bundles and fascicles helicoidally arranged along the largest axis of the tendon. The biomechanical properties of tendons are directly related to the organization of the collagen molecules that aggregate to become a super-twisted cord. In addition to collagen, the ECM of tendons is composed of non-fibrillar components, such as proteoglycans and non-collagenous glycoproteins. The capacity of tendons to resist mechanical stress is directly related to the structural organization of the ECM. Collagen is a biopolymer and presents optical anisotropies, such as birefringence and linear dichroism, that are important optical properties in the characterization of the supramolecular organization of the fibers. The objective of this study was to present a review of the composition and organization of the ECM of tendons and to highlight the importance of the anisotropic optical properties in the study of alterations in the ECM.     

Controlled assembly of DNA nanostructures on silanized silicon and mica surfaces for future molecular devices

In order to establish key technology for future molecular devices, we have explored the assembly behaviour of λ-deoxyribonucleic acid (DNA) molecules adsorbed on silanized mica and silanized oxide silicon surfaces by using atomic force microscopy (AFM). AFM experiments show that λ-DNA molecules can be hardly adsorbed on untreated mica and oxidized silicon surfaces, but can be strongly adsorbed onto aminosilanized mica and oxidized silicon surfaces. Importantly, DNA molecules can be assembled into linear DNA alignment, and can also self-assemble into various network structures on the silanized surfaces. Our experimental observations have demonstrated the feasibility of assembling DNA-based nanostructures by varying surface chemistry of substrates, and offer useful clues in constructing DNA-based nanodevices for nanoelectronics and biomolecular computation as well as quantum computation.     

PAC Studies of BSA Conformational Changes

The structure of biological molecules plays an important role in many biological processes. The variation of ambient parameters such as pH, temperature or pressure can influence important properties of protein molecules like conformation or stability. By means of the perturbed angular correlation (PAC) technique and atomic force microscopy (AFM) a conformation change of bovine serum albumin (BSA) molecules has been studied as a function of the pH value of the BSA solution. The observed decrease of the rotational correlation time and the increase of molecule diameter as a function of pH were attributed to conformational changes of bovine serum albumin induced by different pH values of the BSA solution.     

Electrostatic assembly of protein lysozyme on DNA visualized by atomic force microscopy

In the present work, atomic force microscopy (AFM) has been used to study the assembly of protein lysozyme on DNA molecule. Based on the electrostatic interaction, the positively charged lysozyme can easily bind onto the negatively charged DNA molecule surface. The protein molecules appear as globular objects on the DNA scaffold, which are distinguishable in the AFM images. At the same time, lysozyme molecules can be assembled onto DNA as dense or sporadic pattern by varying the protein concentration. This work may provide fundamental aspects for building protein nanostructures and studying of DNA-protein interaction.     

7Li和12C离子致DNA链断裂的研究

选用HI-13串列加速器产生的不同传能线密度的⁷Li和¹²C重离子,以不同的剂量对纯化的质粒DNA水溶液进行了辐照.利用原子力显微镜对这两种重离子诱发的DNA损伤进行了纳米水平的结构分析,并用ScionImage分析软件完成了DNA碎片长度的测量.得到了DNA分子超螺旋、开环和线性三种形态随剂量的变化情况以及DNA碎片长度的分布函数,并用Tsallis熵统计理论对实验结果进行了拟合.     

Study on the interactions between anti-cancer drug oxaliplatin and DNA by atomic force microscopy

Oxaliplatin is one of the most important anticancer drugs at present. However, the mechanism of action of oxaliplatin is still controversial. In this study, the interactions between oxaliplatin and a plasmid DNA have been studied so as to reveal the structural basis of its activity. The structural characteristic of pUC19 DNA (2 ng/μL) incubated with 100 μmol/L and 1000 μmol/L of oxaliplatin for the different time on a freshly cleaved highly ordered pyrolytic graphite (HOPG) surface was investigated by atomic force microscopy (AFM). High resolution AFM observation indicated that oxaliplatin can induce pUC19 DNA molecules change from the extended conformation to the entangled structures with many nodes, and finally to the compact particles. The present AFM results provide structural evidence about the interactions between oxaliplatin and circular duplex DNA containing multiple targets.     

From DNA to transistors

The rapid advance in molecular biology and nanotechnology opens up the possibility to explore the interface between biology and electronics at the single-molecule level. We focus on the organization of molecular electronic circuits. Interconnecting an immense number of molecular devices into a functional circuit and constructing a framework for integrated molecular electronics requires new concepts. A promising avenue relies on bottom-up assembly where the information for the circuit connectivity and functionality is embedded in the molecular building blocks. Biology can provide concepts and mechanisms for advancing this approach, but there is no straightforward way to apply them to electronics since biological molecules are essentially electrically insulating. Bridging the chasm between biology and electronics therefore presents great challenges. Circuit organization on the molecular scale is considered and contrasted with the levels of organization presented by the living world. The discussion then focuses on our proposal to harness DNA and molecular biology to construct the scaffold for integrated molecular electronics. DNA metallization is used to convert the DNA scaffold into a conductive one. We present the framework of sequence-specific molecular lithography based on the biological mechanism of homologous genetic recombination and carried out by the bacterial protein RecA. Molecular lithography enables us to use the information encoded in the scaffold DNA molecules for directing the construction of an electronic circuit. We show that it can lead all the way from DNA molecules to working transistors in a test-tube. Carbon nanotubes are incorporated as the active electronic components in the DNA-templated transistors. Our approach can, in principle, be applied to the fabrication of larger-scale electronic circuits. The realization of complex DNA-based circuits will, however, require new concepts and additional biological machinery allowing, for example, feedback from the electronic functionality to direct the assembly process and adaptation mechanisms.     

Imaging and manipulation of biological structures with the AFM

Many biologists have dreamt of physically touching and manipulating the biomolecules they were investigating. With the invention of the atomic force microscope (AFM), this dream has come true. Here, recent applications of the AFM to image and to manipulate biological systems at the nanometer scale are reviewed. Macromolecular biological assemblies as well as individual biomolecules can be subjected to controlled nanomanipulation. Examples of AFM application in imaging and nanomanipulation include the extraction of chromosomal DNA for genetic analysis, the disruption of antibody--antigen bonds, the dissection of biological membranes, the nanodissection of protein complexes, and the controlled modulation of protein conformations. Also reviewed is the novel combination of single molecule imaging and force spectroscopy which allows biomolecules to be imaged, and inter- and intramolecular forces to be measured. Future application of these nanotechniques will reveal new information on the structure, function and assembly of biomolecules.     

Characterising the throat diameter of through-pores in network structures using a percolation criterion

We present a method for measuring the pore throat diameter of a simulated porous material. The pore throat diameter is the size of the narrowest pore that has both an entrance and an exit in a network structure. Knowledge of the pore throat diameter allows estimation of the size of the largest molecules that can travel through a network structure without interruption. In this method, a chain of virtual circles (in 2-dimensions) or spheres (in 3-dimensions) is constructed along a percolated path through the pores in a network. The diameter of the largest circle or sphere for which this is possible is the pore throat diameter. The method is applied to two 2-dimensional models (one where we know the pore throat diameter and one where we do not), and well predicts the pore throat diameters in each case. The pore throat diameter of a 3-dimensional DNA-mediated hydrogel model is also determined. This method is applicable to any porous structure for which molecular coordinate information is available. The ability to predict pore throat diameters in simulation could be useful for determining the size of molecules that can safely be administered by hydrogel drug delivery systems.     

Humidity Effects on Imaging and Nanomanipulation of Individual DNA Molecules on HOPG Surface

Single DNA molecules are aligned on highly ordered pyrolytic graphite （HOPG） surface in ambient air. It is shown that environmental humidity has a remarkable influence on the measured height of DNA by atomic force microscopy （AFM）, probably due to the conformation transition of DNA. We also demonstrate that DNA molecules deposited on HOPG surface can be ＇pushed＇ much more easily by AFM tip at high humidity than at 10W one.     

生物分子结合水的结构与动力学研究进展

生物结合水在维护生物大分子的结构、稳定性以及调控动力学性质和生理功能等方面起着决定性的作用.从分子水平上理解生物结合水分子的结构与性质及其影响生物结构和功能的本质与规律,是揭示生物大分子生理功能机理的关键.目前生物结合水的结构与动力学相关研究尚处于初步阶段.本文从三个方面介绍当前生物结合水的相关研究及其进展:首先介绍结合水对蛋白质折叠、质子给予与迁移、配体结合与药物设计以及变构效应等生物结构和功能的影响;然后介绍生物分子周围的水分子结构研究情况;最后从时间尺度、动力学属性、生物分子与水分子之间的动力学耦合作用、蛋白质表面结合水次扩散运动等角度介绍生物分子水合动力学的研究进展,并归纳出一些目前尚待进一步解决的科学问题.     

Noninvertibility and resonance in discrete-time neural networks for time-series processing

We present a computer-assisted study emphasizing certain elements of the dynamics of artificial neural networks (ANNs) used for discrete time-series processing and nonlinear system identification. The structure of the network gives rise to the possibility of multiple inverses of a phase point backward in time; this is not possible for the continuous-time system from which the time series are obtained. Using a two-dimensional illustrative model in an oscillatory regime, we study here the interaction of attractors predicted by the discrete-time ANN model (invariant circles and periodic points locked on them) with critical curves. These curves constitute a generalization of critical points for maps of the interval (in the sense of Julia-Fatou); their interaction with the model-predicted attractors plays a crucial role in the organization of the bifurcation structure and ultimately in determining the dynamic behavior predicted by the neural network.     

Characterization of DNA chips on the molecular scale before and after hybridization with an atomic force microscope

Using two different 25-mer oligonucleotide probes covalently grafted on a silicon substrate, we demonstrate how efficient atomic force microscopy (AFM) can be for monitoring each step of DNA chip preparation: from probe immobilization to hybridization on the molecular scale. We observed the probe-molecule organization on the chip after immobilization, and the target molecules, which hybridized with probes could be individually identified. This article presents a method of straightforwardly identifying not only single and double DNA strands, but also, and more significantly, the hybridized part on them.     

用单分子技术研究抗癌药物顺铂对DNA结构的影响

文章作者用磁镊与原子力显微镜研究了抗癌药物顺铂对单个DNA分子结构的影响.当顺铂浓度较低时,DNA链变得柔软,驻留长度从～52 nm显著缩短到～15 nm;当顺铂浓度较高时,DNA表现出凝聚现象.基于单分子拉伸和原子力显微镜(AFM)成像两方面的实验结果,文章作者提出一个顺铂导致的DNA变软(softening)-成环(looping)-缩短(shortening)-凝聚(condensing)模型(简写为SLSC模型)来解释观察到的DNA凝聚,并认为通过远程交联使DNA形成小环结构是铂类抗癌药物作用的重要特征.     

Application of self-consistent field theory to self-assembled bilayer membranes

Bilayer membranes self-assembled from amphiphilic molecules such as lipids, surfactants, and block copolymers are ubiquitous in biological and physiochemical systems. The shape and structure of bilayer membranes depend crucially on their mechanical properties such as surface tension, bending moduli, and line tension. Understanding how the molecular properties of the amphiphiles determine the structure and mechanics of the self-assembled bilayers requires a molecularly detailed theoretical framework. The self-consistent field theory provides such a theoretical framework, which is capable of accurately predicting the mechanical parameters of self-assembled bilayer membranes. In this mini review we summarize the formulation of the self-consistent field theory, as exemplified by a model system composed of flexible amphiphilic chains dissolved in hydrophilic polymeric solvents, and its application to the study of self-assembled bilayer membranes.     

Assessing the structure and function of single biomolecules with scanning transmission electron and atomic force microscopes

The scanning transmission electron microscope (STEM) and the atomic force microscope (AFM) have provided a wealth of useful information on a wide variety of biological structures. These instruments have in common that they raster-scan a probe over a sample and are able to address single molecules. In the STEM the probe is a focused electron beam that is deflected by the scan-coils. Detectors collecting the scattered electrons provide quantitative information for each sub-nanometer sized sample volume irradiated. These electron scattering data can be reconstituted to images of single macromolecules or can be integrated to provide the mass of the macromolecules. Samples need to be dehydrated for such quantitative STEM imaging. In contrast, the AFM raster-scans a sharp tip over a sample surface submerged in a buffer solution to acquire information on the sample's surface topography at sub-nanometer resolution. Direct observation of function-related structural changes induced by variation of temperature, pH, ionic strength, and applied force provides insight into the structure-function relationship of macromolecules. Further, the AFM allows single molecules to be addressed and quantitatively unfolded using the tip as nano-tweezers. The performance of these two scanning probe approaches is illustrated by several examples including the chaperonin GroEL, bacterial surface layers, protein crystals, and bacterial appendices.     

The re-entrant cholesteric phase of DNA

The character of packing of double-stranded DNA molecules in particles of liquid-crystal dispersions formed as a result of the phase exclusion of DNA molecules from aqueous salt polyethylene glycol solutions has been estimated by comparing the circular dichroism (CD) spectra of these dispersions recorded at different osmotic pressures and temperatures. It is shown that the first cycle of heating of dispersion particles with hexagonally packed double-stranded DNA molecules leads to the occurrence of abnormal optical activity of these particles, which manifests itself in the form of a strong negative CD band, characteristic of DNA cholesterics. Moreover, subsequent cooling is accompanied by a further increase in the abnormal optical activity, which indicates the existence of the “hexagonal → cholesteric packing” phase transition, controlled by both the osmotic pressure of the solution and its temperature. The result obtained can be described in terms of “quasi-nematic” layers composed of orientationally ordered DNA molecules in the structure of dispersion particles. There are two possible ways of packing for these layers, which determine their hexagonal or cholesteric spatial structure. The second heating → cooling cycle confirms these results and is indicative of possible differences in the packing of double-stranded DNA molecules in the hexagonal phase, which depend on the osmotic pressure of the solution.     

Raman optical activity of an achiral element in a chiral environment

Raman optical activity (ROA) is a relatively new technique used to determine the structure of chiral molecules and is proving useful in the study of biological molecules such as proteins and DNA/RNA. Here, for the first time, we demonstrate the applicability of ROA as a technique to study achiral groups in chiral environments, detecting the induced chirality of N‐(fluorenyl‐9‐methoxycarbonyl) (Fmoc) in a chiral self‐assembled structure of Fmoc‐dipeptides. This technique is therefore of interest to those studying self‐assembled systems that adopt a chiral structure. Copyright © 2009 John Wiley & Sons, Ltd.