Surface modification of thermoplastics--towards the plastic biochip for high throughput screening devices

Microarrays have become one of the most convenient tools for high throughput screening, supporting major advances in genomics and proteomics. Other important applications can be found in medical diagnostics, detection of biothreats, drug discovery, etc. Integration of microarrays with microfluidic devices can be highly advantageous in terms of portability, shorter analysis time and lower consumption of expensive biological analytes. Since fabrication of microfluidic devices using traditional materials such as glass is rather expensive, there is great interest in employing polymeric materials as a low cost alternative that is suitable for mass production. A number of commercially available plastic materials were reviewed for this purpose and poly(methylmethacrylate) Zeonor 1060R and Zeonex E48R were identified as promising candidates, for which methods for surface modification and covalent immobilization of DNA oligonucleotides were developed. In addition, we present proof-of-concept plastic-based microarrays with and without integration with microfluidics.     

Microarray technology as a universal tool for high-throughput analysis of biological systems

Over the last years microarray technology has become one of the principal platform technologies for the high-throughput analysis of biological systems. Starting with the construction of first DNA microarrays in the 1990s, microarray technology has flourished in the last years and many different new formats have been developed. Peptide and protein microarrays are now applied for the elucidation of interaction partners, modification sites and enzyme substrates. Antibody microarrays are envisaged to be of high importance for the high-throughput determination of protein abundances in translational profiling approaches. First cell microarrays have been constructed to transform microarray technology from an in vitro technology to an in vivo functional analysis tool. All of these approaches share a common prerequisite: the solid support on which they are generated. The demands on this solid support are thereby as manifold as the applications themselves. This review is aimed to display the recent developments in surface chemistry and derivatization, and to summarize the latest developments in the different application areas of microarray technology.     

Applications of protein microarray technology

Protein microarrays, an emerging class of proteomic technologies, are quickly becoming essential tools for large-scale and high throughput biochemistry and molecular biology. Recent progress has been made in all the key steps of protein microarray fabrication and application, such as the large-scale cloning of expression-ready prokaryotic and eukaryotic ORFs, high throughput protein purification, surface chemistry, protein delivery systems, and detection methods. Two classes of protein microarrays are currently available: analytical and functional protein microarrays. In the case of analytical protein microarrays, well-characterized molecules with specific activity, such as antibodies, peptide-MHC complexes, or lectins, are used as immobilized probes. These arrays have become one of the most powerful multiplexed detection platforms. Functional protein microarrays are being increasingly applied to many areas of biological discovery, including drug target identification/validation and studies of protein interaction, biochemical activity, and immune responses. Great progress has been achieved in both classes of protein microarrays in terms of sensitivity and specificity, and new protein microarray technologies are continuing to emerge. Finally, protein microarrays have found novel applications in both scientific research and clinical diagnostics.     

Microarray and nanotechnology applications of functional nanoparticles

Microarrays are a sensitive, specific, miniaturized devices that may be used to detect selected DNA sequences and proteins, or mutated genes associated with human diseases. Several methods have been developed to detect the binding of complementary molecules to microarrays by generating an optical signal. One of the most commonly used molecular labeling methods at present is fluorescence, but its application is expensive due to sophisticated equipment required to design the platform, hybridize it, and interpret the images derived from microarray-based studies. This is a drawback for its use in laboratories and clinical services. Another less expensive procedure having similar sensitivity and specificity is DNA and protein functional nanoparticles (FNP). Nanoparticles are sphere-like biocompatible materials made of inert silica, metal or crystals of a nanometer in size, which are generally coated with a thin gold layer. They may be used as hybridization probes in single nucleotide polymorphism (SNP) screening and to detect biological markers for cancer, infection, and cardiovascular diseases.     

Structure-related clustering of gene expression fingerprints of thp-1 cells exposed to smaller polycyclic aromatic hydrocarbons

This study was undertaken to test the hypothesis that structurally similar PAHs induce similar gene expression profiles. THP-1 cells were exposed to a series of 12 selected PAHs at 50 microM for 24 hours and gene expressions profiles were analyzed using both unsupervised and supervised methods. Clustering analysis of gene expression profiles revealed that the 12 tested chemicals were grouped into five clusters. Within each cluster, the gene expression profiles are more similar to each other than to the ones outside the cluster. One-methylanthracene and 1-methylfluorene were found to have the most similar profiles; dibenzothiophene and dibenzofuran were found to share common profiles with fluorine. As expression pattern comparisons were expanded, similarity in genomic fingerprint dropped off dramatically. Prediction analysis of microarrays (PAM) based on the clustering pattern generated 49 predictor genes that can be used for sample discrimination. Moreover, a significant analysis of Microarrays (SAM) identified 598 genes being modulated by tested chemicals with a variety of biological processes, such as cell cycle, metabolism, and protein binding and KEGG pathways being significantly (p < 0.05) affected. It is feasible to distinguish structurally different PAHs based on their genomic fingerprints, which are mechanism based.     

化学生物学中光敏分子微阵列的表面构建与应用

分子微阵列是有机合成（特别是组合化学合成）方法应用于生物和医学研究而发展起来的高科技集成技术,通过把微电子、微加工技术和有机化学合成反应相结合,在固体基质（如硅片、玻片、瓷片等）表面构建微型的生物有机化学分子系统,以实现对细胞、蛋白质、核酸及其他生物组分进行快速、敏感、高效地处理．近年来,随着表面化学构建策略研究的不断深入和迅猛发展,分子微阵列技术的应用领域不断拓展,已从最初用于核酸分子的杂交测序延伸到基因组功能研究的各个方面．本文着重综述了光敏分子微阵列的表面化学构建策略研究及其在化学生物学分析中应用的最新进展,并展望了其发展的未来趋势．内容主要包括：小分子与多肽分子微阵列、蛋白质分子微阵列、核酸分子微阵列和糖分子微阵列等．     

Automated analytical microarrays: a critical review

Microarrays provide a powerful analytical tool for the simultaneous detection of multiple analytes in a single experiment. The specific affinity reaction of nucleic acids (hybridization) and antibodies towards antigens is the most common bioanalytical method for generating multiplexed quantitative results. Nucleic acid-based analysis is restricted to the detection of cells and viruses. Antibodies are more universal biomolecular receptors that selectively bind small molecules such as pesticides, small toxins, and pharmaceuticals and to biopolymers (e.g. toxins, allergens) and complex biological structures like bacterial cells and viruses. By producing an appropriate antibody, the corresponding antigenic analyte can be detected on a multiplexed immunoanalytical microarray. Food and water analysis along with clinical diagnostics constitute potential application fields for multiplexed analysis. Diverse fluorescence, chemiluminescence, electrochemical, and label-free microarray readout systems have been developed in the last decade. Some of them are constructed as flow-through microarrays by combination with a fluidic system. Microarrays have the potential to become widely accepted as a system for analytical applications, provided that robust and validated results on fully automated platforms are successfully generated. This review gives an overview of the current research on microarrays with the focus on automated systems and quantitative multiplexed applications. Figure MCR 3: A fully automated chemiluminescence microarray reader for analytical microarrays     

Structure-related clustering of gene expression fingerprints of thp-1 cells exposed to smaller polycyclic aromatic hydrocarbons

This study was undertaken to test the hypothesis that structurally similar PAHs induce similar gene expression profiles. THP-1 cells were exposed to a series of 12 selected PAHs at 50 µM for 24 hours and gene expressions profiles were analyzed using both unsupervised and supervised methods. Clustering analysis of gene expression profiles revealed that the 12 tested chemicals were grouped into five clusters. Within each cluster, the gene expression profiles are more similar to each other than to the ones outside the cluster. One-methylanthracene and 1-methylfluorene were found to have the most similar profiles; dibenzothiophene and dibenzofuran were found to share common profiles with fluorine. As expression pattern comparisons were expanded, similarity in genomic fingerprint dropped off dramatically. Prediction analysis of microarrays (PAM) based on the clustering pattern generated 49 predictor genes that can be used for sample discrimination. Moreover, a significant analysis of Microarrays (SAM) identified 598 genes being modulated by tested chemicals with a variety of biological processes, such as cell cycle, metabolism, and protein binding and KEGG pathways being significantly (p < 0.05) affected. It is feasible to distinguish structurally different PAHs based on their genomic fingerprints, which are mechanism based.     

Cubanes: Starting Materials for the Chemistry of the 1990s and the New Century

The study of non-natural products has led to a broad understanding of bonding and reactivity in organic chemistry. Many times, compounds thought impossible have been realized in the course of such studies. Cubane, a landmark in the world of “impossible” compounds, has been found to have a rich chemistry, full of the unexpected. The recent renaissance of cubane chemistry, triggered by potential applications of the system to the production of high-energy fuels and the like, has led to many discoveries including the first methods for systematic substitution on strained, saturated systems and a new process for the metalation of arenes, ortho magnesiation. Reactive intermediates with exceptional bonding parameters have been uncovered and characterized including 1(9)-homocubene, the most twisted olefin; cubene, the most pyramidalized olefin; cubyl cation, once the “least likely” cation; cubylmethyl radical, a saturated radical that rearranges on the picosecond timescale; and many other extraordinary species. There is certainly good reason to believe that future work in the cubane arena will be at least as productive (probably more so), and that it will help develop a deeper understanding of chemistry.     

Reading Polymers: Sequencing of Natural and Synthetic Macromolecules

The sequencing of biopolymers such as proteins and DNA is among the most significant scientific achievements of the 20th century. Indeed, modern chemical methods for sequence analysis allow reading and understanding the codes of life. Thus, sequencing methods currently play a major role in applications as diverse as genomics, gene therapy, biotechnology, and data storage. However, in terms of fundamental science, sequencing is not really a question of molecular biology but rather a more general topic in macromolecular chemistry. Broadly speaking, it can be defined as the analysis of comonomer sequences in copolymers. However, relatively different approaches have been used in the past to study monomer sequences in biological and manmade polymers. Yet, these “cultural” differences are slowly fading away with the recent development of synthetic sequence‐controlled polymers. In this context, the aim of this Minireview is to present an overview of the tools that are currently available for sequence analysis in macromolecular science.     

Microbial and Enzymatic Processes for the Production of Biologically and Chemically Useful Compounds [New Synthetic Methods (69)]

In recent years, the most significant development in the field of synthetic organic chemistry has been the application of biological systems to chemical reactions. Reactions catalyzed by enzymes and enzyme systems display far greater specificities than more conventional organic reactions. Biological and/or enzymatic syntheses and transformations, that is, “microbial transformations,” have great potential. Some of these reactions have already been shown to have useful applications in the fields of synthetic organic chemistry and biotechnology. This article reviews the current status of the rapidly developing field of microbial transformation, the methodology, available technological procedures, and fields of application being described especially in relation to conventional organic synthesis methods.     

New routes in the synthesis of metal oxides,I

Single crystals of numerous new metal oxides “rich in cations” are prepared by using methods such as dis- or conproportionation, thermal decomposition of higher valence oxides, or oxidation of metals and intermetallic compounds (“reactions with the wall”). Exchange reactions allow growth of single crystals even outside of thermodynamic equilibrium. The role of vacancies in structural chemistry as well as in “tailor-made” syntheses is emphasized and illustrated. Molecular aspects of solid state chemistry are demonstrated by cutting chains or rings and by dimerization of small entities. Many examples are provided.     

分析化学进展

随着纳米材料、膜材料、有机功能材料、离子液体,以及光电技术、计算机科学的发展,分析化学在色谱、质谱、光谱、电分析等各分支领域都取得了重要进展。当然,分析化学的发展也有力地推动了我国的生命科学、材料科学、医学、生态与环境化学、矿产、食品安全等许多领域和学科的发展和进步。近年来,我国分析化学学科在与生命科学的学科交叉研究十分活跃,主要集中在蛋白质组学、代谢组学、金属组学中的新分析方法和新分析技术,例如纳米生物技术、生物传感器、微流控系统与芯片技术等,取得了一大批重要的研究成果。此外,针对食品安全、生态环境监测、药品检测、流行疾病应急响应等人们关注的热点开发了许多新的实用技术与方法;在大中型分析仪器的研发方面也取得喜人的进步。共引用97篇参考文献。     

Analysis of Low Molecular Weight Homologues of Fiber-Forming Polycondensates

Oligomers belong to the gray area between low molecular weight chemistry and macromolecular chemistry. Although they represent an undesirable “natural impurity” in fiber-forming polycondensates, they serve as useful model compounds for the corresponding polymers in fundamental research. Whereas for many years new classes of oligomers were being made preparatively accessible and the isolation of higher oligomers in pure form was being pursued, at the present time the emphasis is on analysis. By a combination of classical chemical and instrumental methods of analysis from polymer and organic chemistry, the identification of oligomers of unknown structure, the analytical control of their synthesis and the determination of their content in technical polymers has meanwhile become a routine task.     

Methods for the determination of water in polymers

Water may be “weakly” or “strongly” bound to other substances by physical or chemical forces. Knowledge of the amount of water and the type of bonding in polymeric materials is very important in control of many polymerization processes and in the physical behavior of the polymer. Hundreds of methods have been proposed for the determination of water in concentrations ranging from p.p.b. to high percentages. Some are direct; others require preliminary concentration or chemical reaction. The most useful methods of analysis for water in polymers are based on chemical, spectroscopic, gravimetric, thermal, electrical, and physical techniques. Chemical methods are represented by Karl Fischer titration, acylation, and nitride reactions. Infrared, nuclear magnetic resonance, and mass spectrometry are the principal spectroscopic approaches. Other useful methods include direct weight loss, thermogravimetry, differential thermal analysis, thermal evolution analysis, dielectric constant, conductance, coulometry, chromatography, azeotropic distillation, piezoelectric, manometric, and volumetric procedures. Recent developments are described with emphasis on applications of these techniques.     

Modern Analysis

The important advances being made in modern analytical methods are indicative of the fundamental changes that are occuring in the theory and practice of “analytical chemistry”. “Information optimization” demands a new approach in teaching and research, and calls for the intergration of chemistry with other scientific and technical disciplines.     

理论化学与下世纪“化学学科重组”前瞻

本文展望了理论化学的发展趋势并预言了下个世纪“化学学科的重组”。作者建议了现代化学的定义：化学是研究从原子,分子片,分子,超分子,生物大分子到分子的各种不同尺度和不同程度的聚集态的合成和反应,分离和分析,结构和形态,物理性能和生物活性及其规律和应用的科学． 根据这个定义,从化学的研究对象不同,在２１ 世纪化学分支学科可能发生重组,因此化学可以划分为如下八个层次：１） 原子层次的化学; ２） 分子片层次的化学; ３） 分子层次的化学; ４） 超分子层次的化学; ５）生物与分子层次的化学; ６） 宏观聚集态化学; ７） 介观聚集态化学和８） 复杂分子体系的化学     

Spin-chemical approach to photochemistry: reaction control by spin quantum operation

In this review, the contribution of spin chemistry (in particular, magnetic resonance-related chemistry) to the photochemical field is briefly introduced. First, the development of a time-resolved EPR method and its significant application to radical-related physical phenomena and chemical reactions are presented. Second, a reaction-control method by means of electron spin operations is introduced, and several reaction yield-detected magnetic resonance (RYDMR) methods are presented as applications of this concept. One of the most important physical conclusions is the introduction of the concept of “spin phase relaxation” termed singlet–triplet (S–T) and triplet–triplet (T–T) dephasing, instead of the traditional concepts of longitudinal (T₁) and transversal relaxations (T₂). The effects of strong microwave power on the RYDMR spectrum and time-domain data are analyzed according to this concept. Furthermore, a new detection method is introduced, termed “photoconductivity detected magnetic resonance” (PCDMR), which is applicable exclusively to the system of charge transfer reactions.     

Starburst Dendrimers: Molecular-Level Control of Size,Shape, Surface Chemistry,Topology, and Flexibility from Atoms to Macroscopic Matter

Starburst dendrimers are three-dimensional, highly ordered oligomeric and polymeric compounds formed by reiterative reaction sequences starting from smaller molecules—“initiator cores” such as ammonia or pentaerythritol. Protecting group strategies are crucial in these syntheses, which proceed via discrete “Aufbau” stages referred to as generations. Critical molecular design parameters (CMDPs) such as size, shape, and surface chemistry may be controlled by the reactions and synthetic building blocks used. Starburst dendrimers can mimic certain properties of micelles and liposomes and even those of biomolecules and the still more complicated, but highly organized, building blocks of biological systems. Numerous applications of these compounds are conceivable, particularly in mimicking the functions of large biomolecules as drug carriers and immunogens. This new branch of “supramolecular chemistry” should spark new developments in both organic and macromolecular chemistry.