The developing biosensor arena

The inherent specificity of biological molecules is currently being successfully exploited in the development of analytical biosensors. The physicochemical changes that occur when enzymes or antibodies recognize and respond to their substrates is being monitored in a variety of innovative devices in which the biological species is coupled with a suitable transducer, converting the concentration of analyte into a quantifiable electrical signal. The development of these biosensors is proceeding alongside the semiconductor and fibre-optic revolutions and represents a union of expertise from the fields of microelectronics, electrochemistry, optics and of course biochemistry.     

Applications of cell-free protein synthesis in synthetic biology: Interfacing bio-machinery with synthetic environments

Synthetic biology is built on the synthesis, engineering, and assembly of biological parts. Proteins are the first components considered for the construction of systems with designed biological functions because proteins carry out most of the biological functions and chemical reactions inside cells. Protein synthesis is considered to comprise the most basic levels of the hierarchical structure of synthetic biology. Cell-free protein synthesis has emerged as a powerful technology that can potentially transform the concept of bioprocesses. With the ability to harness the synthetic power of biology without many of the constraints of cell-based systems, cell-free protein synthesis enables the rapid creation of protein molecules from diverse sources of genetic information. Cell-free protein synthesis is virtually free from the intrinsic constraints of cell-based methods and offers greater flexibility in system design and manipulability of biological synthetic machinery. Among its potential applications, cell-free protein synthesis can be combined with various man-made devices for rapid functional analysis of genomic sequences. This review covers recent efforts to integrate cell-free protein synthesis with various reaction devices and analytical platforms.     

微流控器件-质谱联用接口技术研究进展与应用

生物分析是生命科学研究中的重要环节,分析仪器的小型化是提高生物分析灵敏度、速度、通量和降低成本的有效途径之一.微流控技术能够方便地操纵微量样品,具有集成度高、样品耗量小、污染少等诸多其他常量流控技术难以具备的优点,适用于进行多通道样品处理和高通量分析.除广泛采用的光学和电化学检测手段外,质谱也被用作这些微流控器件的检测器,并逐渐形成了微流控器件-质谱联用技术专门研究领域,进一步促进了自动化程度好、灵敏度高、特异性强的高通量生物分析方法的迅速发展.在大量调研国内外文献的基础上,对微流控器件-质谱联用领域的研究背景和现状进行了综述,不但介绍了微流控器件的制造技术还着重介绍了微流控器件-质谱联用技术在蛋白质组学等生物质谱分析方面的应用和新近进展,评述了可能的发展趋势.     

Ion mobility mass spectrometry for peptide analysis

The use of ion mobility mass spectrometry has grown rapidly over the last two decades. This powerful analytical platform now forms an attractive prospect for comprehensive analysis of many different molecular species, including chemically complex biological molecules. This paper describes the application of IM-MS to the study of peptides. We focus on three different ion mobility devices that are most frequently found in tandem with mass spectrometers. These are instruments using linear drift tubes (LDT), those using travelling wave ion guides (TWIGS) and those employing high field asymmetric ion mobility spectrometry (FAIMS). Each technique is described. Examples are given on the use of IM-MS for the determination of peptide structure, the study of peptides that form amyloid fibrils, and the study of complex peptide mixtures in proteomic investigations. We describe and comment on the methodologies used and the outlook for this developing analytical technique.     

Fabrication of silicon nanowire devices for ultrasensitive, label-free, real-time detection of biological and chemical species

Detection and quantification of biological and chemical species are central to many areas of healthcare and the life sciences, ranging from diagnosing disease to discovery and screening of new drug molecules. Semiconductor nanowires configured as electronic devices have emerged as a general platform for ultra-sensitive direct electrical detection of biological and chemical species. Here we describe a detailed protocol for realizing nanowire electronic sensors. First, the growth of uniform, single crystal silicon nanowires, and subsequent isolation of the nanowires as stable suspensions are outlined. Second, fabrication of addressable nanowire device arrays is described. Third, covalent modification of the nanowire device surfaces with receptors is described. Fourth, an example modification and measurements of the electrical response from devices are detailed. The silicon nanowire (SiNW) devices have demonstrated applications for label-free, ultrasensitive and highly-selective real-time detection of a wide range of biological and chemical species, including proteins, nucleic acids, small molecules and viruses.     

Towards computing with proteins

Can proteins be used as computational devices to address difficult computational problems? In recent years there has been much interest in biological computing, that is, building a general purpose computer from biological molecules. Most of the current efforts are based on DNA because of its ability to self‐hybridize. The exquisite selectivity and specificity of complex protein‐based networks motivated us to suggest that similar principles can be used to devise biological systems that will be able to directly implement any logical circuit as a parallel asynchronous computation. Such devices, powered by ATP molecules, would be able to perform, for medical applications, digital computation with natural interface to biological input conditions. We discuss how to design protein molecules that would serve as the basic computational element by functioning as a NAND logical gate, utilizing DNA tags for recognition, and phosphorylation and exonuclease reactions for information processing. A solution of these elements could carry out effective computation. Finally, the model and its robustness to errors were tested in a computer simulation. Proteins 2006. © 2006 Wiley‐Liss, Inc.     

New tools and new biology: Recent miniaturized systems for molecular and cellular biology

Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology.     

Introduction to the principles and applications of biosensors

A biosensor is an analytical device that responds to an analyte in an appropriate sample and interprets its concentration as an electrical signal via a suitable combination of a biological recognition system and an electrochemical transducer. As a result of recent scientific and technological progress, such devices are likely to play an increasingly important role in generating analytical information in all sectors of human endeavour, from medicine to the military. In particular, biosensors will form the basis of cheap, simple devices for acquiring chemical information, bringing sophisticated analytical capabilities to the non-specialist and general public alike. The market opportunities for the rapid exploitation of novel developments in this sector are substantial. Biosensor research is also likely to have a significant impact on the development of modern electronics.     

Do biomolecules process information differently than synthetic organic molecules?

This paper compares information/signal processing in synthetic and biological molecules. The role of conformation-based (shape-based) mechanisms and electrostatic interactions in molecular recognition is discussed. In biological electron transfer, the 'electron shuttle'-mediated mechanism is contrasted with the mechanism based on pre-formed 'electron wires'. While biological information processing is thought to be more distributed (less discrete), an example of molecular switch is presented: visual transduction. We further speculate that visual transduction may be implemented in the form of a switch based on electrostatic interactions. The concept of intelligent materials is discussed with the well-known Bohr effect of hemoglobin oxygenation. Based on these examples, we argue that there are no fundamental differences between synthetic and biological molecules in their mode of information processing. In the pursuit of novel paradigms of molecular information processing, we also perceive no conflicts in developing molecular devices that emulate the switching function of conventional microelectronic devices.     

Biosensors

Biosensors are analytical devices that respond selectively to analytes in an appropriate sample and convert their concentration into an electrical signal via a combination of a biological recognition system and an electrochemical, optical or other transducer. Such devices will find application in medicine, agriculture, environmental monitoring and the bioprocessing industries. The last few years have seen great advances in the design of sensor architectures, the marriage of biological systems with monolithic silicon and optical technologies, the development of effective electron-transfer systems and the configuration of direct immunosensors. Recent progress in these areas has already led to the introduction of new-generation biosensors into the competitive diagnostics market place.     

适配体的筛选及在生命分析化学中的应用

指数级富集的配体系统进化技术（SELEX）是近年来发展的获得能够与靶分子高特异性和高亲力结合的寡核苷酸序列（适配体）的筛选技术。目前多种靶分子的适配体如蛋白或小分子,都已经通过SELEX技术筛选获得,使适配体在蛋白质组研究、临床医学、药物研发及基因调控等领域已经成为重要的研究工具。本文就近几年适配体的筛选技术及在生命分析化学中的应用发展方面进行了综述。     

Selecting peptides for use in nanoscale materials using phage-displayed combinatorial peptide libraries

Materials that combine inorganic components and biological molecules provide a new paradigm for synthesizing nanoscale and larger structures with tailored physical properties. These synthesis techniques utilize the molecular recognition properties of many biological molecules to nucleate and control growth of the nanoscale structure. Phage-displayed peptide libraries are a powerful tool to identify peptides that selectively recognize and bind to a variety of inorganic surfaces that are utilized in electronic and photonic devices. These libraries have been used extensively to study the peptide-mediated nucleation and growth of some metallic and semiconducting materials, and the application to designed nanostructures has been demonstrated.     

Monitoring and Control of Bioproducts from Conception to Production in Real‐time Using an Optical Biosensor

The ability to observe biological interactions in real‐time using optical biosensor technology provides the scientist/engineer with a valuable analytical tool to analyze biological molecules. Production of biological products is a growing area, but the course of discovery through to production is lengthy and complex, especially for therapeutic products. However, the economics of developing new products are clear, time to market for a new product is the primary consideration. Limited patent lifetimes, the need to get a return on the investment in research and gain competitive advantage by launching products before competitors all contribute to the necessity to get products to market. The ability of biosensor technology to give rapid, direct information on key biological parameters, (such as product concentration), makes it a suitable analytical tool to help accelerate the development of biological products. It is difficult to conceive how direct measurements of this speed and selectivity can be possible with other analytical methods. This paper aims to describe how this potential can be brought to use from biological product conception and discovery all the way through to process operation and quality control.     

Protein arrays: Concepts and subjects

To adapt proteins, the materials in life, for use as materials in science and technology, we focused not only on the biological aspects (functional aspects) but also on the material aspects as matter (structural and physical aspects). Engineering with protein arrays will develop under such consideration and advance toward stable devices made of protein molecules. The protein arrays with 2D crystalline order provide a primary model of macroscopic protein-based devices. The combination of protein engineering, the leading edge of life science, and array engineering, the leading edge of materials science, will provide clues to the controlled integration of protein molecules to a form of functional supramolecules on proper surfaces.     

Application of multilayer films to molecular sensors: some examples of bioengineering at the molecular level

The Langmuir-Blodgett technique is now a well established method for producing ultra-thin organic films on solid surfaces. These layers could find wide ranging uses in electronic and optoelectronic devices, or even as the basis of artificial biological systems. In this paper the film deposition process is briefly reviewed. Examples of multilayers incorporating biological molecules are presented and possible applications for such films in sensing structures are briefly discussed.     

Surface modification of polymers: chemical, biological and surface analytical challenges

Surface modification methods can optimise the biocompatibility or the specificity of biointeraction of a biosensor or medical device. With only the surface modified, the manufacture and implantation protocol remain unchanged. This review article summarises some of the chemical, surface analytical and biological challenges associated with surface modification of biosensors and biomedical devices.     

Fluorescence correlation spectroscopy for ultrasensitive DNA analysis in continuous flow capillary electrophoresis

Continuous flow capillary electrophoresis (CFCE) is non-separations based analytical technique based on the free solution electrophoretic mobility of biological molecules such as DNA, RNA, peptides, and proteins. The electrophoretic mobilities and translational diffusion constants of the analyte molecules are determined using single molecule detection methods, including fluorescence correlation spectroscopy (FCS). CFCE is used to resolve multiple components in a mixture of analytes, measure electrophoretic mobility shifts due to binding interactions, and study the hydrodynamic and electrostatic properties of biological molecules in solution. Often this information is obtained with greater speed and sensitivity than conventational separations-based capillary-zone electrophoresis. This paper will focus on the application of two-beam fluorescence cross-correlation spectroscopy as a versatile detection method for CFCE and explore several applications to the study of the solution properties of single-stranded DNA.     

BIOSENSORS: BLESSING OR BANE?

Biosensor technology is changing the methodology used to detect or characterize many microorganisms and/or their metabolites of importance to food microbiologists and the food industry. Biosensors have been developed to monitor the freshness of meat and fish. ATP and glucose concentrations have been monitored as well as continuous control operations in food processing. Enzyme-substrate transformations, DNA or RNA hybridizations and antibody-antigen interactions are examples of the types of molecules used in biosensor systems. Instrumentation coupled to the biological molecules and measuring the changes that occur include reactions on simple ion-sensing electrodes, as well as complex chips, optical fibers or piezoelectric crystals. In most cases, data can be obtained within a few minutes on very small amounts of compounds. However, the long term stability of the biological molecules involved in these procedures presents a major stumbling block. Partially or completely disposable devices are under consideration.     

Immobilization of immunoglobulins on silica surfaces. Stability.

The development of new immunosensors based on surface-concentration-measuring devices requires a stable and reproducible immobilization of antibodies on well-characterized solid surfaces. We here report on the immobilization of immunoglobulin G (IgG) on chemically modified silica surfaces. Such surfaces may be used in various surface-oriented analytical methods. Reactive groups were introduced to the silica surfaces by chemical-vapour deposition of silane. The surfaces were characterized by ellipsometry, contact-angle measurements and scanning electron microscopy. IgG covalently bound by the use of thiol-disulphide exchange reactions, thereby controlling the maximum number of covalent bonds to the surface, was compared with IgG adsorbed on various silica surfaces. This comparison showed that the covalently bound IgG has a superior stability when the pH was lowered or incubation with detergents, urea or ethylene glycol was carried out. The result was evaluated by ellipsometry, an optical technique that renders possible the quantification of amounts of immobilized IgG. The results outline the possibilities of obtaining a controlled covalent binding of biomolecules to solid surfaces with an optimal stability and biological activity of the immobilized molecules.     

DNA adduct profiles: chemical approaches to addressing the biological impact of DNA damage from small molecules

Diverse small molecules alkylate DNA and form covalently linked adducts that can influence crucial biological processes, contributing to toxicity and mutation. Understanding the chemical reactivity dictating DNA alkylation and interactions of adducts with biological pathways can impact disease prevention and treatment. The ambident reactivity of DNA-alkylating small molecules, and of DNA itself, often results in formation of multiple adducts. Determining which structures impart biological responses is important for understanding the underlying relationships between small-molecule structure and biology. With application of sensitive and structure-specific experimental and analytical methodology, such as heteronuclear NMR spectroscopy and mass spectrometry, there are increasing numbers of studies that evaluate DNA alkylation from the perspective of resulting adduct profiles. DNA adduct profiles have been examined for both exogenous and endogenous reactive small molecules. Examples of recent findings are in the areas of tobacco-specific carcinogens, lipid peroxidation products, environmental and dietary chlorophenols, and natural-product-derived antitumor therapies. As more profile data are obtained, correlations with biological impact are being observed that would not be identified by a simplified single agent/single adduct approach.