Survey of the year 2003 commercial optical biosensor literature

Waveguide-based total internal reflection fluorescence microscope enabling cellular imaging under cryogenic conditions

Total internal reflection fluorescence (TIRF) microscopy is an important imaging tool for the investigation of biological structures, especially the study on cellular events near the plasma membrane. Imaging at cryogenic temperatures not only enables observing structures in a near-native and fixed state but also suppresses irreversible photo-bleaching rates, resulting in increased photo-stability of fluorophores. Traditional TIRF microscopes produce an evanescent field based on high numerical aperture immersion objective lenses with high magnification, which results in a limited field of view and is incompatible with cryogenic conditions. Here, we present a waveguide-based TIRF microscope, which is able to generate a uniform evanescent field using high refractive index waveguides on photonic chips and to obtain cellular observation at cryogenic temperatures. Our method provides an inexpensive way to achieve total-internal-reflection fluorescence imaging under cryogenic conditions.

Half-life extension of efficiently produced DARPin serum albumin fusions as a function of FcRn affinity and recycling

Serum albumin shows slow clearance from circulation due to neonatal Fc receptor (FcRn)-mediated recycling and has been used for half-life extension. We report here fusions to a high-affinity DARPin, binding to Epithelial Cell Adhesion Molecule (EpCAM). We developed a novel, efficient expression system for such fusion proteins in Pichia pastoris with titers above 300 mg/L of lab-scale shake-flask culture. Since human serum albumin (HSA) does not bind to the murine FcRn, half-lives of therapeutic candidates are frequently measured in human FcRn transgenic mice, limiting useable tumor models. Additionally, serum albumins with extended half-life have been designed. We tested HSA7, motivated by its previously claimed extraordinarily long half-life in mice, which we could not confirm. Instead, we determined a half-life of only 29 h for HSA7, comparable to MSA. The fusion of HSA7 to a DARPin showed a similar half-life. To rationalize these findings, we measured binding kinetics and affinities to murine and human FcRn. Briefly, HSA7 showed affinity to murine FcRn only in the micromolar range, comparable to MSA to its cognate murine FcRn, and an affinity in the nanomolar range only to the human FcRn. This explains the comparable half-life of MSA and HSA7 in mice, while wild-type-HSA has a half-life of only 21 h, as it does not bind the murine FcRn and is not recycled. Thus, HSA-fusions with improved FcRn-affinity, such as HSA7, can be used for preclinical experiments in mice when FcRn transgenes cannot be used, as they reflect better the complex FcRn-mediated recycling and distribution mechanisms.

Carbodiimide-mediated immobilization of acidic biomolecules on reversed-charge zwitterionic sensor chip surfaces

The carbodiimide-mediated amine coupling of protein ligands to sensor chips coated with anionic polycarboxylate hydrogels, such as carboxymethyl dextran, is the predominant covalent immobilization procedure utilized in optical biosensors, namely surface plasmon resonance (SPR) biosensors. Usually, electrostatic interactions at a slightly acidic pH and low ionic strength are employed to efficiently accumulate neutral and basic ligands on the chip surface, which are then covalently coupled by surface-bound active N-hydroxysuccinimide (NHS) esters. Unfortunately, this approach is not suitable for acidic proteins or other ligands with low isoelectric points (IEPs), such as nucleic acids, because the charge density of the polycarboxylates is greatly reduced at acidic pH or because electrostatic attraction cannot be achieved. To overcome these drawbacks, we have established a charge-reversal approach that allows the preconcentration of acidic proteins above their IEPs. A precisely controlled amount of tertiary amines is applied to reverse the previous anionic surface charge while maintaining carbodiimide compatibility with future protein immobilization. The mechanism of this reversed-charge immobilization approach was demonstrated employing protein A as a model protein and using attenuated total reflectance Fourier transform infrared spectroscopy, dynamic contact angle measurements, colorimetric quantification, and SPR analysis to characterize surface derivatization. Furthermore, even though it had previously proven impossible to preconcentrate DNA electrostatically and to covalently couple it to polyanionic chip surfaces, we demonstrated that our approach allowed DNA to be preconcentrated and immobilized in good yields. Graphical abstract Principle of the covalent immobilization of acidic ligands on reversed-charge zwitterionic sensor chip surfaces.

(S)Pinning down protein interactions by NMR

Protein molecules are highly diverse communication platforms and their interaction repertoire stretches from atoms over small molecules such as sugars and lipids to macromolecules. An important route to understanding molecular communication is to quantitatively describe their interactions. These types of analyses determine the amounts and proportions of individual constituents that participate in a reaction as well as their rates of reactions and their thermodynamics. Although many different methods are available, there is currently no single method able to quantitatively capture and describe all types of protein reactions, which can span orders of magnitudes in affinities, reaction rates, and lifetimes of states. As the more versatile technique, solution NMR spectroscopy offers a remarkable catalogue of methods that can be successfully applied to the quantitative as well as qualitative descriptions of protein interactions. In this review we provide an easy-access approach to NMR for the non-NMR specialist and describe how and when solution state NMR spectroscopy is the method of choice for addressing protein ligand interaction. We describe very briefly the theoretical background and illustrate simple protein-ligand interactions as well as typical strategies for measuring binding constants using NMR spectroscopy. Finally, this review provides examples of caveats of the method as well as the options to improve the outcome of an NMR analysis of a protein interaction reaction.

Measuring Protein-Protein Interactions Using Biacore

The use of optical biosensors for studying macromolecular interactions is gaining increasing popularity. In one study, 1514 papers that involved the application of biosensor data were identified for the year 2009 alone (Rich and Myszka, J Mol Recognit 24:892-914, 2011), the sheer volume and variety of which present a daunting task for the burgeoning biosensor user to accumulate and decipher. This chapter is designed to provide the reader with the tools necessary to prepare, design, and efficiently execute a kinetic experiment on Biacore. It is written to guide the Biacore user through basic theory, system maintenance, and assay setup while also offering some practical tips that we find useful for Biacore-based studies. Many kinetic-based screening assays require rigorous sample preparation and purification prior to analysis. To highlight these procedures, this protocol describes the kinetic characterization of single chain Fv (scFv) antibody fragments from crude bacterial lysates using an antibody affinity capture approach. Even though we specifically describe the capture of HA-tagged scFv antibody fragments to an anti-HA tag monoclonal antibody-immobilized surface prior to kinetic analysis, the same methodologies are universally applicable and can be used for practically any affinity pair and most Biacore systems.

Studying protein-protein interactions using surface plasmon resonance

Protein-protein interactions regulate many important cellular processes, including carbohydrate and lipid metabolism, cell cycle and cell death regulation, protein and nucleic acid metabolism, signal transduction, and cellular architecture. A complete understanding of cellular function depends on full characterization of the complex network of cellular protein-protein interactions, including measurements of their kinetic and binding properties. Surface plasmon resonance (SPR) is one of the commonly used technologies for detailed and quantitative studies of protein-protein interactions and determination of their equilibrium and kinetic parameters. SPR provides excellent instrumentation for a label-free, real-time investigation of protein-protein interactions. This chapter details the experimental design and proper use of the instrumentation for a kinetic experiment. It will provide readers with basic theory, assay setup, and the proper way of reporting this type of results with practical tips useful for SPR-based studies. A generic protocol for immobilizing ligands using amino coupling chemistry, also useful if an antibody affinity capture approach is used, performing kinetic studies, and collecting and analyzing data is described.

Plasmonic biosensors

The unique optical properties of plasmon resonant nanostructures enable exploration of nanoscale environments using relatively simple optical characterization techniques. For this reason, the field of plasmonics continues to garner the attention of the biosensing community. Biosensors based on propagating surface plasmon resonances (SPRs) in films are the most well-recognized plasmonic biosensors, but there is great potential for the new, developing technologies to surpass the robustness and popularity of film-based SPR sensing. This review surveys the current plasmonic biosensor landscape with emphasis on the basic operating principles of each plasmonic sensing technique and the practical considerations when developing a sensing platform with the various techniques. The 'gold standard' film SPR technique is reviewed briefly, but special emphasis is devoted to the up-and-coming localized surface plasmon resonance and plasmonically coupled sensor technology.

Biosensor-Based Approach to the Identification of Protein Kinase Ligands with Dual-Site Modes of Action

The authors have used a surface plasmon resonance (SPR)–based biosensor approach to identify and characterize compounds with a unique binding mode to protein kinases. Biacore was used to characterize hits from an enzymatic high-throughput screen of the Tec family tyrosine kinase, IL2-inducible T cell kinase (ITK). Complex binding kinetics was observed for some compounds, which led to identification of compounds that bound simultaneously at both the adenosine triphosphate (ATP) binding site and a second, allosteric site on ITK. The presence of the second binding site was confirmed by X-ray crystallography. The second site is located in the N-terminal lobe of the protein kinase catalytic domain, adjacent to but distinct from the ATP site. To enable rapid optimization of binding properties, a competition-based Biacore assay has been developed to successfully identify second site noncompetitive binders that have been confirmed by X-ray crystallographic studies. The authors have found that SPR technology is a key method for rapid identification of compounds with dual-site modes of action.

Measuring protein-protein interactions using Biacore

The use of optical biosensors for studying macromolecular interactions is gaining increasing popularity. In one study, 1,179 papers that involved the application of biosensor data were identified for the year 2007 alone (Rich and Myszka, J Mol Recognit 21:355-400, 2008), the sheer volume and variety of which present a daunting task for the burgeoning biosensor user to accumulate and decipher. This chapter is designed to provide the reader with the tools necessary to prepare, design, and efficiently execute a kinetic experiment on Biacore. It is written to guide the Biacore user through basic theory, system maintenance, and assay set-up while also offering some practical tips that we find useful for Biacore-based studies. Many kinetic-based screening assays require rigorous sample preparation and purification prior to analysis. To highlight these procedures, this protocol describes the kinetic characterisation of single chain Fv (scFv) antibody fragments from crude bacterial lysates using an antibody affinity capture approach. Even though we specifically describe the capture of HA-tagged scFv antibody fragments to an anti-HA tag monoclonal antibody-immobilised surface prior to kinetic analysis, the same methodologies are universally applicable and can be used for practically any affinity pair and most Biacore systems.

Surface plasmon resonance spectroscopy: a new lead in studying the membrane binding of amyloidogenic transthyretin

Surface plasmon resonance (SPR) employs the optical principle of SPR to measure changes in mass on a sensor chip surface in real time. Surface chemistry has been developed which enables the immoblization of lipid bilayers and determination of protein-membrane interactions in real time. In the last decade, the plasma membrane has been demonstrated to play an important role in amyloidogenesis and cytotoxicity induced by amyloidogenic proteins. SPR provides an ideal way to study the membrane binding of amyloidogenic proteins. In this chapter, we describe the application of SPR to the study of amyloidogenic transthyretin binding to the plasma membrane and artificial lipid bilayers.

Surface plasmon resonance for vaccine design and efficacy studies: recent applications and future trends

The lack of a clear correlation between design and protection continues to present a barrier to progress in vaccine research. In this article, we outline how surface plasmon resonance (SPR) biosensors are emerging as tools to help resolve some of the key biophysical determinants of protection and, thereby, facilitate more rational vaccine design campaigns. SPR technology has contributed significantly to our understanding of the complex biophysical determinants of HIV neutralization and offers a platform for preclinical evaluation of vaccine candidates. In particular, the concept of reverse-engineering HIV vaccine targets based on known broadly neutralizing antibody modalities is explored and extended to include other infectious diseases, such as malaria and influenza, and other diseases such as cancer. The analytical capacity afforded by SPR includes serum screening to monitor immune responses and highly efficient quality-control surveillance measures. These are discussed alongside key technological advances, such as developments in sample throughput, and a perspective predicting continued growth and diversification of the role of SPR in vaccine development is proposed.

Surface plasmon resonance biosensorics in urine proteomics

Surface plasmon resonance (SPR) is a novel biophysical detection method. In combination with sophisticated surface chemistries and sensing instrumentations, SPR biosensors are approved as tools for molecular interaction studies. SPR plays also a role in interaction proteomics. Once being detected in urine, SPR helps to unravel the functions of new proteins. Due to its outstanding analytical characteristics, SPR also moves more and more into the realm of quantitative analyses in the clinical laboratory. Complex urine determinations of proteins and/or metabolites will bring the SPR biosensor both to the core lab and to point-of-care-testing.This review delineates first the optical phenomena of SPR near to the gold surface, and also the main features of bioconjugation chemistry on a solid-state surface. Then the kinetic calculation of molecular interaction analysis using SPR is introduced. In order to portray the capability of the method, new applications in urine proteomics and proteinuria diagnostics are finally described in detail.

Reactive surface coatings based on polysilsesquioxanes: controlled functionalization for specific protein immobilization

The key designing in reliable biosensors is the preparation of thin films in which biomolecular functions may be immobilized and addressed in a controlled and reproducible manner. This requires the controlled preparation of specific binding sites on planar surfaces. Poly(methylsilsesquioxane)-poly(pentafluorophenyl acrylates) (PMSSQ-PFPA) are promising materials to produce stable and adherent thin reactive coatings on various substrates. Those reactive surface coatings could be applied onto various materials, for example, gold, polycarbonate (PC), poly(tetrafluoroethylene) (PTFE), and glass. By dipping those substrates in a solution of a desired amine, specific binding sites for protein adsorption could be immobilized on the surface. The versatile strategy allowed the attachment of various linkers, for example, biotin, l-thyroxine, and folic acid. The adsorption processes of streptavidin, pre-albumin, and folate-binding protein were monitored using surface plasmon resonance (SPR), Fourier transform infrared (FTIR) spectroscopy, fluorescence spectroscopy, and atomic force microscopy (AFM). The presented protein immobilization strategy, consisting of four steps (a) spin-coating of PMSSQ-PFPA hybrid polymer from tetrahydrofuran (THF) solution, (b) annealing at 130 degrees C for 2 h to induce thermal cross-linking of the PMSSQ part, (c) surface analogues reaction with different amino-functionalized specific binding sites for proteins, and (d) controlled assembly of proteins on the surface, may find various applications in future biosensor design.

Noncompetitive peak decay analysis of drug-protein dissociation by high-performance affinity chromatography

The peak decay method is an affinity chromatographic technique that has been used to examine the dissociation of solutes from immobilized ligands in the presence of excess displacing agent. However, it can be difficult to find a displacing agent that does not interfere with detection of the eluting analyte. In this study, a noncompetitive peak decay method was developed in which no displacing agent was required for analyte elution. This method was evaluated for the study of drug-protein interactions by using it along with high-performance affinity chromatography to measure the dissociation rate constants for R- and S-warfarin from columns containing immobilized HSA. Several factors were considered in the optimization of this method, including the amount of applied analyte, the column size, and the flow rate. The dissociation rate constants for R- and S-warfarin from HSA were measured at several temperatures by this approach, giving values of 0.56 (+/-0.01) and 0.66 (+/-0.01) s(-1) at pH 7.4 and 37 degrees C. These results were in good agreement with previous values obtained by other methods. This approach is not limited to warfarin and HSA but could be employed in studying additional drug-protein interactions or other systems with weak-to-moderate binding.

Exploiting Surface Plasmon Resonance (SPR) Technology for the Identification of Fibroblast Growth Factor-2 (FGF2) Antagonists Endowed with Antiangiogenic Activity

Angiogenesis, the process of new blood vessel formation, is implicated in various physiological/pathological conditions, including embryonic development, inflammation and tumor growth. Fibroblast growth factor-2 (FGF2) is a heparin-binding angiogenic growth factor involved in various physiopathological processes, including tumor neovascularization. Accordingly, FGF2 is considered a target for antiangiogenic therapies. Thus, numerous natural/synthetic compounds have been tested for their capacity to bind and sequester FGF2 in the extracellular environment preventing its interaction with cellular receptors. We have exploited surface plasmon resonance (SPR) technique in search for antiangiogenic FGF2 binders/antagonists. In this review we will summarize our experience in SPR-based angiogenesis research, with the aim to validate SPR as a first line screening for the identification of antiangiogenic compounds.

Waveguide-based biosensors for pathogen detection

Optical phenomena such as fluorescence, phosphorescence, polarization, interference and non-linearity have been extensively used for biosensing applications. Optical waveguides (both planar and fiber-optic) are comprised of a material with high permittivity/high refractive index surrounded on all sides by materials with lower refractive indices, such as a substrate and the media to be sensed. This arrangement allows coupled light to propagate through the high refractive index waveguide by total internal reflection and generates an electromagnetic wave-the evanescent field-whose amplitude decreases exponentially as the distance from the surface increases. Excitation of fluorophores within the evanescent wave allows for sensitive detection while minimizing background fluorescence from complex, "dirty" biological samples. In this review, we will describe the basic principles, advantages and disadvantages of planar optical waveguide-based biodetection technologies. This discussion will include already commercialized technologies (e.g., Corning's EPIC(®) Ô, SRU Biosystems' BIND(™), Zeptosense(®), etc.) and new technologies that are under research and development. We will also review differing assay approaches for the detection of various biomolecules, as well as the thin-film coatings that are often required for waveguide functionalization and effective detection. Finally, we will discuss reverse-symmetry waveguides, resonant waveguide grating sensors and metal-clad leaky waveguides as alternative signal transducers in optical biosensing.

Approach for reliable evaluation of drug proteins interactions using surface plasmon resonance technology

The surface plasmon resonance (SPR) biosensor was recently introduced to the analytical biochemical society for measuring small drug-protein interactions. However, the technique has many times been used without specifying the type of enantiomeric form of the chiral drug measured and/or with using a too narrow drug concentration range resulting in biased values of binding coefficients and sometimes even assumptions about single-site bindings although the binding in reality comprises a multisite interaction. In this study we will give guidelines for reliable experimental and methodological approaches to avoid these pitfalls. For this purpose, we also introduce a new tool, based on physical chemistry, to the sensor community; the calculation of the adsorption energy distribution (AED). The AED-calculations reveal the degree of heterogeneity directly from the SPR raw data and thus guide us into a narrower selection of probable models before the rival model fitting procedure. We demonstrate how to measure reliable equilibrium data for the two typically different cases: drug binding to (i) transport (plasma) proteins and to (ii) a target protein. Both the binding of the chiral beta-blocker propranolol to alpha(1)-acid glycoprotein (AGP) and that of the anticoagulant warfarin to human serum albumin were heterogeneous, with a few strong enantioselective sites and many weak nonselective sites. We also demonstrate how the multisite binding rapidly falsely turns to single-site as the concentration range is narrowed and how adding dimethyl sulfoxide to the buffer affects multisite drug-protein data. The binding of the enantiomers of the thrombin inhibitor melagatran was investigated on both thrombin and the transport proteins, revealing clear enantioselectivity for thrombin in favor of the active enantiomer, but almost similar binding properties for both enantiomers to the transport protein AGP. The AED-calculations verified that both these system has a unimodal energy distribution and are best described with a homogeneous adsorption model.

Phenolics: occurrence and immunochemical detection in environment and food

Phenolic compounds may be of natural or anthropogenic origin and be present in the environment as well as in food. They comprise a large and diverse group of compounds that may be either beneficial or harmful for consumers. In this review first a non-exhausting overview of interesting phenolics is given, in particular with regards to their presence in environment and food. For some of these compounds, beneficial, toxicological and/or optionally endocrine disrupting activities will be presented. Further, immunochemical detection and/or isolation methods developed will be discussed, including advantages and disadvantages thereof in comparison with conventional analytical methods such as HPLC, GC, MS. A short overview of new sensor-like methods will also be included for present and future application.

Detergent screening of a G-protein-coupled receptor using serial and array biosensor technologies

We describe the benefits and limitations of two biosensor approaches for screening solubilization conditions for G-protein-coupled receptors (GPCRs). Assays designed for a serial processing instrument (Biacore 2000/3000/T100) and an array platform (Biacore Flexchip) were used to examine how effectively 96 different detergents solubilized the chemokine receptor CCR5 while maintaining its binding activity for a conformationally sensitive Fab (2D7). Using the serial processing instrument, we were able to analyze three samples in each 30-min binding cycle, thereby requiring approximately 24h to screen an entire 96-well plate of conditions. In-line capturing allowed us to normalize the 2D7 binding responses for different receptor capture levels. In contrast, with the array system, we could characterize the effects of all 96 detergents simultaneously, completing the assay in less than 1h. But the current array technology requires that we capture the GPCR preparations off-line, making it more challenging to normalize for receptor capture levels. Also, the array platform is less sensitive than the serial platforms, thereby limiting the size of the analyte to larger molecules (>5000Da). Overall, the two approaches proved to be highly complementary; both assays identified identical detergents that produced active solubilized CCR5 as well as those detergents that either were ineffective solubilizers or inactivated the receptor.

Chemical strategies for generating protein biochips

Protein biochips are at the heart of many medical and bioanalytical applications. Increasing interest has been focused on surface activation and subsequent functionalization strategies for immobilizing these biomolecules. Different approaches using covalent and noncovalent chemistry are reviewed; particular emphasis is placed on the chemical specificity of protein attachment and on retention of protein function. Strategies for creating protein patterns (as opposed to protein arrays) are also outlined. An outlook on promising and challenging future directions for protein biochip research and applications is also offered.

Integrated Optic Surface Plasmon Resonance Measurements in a Borosilicate Glass Substrate

The surface plasmon resonance (SPR) technique is a well-known optical method that can be used to measure the refractive index of organic nano-layers adsorbed on a thin metal film. Although there are many configurations for measuring biomolecular interactions, SPR-based techniques play a central role in many current biosensing experiments, since they are the most suited for sensitive and quantitative kinetic measurements. Here we give some results from the analysis and numerical elaboration of SPR data from integrated optics experiments in a particular borosilicate glass, chosen for its composition offering the rather low refractive index of 1.4701 at 633 nm wavelength. These data regard the flow over the sensing region (metal window) of different solutions with refractive indexes in the range of interest (1.3÷1.5) for the detection of contaminants in aqueous solutions. After a discussion of the principles of SPR, of the metal window design optimization by means of optical interaction numerical modeling, and of waveguide fabrication techniques, we give a description of system setup and experimental results. Optimum gold film window thickness and width in this guided-wave configuration has been for the first time derived and implemented on an integrated optic prototype device. Its characterization is given by means of the real time waveguide output intensity measurements, which correspond to the interaction between the sensing gold thin film window and the flowing analyte. The SPR curve was subsequently inferred. Finally, a modified version of the device is reported, with channel waveguides arranged in a Y-junction optical circuit, so that laser source stability requirements are lowered by a factor of 85 dB, making possible the use of low cost sources in practical applications.

Using Biacore to measure the binding kinetics of an antibody-antigen interaction

The optical phenomenon of surface plasmon resonance (SPR) used by Biacore systems enables the detection and measurement of protein-protein interactions in real time, without the use of labels. In this unit, the application of Biacore technology to measure a protein-protein interaction is described using an antibody and its antigen as an example. The affinity of the antibody for its antigen is determined by measuring the binding kinetics of the interaction. The protocols are divided into three major steps that are required for measuring binding kinetics using Biacore: (1) surface preparation, (2) assay development, and (3) kinetic analysis.

MicroParticle photophysics illuminates viral bio-sensing

The authors present an approach for specific and rapid unlabeled detection of a virus by using a microsphere-based whispering gallery mode sensor that transduces the interaction of a whole virus with an anchored antibody. They show theoretically that this sensor can detect a single virion below the mass of HIV. A micro-fluidic device is presented that enables the discrimination between viruses of similar size and shape.

Evanescent field Sensors Based on Tantalum Pentoxide Waveguides - A Review

Evanescent field sensors based on waveguide surfaces play an important rolewhere high sensitivity is required. Particularly tantalum pentoxide (Ta₂O₅) is a suitablematerial for thin-film waveguides due to its high refractive index and low attenuation.Many label-free biosensor systems such as grating couplers and interferometric sensors aswell as fluorescence-based systems benefit from this waveguide material leading toextremely high sensitivity. Some biosensor systems based on Ta₂O₅ waveguides alreadytook the step into commercialization. This report reviews the various detection systems interms of limit of detection, the applications, and the suitable surface chemistry.

Biosensor-surface plasmon resonance methods for quantitative analysis of biomolecular interactions

The surface plasmon resonance (SPR) biosensor method has emerged as a very flexible and powerful approach for detecting a wide diversity of biomolecular interactions. SPR monitors molecular interactions in real time and provides significant advantages over optical or calorimetric methods for systems with strong binding and low spectroscopic signals or reaction heats. The SPR method simultaneously provides kinetic and equilibrium characterization of the interactions of biomolecules. Such information is essential for development of a full understanding of molecular recognition as well as for areas such as the design of receptor-targeted therapeutics. This article presents basic, practical procedures for conducting SPR experiments. Initial preparation of the SPR instrument, sensor chips, and samples are described. This is followed by suggestions for experimental design, data analysis, and presentation. Steady-state and kinetic studies of some small molecule-DNA complexes are used to illustrate the capability of this technique. Examples of the agreement between biosensor-SPR and solution studies are presented.

Molecular interactions in the insulin-like growth factor (IGF) axis: a surface plasmon resonance (SPR) based biosensor study

This review describes a comprehensive analysis of a surface plasmon resonance (SPR)-based biosensor study of molecular interactions in the insulin-like growth factor (IGF) molecular axis. In this study, we focus on the interaction between the polypeptide growth factors IGF-I and IGF-II with six soluble IGF binding proteins (IGFBP 1-6), which occur naturally in various biological fluids. We have describe the conditions required for the accurate determination of kinetic rate constants for these interactions and highlight the experimental and theoretical pitfalls, which may be encountered in the early stages of such a study. We focus on IGFBP-5 and describe a site-directed mutagenesis study, which examines the contribution of various residues in the protein to high affinity interaction with IGF-I and -II. We analyse the interaction of IGFBP-5 (and IGFBP-3) with heparin and other biomolecules and describe experiments, which were designed to monitor multi-protein complex formation in this molecular axis.

Biosensor-surface plasmon resonance: Quantitative analysis of small molecule–nucleic acid interactions

Surface plasmon resonance (SPR)-biosensor techniques directly provide essential information for the study and characterization of small molecule-nucleic acid interactions, and the use of these methods is steadily increasing. The method is label-free and monitors the interactions in real time. Both dynamic and steady-state information can be obtained for a wide range of reaction rates and binding affinities. This article presents the basics of the SPR technique, provides suggestions for experimental design, and illustrates data processing and analysis of results. A specific example of the interaction of a well-known minor groove binding agent, netropsin, with DNA is evaluated by both kinetic and steady-state SPR methods. Three different experiments are used to illustrate different approaches and analysis methods. The three sets of results show the reproducibility of the binding constants and agreement from both steady-state and kinetic analyses. These experiments also show that reliable kinetic information can be obtained, even with difficult systems, if the experimental conditions are optimized to minimize mass transport effects. Limitations of the biosensor-SPR technique are also discussed to provide an awareness of the care needed to conduct a successful experiment.

Construction of nanogold hollow balls with dendritic surface as immobilized affinity support for protein adsorption

This contribution introduced the construction of nanosize gold hollow balls (NGB) with dendritic surface as the immobilized affinity support for aflatoxin B(1) antibody (anti-AFB(1)) adsorption, as a model protein, in biorecognition interface. The interaction between nanogold hollow balls and anti-AFB(1) was characterized by cyclic voltammetry, electrochemical impedance spectroscopy, and quartz crystal microbalance (QCM) technique. The deposited mass of anti-AFB(1) on the nanogold hollow ball-modified electrodes was more than that on the nanogold particle-modified electrodes via QCM analysis. The cyclic voltammogram tends to be more irreversible with anti-AFB(1) concentration increased. The antigen-antibody interaction was examined by using the nanogold hollow ball-modified QCM probes. Experimental results show that the developed protein assay system is sensitive to the concentration of AFB(1) as low as 0.05 ng mL(-1). Thus, the nanogold hollow ball is a useful matrix, and can be used as the immobilized affinity support for the adsorption of other proteins.

The rational design of biological complexity: A deceptive metaphor

Biologists often claim that they follow a rational design strategy when their research is based on molecular knowledge of biological systems. This claim implies that their knowledge of the innumerable causal connections present in biological systems is sufficient to allow them to deduce and predict the outcome of their experimental interventions. The design metaphor is shown to originate in human intentionality and in the anthropomorphic fallacy of interpreting objects, events, and the behavior of all living organisms in terms of goals and purposes. Instead of presenting rational design as an effective research strategy, it would be preferable to acknowledge that advances in biomedicine are nearly always derived from empirical observations based on trial and error experimentation. The claim that rational design is an effective research strategy was tested in the case of current attempts to develop synthetic vaccines, in particular against human immunodeficiency virus. It was concluded that in this field of biomedicine, trial and error experimentation is more likely to succeed than a rational design approach. Current developments in systems biology may give us eventually a better understanding of the immune system and this may enable us in the future to develop improved vaccines.

Enhanced sensitivity of self-assembled-monolayer-based SPR immunosensor for detection of benzaldehyde using a single-step multi-sandwich immunoassay

This paper describes the fabrication and sensing characteristics of a self-assembled monolayer (SAM)-based surface plasmon resonance (SPR) immunosensor for detection of benzaldehyde (BZ). The functional sensing surface was fabricated by the immobilization of a benzaldehyde-ovalbumin conjugate (BZ-OVA) on Au-thiolate SAMs containing carboxyl end groups. Covalent binding of BZ-OVA on SAM was found to be dependent on the composition of the base SAM, and it is improved very much with the use of a mixed monolayer strategy. Based on SPR angle measurements, the functional sensor surface is established as a compact monolayer of BZ-OVA bound on the mixed SAM. The BZ-OVA-bound sensor surface undergoes immunoaffinity binding with anti-benzaldehyde antibody (BZ-Ab) selectively. An indirect inhibition immunoassay principle has been applied, in which analyte benzaldehyde solution was incubated with an optimal concentration of BZ-Ab for 5 min and injected over the sensor chip. Analyte benzaldehyde undergoes immunoreaction with BZ-Ab and makes it inactive for binding to BZ-OVA on the sensor chip. As a result, the SPR angle response decreases with an increase in the concentration of benzaldehyde. The fabricated immunosensor demonstrates a low detection limit (LDL) of 50 ppt (pg mL(-1)) with a response time of 5 min. Antibodies bound to the sensor chip during an immunoassay could be detached by a brief exposure to acidic pepsin. With this surface regeneration, reusability of the same sensor chip for as many as 30 determination cycles has been established. Sensitivity has been enhanced further with the application of an additional single-step multi-sandwich immunoassay step, in which the BZ-Ab bound to the sensor chip was treated with a mixture of biotin-labeled secondary antibody, streptavidin and biotin-bovine serum albumin (Bio-BSA) conjugate. With this approach, the SPR sensor signal increased by ca. 12 times and the low detection limit improved to 5 ppt with a total response time of no more than ca. 10 min. Figure A single-step multi-sandwich immunoassay step increases SPR sensor signal by ca. 12 times affording a low detection limit for benzaldehyde of 5 ppt.

Inhibition of the mitogenic, angiogenic and tumorigenic activities of pleiotrophin by a synthetic peptide corresponding to its C-thrombospondin repeat-I domain

Pleiotrophin (PTN), is a heparin-dependent growth factor involved in angiogenesis and tumor growth. PTN contains a thrombospondin repeat-I (TSR-I) motif in its two beta-sheet domains that are involved in its binding to heparin and its neurite outgrowth activity. Based on the importance of the binding of PTN to heparin in its dimerization and biological activities, we have designed two synthetic peptides, P(13-39) and P(65-97) corresponding to a part of the N-terminal and C-terminal TSR-I motif of PTN, respectively. P(65-97) inhibited the mitogenic, tumorigenic and angiogenic activities of PTN, as well as the mitogenic and an angiogenic activity of fibroblast growth factor-2 (FGF-2). However, P(65-97) had no effect on the mitogenic activity of epidermal growth factor, which does not bind heparin. P(65-97) but not P(13-39) inhibited the binding of PTN and to a lesser extent of FGF-2 to heparin using an immunoassay and an optical biosensor assay and bound directly to heparin with a K(d) of 120 nM. These findings suggest that P(65-97), containing amino acids 65-97 of the TSR-I motif of the C-terminal domain of PTN, inhibits the activities of PTN and FGF-2 by virtue of its ability to bind heparin very effectively and so compete with the growth factors for their polysaccharide co-receptor.

SPR-based biosensors: a tool for biodetection of hormonal compounds

Novel cancer treatments, prevention of postmenopausal disorder, and prescription of oral contraceptives are the main developments in the design of synthetic estrogenic medication. The increasing consumption of these synthetic pharmaceuticals, in addition to human and animal natural estrogenic compound excretion, contribute to their environmental dissemination worldwide. Their assimilation as a result of consumption of food and water perturbs normal endocrine systems and leads to the emergence of human and animal diseases and malformations. These compounds are active in the organism at low concentrations. Accordingly, daily low-level exposure disrupts the natural equilibrium in the endocrine system. A method enabling quantification at such products at low levels (from pg L(-1) to ng L(-1)) is therefore required for these products. Surface plasmon resonance, essentially used for comprehension of molecular mechanisms and in drug discovery, can also be used for environmental pollutant monitoring. This technology has already been used for evaluation of the effects of chemical pollutants on specific nuclear receptors. It has been possible to determine the role of each individual compound on the disruption of the estrogen-activated cellular pathway. Development of SPR screening methods enables application of such an approach for quantification of these compounds in water.

Optical immunosensors for environmental monitoring: How far have we come?

Immunosensing has proved to be a very interesting research area. This review discusses what has actually been achieved in the field of optical immunosensing for environmental screening, and what still needs to be done. The review is presented from a practical point of view. In terms of the basic design of the immunosensor, there is a trend towards decreasing assay time; indeed, this has been reduced from 15-20 minutes to less than 5 minutes. Another goal is to simplify the manifold, and label-free approaches combining indirect assay formats and the detection of antibody binding are popular. Rapid displacement assays have also been investigated thoroughly. In terms of some important features of immunosensing devices, the reusability of the sensing element has been studied in great depth, and working lifetimes of more than five hundred assays can now be found for all assay formats. Multianalyte assays are now being investigated, and current systems are able to monitor 2-3 target compounds, although this number is set to increase greatly (to >30) in the near future. In this sense, an increasing number of publications can be found on microarrays intended for multianalyte determinations. The application of immunosensing to real situations is the main challenge. Immunosensors are barely commercialized and are yet to be established as research or routine tools, due to a lack of validated protocols for a wide range of sample matrices. Regarding compounds considered as analytes, some significant pollutants such as dioxins or pharmaceuticals are rarely chosen as targets, although the current tendency is towards a broader spectrum of analytes. New immunoreagents should be raised for these compounds, for use in immunosensors that can be used as screening tools.

Optical biosensors: where next and how soon?

From a direct comparison of the technical benefits of labelled reporter assays with the benefits of label-free assays, label-free appears to have significant advantages. Faster assay development times; accurate, high information content data; and less interference from labels. However, optical label-free platforms have not yet made a major impact in the drug discovery technology markets; are often viewed as having poor throughput, limited application; and are difficult to learn and use effectively.

Binding assays with artificial tethered membranes using surface plasmon resonance

Surface sensitive optical techniques based on surface plasmon resonance have become interesting for biosciences in the context of biorecognition and binding studies at functional surfaces. We use surface plasmon resonance spectroscopy (SPS) in combination with surface plasmon enhanced fluorescence spectroscopy (SPFS) for the characterization of interaction processes associated with biomembranes. The biological membrane is mimicked by a tethered membrane consisting of a planar lipid bilayer attached to a gold surface via a hydrophilic anchor peptide. The interaction between membrane-bound hydrophobic compounds and free hydrophilic molecules is monitored in real-time and with high sensitivity and selectivity by combined SPS/SPFS. In this review we shortly discuss the principles of surface plasmon resonance and its utilization in SPS and SPFS. A detailed description of the required instrumentation for combined SPS and SPFS is presented. Furthermore, we outline the design of a binding assay with a tethered bilayer and the procedure of the artificial membrane system built-up is delineated. We also present examples that demonstrate the potential of combined SPS/SPFS assays with artificial tethered membranes. The method provides insight into the interaction of integral membrane proteins with various hydrophilic ligands and the specific recognition of small lipophilic molecules by soluble proteins.

Comparative analysis of 10 small molecules binding to carbonic anhydrase II by different investigators using Biacore technology

In this benchmark study, 26 investigators were asked to characterize the kinetics and affinities of 10 sulfonamide inhibitors binding to the enzyme carbonic anhydrase II using Biacore optical biosensors. A majority of the participants collected data that could be fit to a 1:1 interaction model, but a subset of the data sets obtained from some instruments were of poor quality. The experimental errors in the k(a), k(d), and K(D) parameters determined for each of the compounds averaged 34, 24, and 37%, respectively. As expected, the greatest variation in the reported constants was observed for compounds with exceptionally weak affinity and/or fast association rates. The binding constants determined using the biosensor correlated well with solution-based titration calorimetry measurements. The results of this study provide insight into the challenges, as well as the level of experimental variation, that one would expect to observe when using Biacore technology for small molecule analyses.

Looking towards label-free biomolecular interaction analysis in a high-throughput format: a review of new surface plasmon resonance technologies

Surface plasmon resonance (SPR) biosensors have enabled a wide range of applications in which researchers can monitor biomolecular interactions in real time. Owing to the fact that SPR can provide affinity and kinetic data, unique features in applications ranging from protein-peptide interaction analysis to cellular ligation experiments have been demonstrated. Although SPR has historically been limited by its throughput, new methods are emerging that allow for the simultaneous analysis of many thousands of interactions. When coupled with new protein array technologies, high-throughput SPR methods give users new and improved methods to analyze pathways, screen drug candidates and monitor protein-protein interactions.

Protein adsorption from flowing solutions on pure and maleic acid copolymer modified glass particles

The adsorption of human serum albumin (HSA) and lysozyme (LSZ) on pure as well as maleic acid (MA) copolymer coated spherical soda lime glass particles was investigated under flowing conditions. Coating the glass particles with two different maleic acid copolymers alters the properties of the particle surface concerning its charge and hydrophobicity in a well-defined gradation. Frontal chromatography was used to determine the surface concentration of the adsorbed proteins and to establish adsorption isotherms. The introduced methodology was demonstrated to provide a powerful means to study protein adsorption at solid/liquid interfaces. Investigations with virginal and protein-preadsorbed glass particles revealed that even under streaming conditions HSA is irreversibly adsorbed, whereas LSZ partially desorbs. For LSZ and HSA the adsorbed amounts and the isotherms strongly depend on the surface "history", i.e. the presence or absence of preadsorbed protein layers, and the kind of surface modification of the glass. Compared to the soda lime glass surface the adsorption of HSA was strongly increased on surfaces modified with a hydrophobic maleic acid copolymer indicating a strong hydrophobic protein-surface interaction. By coating the surface with a hydrophilic and more negatively charged maleic acid copolymer the adsorption of HSA to that surface was lower and comparable to the adsorption onto plain glass due to the electrostatic repulsion between HSA and the modified surface. In contrast the affinity to any of the investigated particle surfaces was generally higher for LSZ than for HSA which can be mainly attributed to the electrostatic attraction between LZS and the surface. The adsorbed amount of LSZ on the copolymer coated particle surfaces was much higher than on the pure soda lime glass particles indicating superposed hydrophobic interactions in the case of the hydrophobic MA copolymer layer and an increased density of anionic sites as well as interactions of LSZ within the three-dimensional (swollen), hydrophilic MA copolymer layer.

Analyzing ligand and small molecule binding activity of solubilized GPCRs using biosensor technology

We used Biacore technology to measure directly the binding of natural ligands and small molecules to the chemokine receptors CXCR4 and CCR5. Both G protein-coupled receptors were solubilized from whole cell pellets and captured on antibody surfaces for analysis. Our solubilization conditions maintained high-affinity binding of chemokines SDF-1alpha and RANTES to CXCR4 and CCR5, respectively. Surface density- and buffer-dependent binding responses, along with binding data for a selective ligand (RCP-168), further validated the biosensor assay. In addition, we showed that it is possible to collect high-quality binding responses for the archetypal small molecule inhibitors JM-2987 and TAK-779. Finally, using our biosensor-based method, we characterized the kinetics of 19 novel small molecule inhibitors of CCR5 and showed that their affinities correlated with values determined for the membrane-associated receptor. Together, the chemokine and small molecule binding data provide evidence that the solubilized receptors maintain native binding properties. These solubilized receptor preparations could be useful reagents for biophysical studies as well as for structural analysis.