Optical evanescent wave methods for the study of biomolecular interactions

Principles and pitfalls of high-throughput analysis of microRNA-binding thermodynamics and kinetics by RNA Bind-n-Seq

RNA Bind-n-Seq (RBNS) is a cost-effective, high-throughput method capable of identifying the sequence preferences of RNA-binding proteins and of qualitatively defining relative dissociation constants. Although RBNS is often described as an unbiased method, several factors may influence the outcome of the analysis. Here, we discuss these biases and present an analytical strategy to estimate absolute binding affinities from RBNS data, extend RBNS to kinetic studies, and develop a framework to compute relative association and dissociation rate constants. As proof of principle, we measured the equilibrium binding properties of mammalian Argonaute2 (AGO2) guided by eight microRNAs (miRNAs) and kinetic parameters for let-7a. The miRNA-binding site repertoires, dissociation constants, and kinetic parameters calculated from RBNS data using our methods correlate well with values measured by traditional ensemble and single-molecule approaches. Our data provide additional quantitative measurements for Argonaute-bound miRNA binding that should facilitate development of quantitative targeting rules for individual miRNAs.

Measuring Protein Interactions by Optical Biosensors

This unit gives an introduction to the basic techniques of optical biosensing for measuring equilibrium and kinetics of reversible protein interactions. Emphasis is placed on description of robust approaches that will provide reliable results with few assumptions. How to avoid the most commonly encountered problems and artifacts is also discussed. © 2017 by John Wiley & Sons, Inc.

Analysis of Surface Plasmon Resonance Curves with a Novel Sigmoid-Asymmetric Fitting Algorithm

The present study introduces a novel curve-fitting algorithm for surface plasmon resonance (SPR) curves using a self-constructed, wedge-shaped beam type angular interrogation SPR spectroscopy technique. Previous fitting approaches such as asymmetric and polynomial equations are still unsatisfactory for analyzing full SPR curves and their use is limited to determining the resonance angle. In the present study, we developed a sigmoid-asymmetric equation that provides excellent curve-fitting for the whole SPR curve over a range of incident angles, including regions of the critical angle and resonance angle. Regardless of the bulk fluid type (i.e., water and air), the present sigmoid-asymmetric fitting exhibited nearly perfect matching with a full SPR curve, whereas the asymmetric and polynomial curve fitting methods did not. Because the present curve-fitting sigmoid-asymmetric equation can determine the critical angle as well as the resonance angle, the undesired effect caused by the bulk fluid refractive index was excluded by subtracting the critical angle from the resonance angle in real time. In conclusion, the proposed sigmoid-asymmetric curve-fitting algorithm for SPR curves is widely applicable to various SPR measurements, while excluding the effect of bulk fluids on the sensing layer.

Preliminary studies and potential applications of localized surface plasmon resonance spectroscopy in medical diagnostics

Miniature optical sensors that specifically identify low concentrations of environmental and biological substances are in high demand. Currently, there is no optical sensor that provides identification of the aforementioned species without amplification techniques at naturally occurring concentrations. Recently, it has been demonstrated that triangular silver nanoparticles have remarkable optical properties and that their enhanced sensitivity to their nanoenvironment has been used to develop a new class of optical sensors using localized surface plasmon resonance spectroscopy. The examination of both model and nonmodel biological assays using localized surface plasmon resonance spectroscopy will be presented in this review. It will be demonstrated that the use of a localized surface plasmon resonance nanosensor rivals the sensitivity and selectivity of, and provides a low-cost alternative to, commercially available sensors.

Nonmonotonous variation of DNA angular separation during asymmetric pulsed field electrophoresis

Asymmetric pulsed field electrophoresis within crystalline arrays is used to generate angular separation of DNA molecules. Four regimes of the frequency response are observed, a low frequency rise in angular separation, a plateau, a subsequent decline, and a second plateau at higher frequencies. It is shown that the frequency response for different sized DNA is governed by the relation between pulse time and the reorientation time of DNA molecules. The decline in angular separation at higher frequencies has not previously been analyzed. Real-time videos of single DNA molecules migrating under high frequency-pulsed electric field show the molecules no longer follow the head to tail switching, ratchet mechanism seen at lower frequencies. Once the pulse period is shorter than the reorientation time, the migration mechanism changes significantly. The molecule reptates along the average direction of the two electric fields, which reduces the angular separation. A freely jointed chain model of DNA is developed where the porous structure is represented with a hexagonal array of obstacles. The model qualitatively predicts the variation of DNA angular separation with respect to frequency.

Amplified surface plasmon resonance based DNA biosensors, aptasensors, and Hg2+ sensors using hemin/G-quadruplexes and Au nanoparticles

Thiolated nucleic acid hairpin nanostructures that include in their stem region a "caged" G-quadruplex sequence, and in their single-stranded loop region oligonucleotide recognition sequences for DNA, adenosine monophosphate (AMP), or Hg(2+) ions were linked to bare Au surfaces or to Au nanoparticles (NPs) linked to Au surfaces. The opening of the hairpin nanostructures associated with the bare Au surface by the complementary target DNA, AMP substrate, or Hg(2+) ions, in the presence of hemin, led to the self-assembly of hemin/G-quadruplexes on the surface. The resulting dielectric changes on the surface exhibited shifts in the surface plasmon resonance (SPR) spectra, thus providing a readout signal for the recognition events. A similar opening of the hairpin nanostructures, immobilized on the Au NPs associated with the Au surface, by the DNA, AMP, or Hg(2+) led to an ultrasensitive SPR-amplified detection of the respective analytes. The amplification originated from the coupling between the localized surface plasmon associated with the NPs and the surface plasmon wave, an effect that cooperatively amplifies the SPR shifts that result from the formation of the hemin/G-quadruplexes. The different sensing platforms reveal impressive sensitivities and selectivities toward the target analytes.

Short time-scale bacterial adhesion dynamics

In natural conditions many bacterial populations are found as surface-attached communities exhibiting features distinct from those of planktonic cells. We focus here on the question of initial adhesion, the mechanisms of which are still far from being fully understood. Recently, the frontier between microbiologists and physicists has become increasingly permeable, boosting implementation of new methodological approaches for better elucidating the intricate aspects of initial bacterial adhesion. After discussing briefly the main sources of complexity that confuse the understanding of the early steps of cell-surface attachment, we present a selection of physical methods enabling real-time measurement of early adhesion kinetics in live cells. We also discuss the limitations and pitfalls that might appear when applying such methodologies - initially designed for studying physically ideal systems - to analysis of these, more complex, living systems. We address mainly on the use of dispersed-surfaces flow cytometry (DS-FCM), quartz microbalance (QCM) and surface plasmon resonance (SPR) approaches, and give a brief survey of new perspectives in optical microscopy. We conclude that the use of combined and multiparametric technical approaches will lead to significant advances in providing a comprehensive understanding of the early events in bacterial adhesion.

A surface plasmon resonance-based technical platform for the detection of chromosome aneuploidy

Surface plasmon resonance (SPR)-based technologies have been widely used to study biomolecular interactions including receptor-ligand, DNA-protein, and protein-protein interactions. In this pilot study, we used chromosome 21 as the genetic marker to appreciate the value of using SPR technology for the detection of chromosome aneuploidy. Four normal and four trisomy 21 samples were used in this study. Chromosomes 1- (as the internal control) and 21-specific sequence-tagged sites were used as markers for detection. Resonance unit ratios of chromosome 21 sequence-tagged site (STS) to chromosome 1 STS were calculated to interpret analytic results. The ratios in the normal samples ranged from 0.96 to 2.83, whereas in trisomy 21 samples, the ratios were from 6.96 to 16.30, significantly higher than those of the normal samples. These findings strongly indicate that SPR technology is suitable for the detection of trisomy 21.

Surface plasmon optical study of the interfacial phase transition of elastinlike polypeptide grafted on gold

The conformational changes in elastinlike polypeptides (ELPs) grafted to a solid/solution interface via different architectures were studied using surface plasmon resonance spectroscopy and surface plasmon field-enhanced fluorescence spectroscopy (SPFS). SPFS provides a simple and convenient optical method to study the influence of the grafting method and the graft density on the conformational changes in ELPs at the solid-solution interface as a function of environmental variables. A typical response of the ELP, consistent with its stimuli responsiveness, was a gradual collapse upon increasing the ionic strength; this effect was inversely correlated with the surface graft density of the ELP.

Designing efficient zero calibration point for phase-sensitive surface plasmon resonance biosensing

This work is related to the development of phase-sensitive methodologies in Surface Plasmon Resonance (SPR) biosensing. We take advantage of a specific angular dependence of phase of light, reflected under SPR geometry, on parameters of the SPR-supporting metal, and propose a polarimetry-based methodology to easily determine the optimal calibration zero point, corresponding to the maximal phase sensitivity. The proposed methodology can significantly facilitate the calibration of the system in field and multi-channel sensing, broaden the dynamic range, as well as contribute to the development of feedback loops.

Analysis of membrane-localized binding kinetics with FRAP

Interactions between plasma membrane-associated proteins on interacting cells are critical for many important biological processes. Few experimental techniques, however, can accurately determine the association and the dissociation rates between such interacting pairs when the two molecules diffuse on apposing membranes or lipid bilayers. In this study, we give a theoretical description of how and when fluorescence recovery after photobleaching (FRAP) experiments can be used to quantify these reaction rates. We analyze the effect of binding on FRAP recovery curves with a reaction-diffusion model and systematically identify different regimes in the parameter space of the association and the dissociation constants for which the full model simplifies into equivalent one-parameter models. Based on this analysis, we propose an experimental protocol that may be used to identify the kinetic parameters of binding in the appropriate parameter regime. We present simulated experiments illustrating our protocol and lay down guidelines for parameter estimation.

Enzymatically biocatalytic precipitates amplified antibody-antigen interaction for super low level immunoassay: an investigation combined surface plasmon resonance with electrochemistry

We demonstrated a simple and efficient strategy, which based on the enzymatically biocatalytic precipitates amplified antibody-antigen interaction, for improving the response signals of surface plasmon resonance (SPR) immunosensing. The antibody-antigen-alkaline phosphatase (AP) labeled secondary antibody sandwich were successfully prepared and characterized by SPR, cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The SPR signal amplification was accomplished through probing resonance angle shift and Faradaic electron impedance of [Fe(CN)(6)](3-/4-) redox pair after the enzymatically biocatalytic products precipitating on the immunosensing electrode surface. As a result, the accumulation of the enzymatically biocatalytic precipitates leads to significantly resonance angle shift and increase of electron transfer impedance of [Fe(CN)(6)](3-/4-) probe. The precipitates-enhanced sandwich SPR immunoassay for mouse immunoglobulin G (m-IgG) can easily detect solution protein concentrations in the linear range of 0.02-40 ng mL(-1) and with a detection limit of 200 fg mL(-1), which is more than four-orders and 10 times better compared with the values using streptavidin-biotinylated protein complex and biotinylated HRP biocatalyzation amplification methods. Moreover, this method is generally applicable to other sandwich immunoassays and also can be expanded to monitor other antibody-antigen interaction for immunosensing detection at low concentrations.

Steric hindrance effects on surface reactions: applications to BIAcore

Because surface-volume reactions occur in many biological and industrial processes, understanding the rate of such reactions is important. The BIAcore surface plasmon resonance (SPR) biosensor for measuring rate constants has such a geometry. Though several models of the BIAcore have been presented, few take into account that large ligand molecules can block multiple receptor sites, thus skewing the sensogram data. In this paper some general mathematical principles are stated for handling this phenomenon, and a surface-reaction model is presented explicitly. An integro-partial differential equation results, which can be simplified greatly using perturbation techniques, yielding linear and nonlinear integrodifferential equations. Explicit and asymptotic solutions are constructed for cases motivated by experimental design. The general analysis can provide insight into surface-volume reactions occurring in various contexts. In particular, the steric hindrance effect can be quantified with a single dimensionless parameter.

Bimodal Swelling Responses in Microgel Thin Films

A series of studies on microgel thin films is described, wherein quartz crystal microgravimetry (QCM), surface plasmon resonance (SPR), and atomic force microscopy (AFM) have been used to probe the properties of microstructured polymer thin films as a function of film architecture and solution pH. Thin films composed of pNIPAm-co-AAc microgels were constructed by using spin-coating layer-by-layer (scLbL) assembly with poly(allylamine hydrochloride) (PAH) as a polycationic "glue". Our findings suggest that the interaction between the negatively charged microgels and the positively charged PAH has a significant impact on the pH responsivity of the film. These effects are observable in both the optical and mechanical behaviors of the films. The most significant changes in behavior are observed when the motional resistance of a quartz oscillator is monitored via QCM experiments. Slight changes to the film architecture and alternating the pH of the environment significantly changes the QCM and SPR responses, suggesting a pH-dependent swelling that is dependent on both particle swelling and polyelectrolyte de-complexation. Together, these studies allow for a deeper understanding of the morphological changes that take place in environmentally responsive microgel-based thin films.

Phase-sensitive time-modulated surface plasmon resonance polarimetry for wide dynamic range biosensing

A novel polarimetry scheme is proposed to improve the performance of phase-sensitive Surface Plasmon Resonance (SPR) biosensors. The scheme uses s-polarized light, not affected by SPR, as a reference beam, while information on the phase of the p-polarized component is obtained from an analysis of phase-polarization state of light of mixed polarization. We utilize temporal modulation of the beam reflected under SPR by a photo-elastic modulator and show that, under certain birefringent geometry, the signals at the 2nd and 3rd harmonics of modulated frequency can provide ultra-sensitive phase-based response to changes of the refractive index (thickness) of thin films on gold. We also show that the proposed configuration significantly improves detection limit compared to conventional intensity-sensitive SPR, yet enables to maintain wide dynamic range of measurements, which is normally difficult with phase-sensitive SPR schemes. Biosensing applications of the proposed scheme are illustrated in a biological model reaction of avidin - biotin binding on gold.

A theoretical and experimental study of competition between solution and surface receptors for ligand in a Biacore flow cell

Rate constants that characterize the kinetics of binding and dissociation between biomolecules carry fundamental information about the biological processes these molecules are involved in. An instrument that is widely used to determine these rate constants is the Biacore. In a Biacore experiment, one of the reactants, which we will call the receptor, is immobilized on a sensor chip. During the binding phase of the experiment the other reactant flows past the chip. After binding, buffer alone is introduced into the flow cell and dissociation is monitored. Often surface-based binding assays are influenced by the transport of the reactant in solution, complicating the determination of the chemical rate constants from the observed binding kinetics. We propose a new way to determine the dissociation rate constant by adding soluble receptor during dissociation. The method is tested first on simulated data and then on Biacore experiments where the lac repressor protein binds and dissociates from a stretch of double stranded DNA containing the lac repressor binding site. With this method we find a dissociation rate constant k(d)=0.075 +/- 0.005s(-1), a value that is faster than previously obtained from Biacore experiments. In developing our method to analyze these experiments we obtain an expression for the transport limited rate constant for a Biacore experiment when soluble receptor is present during dissociation.

Evaluation of α-d-mannopyranoside glycolipid micelles–lectin interactions by surface plasmon resonance method

It is established that achieving higher binding affinities in carbohydrate-protein interactions requires multivalent presentations of the sugar ligands at the receptor binding site. Several inhibition, calorimetric, mass balance, and other studies have reiterated the beneficial effects of molecular level clustering of the sugar ligands for tight binding to the receptors. We have undertaken an effort to study the multivalent effects involving larger assemblies, represented by micelles, and their lectin interactions. The micelles were constituted with monomer bearing one- or two-sugar moieties at the monomolecular level and with varying the distances between the sugar moieties. Micellar aggregation studies and dynamic light scattering (DLS) studies afforded details of the aggregation numbers and the hydrodynamic diameters of various glycolipid (GL) micelles. The GL micelles were used as analytes of surface plasmon resonance (SPR) experiments on a lectin concanavalin A (Con A)-immobilized surface. SPR studies of the micelle-lectin interactions demonstrate that the ligand-receptor binding can be fit into the bivalent analyte model of interaction. Furthermore, micelles formed from two-sugar containing GLs are able to elicit favorable kinetic association rate constants in comparison to the micelles constituted with one-sugar containing GLs. The kinetic rate constants across the micelles and the effect of the sugar valencies in the GLs are discussed.

Surface plasmon optical studies of carboxymethyl dextran brushes versus networks

The conformational changes of carboxymethyl dextran (CMD) substrates induced by variations in pH and ionic strength were studied using surface plasmon field-enhanced fluorescence spectroscopy (SPFS). A typical response was an increase in swelling upon increasing the pH and decreasing the ionic strength. Furthermore, the effects of the surface charge and cross-link density of the CMD on the degree of stimulus responses were investigated. The swelling/collapse ratio decreased with decreasing carboxyl group surface concentration and increasing cross-link density.

Lectin-based structural glycomics: glycoproteomics and glycan profiling

Structural glycomics (SG) plays a fundamental part of concurrent glycobiology aiming at comprehensive elucidation of glycan functions ( i.e. , functional glycomics) in the context of post-genome sciences. The SG project started in April 2003 and will continue for 3 years in the framework of NEDO (New Energy and Industrial Technology Organization) under the METI (the Ministry of Economy, Trade, and Industry), Japan. The main purpose of the project is the development of high-throughput and robust machines, which should greatly contribute to the structural analysis of complex glycans. In this chapter, 2 major research items, i.e. , (1) glycoproteomics, which enables comprehensive analysis of glycoproteins, and (2) "glycan profiling" by means of lectins, are described. For the latter, frontal affinity chromatography has been adopted as a starting tool for comprehensive analysis of the interaction of 100 lectins and 100 oligosaccharides under the concept of "hect-by-hect," which refers to 100 x 100.

Single Amino Acid Substitutions in Procollagen VII Affect Early Stages of Assembly of Anchoring Fibrils

Procollagen VII is a homotrimer of 350-kDa pro-alpha1(VII) chains, each consisting of a central collagenous domain flanked by the noncollagenous N-terminal NC1 domain and the C-terminal NC2 domain. After secretion from cells, procollagen VII molecules form anti-parallel dimers with a C-terminal 60-nm overlap. Characteristic alignment of procollagen VII monomers forming a dimer depends on site-specific binding between the NC2 domain and the triple-helical region adjacent to Cys-2634 of the interacting procollagen VII molecules. Formation of the intermolecular disulfide bonds between Cys-2634 and either Cys-2802 or Cys-2804 is promoted by the cleavage of the NC2 domain by procollagen C-proteinase. By employing recombinant procollagen VII variants harboring G2575R, R2622Q, or G2623C substitutions previously disclosed in patients with dystrophic epidermolysis bullosa, we studied how these amino acid substitutions affect intermolecular interactions. Binding assays utilizing an optical biosensor demonstrated that the G2575R substitution increased affinity between mutant molecules. In contrast, homotypic binding between the R2622Q or G2623C molecules was not detected. In addition, kinetics of heterotypic binding of all analyzed mutants to wild type collagen VII were different from those for binding between wild type molecules. Moreover, solid-state binding assays demonstrated that R2622Q and G2623C substitutions prevent formation of stable assemblies of procollagen C-proteinase-processed mutants. These results indicate that single amino acid substitutions in procollagen VII alter its self-assembly and provide a basis for understanding the pathomechanisms leading from mutations in the COL7A1 gene to fragility of the dermal-epidermal junction seen in patients with dystrophic forms of epidermolysis bullosa.

Analysis of protein interactions on protein arrays by a wavelength interrogation-based surface plasmon resonance biosensor

We have investigated whether surface plasmon resonance (SPR) sensors based on the wavelength interrogation are able to analyze protein interactions on protein arrays. The spectral SPR sensor was self-constructed and its detection limit, expressed as the minimal refractive index variation, was calculated to be 6.6x10(-5) with the signal fluctuation of 1.0x10(-5). The protein array surface was modified by a mixed thiol monolayer to immobilize proteins. Protein arrays were analyzed by the line-scanning mode of the SPR sensor, which scanned every 100 microm along the central line of array spots and the scanned results were presented by color spectra from blue to red. Glutathione S-transferase (GST)-rac1 caused a concentration-dependent increase of SPR wavelength shift on protein arrays. The surface structure of the protein arrays was analyzed by atomic force microscopy. Specific interactions of antigens with antibodies were analyzed on the protein arrays by using three antibodies and eight proteins. These results suggest that the wavelength interrogation-based SPR sensor can be used as the biosensor for the high-throughput analysis of protein interactions on protein arrays.

Quantitative methods for spatially resolved adsorption/desorption measurements in real time by surface plasmon resonance microscopy

A simple method for converting local reflectivity changes measured in surface plasmon resonance (SPR) microscopy to effective adlayer thicknesses and absolute surface coverages of adsorbed species is presented. For a range of high-contrast angles near the SPR resonance where the local metal surface's reflectivity changes linearly with angle, the change in reflectivity at fixed angle is proportional to the change in effective refractive index (eta(eff)) near the surface. This change in eta(eff) can be converted to absolute adsorbate coverage using methods developed for quantitative SPR spectroscopy. A measurement of the change in reflectivity due to changes in refractive index of bulk solutions, i.e., percent reflectivity change per refractive index unit (RIU), is the only calibration required. Application of this method is demonstrated for protein adsorption onto protein/DNA arrays on gold from aqueous solution using an SPR microscope operating at 633 nm. A detection limit of 0.072% change in absolute reflectivity is found for simultaneous measurements of all 200 microm x 200 microm areas within the 24-mm(2) light beam with 1-s time averaging. This corresponds to a change in effective refractive index of 1.8 x 10(-5) and a detection limit for protein adsorption of 1.2 ng/cm(2) (approximately 0.5 pg in a 200-microm spot). The linear dynamic range is Deltaeta(eff) = approximately 0.011 RIU or approximately 720 ng/cm(2) of adsorbed protein. Using a nearby spot as a reference channel, one can correct for instrumental drift and changes in refractive index of the solutions in the flow cell.

Silicon-based surface plasmon resonance sensing with two surface plasmon polariton modes

Surface plasmon resonance (SPR) sensing on a silicon-based platform is considered. We have studied properties of SPR in a combined silicon-dielectric layer-gold film-sample medium structure and established conditions of the simultaneous excitation of two plasmon polariton modes that provide narrow and well-separated minima of the reflected intensity. It has been shown that the external mode over the gold-sample medium interface demonstrates a highly sensitive response to a change in the refractive index of the sample medium, whereas the internal mode over the dielectric-gold interface is almost insensitive to medium parameters. We propose that the internal mode can be used as an effective reference zero point for miniature and portable SPR-based systems designed for field and multichannel sensing.

Highly sensitive biosensing using a supercritical angle fluorescence (SAF) instrument

We present a new optical biosensor for probing molecular binding to a water/glass interface. The system is designed to measure the kinetics of surface reactions down to low analyte concentrations straightforwardly. The selective detection of surface bound fluorescence is achieved by collecting supercritical angle fluorescence (SAF) emission of surface bound molecules into the glass. Thereby the expansion of the detection volume into the aqueous probe is reduced to about one sixth of the fluorescence wavelength, consequently bulk fluorescence from the solution is rejected successfully. The SAF-signal is captured by a parabolic glass lens, which leads to high spatial collection efficiency and detection sensitivity. The sensor has an inverted optical design and is compatible with common glass cover slips, which strongly facilitates operation for the user working in the biological and biochemical fields. The performance of the system is demonstrated by real time measurements of antibody-antigen reactions. Rate constants of the reaction were extracted. Antigen concentrations were detected down to 10(-13) mol/l.

Properties and sensing characteristics of surface-plasmon resonance in infrared light

Conditions of surface-plasmon resonance (SPR) production with use of IR pumping light (800-2300 nm) in the Kretschmann-Raether prism arrangement were investigated. Both calculations and experimental data showed that SPR characteristics in the IR are strongly influenced by the properties of the coupling prism material. Indeed, quite different regularities of plasmon excitation, polarity of sensing response, and sensitivity are observed for two different glasses and silicon. The observed differences in SPR properties are related to essentially different behavior of dispersion characteristics of materials near the SPR coupling point. Methods for improving sensor performance and miniaturizing the SPR technique using novel coupling materials (silicon) are discussed.

Real-time detection of nucleic acid interactions by total internal reflection fluorescence

This paper describes the development of an optical readout system for the real-time analysis of fluorescent-labeled DNA microarrays is described. The system is targeted toward research applications in genomics, agriculture, and life sciences, where the end-point detection of state-of-the-art readout systems does not provide sufficient information on the hybridization process. The hybridization progress of molecules from the liquid phase in a flow cell to immobilized oligonucleotides on a transducer surface can be observed. The excitation of fluorochromes is realized by a semiconductor laser, and the fluorescence emission is collected by a cooled CCD camera. Quantitative data can be extracted from the images for analysis of the microarray. For the signal transduction, the principle of total internal reflection is used. With a multiple internal reflection arrangement, the sensor chip was adapted to the standard microscope slide format and a homogeneous evanescent illumination of the active area of the sensor surface was achieved. An application measurement was carried out with this readout system. The hybridization of Cy5-labeled 30-mer single-stranded oligonucleotides to fully complementary immobilized strands was observed in real time. A kinetic analysis was demonstrated with the recorded data. Melting curves of a 140-mer PCR product from a hemochromatosis patient sample hybridized to immobilized wild-type mutant 15- and 17-mer oligonucleotides were recorded and single-point mutations could be detected.

Hybridization enhancement using cavitation microstreaming

Conventional DNA microarray hybridization relies on diffusion of target to surface-bound probes, and thus is a rate-limited process. In this paper, a micromixing technique based on cavitation microstreaming principle that was developed to accelerate hybridization process is explained. Fluidic experiments showed that air bubbles resting on a solid surface and set into vibration by a sound field generated steady circulatory flows, resulting in global convection flows and, thus, rapid mixing. The time to fully mix dyed solutions in a 50-microL chamber using cavitation microstreaming was significantly reduced from hours (a pure diffusion-based mixing) to 6 s. Cavitation microstreaming was implemented to enhance DNA hybridization in both fluorescence-detection-based and electrochemical-detection-based DNA microarray chips. The former showed that cavitation microstreaming results in up to 5-fold hybridization signal enhancement with significantly improved signal uniformity, as compared to the results obtained in conventional diffusion-based biochips for a given time (2 h). Hybridization kinetics study in the electrochemical detection-based chips showed that acoustic microstreaming results in up to 5-fold kinetics acceleration. Acoustic microstreaming has many advantages over most existing techniques used for hybridization enhancement, including a simple apparatus, ease of implementation, low power consumption (approximately 2 mW), and low cost.

Binding of small peptides to immobilized antibodies: kinetic analysis by surface plasmon resonance

This unit describes a method for screening small viral peptides as specific antigens using a surface plasmon resonance (SPR) biosensor. The basic protocol in this unit is suited for direct single-step SPR analysis of small ligand-large receptor interactions, where small peptides are used as analytes (injected in the continuous buffer flow) and monoclonal antibodies (MAbs) are immobilized on the SPR sensor chip surface. An alternate protocol is included for situations where kinetic analysis is not possible and uses a surface competition assay to indirectly measure the kinetics of small analyte binding.

A nanoscale optical biosensor: sensitivity and selectivity of an approach based on the localized surface plasmon resonance spectroscopy of triangular silver nanoparticles

Triangular silver nanoparticles ( approximately 100 nm wide and 50 nm high) have remarkable optical properties. In particular, the peak extinction wavelength, lambda(max) of their localized surface plasmon resonance (LSPR) spectrum is unexpectedly sensitive to nanoparticle size, shape, and local ( approximately 10-30 nm) external dielectric environment. This sensitivity of the LSPR lambda(max) to the nanoenvironment has allowed us to develop a new class of nanoscale affinity biosensors. The essential characteristics and operational principles of these LSPR nanobiosensors will be illustrated using the well-studied biotin-streptavidin system. Exposure of biotin-functionalized Ag nanotriangles to 100 nM streptavidin (SA) caused a 27.0 nm red-shift in the LSPR lambda(max). The LSPR lambda(max) shift, DeltaR/DeltaR(max), versus [SA] response curve was measured over the concentration range 10(-)(15) M < [SA] < 10(-)(6) M. Comparison of the data with the theoretical normalized response expected for 1:1 binding of a ligand to a multivalent receptor with different sites but invariant affinities yielded approximate values for the saturation response, DeltaR(max) = 26.5 nm, and the surface-confined thermodynamic binding constant K(a,surf) = 10(11) M(-)(1). At present, the limit of detection (LOD) for the LSPR nanobiosensor is found to be in the low-picomolar to high-femtomolar region. A strategy to amplify the response of the LSPR nanobiosensor using biotinylated Au colloids and thereby further improve the LOD is demonstrated. Several control experiments were performed to define the LSPR nanobiosensor's response to nonspecific binding as well as to demonstrate its response to the specific binding of another protein. These include the following: (1) electrostatic binding of SA to a nonbiotinylated surface, (2) nonspecific interactions of prebiotinylated SA to a biotinylated surface, (3) nonspecific interactions of bovine serum albumin to a biotinylated surface, and (4) specific binding of anti-biotin to a biotinylated surface. The LSPR nanobiosensor provides a pathway to ultrasensitive biodetection experiments with extremely simple, small, light, robust, low-cost instrumentation that will greatly facilitate field-portable environmental or point-of-service medical diagnostic applications.

Application of different surface plasmon resonance biosensor chips to monitor the interaction of the CaM-binding site of nitric oxide synthase I and calmodulin

Surface plasmon resonance biosensors depend on modified gold surfaces to allow immobilization of proteins or peptides for interaction analysis. We investigated sensor chip surfaces that differ in the geometry of the immobilization matrix: two contain a three-dimensional coupling matrix and two have a surface with immobilization sites on a two-dimensional plane. Properties of sensor chips were compared by studying the interaction of calmodulin with a peptide representing the calmodulin-binding site of nitric oxide synthase I. Apparent K(D) values were determined by three different procedures in order to apply tests for self-consistency. At low surface densities (5-8 fmol/mm(2)) on three of the four tested surfaces, estimated K(D) values were within one order of magnitude and similar to the value found in solution (K(D) = 1-3 nM). When immobilization densities were increased by one to two orders of magnitude, apparent association rate constants were less distorted on a flat carboxymethylated surface than on dextran-coated sensor chips.

Use of optical biosensors for the study of mechanistically concerted surface adsorption processes

The advent of commercial optical biosensors, such as the BIAcore from Pharmacia and IAsys from Affinity Sensors, has made available to the biochemist a powerful means to examine and characterize the interaction of biological macromolecules with a binding surface. By analysis of the kinetic and equilibrium aspects of the observed experimental adsorption isotherms, rate and affinity constants can be determined. This Review focuses on pertinent aspects of the technology and its use for the performance and quantitative characterization of some various types of mechanistically concerted adsorption behavior.

Molecular analysis of peptides from the GH loop of foot-and-mouth disease virus C-S30 using surface plasmon resonance: a role for kinetic rate constants

A foot-and-mouth disease virus (FMDV) field variant, isolate C-S30 (also named C(1)-Barcelona), is known to contain four changes within the main antigenic site A (GH loop of capsid protein VP1, residues 136-150), at least one of which (Leu147-->Val) involves a highly conserved position, critical for antibody recognition in the reference strain C-S8c1. However, immunoenzymatic analysis of FMDV C-S30 showed it was recognised by 4C4, a monoclonal antibody that specifically targets site A. This remarkable behaviour has led us to analyse the individual and combined contributions of the four mutations to the antigenicity of C-S30, by surface plasmon resonance (SPR) and enzyme-linked immunosorbent assay (ELISA) studies of pentadecapeptides displaying all possible combinations of the four replacements. Analysis of this family of C-S30-derived analogues shows a certain level of antibody recognition by SPR. In addition, SPR data suggest that kinetic rate constants provide an indirect measure, on the one hand, of paratope accessibility (association rate constant) and, on the other hand, of peptide fitness to the same paratope (dissociation rate constant).

High affinity of anti-GBM antibodies from Goodpasture and transplanted Alport patients to alpha3(IV)NC1 collagen

BACKGROUND

Anti-glomerular basement membrane (anti-GBM) antibody-mediated diseases are characterized by rapidly progressive glomerulonephritis (RPGN) that often results in irreversible loss of renal function and renal failure. Although many factors contribute to the fulminant nature and treatment resistance of this disease, we questioned whether high affinity autoantibody-alpha3(IV) collagen interactions lead to persistent antibody deposition, thereby perpetuating inflammation. To address this hypothesis, the binding kinetics of human anti-GBM antibodies (Ab) to alpha3(IV)NC1 were evaluated using an optical biosensor interaction analysis.

METHODS

Polyclonal anti-GBM Abs were purified by alpha3(IV)NC1 affinity chromatography from the sera of patients with anti-GBM AB-mediated diseases, including individuals with Goodpasture syndrome (GS), idiopathic RPGN (N = 7), and Alport syndrome (AL) following kidney transplantation (N = 4). The affinity-binding characteristics of the autoantibodies were determined using a biosensor analysis system, with immobilized bovine alpha3(IV)NC1 dimers.

RESULTS

All of the autoantibody preparations bound to alpha3(IV)NC1, whereas none bound to alpha1(IV)NC1 (control). Purified, normal serum IgG did not bind to either antigen. Estimated dissociation constants (Kd) for the purified autoantibodies were 1.39E-04 +/- 7.30E-05 s-l (GS) and 8. 90E-05 +/- 2.80E-05 s-l (AL). Their estimated association constants (Ka) were 2.67E+04 +/- 1.8E+04 (M-ls-l) and 2.76E+04 +/- 1. 70E+04(M-ls-l) for GS and AL patients, respectively. By comparison with other Ab interactions, these Abs demonstrated high affinity, with relatively high on (binding) rates and slow off (dissociation) rates.

CONCLUSIONS

The results suggest that anti-GBM Abs bind rapidly and remain tightly bound to the GBM in vivo. This property likely contributes to both the fulminant nature of this disease and its resistance to therapy, because persistent glomerular Ab deposition has the potential to produce continuous inflammation, despite removal of circulating Abs and adequate immunosuppression.

Analysis of the interaction between monoclonal antibodies and human hemoglobin (native and cross-linked) using a surface plasmon resonance (SPR) biosensor

To develop a stable immuno-assay system for quantification of human hemoglobin (Hb), the interaction between various antibodies and Hb was studied using a surface plasmon resonance (SPR) biosensor in the BIAcore equipment (Amersham Pharmacia Biotech) with an immobilized anti-Hb antibody sensor chip. When polyclonal antibodies were used, the immuno-reactivity of purified and commercially available Hb decreased drastically with incubation times up to 14 h. This instability of immuno-reactivity of Hb is attributable to the conformational changes in Hb induced by oxidation. On the other hand, of the sixteen monoclonal antibodies tested, four antibodies (MSU-102, -103, -106 and -115) were found to maintain their immuno-reactivities at least up to 24 h. During long-term storage, however, the immuno-reactivity of Hb with these monoclonal antibodies decreased significantly. The chemical betabeta-cross-linking of Hb was effectively able to stabilize the structure of Hb and immuno-reactivity with monoclonal antibodies such as MSU-103 for periods at least up to 70 days. Therefore, the combination of specific monoclonal antibodies such as MSU-103 and a betabeta-cross-linked Hb standard could be used for the quantification of Hb.