Bivalent kinetic binding model to surface plasmon resonance studies of antigen-antibody displacement reactions

Toward the Development of Rapid, Specific, and Sensitive Microfluidic Sensors: A Comprehensive Device Blueprint

Recent advances in nano/microfluidics have led to the miniaturization of surface-based chemical and biochemical sensors, with applications ranging from environmental monitoring to disease diagnostics. These systems rely on the detection of analytes flowing in a liquid sample, by exploiting their innate nature to react with specific receptors immobilized on the microchannel walls. The efficiency of these systems is defined by the cumulative effect of analyte detection speed, sensitivity, and specificity. In this perspective, we provide a fresh outlook on the use of important parameters obtained from well-characterized analytical models, by connecting the mass transport and reaction limits with the experimentally attainable limits of analyte detection efficiency. Specifically, we breakdown when and how the operational (e.g., flow rates, channel geometries, mode of detection, etc.) and molecular (e.g., receptor affinity and functionality) variables can be tailored to enhance the analyte detection time, analytical specificity, and sensitivity of the system (i.e., limit of detection). Finally, we present a simple yet cohesive blueprint for the development of high-efficiency surface-based microfluidic sensors for rapid, sensitive, and specific detection of chemical and biochemical analytes, pertinent to a variety of applications.

Data evaluation for surface-sensitive label-free methods to obtain real-time kinetic and structural information of thin films: A practical review with related software packages

Interfacial layers are important in a wide range of applications in biomedicine, biosensing, analytical chemistry and the maritime industries. Given the growing number of applications, analysis of such layers and understanding their behavior is becoming crucial. Label-free surface sensitive methods are excellent for monitoring the formation kinetics, structure and its evolution of thin layers, even at the nanoscale. In this paper, we review existing and commercially available label-free techniques and demonstrate how the experimentally obtained data can be utilized to extract kinetic and structural information during and after formation, and any subsequent adsorption/desorption processes. We outline techniques, some traditional and some novel, based on the principles of optical and mechanical transduction. Our special focus is the current possibilities of combining label-free methods, which is a powerful approach to extend the range of detected and deduced parameters. We summarize the most important theoretical considerations for obtaining reliable information from measurements taking place in liquid environments and, hence, with layers in a hydrated state. A thorough treamtmaent of the various kinetic and structural quantities obtained from evaluation of the raw label-free data are provided. Such quantities include layer thickness, refractive index, optical anisotropy (and molecular orientation derived therefrom), degree of hydration, viscoelasticity, as well as association and dissociation rate constants and occupied area of subsequently adsorbed species. To demonstrate the effect of variations in model conditions on the observed data, simulations of kinetic curves at various model settings are also included. Based on our own extensive experience with optical waveguide lightmode spectroscopy (OWLS) and the quartz crystal microbalance (QCM), we have developed dedicated software packages for data analysis, which are made available to the scientific community alongside this paper.

Structure and dsRNA-binding activity of the Birnavirus Drosophila X Virus VP3 protein

The Birnavirus multifunctional protein VP3 plays an essential role coordinating the virus life cycle, interacting with the capsid protein VP2, with the RNA-dependent RNA polymerase VP1 and with the dsRNA genome. Furthermore, the role of this protein in controlling host cell responses triggered by dsRNA and preventing gene silencing has been recently demonstrated. Here we report the X-ray structure and dsRNA-binding activity of the N-terminal domain of Drosophila X virus (DXV) VP3. The domain folds in a bundle of three α-helices and arranges as a dimer, exposing to the surface a well-defined cluster of basic residues. Site directed mutagenesis combined with Electrophoretic Mobility Shift Assays (EMSA) and Surface Plasmon Resonance (SPR) revealed that this cluster, as well as a flexible and positively charged region linking the first and second globular domains of DXV VP3, are essential for dsRNA-binding. Also, RNA silencing studies performed in insect cell cultures confirmed the crucial role of this VP3 domain for the silencing suppression activity of the protein.IMPORTANCE The Birnavirus moonlighting protein VP3 plays crucial roles interacting with the dsRNA genome segments to form stable ribonucleoprotein complexes and controlling host cell immune responses, presumably by binding to and shielding the dsRNA from recognition by the host silencing machinery. The structural, biophysical and functional data presented in this work has identified the N-terminal domain of VP3 as responsible for the dsRNA-binding and silencing suppression activities of the protein in Drosophila X virus.

Sensitivity and reproducibility enhancement in enzyme immunosorbent assays based on half fragment antibodies

The free sulfhydryl groups of the hinge region of monovalent antibody fragments (rIgG) allow the orientation of rIgG on functionalized surfaces in immunosensors. To evaluate the contribution of reduction and orientation on signal enhancement we compared the performance of whole antibodies and their rIgG in ELISA performed on polystyrene or maleimide-functionalized microplates. Monoclonal anti-horseradish peroxidase (anti-HRP) and monoclonal anti-fPSA antibodies (1 mg/mL) were reduced with 2-mercaptoethylamine (53 mM). Western blot confirmed the presence of rIgG as a band at 75 kDa, detectable only by anti-heavy chain but not by anti-light chain antibodies, suggesting a possible folding rearrangement. Using anti-HRP we confirmed the retention of the antigen binding capacity of rIgG. Moreover, we observed a signal enhancement for rIgG even if randomly absorbed on polystyrene [linear regression slope (95%CI): rIgG 0.524 (0.434-0.614), IgG 0.370 (0.430-0.399); P = 0.0016] suggesting that chemical reduction might affect the antigen binding capacity of antibodies. ELISA with anti-fPSA rIgG coated on polystyrene confirmed these observations. Oriented anti-fPSA rIgG on a maleimide surface showed comparable signals to the assay performed on polystyrene for each analyzed concentration of antigen (P_ANOVA = 0.1980), anyway, with a significant improvement of the repeatability likely providing a more homogeneous capturing surface (SD rIgG_maleimide-rIgG_polystirene: fPSA 0.725 ng/mL:0.74-2.89; 1.45 ng/mL:1.56-8.69; 3.625 ng/mL:3.52-15.03; 7.25 ng/mL:7.78-18.44).

Surface plasmon resonance biosensors for detection of Alzheimer's biomarkers; an effective step in early and accurate diagnosis

The rapid and direct detection of biomarkers in biofluids at clinically relevant concentrations faces serious limitations to develop diagnostic criteria for neurodegenerative diseases such as Alzheimer's disease (AD). In this regard, the early detection of biomarkers correlated with AD using novel modalities and instruments is at the center of attention. Recently, some newly invented optical-based biosensors namely Surface Plasmon Resonance (SPR) has been extensively investigated for the detection of biomarkers using a label-free method or by checking interaction between ligand and analyte. These approaches can sense a very small amount of target molecules in the blood and cerebrospinal fluids samples. In this review, the different hypothesis related to AD, and the structural properties of AD biomarkers was introduced. Also, we aim to highlight the specific role of available SPR-based sensing methods for early detection of AD biomarkers such as aggregated β-amyloid and tau proteins. Efforts to better understand the accuracy and efficiency of optical-based biosensors in the field of neurodegenerative disease enable us to accelerate the advent of novel modalities in the clinical setting for therapeutic and diagnostic purposes.

SPR signals enhancement by gold nanorods for cell surface marker detection

Introduction: The detection of micrometer-sized particles like cells is limited by surface plasmon resonance (SPR) biosensors because of having a depth of evanescent wave <500 nm. In this study, for the first time, we exhibited the use of streptavidin-functionalized gold nanorods (GNRs) as intensification labels for detection of cell surface markers in SPR-based biosensors.

Methods: The GNRs (ʎ max: 735 nm) were modified with streptavidin using EDC/NHS coupling method and human umbilical vein endothelial cells (HUVECs) were selected as the cell model for detecting VE-cadherin on cell surface using real-time SPR device in the 785 nm wavelength of the laser source.

Results: The investigations revealed that the plasmonic field extension produced from the gold layer and GNRs resulted in multiple enhancement of SPR signals when the wavelength of laser source in SPR instrument was matched with the wavelength of maximum absorbance in GNRs. Moreover, the results showed that the growth of ∆RU value in specific and non-specific bindings for various cell number injections were produced with increasing the cell number.

Conclusion: The results displayed that cell detection can be performed in real- time form without any need to a time-consuming process used in conventional methods like immunocytochemistry, flow cytometry, and western blotting.

Ultra-sensitive detection by metal nanoparticles-mediated enhanced SPR biosensors

Surface plasmon resonance (SPR), as an optical technique, has widely been used for the detection of biomarkers. Various investigations have been conducted to address the impacts of SPR on the kinetics of biological interactions between the ligand and its cognate bio-element. Up until now, different biofunctionalized metal nanoparticles (NPs) have been used for the ultrasensitive detection of biomarkers in the enhanced SPR. The enhancement of plasmonic properties and refractive index by means of metal NPs in SPR-based biosensors have significantly improved the diagnosis and monitoring of molecular markers in different disesaes including malignancies. In all the enhanced SPR systems utilized for the direct/sandwich assay, each NP is covalently modified with the analyte molecules like antibody (Ab) or a nucleic acid such as DNA/RNA aptamer (Ap) capable of interaction with the related biomarker(s). The increasing of density near the gold surface and plasmonic coupling of gold film and NPs can provide a large shift in the refractive index enhancing the plasmonic resonance because the SPR response unit is sensitive to alteration of the refractive index and the mass shifting onto the chip surface. In this study, we review the potential applications of two major NPs for enhancing the SPR signals for the detection of molecular biomarkers, including gold and magnetic NPs.

Mathematical Modeling of Bioassays

The high affinity and specificity of biological receptors determine the demand for and the intensive development of analytical systems based on use of these receptors. Therefore, theoretical concepts of the mechanisms of these systems, quantitative parameters of their reactions, and relationships between their characteristics and ligand-receptor interactions have become extremely important. Many mathematical models describing different bioassay formats have been proposed. However, there is almost no information on the comparative characteristics of these models, their assumptions, and predictive insights. In this review we suggested a set of criteria to classify various bioassays and reviewed classical and contemporary publications on these bioassays with special emphasis on immunochemical analysis systems as the most common and in-demand techniques. The possibilities of analytical and numerical modeling are discussed, as well as estimations of the minimum concentrations that may be detected in bioassays and recommendations for the choice of assay conditions.

Quantifying Weak Glycan-Protein Interactions Using a Biolayer Interferometry Competition Assay: Applications to ECL Lectin and X-31 Influenza Hemagglutinin

This chapter introduces two formats using bio-layer interferometry competition assays to determine the solution K _D values of weak glycan-protein interactions. This approach overcomes the challenge of determining weak interactions while minimizing the amount of reagents required. Accurate solution K _D values aid in understanding the complex relationships between monomeric versus multimeric interactions and affinity versus avidity. The assays have been applied to a well-studied lectin (Erythrina crista-galli lectin) and influenza hemagglutinin (X-31). The solution K _D values determined from this approach are in good agreement with previous reported literature values from isothermal titration calorimetry and NMR. Additionally, this approach appears robust and precise.

Analysis of Protein Interactions by Surface Plasmon Resonance

Surface plasmon resonance is an optical technique that is utilized for detecting molecular interactions, such as interactions that occur between proteins or other classes of molecules. Binding of a mobile molecule (analyte) to a molecule immobilized on a thin metal film (ligand) changes the refractive index of the film. The angle of extinction of light that is completely reflected after polarized light impinges upon the film, is altered and monitored as a change in detector position for a dip in reflected intensity (the surface plasmon resonance phenomenon). Because the method strictly detects mass, there is no need to label the interacting components, thus eliminating possible changes of their molecular properties. In this chapter, we review essential SPR methodology and present applications to basic science and human disease.