Dynamics of fluorescence dequenching of ostrich-quenched fluorescein biotin: A multifunctional quantitative assay for biotin

Dually Labeled Biomolecules for Characterizing Biotinylated Species through Competitive Binding Reactions

The capability of biotinylated molecules to bind streptavidin may be a more functional measure of the success of target biotinylation than titration of total bound biotins per molecule. It was demonstrated that the binding capability could be assessed by a competitive assay, in which a biotinylated antibody (BA) (or protein, ligand, receptor etc.) of interest competed with a reference antibody (or a protein) dually labeled with biotin and electrochemiluminescence (ECL) moieties for the binding sites of streptavidin coated on the surface of magnetic beads. Inversely related to the ECL signal, the binding capability of a biotinylated antibody can be reproducibly evaluated by multiple sets of easily acquired data series rather than by a single measurement. This method can be employed in an ordinary laboratory with an automated ECL analyzer or other readout instruments for routine characterization of any biotinylated species, such as proteins, ligands, receptors, and polypeptides.

Biotin oligonucleotide labeling reactions: A method to assess their effectiveness and reproducibility

The strong molecular interaction between biotin and streptavidin is widely used in the growing field of nucleic acid nanotechnology. Several biotin labeled oligonucleotide tools have been developed for the detection of biological molecules as well as for protein purification. For these reasons, biotinylation can be considered one of the main chemical reactions for nucleic acid labeling. However, despite its widespread application and the presence on the market of many reagents for the conjugation of biotin to oligonucleotides, it is not yet available a cheap, easy and sensitive system able to assess the effectiveness and reproducibility of this reaction. Here, we present an accurate and reliable method to achieve a qualitative and quantitative analysis of oligonucleotide biotinylation. The protocol employs basic laboratory instruments and standard software for molecular biology applications and does not require advanced expertise for its execution. Most importantly, our method is independent from complex kinetic equilibrium parameters and shows a limit of detection more than one order of magnitude lower than the current fluorometric gold standard assay. Therefore, this method could become a standard, inexpensive and routinely used quality test for post-synthesis evaluation of biotin conjugation reactions.

Detailed characterization of the solution kinetics and thermodynamics of biotin, biocytin and HABA binding to avidin and streptavidin

The high affinity (K_D ~ 10⁻¹⁵ M) of biotin for avidin and streptavidin is the essential component in a multitude of bioassays with many experiments using biotin modifications to invoke coupling. Equilibration times suggested for these assays assume that the association rate constant (k_on) is approximately diffusion limited (10⁹ M^-1s^-1) but recent single molecule and surface binding studies indicate that they are slower than expected (10⁵ to 10⁷ M^-1s^-1). In this study, we asked whether these reactions in solution are diffusion controlled, which reaction model and thermodynamic cycle describes the complex formation, and if there are any functional differences between avidin and streptavidin. We have studied the biotin association by two stopped-flow methodologies using labeled and unlabeled probes: I) fluorescent probes attached to biotin and biocytin; and II) unlabeled biotin and HABA, 2-(4’-hydroxyazobenzene)-benzoic acid. Both native avidin and streptavidin are homo-tetrameric and the association data show no cooperativity between the binding sites. The k_on values of streptavidin are faster than avidin but slower than expected for a diffusion limited reaction in both complexes. Moreover, the Arrhenius plots of the k_on values revealed strong temperature dependence with large activation energies (6–15 kcal/mol) that do not correspond to a diffusion limited process (3–4 kcal/mol). Accordingly, we propose a simple reaction model with a single transition state for non-immobilized reactants whose forward thermodynamic parameters complete the thermodynamic cycle, in agreement with previously reported studies. Our new understanding and description of the kinetics, thermodynamics, and spectroscopic parameters for these complexes will help to improve purification efficiencies, molecule detection, and drug screening assays or find new applications.

Recognition kinetics of biomolecules at the surface of different-sized spheres

Bead-based assay is widely used in many bioanalytical applications involving the attachment of proteins and other biomolecules to the surface. For further understanding of the formation of a sphere-biomolecule complex and easily optimizing the use of spheres in targeted biological applications, it is necessary to know the kinetics of the binding reaction at sphere/solution interface. In our presented work, a simple fluorescence analysis method was employed to measure the kinetics for the binding of biotin to sphere surface-bound FITC-SA, based on the fact that the fluorescence intensity of FITC was proportionally enhanced by increasing the binding amount of biotin. By monitoring the time-dependent changes of FITC fluorescence, it was found that the binding rate constant of biotin to sphere surface-immobilized FITC-SA was much smaller than that of biotin to freely diffusing FITC-SA. This can be attributed to the decreased encounter frequency of the reaction pair, restricted motion of the attached biomolecule, and the weakened steric accessibility of the binding site. These factors would become more obvious when increasing the size of the sphere upon which the FITC-SA was immobilized. Additionally, the effect of nanoparticles on the diffusion-controlled bimolecular binding reaction was more evident than that on the chemical recognition-controlled binding reaction.

Chapter 11. Subsecond analyses of G-protein coupled-receptor ternary complex dynamics by rapid mix flow cytometry

The binding of full and partial agonist ligands (L) to G-protein-coupled receptors (GPCRs) initiates the formation of ternary complexes with G-proteins (LRG complexes). We describe the assembly of detergent-solubilized LRG complexes on beads. Rapid mix flow cytometry is used to analyze the subsecond dynamics of guanine nucleotide-mediated ternary complex disassembly. Ternary complexes were assembled with three formyl peptide receptor constructs (wild type, FPR-Galpha(i2) fusion, and FPR-GFP fusion) and two isotypes of the alpha subunit (alpha(i2) and alpha(i3)) and betagamma dimer (beta(i)(1)gamma(2) and beta(4)gamma(2)). Experimental evidence suggests that thermodynamic stability of ternary complexes depends on subunit isotype. Comparison of assemblies derived from the three constructs of FPR and G-protein heterotrimers composed of the available subunit isotypes demonstrate that the fast step is associated with the separation of receptor and G-protein and that the dissociation of the ligand or of the alpha and betagamma subunits was slower. These results are compatible with a cell activation model involving G-protein conformational changes rather than disassembly of Galphabetagamma heterotrimer.

Fluorometric assay for quantitation of biotin covalently attached to proteins and nucleic acids

As a component of the (strept)avidin affinity system, biotin is often covalently linked to proteins or nucleic acids. We describe here a microplate-based high-throughput fluorometric assay for biotin linked to either proteins or nucleic acids based on fluorescence resonance energy transfer (FRET). This assay utilizes a complex of Alexa Fluor® 488 dye-labeled avidin with a quencher dye, 2-(4′-hydroxyazobenzene) benzoic acid (HABA), occupying the biotin binding sites of the avidin. In the absence of biotin, HABA quenches the fluorescence emission of the Alexa Fluor 488 dyes via FRET. HABA is displaced when biotin binds to the Alexa Fluor 488 dye-labeled avidin, resulting in decreased FRET efficiency. This mechanism results in an increase in fluorescence intensity directly related to the amount of biotin present in the sample. The assay is able to detect as little as 4 pmol biotin in a 0.1 mL volume within 15 min of adding sample to the reagent, with a Z-factor >0.9.

Some mechanistic insights into GPCR activation from detergent-solubilized ternary complexes on beads

The binding of full and partial agonist ligands (L) to G protein-coupled receptors (GPCRs) initiates the formation of ternary complexes with G proteins [ligand-receptor-G protein (LRG) complexes]. Cyclic ternary complex models are required to account for the thermodynamically plausible complexes. It has recently become possible to assemble solubilized formyl peptide receptor (FPR) and beta(2)-adrenergic receptor (beta(2)AR) ternary complexes for flow cytometric bead-based assays. In these systems, soluble ternary complex formation of the receptors with G proteins allows direct quantitative measurements which can be analyzed in terms of three-dimensional concentrations (molarity). In contrast to the difficulty of analyzing comparable measurements in two-dimensional membrane systems, the output of these flow cytometric experiments can be analyzed via ternary complex simulations in which all of the parameters can be estimated. An outcome from such analysis yielded lower affinity for soluble ternary complex assembly by partial agonists compared with full agonists for the beta(2)AR. In the four-sided ternary complex model, this behavior is consistent with distinct ligand-induced conformational states for full and partial agonists. Rapid mix flow cytometry is used to analyze the subsecond dynamics of guanine nucleotide-mediated ternary complex disassembly. The modular breakup of ternary complex components is highlighted by the finding that the fastest step involves the departure of the ligand-activated GPCR from the intact G protein heterotrimer. The data also show that, under these experimental conditions, G protein subunit dissociation does not occur within the time frame relevant to signaling. The data and concepts are discussed in the context of a review of current literature on signaling mechanism based on structural and spectroscopic (FRET) studies of ternary complex components.