Nanoparticles as Fluorescence Labels: Is Size All that Matters?

Fluorescent labels are often used in bioassays as a means to detect and characterize ligand-receptor binding. This is due in part to the inherently high sensitivity of fluorescence-based technology and the relative accessibility of the technique. There is often little concern raised as to whether or not the fluorescent label itself affects the ligand-receptor binding dynamics and equilibrium. This may be particularly important when considering nanoparticle labels. In this study, we examine the affects of nanoparticle (quantum dots and polymer nanospheres) fluorescent labels on the streptavidin-biotin binding system. Since the nanoparticle labels are larger than the species they tag, one could anticipate significant perturbation of the binding equilibrium. We demonstrate, using fluorescence cross-correlation spectroscopy, that although the binding equilibria do change, the relative changes are largely predictable. We suggest that the nanoparticles’ mesoscopic size and surface tension effects can be used to explain changes in streptavidin-biotin binding.     

Reevaluation of ANS binding to human and bovine serum albumins: key role of equilibrium microdialysis in ligand - receptor binding characterization

In this work we return to the problem of the determination of ligand-receptor binding stoichiometry and binding constants. In many cases the ligand is a fluorescent dye which has low fluorescence quantum yield in free state but forms highly fluorescent complex with target receptor. That is why many researchers use dye fluorescence for determination of its binding parameters with receptor, but they leave out of account that fluorescence intensity is proportional to the part of the light absorbed by the solution rather than to the concentration of bound dye. We showed how ligand-receptor binding parameters can be determined by spectrophotometry of the solutions prepared by equilibrium microdialysis. We determined the binding parameters of ANS - human serum albumin (HSA) and ANS - bovine serum albumin (BSA) interaction, absorption spectra, concentration and molar extinction coefficient, as well as fluorescence quantum yield of the bound dye. It was found that HSA and BSA have two binding modes with significantly different affinity to ANS. Correct determination of the binding parameters of ligand-receptor interaction is important for fundamental investigations and practical aspects of molecule medicine and pharmaceutics. The data obtained for albumins are important in connection with their role as drugs transporters.     

Energy landscape of streptavidin-biotin complexes measured by atomic force microscopy

The dissociation of ligand and receptor involves multiple transitions between intermediate states formed during the unbinding process. In this paper, we explored the energy landscape of the streptavidin-biotin interaction by using the atomic force microscope (AFM) to measure the unbinding dynamics of individual ligand-receptor complexes. The rupture force of the streptavidin-biotin bond increased more than 2-fold over a range of loading rates between 100 and 5000 pN/s. Moreover, the force measurements showed two regimes of loading in the streptavidin-biotin force spectrum, revealing the presence of two activation barriers in the unbinding process. Parallel experiments carried out with a streptavidin mutant (W120F) were used to investigate the molecular determinants of the activation barriers. From these experiments, we attributed the outer activation barrier in the energy landscape to the molecular interaction of the '3-4' loop of streptavidin that closes behind biotin.     

The binding of the B-chain of ricin to Burkitt lymphoma cells. A new approach to ligand-receptor interaction studies

It is shown that conformational changes of receptor proteins brought about by binding of a ligand induce changes in the lipid environment of the receptor that can be monitored by fluorescent lipid probes. On this basis a new approach to studies of ligand-receptor binding is proposed. Using the interaction of the ricin B-chain with Burkitt lymphoma cells as an example and fluorescent labelled sphingomyelin as a probe, the ligand-induced changes of fluorescence anisotropy were shown to be concentration-dependent and to permit determination of the binding constant and the number of receptor-binding sites. The method was found to be specific and highly sensitive, allowing detection of the action of one RB molecule per cell. Scatchard analysis of the binding of 125I-RB demonstrated the presence on the cell surface of two binding sites with Kd approximately 10(-10) and approximately 10(-8) M, respectively. Only the high-affinity sites were detected by the fluorescence technique. Saturation of these sites resulted in maximum inhibition of protein synthesis.     

Kinetic analysis of heparin and glucan sulfates binding to P-selectin and its impact on the general understanding of selectin inhibition

P-Selectin, expressed on activated endothelial cells and platelets, is a high kinetic adhesion receptor involved in leukocyte rolling of the inflammatory response, or in tumor cell binding in the course of metastasis. Thus, P-selectin inhibition is a promising therapeutic target. The anti-inflammatory and anti-metastatic activities of heparin have partly been related to the inhibition of P-selectin binding. Here we apply a quartz crystal microbalance (QCM) biosensor to determine the kinetic constants of heparin and other sulfated polysaccharides binding to immobilized P-selectin. Binding kinetics of the derivatives were correlated with their inhibitory capacity in a P-selectin cell rolling assay. Three commercial heparins differ in cell rolling inhibition and display slightly different affinities (KD 1.21 x 10(-6) M to 5.86 x 10(-7) M). Inhibitory capacity appears to be mainly driven by a slow off-rate from the receptor (2.27 x 10(-3) s-1 to 1.23 x 10(-3) s-1). To correlate the impact of binding kinetics on inhibitory capacity structurally, we analyzed six semisynthetic glucan sulfates. They display different degrees of sulfation (DS), which has a strong influence on inhibitory activity. Kinetic data illustrate that the inhibitory capacity correlates excellently with the off-rate of these polysaccharides (R = 0.99), while the association (on-rate) affects activity to a lesser extent. In general, the consideration of binding kinetics sheds new light on the mechanism of selectin inhibition. A much slower dissociation of the inhibitors from the receptor than the physiological ligands is key for inhibitory capacity. Structurally, highly charged compounds with a slow off-rate, such as heparin or glucan sulfates, appear as potent candidates for P-selectin inhibition.     

Cascade blue derivatives: water soluble, reactive, blue emission dyes evaluated as fluorescent labels and tracers.

Fluorescent dyes based on the pyrenyloxytrisulfonic acid (Cascade Blue) structure were prepared and evaluated. The dyes contain functional groups that react with amines, thiols, acids, aldehydes, and ketones, forming covalently bonded, fluorescent derivatives of molecules with broad biological interest. Reactive groups in the Cascade Blue dyes include carboxylic acids and activated esters, amines, hydrazides, alcohols, photoaffinity reagents, acrylamides, and haloacetamides. The dyes exhibited absorption maxima at 374-378 nm and 399-403 nm, with extinction coefficients in the range of 1.9 x 10(4)-2.4 x 10(4) M-1cm-1 and 2.3 x 10(4)-3.0 x 10(4) M-1cm-1, respectively. Emission maxima ranged from 422-430 nm. The spectral properties of the fluorescent dyes are sufficiently different from fluorescein to permit simultaneous use of both dyes with minimum spectral interference. The Cascade Blue derivatives have narrower spectral bandwidths and smaller Stokes' shifts than other reactive dyes with similar spectral properties, do not show appreciable sensitivity to pH, have higher solubilities in aqueous solution, and have good to excellent quantum yields. Cascade Blue conjugates of a number of histochemically and biologically useful molecules were prepared, including dextrans, albumins, Fc receptor binding proteins, antibodies, lectins, membrane receptor binding proteins, and biotin binding proteins, as well as biological particles and bacteria. Cascade Blue conjugates of secondary and tertiary labels yielded specific fluorescence localization in the indirect immunofluorescent staining of human epithelial cell (HEp-2) nuclei.     

Mapping the binding sites of peptide and non-peptide molecules to G protein-coupled receptors by fluorescence

Summary Novel fluorescence approaches to investigate ligand recognition and structure of G protein-coupled receptors in native membranes have been developed. These methods combine the biosynthetic incorporation of unnatural fluorescent amino acids at known sites in receptors with the technique of fluorescence energy transfer for distance measurement. This permits one to fix the ligand in space and to define the structure of the receptor in a model of ligand-receptor interactions. Subdomains of ligand binding sites on NK1 and NK2 receptors were also characterized using environment-sensitive fluorophores and the techniques of collisional quenching and anisotropy. Antagonists and agonists have different binding sites on NK1 and NK2.     

dsDNA-coated quantum dots

Because of their unique spectral properties, quantum dots (QDs) have recently proved useful as fluorescent labels for biosensing probes. We developed a versatile QD label by modifying dsDNA with biotin and thiol groups at opposite ends and attaching it to quantum dots via a metal-thiol bond. These dsDNA-coated QDs fluorescently label their targets through biotin-streptavidin binding and show excellent histological results when used to detect biotin-labeled chromosome probes. The dsDNA coating also circumvented the common problems of aggregation and steric hindrance that occur with other QD probes.     

Lanthanide-based luminescent assays for ligand-receptor interactions

The evaluation of receptor ligand interactions is important in the field of drug discovery and development. Currently these interactions are typically measured with cumbersome (low throughput) radiolabels. Higher throughput screens are available such as fluorescent measurements of G-protein coupled receptor-induced Ca2+ increases or fluorescence anisotropy, yet these have limited applicability and/or low signal to noise. Hence, there is a need to develop more widely applicable and more sensitive labels that can be used to monitor ligand-receptor interactions. Lanthanides provide an attractive alternative to the traditional labels used for monitoring ligand-receptor interactions. The incorporation of lanthanide labels into traditional assays used to assess receptor-ligand interactions can make these assays more affordable, less time consuming and amenable to automation. Lanthanides can be coupled to ligands and provide strong luminescent signals that can be detected using time-resolved fluorescence (TRF) methods. This approach takes advantage of the long fluorescence lifetime of the lanthanide and can detect less than one attomole of europium in a multiwell plate sample. This short review provides a basic introduction into lanthanides and TRF and describes some of the recent assays which have utilized lanthanides as labels to assess ligand-receptor interactions.     

Biotinylated-spiperone ligands for quantum dot labeling of the dopamine D2 receptor in live cell cultures

We have synthesized 3 analogs of the dopamine D2 receptor (D2 DR) antagonist spiperone that can be conjugated to streptavidin-coated quantum dots via a pegylated biotin derivative. Using fluorescent imaging we demonstrate that substitution on the spiro position is tolerated, whilst the length and rigidity of a spacer arm attached to spiperone is important in controlling specific labeling as well as minimizing nonspecific labeling to cells and the surface of cell culture dishes. The ligand with the most rigid linker IDT772 (4) had the best binding profile and had high specific binding to D2 DR expressing HEK-293T cells with low nonspecific binding to plates and HEK-293T cells that lacked the D2 DR.     

Benzodiazepine binding studies on living cells: application of small ligands for fluorescence correlation spectroscopy

We demonstrate the applicability of fluorescence correlation spectroscopy (FCS) for receptor binding studies using low molecular weight ligands on the membranes of living nerve cells. The binding of the benzodiazepine Ro 7-1986/602 (N-des-diethyl-fluorazepam), labeled with the fluorophore Alexa 532, to the benzodiazepine receptor was analyzed quantitatively at the membrane of single rat hippocampal neurons. The values obtained for the dissociation constant Kd = (9.9 +/- 1.9) nm and the rate constant for ligand-receptor dissociation kdisS = (1.28 +/- 0.08) x 10(-3) s(-1) show that there is a specific and high affinity interaction between the dye-labeled ligand (Ro-Alexa) and the receptor site. The binding was saturated at approx. 100 nM and displacement of 10 nM Ro-Alexa, with a 1,000-fold excess of midazolam, showed a non-specific binding of 7-10%. Additionally, two populations of the benzodiazepine receptor that differed in their lateral mobility were detected in the membrane of rat neurons. The diffusion coefficients for these two populations [D(bound1) = (1.32 +/- 0.26) microm2/s; D(bound2) = (2.63 +/- 0.63) x 10(-2) microm2/s] are related to binding sites, which shows a mono-exponential decay in a time-dependent dissociation of the ligand-receptor complex.     

Bovine beta-lactoglobulin receptors on transformed mammalian cells (hybridomas MARK-3): characterization by flow cytometry

Flow cytometry was used to demonstrate the presence of beta-lactoglobulin (betaLG) receptors on living murine hybridoma MARK-3 cells using a fluorescein isothiocyanate-betaLG conjugate (FITC-betaLG: molar ratio of 5:1). A site occupation curve was produced using a shift in the mean channel fluorescence at various concentrations of FITC-betaLG. The binding of labelled ligand was concentration dependent and was inhibited by unlabelled betaLG. The on-rate constant was 3.2x10(2) M(-1) min(-1) and the off-rate constant was 0.002 min(-1). Scatchard plot analysis gave a dissociation constant (K(d)) of 44+/-21x10(-7) and 39+/-24x10(-5) M (n=3). Flow cytometry indicated that at least 15% of the FITC-betaLG were internalized for 5 min and that internalization was temperature- and time-dependent. The internalization was confirmed by 3-D fluorescence microscopy (CELLScan system).     

Characterization of benzodiazepine receptors with fluorescent ligands

Fluorescein conjugates of the high-affinity benzodiazepine receptor ligands Ro 15-1788 and Ro 7-1986 were synthesized. The binding of these fluorescent ligands (BD 621 and BD 607) to benzodiazepine receptors was characterized by direct fluorescence measurement. Both the equilibrium dissociation constants (KD) of BD 621 and BD 607 and the maximum number of binding sites (Bmax) estimated by fluorescence monitoring were consistent with values obtained by using radioligand binding techniques. The binding of BD 621 and BD 607 assessed by fluorescence measurement was reversible, abolished by photoaffinity labeling with Ro 15-4513, and unaffected by a variety of substances that do not bind to benzodiazepine receptors. The potencies of chemically diverse benzodiazepine receptor compounds to inhibit fluorescent ligand binding were highly correlated (r = 0.94, P less than 0.001), with potencies obtained from radioligand binding techniques. These findings demonstrate the feasibility of using direct fluorescence measurement techniques to quantitate ligand-receptor interactions.     

Single molecule characterization of P-selectin/ligand binding

P-selectin expressed on activated platelets and vascular endothelium mediates adhesive interactions to polymorphonuclear leukocytes (PMNs) and colon carcinomas critical to the processes of inflammation and blood-borne metastasis, respectively. How the overall adhesiveness (i.e. the avidity) of receptor/ligand interactions is controlled by the affinity of the individual receptors to single ligands is not well understood. Using single molecule force spectroscopy, we probed in situ both the tensile strength and off-rate of single P-selectin molecules binding to single ligands on intact human PMNs and metastatic colon carcinomas and compared them to the overall avidity of these cells for P-selectin substrates. The use of intact cells rather than purified proteins ensures the proper orientation and preserves post-translational modifications of the P-selectin ligands. The P-selectin/PSGL-1 interaction on PMNs was able to withstand forces up to 175 pN and had an unstressed off-rate of 0.20 s(-1). The tensile strength of P-selectin binding to a novel O-linked, sialylated protease-sensitive ligand on LS174T colon carcinomas approached 125 pN, whereas the unstressed off-rate was 2.78 s(-1). Monte Carlo simulations of receptor/ligand bond rupture under constant loading rate for both P-selectin/PSGL-1 and P-selectin/LS174T ligand binding give distributions and mean rupture forces that are in accord with experimental data. The pronounced differences in the affinity for P-selectin/ligand binding provide a mechanistic basis for the differential abilities of PMNs and carcinomas to roll on P-selectin substrates under blood flow conditions and underline the requirement for single molecule affinity measurements.     

Biotin tethered homotryptamine derivatives: high affinity probes of the human serotonin transporter (hSERT)

Quantum dot conjugates of compounds capable of inhibiting the serotonin transporter (SERT) could form the basis of fluorescent probes for live cell imaging of membrane bound SERT. Additionally, quantum dot-SERT antagonist conjugates may be amenable to fluorescence-based, high-throughput assays for this transporter. This Letter describes the synthesis of SERT-selective ligands amenable to conjugation to quantum dots via a biotin-streptavidin binding interaction. SERT selectivity and affinity were incorporated into the ligand via a tetrahydropyridine or cyclohexylamine derivative and the affinity of these compounds for SERT was measured by their ability to produce SERT-dependent currents in Xenopus laveis oocytes.     

Luminescent quantum dots for multiplexed biological detection and imaging

Recent advances in nanomaterials have produced a new class of fluorescent labels by conjugating semiconductor quantum dots with biorecognition molecules. These nanometer-sized conjugates are water-soluble and biocompatible, and provide important advantages over organic dyes and lanthanide probes. In particular, the emission wavelength of quantum-dot nanocrystals can be continuously tuned by changing the particle size, and a single light source can be used for simultaneous excitation of all different-sized dots. High-quality dots are also highly stable against photobleaching and have narrow, symmetric emission spectra. These novel optical properties render quantum dots ideal fluorophores for ultrasensitive, multicolor, and multiplexing applications in molecular biotechnology and bioengineering.     

Surface modification to reduce nonspecific binding of quantum dots in live cell assays

Nonspecific binding is a frequently encountered problem with fluorescent labeling of tissue cultures when labeled with quantum dots. In these studies various cell lines were examined for nonspecific binding. Evidence suggests that nonspecific binding is related to cell type and may be significantly reduced by functionalizing quantum dots with poly(ethylene glycol) ligands (PEG). The length of PEG required to give a significant reduction in nonspecific binding may be as short as 12-14 ethylene glycol units.     

Lateral mobility and specific binding to GABA(A) receptors on hippocampal neurons monitored by fluorescence correlation spectroscopy

The binding behavior of a fluorescently labeled muscimol derivative to the GABA(A) receptor was analyzed at rat hippocampal neurons by fluorescence correlation spectroscopy. After muscimol had been labeled with the fluorophore Alexa Fluor 532, specific binding constants for binding of the dye-labeled ligand (Mu-Alexa) to the GABA(A) receptor were determined. We found a high specific binding affinity of Mu-Alexa with a K(D) value of 3.4 +/- 0.5 nM and a rate constant of ligand-receptor dissociation (k(diss)) of (5.37 +/- 0.95) x 10(-2) s(-1). A rate constant of ligand-receptor association (k(ass)) of (1.57 +/- 0.28) x 10(7) L mol(-1) s(-1) was calculated. The following diffusion coefficients were observed: D(free) = 233 +/- 20 microm(2)/s (n = 66) for free diffusing Mu-Alexa, D(bound1) = 2.8 +/- 0.9 microm(2)/s (n = 64) for the lateral mobility, and D(bound2) = 0.14 +/- 0.05 microm(2)/s (n = 56) for the hindered mobility of the GABA(A) receptor-ligand complex in the cell membrane. Saturation of Mu-Alexa binding was observed at a concentration of 50 nM. A maximum number of binding sites [B(max) = 18.4 +/- -0.4 nM (n = 5)] was found. Similar K(i) values of 4.5 +/- 1.0 nM for nonlabeled muscimol and 8.8 +/- 1.8 nM for Mu-Alexa were found by RRAs using [(3)H]muscimol as a radioligand. A concentration-dependent increase in the level of specific Mu-Alexa binding was demonstrated by the positive cooperative activity of co-incubated midazolam, which was selectively found in GABA(A) receptor-ligand complexes with hindered mobility.     

Stoichiometry of interaction between interferon gamma and its receptor.

The biological response of interferon gamma is mediated by binding to a specific cell-surface receptor. We investigated the stoichiometry of this binding using soluble receptors produced in prokaryotic and eukaryotic expression systems comprising the extracellular ligand-binding domain of the native protein. The ligand-receptor complexes were analyzed by cross-linking, chromatography, analytical ultracentrifugation and laser-light scattering. Cross-linking and chromatography showed that the stoichiometry of the interaction between ligand and receptor depends on the molar ratios of the two components mixed. All approaches confirmed that mixtures of ligand-receptor complexes are formed with one interferon-gamma dimer bound by one or two receptors. The soluble receptor produced in Escherichia coli mainly showed a ligand/receptor stoichiometry of 1:1, while the receptors produced in eukaryotic cells showed a stoichiometry of binding of 1:2. This apparent discrepancy is most likely due to the conformational heterogeneity of the Escherichia-coli-derived protein.     

Functionalized quantum dots to quantify NADPH and their use for NADP+-dependent biocatalyzed transformations

Quantum dots are semiconducting nanoparticles that can be prepared with interesting optical properties. The fluorescent properties of quantum dots are one of the key advantages for their use as optical labels for biorecognition events and biocatalytic processes. We have prepared semiconductor quantum dots conjugated with Nile Blue (NB), and demonstrate that NB-functionalized quantum dots can act as versatile probes to analyze different biocatalyzed transformations, and can be used for the quantitative detection of NADPH as well as NADH. This approach provides a new path for the optical detection of NAD(P)H and for the quantitative analysis of NAD(P)(+)-dependent biotransformations.