Epifluorescent single-molecule counting with Streptavidin-Phycoerythrin conjugates.

Single-molecule methods, specifically single-molecule counting, convey high sensitivity in research applications. However, single-molecule counting experiments require specialized equipment or consumables to perform. We demonstrate the utility of using bright Streptavidin-Phycoerythrin (SA-PE) conjugates and an epifluorescence microscope, for single-molecule counting applications. In this work, we show that we can visualize single-molecules on glass surfaces, perform single-molecule diagnostic assays on magnetic microparticles, and image individual foci on cell surfaces. This approach is simple and effective for researchers interested in single-molecule counting.

Affinity of anti-spike antibodies to three major SARS-CoV-2 variants in recipients of three major vaccines.

Background: Measuring anti-viral antibody affinity in blood plasma or serum is a rational quantitative approach to assess humoral immune response and acquired protection. Three common vaccines against SARS-CoV-2-Comirnaty developed by Pfizer/BioNTech, Spikevax developed by Moderna/NIAID, and Jcovden (previously Janssen COVID-19 Vaccine) developed by Johnson & Johnson/Janssen (J&J)-induce antibodies to a variety of immunogenic epitopes including the epitopes located in the ACE2 receptor-binding domain (RBD) of the spike protein. Blocking RBD with antibodies interferes with the binding of the virus to ACE2 thus protecting against infection. Methods: We perform measurements in the serum of the recipients of Pfizer, Moderna, and J&J vaccines, and we compare the apparent affinities of vaccine-induced antibodies against the RBD of the ancestral SARS-CoV-2 virus and the Delta and Omicron variants. We use our recently published method to determine the apparent affinity of anti-spike protein antibodies directly in human serum. This involves probing antibody-antigen equilibria with a small number of antigen-coated magnetic microparticles and imaging them on a fluorescence microscope. Results: Recipients of two-dose Pfizer and Moderna vaccines, as well as recipients of the single-dose J&J vaccine, develop high-affinity antibodies toward RBD derived from ancestral SARS-CoV-2. Affinities of these antibodies to Delta-RBD are approximately 10 times weaker, and even more drastically reduced (∼1000-fold) toward Omicron-RBD. Conclusions: Vaccine-induced antibodies against ancestral SARS-CoV-2 RBD demonstrate ~10-fold and ~1000-fold weaker affinities toward Delta- and Omicron-RBD, respectively. Our approach offers a direct means for evaluating vaccine-induced adaptive immunity and can be helpful in designing or updating vaccines.

Affinity of anti-spike antibodies in SARS-CoV-2 patient plasma and its effect on COVID-19 antibody assays.

BACKGROUND: Measuring anti-spike protein antibodies in human plasma or serum is commonly used to determine prior exposure to SARS-CoV-2 infection and to assess the anti-viral protection capacity. According to the mass-action law, a lesser concentration of tightly binding antibody can produce the same quantity of antibody-antigen complexes as higher concentrations of lower affinity antibody. Thus, measurements of antibody levels reflect both affinity and concentration. These two fundamental parameters cannot be disentangled in clinical immunoassays, and so produce a bias which depends on the assay format. METHODS: To determine the apparent affinity of anti-spike protein antibodies, a small number of antigen-coated magnetic microparticles were imaged by fluorescence microscopy after probing antigen-antibody equilibria directly in patient plasma. Direct and indirect anti-SARS-CoV-2 immunoassays were used to measure antibody levels in the blood of infected and immunised individuals. FINDINGS: We observed affinity maturation of antibodies in convalescent and vaccinated individuals, showing that higher affinities are achieved much faster by vaccination. We demonstrate that direct and indirect immunoassays for measuring anti-spike protein antibodies depend differently on antibody affinity which, in turn, affects accurate interpretation of the results. INTERPRETATION: Direct immunoassays show substantial antibody affinity dependence. This makes them useful for identifying past SARS-CoV-2 exposure. Indirect immunoassays provide more accurate quantifications of anti-viral antibody levels. FUNDING: The authors are all full-time employees of Abbott Laboratories. Abbott Laboratories provided all operating funds. No external funding sources were used in this study.

Direct single-molecule imaging for diagnostic and blood screening assays.

Every year, over 100 million units of donated blood undergo mandatory screening for HIV, hepatitis B, hepatitis C, and syphilis worldwide. Often, donated blood is also screened for human T cell leukemia-lymphoma virus, Chagas, dengue, Babesia, cytomegalovirus, malaria, and other infections. Several billion diagnostic tests are performed annually around the world to measure more than 400 biomarkers for cardiac, cancer, infectious, and other diseases. Considering such volumes, every improvement in assay performance and/or throughput has a major impact. Here, we show that medically relevant assay sensitivities and specificities can be fundamentally improved by direct single-molecule imaging using regular epifluorescence microscopes. In current microparticle-based assays, an ensemble of bound signal-generating molecules is measured as a whole. By contrast, we acquire intensity profiles to identify and then count individual fluorescent complexes bound to targets on antibody-coated microparticles. This increases the signal-to-noise ratio and provides better discrimination over nonspecific effects. It brings the detection sensitivity down to the attomolar (10-18 M) for model assay systems and to the low femtomolar (10-16 M) for measuring analyte in human plasma. Transitioning from counting single-molecule peaks to averaging pixel intensities at higher analyte concentrations enables a continuous linear response from 10-18 to 10-5 M. Additionally, our assays are insensitive to microparticle number and volume variations during the binding reaction, eliminating the main source of uncertainties in standard assays. Altogether, these features allow for increased assay sensitivity, wide linear detection ranges, shorter incubation times, simpler assay protocols, and minimal reagent consumption.

Acridone and acridinium constructs with red-shifted emission.

Acridinium 9-carboxylic acid derivatives have been extensively used as chemiluminescent labels in diagnostic assays. Triggering acridinium with basic hydrogen peroxide produces a highly strained dioxetanone intermediate, which converts into an acridone in an electronically excited state and emits light at 420-440 nm. Here, we introduce a novel acridinium-fluorescein construct emitting at 530 nm, in which fluorescein is covalently attached to the acridinium N-10 nitrogen via a propyl sulfonamide linker. To characterize the spectral properties of the acridinium-fluorescein chemiluminophores, we synthesized the analogous acridone-fluorescein constructs. Both acridinium and acridone were linked to either 5- or 6-carboxyfluorescein and independently synthesized as individual structural isomers. Using fluorescent acridone-fluorophore tandems, we investigated and optimized the diluent composition to prevent dye aggregation. As monomolecular species, the acridone isomers demonstrated similar absorption, excitation, and emission spectra, as well as the expected fluorescence lifetimes and molecular brightness. Chemical triggering of acridinium-fluorescein tandems, as well as direct excitation of their acridone-fluorescein analogs, resulted in a nearly complete energy transfer from acridone to fluorescein. Acridone-based dyes can be studied with steady-state spectroscopy. Thus, they will serve as useful tools for structure and solvent optimizations, as well as for studying chemiluminescent energy transfer mechanisms in related acridinium-fluorophore tandems. Direct investigations of the light-emitting molecules generated in the acridinium chemiluminescent reaction empower further development of chemiluminescent labels with red-shifted emission. As illustrated by the two-color HIV model immunoassay, such labels can find immediate applications for multicolor detection in clinical diagnostic assays.

A rainbow of acridinium chemiluminescence.

Multicolor chemiluminescent acridinium derivatives were synthesized by attaching various common fluorophores to the N10 -acridinium position through a piperazine linker. Triggering of each acridinium derivative using alkaline hydrogen peroxide resulted in a chemiluminescence spectrum dominated by a strong emission (>95%) from the attached fluorophore. The highly quenched emission from the triggered acridinium, acting as a donor, points to a highly efficient intramolecular energy transfer in acridinium-based chemiluminophore-fluorophore tandems. A variable, and in many cases minimal, spectral overlap between the donor emission and the acceptor absorption may indicate that in such tandems the energy transfer follows the Dexter electron exchange mechanism. Moreover, fluorophores affixed through the acridinium 9-position produce a typical acridinium emission profile, demonstrating the need for close distances and favorable intramolecular orientation of the donor and acceptor moieties for the energy transfer to occur. A family of red-shifted chemiluminescent labels, all sharing a uniform triggering method, will find immediate application in multicolor ligand-receptor assays. Along with the multiplexing capabilities, the red-shifted chemiluminescent detection offers a higher tolerance to green-colored biological interferences and will therefore benefit many screening and diagnostic clinical tests.

Direct single-molecule counting for immunoassay applications.

Single-molecule methods offer specificity in studying complex systems and dynamics, but they also offer high sensitivity for basic enumeration. We apply single-molecule TIRF to immunoassays by counting the number of target molecules captured on a streptavidin surface. We demonstrate the utility of using single-molecule counting on eluted detection conjugate, following the capture and sandwich formation portions of the assay having been completed on microparticles. This approach is simple and effective, and creates the opportunity for a universal detection platform that can be used to perform a variety of diagnostic and blood screening assays. We take advantage of the low volume requirements of single-molecule detection and apply a sample reloading approach to concentrate sample onto the detection surface. Due to the high affinity of the streptavidin-biotin reaction, concentration through reloading is both quick and robust. These findings are demonstrated on a model system and in an HIV p24 antigen assay. Single-molecule detection techniques do not need to be complex to exhibit power and flexibility, and so can become valuable in the field of immunoassay diagnostics.

Characterization of Fluorescently Labeled Protein with Electrospray Ionization-MS and Fluorescence Spectroscopy: How Random is Random Labeling?

Solvent exposed lysine residues are abundantly present in many proteins. Their highly reactive ε-amino groups serve as universal targets for coupling with active esters of various extrinsic labels including a vast arsenal of fluorescent probes. Here, we describe fluorescent properties and preferential localization of two frequently used fluorescent labels, AlexaFluor488 (AF488) and Cy3, on the surface of a small highly soluble serum protein neutrophil gelatinase-associated lipocalin (NGAL), which serves as a diagnostic marker for acute kidney failure. Using a standard protocol for labeling with either AF488-SDP or AF488-NHS, we achieved >95% labeling efficiency of the protein as determined by UV-vis absorption and electrospray ionization (ESI)-MS. However, fluorescence intensity of the labeled protein was less than 10% of the expected value. To understand the unusually high quenching of the probe, we identified the sites of AF488 attachments by means of LC-MS/MS combined with trypsin digestion. Surprisingly, we found that the AF488 label is not randomly distributed among accessible lysines but predominantly bound to the residues K125, K126, or K135, which are located in the NGAL calyx and are likely quenched by neighboring tryptophans and tyrosines. In contrast, when NGAL was labeled with Cy3, the probe's fluorescence was almost fully retained. The LC-MS/MS data indicated that Cy3 was predominately bound to another lysine, K31, on the protein surface on the opposite side of the calyx. Our findings suggest that a combination of the inherent properties of the label and the specifics of the protein microenvironment may selectively lead probes to specific lysine residues and thus challenge the common view that protein labeling is a random process.

Rhodamine-Derived Fluorescent Dye with Inherent Blinking Behavior for Super-Resolution Imaging.

Super-resolution microscopy enables imaging of structures smaller than the diffraction limit. Single-molecule localization microscopy methods, such as photoactivation localization microscopy and stochastic optical reconstruction microscopy, reconstruct images by plotting the centroids of fluorescent point sources from a series of frames in which only a few molecules are fluorescing at a time. These approaches require simpler instrumentation than methods that depend on structured illumination and thus are becoming widespread. The functionalized rhodamine derivative reported in this paper spontaneously converts between a bright and dark state due to pH-dependent cyclization. At pH 7, less than 0.5% of the dye molecules are fluorescent at any given time. Blinking occurs on time scales of seconds to minutes and can therefore be used for single-molecule localization microscopy without sample treatment or activation. The dye is bright and straightforward to use, and it is easy to synthesize and functionalize. Thus, it has potential to become a new and powerful addition to the toolset for super-resolution imaging.

The photostability of the commonly used biotin-4-fluorescein probe.

Biotin-4-fluorescein (B4F) is a commonly used fluorescent probe for studying biotin-(strept)avidin interactions. During a characterization study of an anti-biotin antibody, using B4F as the probe, we noticed a discrepancy in the expected and experimentally determined number of biotin binding sites. Analytical testing showed that the biotin moiety in the probe undergoes a photosensitized oxidation to produce a mixture of biotin sulfoxides which has the potential to impact the quantitation of binding sites using this fluorescent probe.

Three-dimensional structure, binding, and spectroscopic characteristics of the monoclonal antibody 43.1 directed to the carboxyphenyl moiety of fluorescein.

Unlike other known anti-fluorescein antibodies, the monoclonal antibody 43.1 is directed toward the fluorescein's carboxyl phenyl moiety. It demonstrates a very high affinity (KD ∼ 70 pM) and a fast association rate (kon ∼ 2 × 10(7) M(-1 ) s(-1) ). The three-dimensional structure of the Fab 43.1-fluorescein complex was resolved at 2.4 Å resolution. The antibody binding site is exclusively assembled by the CDR loops. It is comprised of a 14 Å groove-shaped entrance leading to a 9 Å by 7 Å binding pocket. The highly polar binding pocket complementary encloses the fluorescein's carboxyphenyl moiety and tightly fixes it by multiple hydrogen bonds. The fluorescein's xanthene ring is embedded in the more hydrophobic groove and stacked between the side chains of Tyr37L and of Arg99H providing conditions for an excited state electron transfer process. In comparison to fluorescein, the absorption spectrum of the complex in the visible region is shifted to the "red" by 23 nm. The complex demonstrates a very weak fluorescence (Φc = 0.0018) with two short lifetime components: 0.03 ns (47%) and 0.8 ns (24%), which reflects a 99.8% fluorescein emission quenching effect upon complex formation. The antibody 43.1 binds fluorescein with remarkable affinity, fast association rate, and strongly quenches its emission. Therefore, it may present a practical interest in applications such as molecular sensors and switches.

Rapid single-molecule imaging in cyclic olefin copolymer channels.

Rapid preparation of high quality capture surfaces is a major challenge for surface-based single-molecule protein binding assays. Here we introduce a simple method to activate microfluidic chambers made from cyclic olefin copolymer for single-molecule imaging with total internal reflection fluorescence microscopy. We describe a surface coating protocol and demonstrate single-molecule imaging in off-the-shelf microfluidic parts that can be activated for binding assays within a few minutes. As the first example, biotinylated protein directly captured on the neutravidin-coated surface was detected using fluorescently labeled antibody. We then showed detection of a fusion construct containing green fluorescence protein and verified its single fluorophore behavior by observing stepwise photobleaching events. Finally, a target protein was identified in the crude cell lysate using antibody-sandwich complex formation. In all experiments, controls were completed to ensure that nonspecific binding to the surface was minimal. Based on our results, we conclude that the simple surface preparation described in this paper enables single-molecule imaging assays without time-consuming coating procedures.

Affinity assisted selection of antibodies for Point of Care TSH immunoassay with limited wash.

BACKGROUND: Molecular binding characteristics of several thyroid stimulating hormone (TSH) antibodies were determined for the TSH antigen, along with its closely related endogenous interfering hormones, follicle stimulating hormone (FSH), luteinizing hormone (LH) and chorionic gonadotropin (CG). METHODS: This data was compared to the same antibodies used in the low wash sandwich ELISA immunoassay system, the Point of Care i-STAT® immunoassay. From this information we developed binding criteria useful in the low wash i-STAT® immunoassay to permit good signal generation from TSH and low cross-reactivity from its interfering hormones. For the TSH Assay we have developed characteristics that enable antibody selection in the i-STAT® immunoassay cartridge. Our antibody screening approach used a dot blot approach as a first screen to select for the most useful antibodies. We then compared a FRET (Förster Resonance Energy Transfer) and electrochemical cartridge approach to determine the appropriate antibody combinations. RESULTS: Both methods generated similar data, but the FRET method was not capable of differentiating the antibody with the best characteristics as a capture antibody or a detection conjugate in a sandwich ELISA assay. Finally, we performed binding characterizations of the antibodies using each of the above mentioned glycoproteins. CONCLUSIONS: We found that we need sub-picomolar detection of TSH, and at least 100 fold or higher values for the cross-reacting species.

Water channel in the binding site of a high affinity anti-methotrexate antibody.

In the present study, we report the structure of the free and drug-bound Fab fragment of a high affinity anti-methotrexate antibody and perform a thermodynamic analysis of the binding process. The anti-methotrexate Fab fragment features a remarkably rigid tunnel-like binding site that extends into a water channel serving as a specialized route to move solvent out and into the site upon ligand binding and dissociation. This new finding in antibody structure-function relationships directly relates to the fast association (1 × 107 M⁻¹ s⁻¹) and slow dissociation (4 × 10⁻5 s⁻¹) rates determined for mAb ADD056, resulting in a very strong binding with a K(D) ~ 3.6 pM at 20 °C. As follows from the X-ray data analysis, the methotrexate-antibody complex is stabilized by an extended network of hydrogen bonds and stacking interactions. The analysis also shows structural involvement of the CDR H3 in formation of the water channel revealing another important role of this hypervariable region. This suggests a new direction in natural affinity maturation and opens a new possibility in antibody engineering. Methotrexate is a widely used therapeutic agent for many malignant diseases and inflammatory disorders. Unfortunately, it may also interfere with central aspects of metabolism and thereby cause inevitable side effects. Therefore, methotrexate therapy requires careful monitoring of drug blood levels, which is traditionally done by immunoassays. An understanding of the structure-function properties of antibodies selected for drug monitoring substantiates the performance and robustness of such tests.

Simplified confocal microscope for counting particles at low concentrations.

We describe a compact scanning confocal fluorescence microscope capable of detecting particles concentrations less than 100 particles∕ml in ~15 min. The system mechanically moves a cuvette containing ~3 ml of sample. A relatively large confocal volume is observed within the cuvette using a 1 mm pinhole in front of a detection PMT. Due to the motion of the sample, particles traverse the confocal volume quickly, and analysis by pattern recognition qualifies spikes in the emission intensity data and counts them as events. We show linearity of detection as a function of concentration and also characterize statistical behavior of the instrument. We calculate a detection sensitivity of the system using 3 µm fluorescent microspheres to be 5 particles/ml. Furthermore, to demonstrate biological application, we performed a dilution series to quantify stained E. coli and yeast cells. We counted E. coli cells at a concentration as low as 30 cells∕ml in 10 min/sample.

Supporting immunoassay design with biophysical tools.

In this article, we demonstrate how the application of biophysical tools facilitates the design of robust immunoassays. The binding characteristics of the reagents used in an immunoassay determine the assay response to the analyte concentrations. We applied several biophysical methods to obtain pertinent equilibrium and kinetic coefficients and used this information in the design of a microparticle-based immunoassay for detection of neutrophil gelatinase-associated lipocalin (NGAL), which is a new diagnostic marker of acute kidney injury (AKI). We characterized the conformational stability of recombinant human NGAL and the solution phase binding properties of six monoclonal antibodies. A preferred antibody pair was selected on the basis of the affinities of the antibodies and their sandwich pairing capabilities. One of the antibodies was coated on magnetic microparticles, and the second antibody was conjugated with a reporter group. The apparent kinetic rates of the immobilized and conjugated antibodies were measured and used to compute the assay calibration plot for the target concentration range of the analyte at specific incubation times. The experimental assay results were found to be in good agreement with the computed data, confirming that applying biophysical tools provides a solid foundation for immunoassay design and optimization.

Studying antibody-antigen interactions with fluorescence fluctuation spectroscopy.

Antibodies are excellent binding proteins that have found numerous applications in biological research, biotechnology, and medicine. Characterization of their ligand binding properties has long been, and continues to be, the focus of many researchers. Antibodies are also perfect test systems which can be used for the evaluation of newly introduced biophysical techniques. Working with many different antibodies, we continuously implement the growing arsenal of methods offered by fluorescence fluctuation spectroscopy (FFS) and apply them for antibody research. In this chapter, we will describe applications of FFS for antibody binding characterization and also provide examples how studying of antibodies helps to develop and enhance the tool set offered by FFS technology. In addition to traditional affinity evaluations, we will describe how resolving molecular populations enables determinations of the binding stoichiometry and provides further information about the system. Even though all our examples include antibodies, the same experimental procedures can also serve well for characterizing various proteins and other ligand binding systems.

Introduction of the mass spread function for characterization of protein conjugates.

Traditionally, characterization of protein molecules conjugated with molecular probes is performed by UV-vis spectroscopy. This method determines the average incorporation ratio but does not yield information about the label distribution. Electrospray ionization mass spectroscopy (ESI-MS) allows direct measurement of the fraction of protein containing a given number of labels. However, for a glycosylated protein, this analysis can be severely limited due to spectral overlap of the labels and carbohydrates. To address this problem, we introduce the mass spread function (MSF) for conjugation analysis. By treating the ESI-MS spectrum of conjugated protein as the spectrum before conjugation convolved with the MSF, we are able to quantify the labeled protein population using a binomial distribution function. We first applied this procedure for characterization of labeled antibody F(ab')(2) fragments which do not contain carbohydrates. We then apply the MSF to fit spectra of entire conjugated monoclonal antibodies and quantify the distribution of labels in the presence of glycans.