Label-enhanced surface plasmon resonance applied to label-free interaction analysis of small molecules and fragments

Integrated Signal Amplification on a Fiber Optic SPR Sensor Using Duplexed Aptamers

Throughout the past decades, fiber optic surface plasmon resonance (FO-SPR)-based biosensors have proven to be powerful tools for both the characterization of biomolecular interactions and target detection. However, as FO-SPR signals are generally related to the mass that binds to the sensor surface, multistep processes and external reagents are often required to obtain significant signals for low molecular weight targets. This increases the time, cost, and complexity of the respective bioassays and hinders continuous measurements. To overcome these requirements, in this work, cis-duplexed aptamers (DAs) were implemented on FO-SPR sensors, which underwent a conformational change upon target binding. This induced a spatial redistribution of gold nanoparticles (AuNPs) upon specific target binding and resulted in an amplified and concentration-dependent signal. Importantly, the AuNPs were covalently conjugated to the sensor, so the principle does not rely on multistep processes or external reagents. To implement this concept, first, the thickness of the gold fiber coating was adapted to match the resonance conditions of the surface plasmons present on the FO-SPR sensors with those on the AuNPs. As a result, the signal obtained due to the spatial redistribution of the AuNPs was amplified by a factor of 3 compared to the most commonly used thickness. Subsequently, the cis-DAs were successfully implemented on the FO-SPR sensors, and it was demonstrated that the DA-based FO-SPR sensors could specifically and quantitatively detect an ssDNA target with a detection limit of 230 nM. Furthermore, the redistribution of the AuNPs was proven to be reversible, which is an important prerequisite for continuous measurements. Altogether, the established DA-based FO-SPR bioassay holds much promise for the detection of low molecular weight targets in the future and opens up possibilities for FO-SPR-based continuous biosensing.

A Versatile One-Step Competitive Fiber Optic Surface Plasmon Resonance Bioassay Enabled by DNA Nanotechnology

Fiber optic surface plasmon resonance (FO-SPR)-based biosensors have emerged as powerful tools for biomarker detection due to their ability for real-time analysis of biomolecular interactions, cost-effectiveness, and user-friendliness. However, as (FO-)SPR signals are determined by the mass of the target molecules, the detection of low-molecular-weight targets remains challenging and currently requires tedious labeling and preparation steps. Therefore, in this work, we established a new concept for low-molecular-weight target detection by implementing duplexed aptamers on an FO-SPR sensor. In this manner, we enabled one-step competitive detection and could achieve significant signals, independent of the weight of the target molecules, without requiring labeling or preprocessing steps. This was demonstrated for the detection of a small molecule (ATP), protein (thrombin), and ssDNA target, thereby reaching detection limits of 72 μM, 36 nM, and 30 nM respectively and proving the generalizability of the proposed bioassay. Furthermore, target detection was successfully achieved in 10-fold diluted plasma, which demonstrated the applicability of the assay in biologically relevant matrices. Altogether, the developed one-step competitive FO-SPR bioassay opens up possibilities for the detection of low-molecular-weight targets in a fast and straightforward manner.

Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications

Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.

Discovery of Orphan Olfactory Receptor 6M1 as a New Anticancer Target in MCF-7 Cells by a Combination of Surface Plasmon Resonance-Based and Cell-Based Systems

Olfactory receptors (ORs) account for 49% of all G protein-coupled receptors (GPCRs), which are important targets for drug discovery, and hence ORs may also be potential drug targets. Various ORs are expressed in breast cancer cells; however, most of them are orphan receptors, and thus, their functions are unknown. Herein, we present an experimental strategy using a surface plasmon resonance (SPR) system and a cell-based assay that allowed the identification of orphan OR6M1 as a new anticancer target in the MCF-7 breast cancer cell line. After the construction of stable OR6M1-expressing cells, the SPR-based screening of 108 chemicals for ligand activity was performed against OR6M1-expressing whole cells (primary screening) or membrane fragments (secondary screening). As a result, anthraquinone (AQ) and rutin were discovered to be new OR6M1 ligands. Based on calcium imaging in OR6M1-expressing Hana3A cells, AQ and rutin were classified as an OR6M1 agonist and antagonist, respectively. Cell viability and live/dead assays showed that AQ induced the death of MCF-7 cells, which was inhibited by rutin. Therefore, OR6M1 may be considered an anticancer target, and AQ may be considered a chemotherapeutic agent. This combined method can be widely used to discover the ligands and functions of other orphan GPCRs.

Ultra-Stable Molecular Sensors by Sub-Micron Referencing and Why They Should Be Interrogated by Optical Diffraction-Part I. The Concept of a Spatial Affinity Lock-in Amplifier

Label-free optical biosensors, such as surface plasmon resonance, are sensitive and well-established for the characterization of molecular interactions. Yet, these sensors require stabilization and constant conditions even with the use of reference channels. In this paper, we use tools from signal processing to show why these sensors are so cross-sensitive and how to overcome their drawbacks. In particular, we conceptualize the spatial affinity lock-in as a universal design principle for sensitive molecular sensors even in the complete absence of stabilization. The spatial affinity lock-in is analogous to the well-established time-domain lock-in. Instead of a time-domain signal, it modulates the binding signal at a high spatial frequency to separate it from the low spatial frequency environmental noise in Fourier space. In addition, direct sampling of the locked-in sensor's response in Fourier space enabled by diffraction has advantages over sampling in real space as done by surface plasmon resonance sensors using the distributed reference principle. This paper and part II hint at the potential of spatially locked-in diffractometric biosensors to surpass state-of-the-art temperature-stabilized refractometric biosensors. Even simple, miniaturized and non-stabilized sensors might achieve the performance of bulky lab instruments. This may enable new applications in label-free analysis of molecular binding and point-of-care diagnostics.

Ultra Stable Molecular Sensors by Submicron Referencing and Why They Should Be Interrogated by Optical Diffraction-Part II. Experimental Demonstration

Label-free optical biosensors are an invaluable tool for molecular interaction analysis. Over the past 30 years, refractometric biosensors and, in particular, surface plasmon resonance have matured to the de facto standard of this field despite a significant cross reactivity to environmental and experimental noise sources. In this paper, we demonstrate that sensors that apply the spatial affinity lock-in principle (part I) and perform readout by diffraction overcome the drawbacks of established refractometric biosensors. We show this with a direct comparison of the cover refractive index jump sensitivity as well as the surface mass resolution of an unstabilized diffractometric biosensor with a state-of-the-art Biacore 8k. A combined refractometric diffractometric biosensor demonstrates that a refractometric sensor requires a much higher measurement precision than the diffractometric to achieve the same resolution. In a conceptual and quantitative discussion, we elucidate the physical reasons behind and define the figure of merit of diffractometric biosensors. Because low-precision unstabilized diffractometric devices achieve the same resolution as bulky stabilized refractometric sensors, we believe that label-free optical sensors might soon move beyond the drug discovery lab as miniaturized, mass-produced environmental/medical sensors. In fact, combined with the right surface chemistry and recognition element, they might even bring the senses of smell/taste to our smart devices.

Gold nanobipyramids integrated ultrasensitive optical and electrochemical biosensor for Aflatoxin B1 detection

This work reports the development of an electrical and optical biosensing for label-free detection of Aflatoxin B₁ (AFB₁) using gold (Au) nanobipyramids (NBPs). AuNBPs were synthesized through a two-step seed-mediated growth process followed by an exchange of capping agent from surfactant to lipoic acid. Pure and monodispersed AuNBPs of 70 nm base length were obtained and deposited on indium tin oxide (ITO)-coated glass substrate modified with self-assembled (3-Aminopropyl) triethoxysilane (APTES) film. The characterization of the obtained surfaces using spectroscopy, microscopy and diffractometry confirms the formation of AuNBPs, the conjugation to ITO electrode substrate and the immobilization of anti-AFB₁ antibodies. AuNBPs modified ITO substrates were used for both electrochemical and Surface Plasmon Resonance biosensing studies. Localized Surface Plasmon Resonance (LSPR) local field enhancement was demonstrated. SPR based AFB₁ detection was found to be linear in the 0.1-500 nM range with a limit of detection of 0.4 nM, whereas, impedimetric AFB₁ detection was shown to be linear in the 0.1-25 nM range with a limit of detection of 0.1 nM. The practical utility of the impedimetric sensor was tested in spiked maize samples and 95-100% recovery percentage was found together with low relative standard deviation, proof of the robustness of this AFB₁ sensor.

Binding Kinetics of Methylene Blue on Monolayer Graphene Investigated by Multiparameter Surface Plasmon Resonance

In this paper, we study the interaction of a small dye molecule, namely, methylene blue (MB) with graphene surfaces using surface plasmon resonance (SPR). We show that by utilizing all of the parameters of the SPR angular dip and exploiting the fact that MB absorbs light at the operating wavelength, it is possible to detect the binding of small molecules that would otherwise not give a significant signal. The binding of MB to unmodified graphene is found to be stronger than that for gold. By studying the interaction at modified surfaces, we demonstrate that electrostatic effects play a dominant role in the binding of MB on to graphene. Furthermore, following the binding kinetics at various concentrations allows us to estimate apparent equilibrium binding and rate constants for the interaction of MB with graphene.

Quantitative monitoring of two simultaneously binding species using Label-Enhanced surface plasmon resonance

Surface plasmon resonance (SPR) is a well-established method for biomolecular interaction studies. SPR monitors the binding of molecules to a solid surface, embodied as refractive index changes close to the surface. One limitation of conventional SPR is the universal nature of the detection that results in an inability to qualitatively discriminate between different binding species. Furthermore, it is impossible to directly discriminate two species simultaneously binding to different sites on a protein, which limits the utility of SPR, for example, in the study of allosteric binders or bi-specific molecules. It is also impossible in principle to discriminate protein conformation changes from actual binding events. Here we demonstrate how Label-Enhanced SPR can be utilized to discriminate and quantitatively monitor the simultaneous binding of two different species - one dye-labeled and one unlabeled - on a standard, single-wavelength SPR instrument. This new technique increases the versatility of SPR technology by opening up application areas where the usefulness of the approach has previously been limited.

Regenerative biosensor for use with biotinylated bait molecules

Label-free biosensors are ideally suited for the quantitative analysis of specific interactions among biomolecules or of biomolecules with drugs, as well as for quantitation of diagnostic markers in biofluids. In contrast to the label-dependent methods, a new assay for a particular prey molecule can be set up within few minutes by immobilizing the corresponding bait molecule on the sensor surface, using one of the common immobilization procedures. Unfortunately, the extensive application of label-free biosensors is still hampered by the fact that the immobilization of the bait molecule is usually irreversible; for that reason, a new chip (which is expensive) is required for every successful or futile attempt. Here, we present a general method for the switchable immobilization of biotinylated bait molecules on a new desthiobiotin surface, using wild-type streptavidin as a robust bridge between the chip and the biotinylated bait. The immobilization of the bait is very stable, so that many cycles of prey injection and subsequent prey removal can be carried out. For the latter, common reagents like HCl, Na₂CO₃, glycine buffer, or SDS are employed. When desired, however, streptavidin plus the biotinylated bait can be completely removed by 3min injections of biotin, guanidinium thiocyanate, pepsin, and SDS, which makes it possible to immobilize new biotinylated bait. The number of in situ regeneration cycles is unlimited during the lifetime of the chip (2-3 weeks). One chip can easily be shared by many users with unrelated tasks (as is typical in academics), or used for the fully automated screening of many different interactions (for example in pharmaceutical research). In comparison to other regenerative chips, the new chip surface has much wider applicability and all of its structural and functional parameters have been disclosed.

A Sensitive and Stable Surface Plasmon Resonance Sensor Based on Monolayer Protected Silver Film

In this paper, we present a stable silver-based surface plasmon resonance (SPR) sensor using a self-assembled monolayer (SAM) as a protection layer and investigated its efficiency in water and 0.01 M phosphate buffered saline (PBS). By simulation, silver-based SPR sensor has a better performance in field enhancement and penetration depth than that of a gold-based SPR sensor, which are 5 and 1.4 times, respectively. To overcome the instability of the bare silver film and investigate the efficiency of the protected layer, the SAM of 11-mercapto-1-undecanol (MUD) was used as a protection layer. Stability experiment results show that the protected silver film exhibited excellent stability either in pure water or 0.01 M PBS buffer. The sensitivity of the silver-based SPR sensor was calculated to be 127.26 deg/RIU (refractive index unit), measured with different concentrations of NaCl solutions. Further, a very high refractive resolution for the silver-based SPR sensor was found to be 2.207 × 10⁻⁷ RIU, which reaches the theoretical limit in the wavelength of 632.8 nm for a SPR sensor reported in the literature. Using a mixed SAM of 16-mercaptohexadecanoic acid (MHDA) and a MUD layer with a ratio of 1:10, this immunosensor for the rabbit immunoglobulin G (IgG) molecule with a limit of detection as low as 22.516 ng/mL was achieved.

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.

Surface plasmon resonance biosensor for enzymatic detection of small analytes

Surface plasmon resonance (SPR) biosensing is based on the detection of small changes in the refractive index on a gold surface modified with molecular recognition materials, thus being mostly limited to detecting large molecules. In this paper, we report on a SPR biosensing platform suitable to detect small molecules by making use of the mediator-type enzyme microperoxidase-11 (MP11) in layer-by-layer films. By depositing a top layer of glucose oxidase or uricase, we were able to detect glucose or uric acid with limits of detection of 3.4 and 0.27 μmol l^-1, respectively. Measurable SPR signals could be achieved because of the changes in polarizability of MP11, as it is oxidized upon interaction with the analyte. Confirmation of this hypothesis was obtained with finite difference time domain simulations, which also allowed us to discard the possible effects from film roughness changes observed in atomic force microscopy images. The main advantage of this mediator-type enzyme approach is in the simplicity of the experimental method that does not require an external potential, unlike similar approaches for SPR biosensing of small molecules. The detection limits reported here were achieved without optimizing the film architecture, and therefore the performance can in principle be further enhanced, while the proposed SPR platform may be extended to any system where hydrogen peroxide is generated in enzymatic reactions.

Identification of C3b-Binding Small-Molecule Complement Inhibitors Using Cheminformatics

The complement system is an elegantly regulated biochemical cascade formed by the collective molecular recognition properties and proteolytic activities of more than two dozen membrane-bound or serum proteins. Complement plays diverse roles in human physiology, such as acting as a sentry against invading microorganisms, priming of the adaptive immune response, and removal of immune complexes. However, dysregulation of complement can serve as a trigger for a wide range of human diseases, which include autoimmune, inflammatory, and degenerative conditions. Despite several potential advantages of modulating complement with small-molecule inhibitors, small-molecule drugs are highly underrepresented in the current complement-directed therapeutics pipeline. In this study, we have employed a cheminformatics drug discovery approach based on the extensive structural and functional knowledge available for the central proteolytic fragment of the cascade, C3b. Using parallel in silico screening methodologies, we identified 45 small molecules that putatively bind C3b near ligand-guided functional hot spots. Surface plasmon resonance experiments resulted in the validation of seven dose-dependent C3b-binding compounds. Competition-based biochemical assays demonstrated the ability of several C3b-binding compounds to interfere with binding of the original C3b ligand that guided their discovery. In vitro assays of complement function identified a single complement inhibitory compound, termed cmp-5, and mechanistic studies of the cmp-5 inhibitory mode revealed it acts at the level of C5 activation. This study has led to the identification of a promising new class of C3b-binding small-molecule complement inhibitors and, to our knowledge, provides the first demonstration of cheminformatics-based, complement-directed drug discovery.