Location-specific nanoplasmonic sensing of biomolecular binding to lipid membranes with negative curvature

Stable trapping of multiple proteins at physiological conditions using nanoscale chambers with macromolecular gates

The possibility to detect and analyze single or few biological molecules is very important for understanding interactions and reaction mechanisms. Ideally, the molecules should be confined to a nanoscale volume so that the observation time by optical methods can be extended. However, it has proven difficult to develop reliable, non-invasive trapping techniques for biomolecules under physiological conditions. Here we present a platform for long-term tether-free (solution phase) trapping of proteins without exposing them to any field gradient forces. We show that a responsive polymer brush can make solid state nanopores switch between a fully open and a fully closed state with respect to proteins, while always allowing the passage of solvent, ions and small molecules. This makes it possible to trap a very high number of proteins (500-1000) inside nanoscale chambers as small as one attoliter, reaching concentrations up to 60 gL-1. Our method is fully compatible with parallelization by imaging arrays of nanochambers. Additionally, we show that enzymatic cascade reactions can be performed with multiple native enzymes under full nanoscale confinement and steady supply of reactants. This platform will greatly extend the possibilities to optically analyze interactions involving multiple proteins, such as the dynamics of oligomerization events.

Nanoplasmonic biosensors: Theory, structure, design, and review of recent applications

Nanoplasmonic biosensing shows an immense potential to satisfy the needs of the global health industry - low-cost, fast, and portable automated systems; highly sensitive and real-time detection; multiplexing and miniaturization. In this review, we presented the theory of nanoplasmonic biosensing for popular detection schemes - SPR, LSPR, and EOT - and underline the consideration for nanostructure design, material selection, and their effects on refractometric sensing performance. Later, we covered the bottom-up and top-down nanofabrication methods for nanoplasmonic biosensors. Subsequently, we reviewed the recent examples of nanoplasmonic biosensors over a wide range of clinically relevant analytes in the diagnosis and prognosis of a wide range of diseases and conditions such as biomarker proteins, infectious bacteria, viral agents. Finally, we discussed the challenges of nanoplasmonic biosensing toward clinical translation and proposed strategic avenues to be competitive against current clinical detection methods. Hopefully, nanoplasmonic biosensing can realize its potential through successful demonstrations of clinical translation in the upcoming years.

Fibre-Optic Surface Plasmon Resonance Biosensor for Monoclonal Antibody Titer Quantification

An extraordinary optical transmission fibre-optic surface plasmon resonance biosensing platform was engineered to improve its portability and sensitivity, and was applied to monitor the concentrations of monoclonal antibodies (Mabs). By refining the fabricating procedure and changing the material of the flow cell and the components of the optical fibre, the biosensor is portable and robust to external interference. After the implementation of an effective template cleaning procedure and precise control during the fabrication process, a consistent sensitivity of 509 ± 5 nm per refractive index unit (nm/RIU) was achieved. The biosensor can detect the Mab with a limit of detection (LOD) of 0.44 µg/mL. The results show that the biosensor is a potential tool for the rapid quantification of Mab titers. The biosensor can be regenerated at least 10 times with 10 mM glycine (pH = 2.5), and consistent signal changes were obtained after regeneration. Moreover, the employment of a spacer arm SM(PEG)2, used for immobilising protein A onto the gold film, was demonstrated to be unable to improve the detecting sensitivity; thus, a simple procedure without the spacer arm could be used to prepare the protein A-based biosensor. Our results demonstrate that the fibre-optic surface plasmon resonance biosensor is competent for the real-time and on-line monitoring of antibody titers in the future as a process analytical technologies (PATs) tool for bioprocess developments and the manufacture of therapeutic antibodies.

Biochemical Sensing with Nanoplasmonic Architectures: We Know How but Do We Know Why?

Here, the research field of nanoplasmonic sensors is placed under scrutiny, with focus on affinity-based detection using refractive index changes. This review describes how nanostructured plasmonic sensors can deliver unique advantages compared to the established surface plasmon resonance technique, where a planar metal surface is used. At the same time, it shows that these features are actually only useful in quite specific situations. Recent trends in the field are also discussed and some devices that claim extraordinary performance are questioned. It is argued that the most important challenges are related to limited receptor affinity and nonspecific binding rather than instrumental performance. Although some nanoplasmonic sensors may be useful in certain situations, it seems likely that conventional surface plasmon resonance will continue to dominate biomolecular interaction analysis. For detection of analytes in complex samples, plasmonics may be an important tool, but probably not in the form of direct refractometric detection.

Unraveling How Multivalency Triggers Shape Deformation of Sub-100 nm Lipid Vesicles

Multivalent ligand-receptor interactions are critical to the function of membrane-enveloped biological and biomimetic nanoparticles, yet resulting nanoparticle shape changes are rarely investigated. Using the localized surface plasmon resonance (LSPR) sensing technique, we tracked the attachment of biotinylated, sub-100 nm lipid vesicles to a streptavidin-functionalized supported lipid bilayer (SLB) and developed an analytical model to extract quantitative details about the vesicle-SLB contact region. The experimental results were supported by theoretical analyses of biotin-streptavidin complex formation and corresponding structural and energetic aspects of vesicle deformation. Our findings reveal how varying the surface densities of streptavidin receptors in the SLB and biotin ligands in the vesicles affects the extent of nanometer-scale vesicle deformation. We also identify conditions, i.e., a critical ligand density, at which appreciable vesicle deformation began, which provides insight into how the membrane bending energy partially counterposes the multivalent binding interaction energy. These findings are generalizable to various multivalent ligand-receptor systems.

Tuning the Thermoresponsive Behavior of Surface-Attached PNIPAM Networks: Varying the Crosslinker Content in SI-ATRP

The synthesis and thermoresponsive properties of surface-attached poly(N-isopropylacrylamide)-co-N,N'-methylene bisacrylamide (PNIPAM-co-MBAM) networks are investigated. The networks are formed via SI-ARGET-ATRP ("grafting-from") on thiol-based initiator-functionalized gold films. This method is reliable, well controlled, fast, and applicable to patterned surfaces (e.g., nanopores) for networks with dry thicknesses >20 nm. Surface-attached PNIPAM-co-MBAM gels are swollen below their volume phase transition temperature but above collapse without complete expulsion of water (retain ∼50 vol %). The swelling/collapse transition is studied using complementary SPR and QCMD techniques. The ratio between swollen and collapsed heights characterizes the thermoresponsive behavior and is shown to not depend on network height but to vary with MBAM content. The higher the proportion of the crosslinker, the lower the magnitude of the phase transition, until all responsiveness is lost at 5 mol % MBAM. The temperature range of the transition is broadened for more crosslinked PNIPAM-co-MBAM gels but remains centered around 32 °C. Upon reswelling, less crosslinked networks display sharp transitions, while for those containing ≥3 mol % MBAM, transitions remain broad. This tunable behavior persists for gels on nanostructured gold surfaces. Investigating PNIPAM-co-MBAM networks on gold plasmonic nanowell arrays is a starting point for expanding their scope as thermo-controlled nanoactuators.

FRET theoretical predictions concerning freely diffusive dyes inside spherical container: how to choose the best pair?

FRET has been massively used to see if biomolecules were bounded or not by labelling both biomolecules by one dye of a FRET pair. This should give a digital answer to the question (fluorescence of the acceptor: high FRET efficency: molecules associated, fluorescence of the donor: low FRET efficency: molecules dissociated). This has been used, inter alia, at the single-molecule scale in containers, such as liposomes. One perspective of the field is to reduce the container's size to study the effect of confinement on binding. The problem is that if the two dyes are encapsulated inside a small liposome, they could have a significant probability to be close one from the other one (and thus to undergo a high FRET efficiency event without binding). This is why we suggest here a theoretical model which gives mean FRET efficiency as a function of liposome radius (the model applies to any spherical container) and Förster radius to help the experimentalist to choose their experimental set-up. Besides, the influence of side effect on mean FRET efficiency has been studied as well. We show here that if this "background FRET" is most of the time non-quantitative, it can remain significant and which makes data analysis trickier. We could show as well that if this background FRET obviously increases when liposome radius decreases, this variation was lower than the one which could be expected because of side effect. We show as well the FRET efficiency function distribution which let the experimentalist know the probability to get one FRET efficiency value.

Scalable Fabrication of Quasi-One-Dimensional Gold Nanoribbons for Plasmonic Sensing

Plasmonic nanostructures have a wide range of applications, including chemical and biological sensing. However, the development of techniques to fabricate submicrometer-sized plasmonic structures over large scales remains challenging. We demonstrate a high-throughput, cost-effective approach to fabricate Au nanoribbons via chemical lift-off lithography (CLL). Commercial HD-DVDs were used as large-area templates for CLL. Transparent glass slides were coated with Au/Ti films and functionalized with self-assembled alkanethiolate monolayers. Monolayers were patterned with lines via CLL. The lifted-off, exposed regions of underlying Au were selectively etched into large-area grating-like patterns (200 nm line width; 400 nm pitch; 60 nm height). After removal of the remaining monolayers, a thin In2O3 layer was deposited and the resulting gratings were used as plasmonic sensors. Distinct features in the extinction spectra varied in their responses to refractive index changes in the solution environment with a maximum bulk sensitivity of ∼510 nm/refractive index unit. Sensitivity to local refractive index changes in the near-field was also achieved, as evidenced by real-time tracking of lipid vesicle or protein adsorption. These findings show how CLL provides a simple and economical means to pattern large-area plasmonic nanostructures for applications in optoelectronics and sensing.

Current and Emerging Technologies for the Detection of Norovirus from Shellfish

Reports of norovirus infections associated with the consumption of contaminated bivalve molluscan shellfish negatively impact both consumers and commercial shellfish operators. Current virus recovery and PCR detection methods can be expensive and time consuming. Due to the lack of rapid, user-friendly and onsite/infield methods, it has been difficult to establish an effective virus monitoring regime that is able to identify contamination points across the production line (i.e., farm-to-plate) to ensure shellfish quality. The focus of this review is to evaluate current norovirus detection methods and discuss emerging approaches. Recent advances in omics-based detection approaches have the potential to identify novel biomarkers that can be incorporated into rapid detection kits for onsite use. Furthermore, some omics techniques have the potential to simultaneously detect multiple enteric viruses that cause human disease. Other emerging technologies discussed include microfluidic, aptamer and biosensor-based detection methods developed to detect norovirus with high sensitivity from a simple matrix. Many of these approaches have the potential to be developed as user-friendly onsite detection kits with minimal costs. However, more collaborative efforts on research and development will be required to commercialize such products. Once developed, these emerging technologies could provide a way forward that minimizes public health risks associated with shellfish consumption.

Nanoplasmonic Sensor Detects Preferential Binding of IRSp53 to Negative Membrane Curvature

Biosensors based on plasmonic nanostructures are widely used in various applications and benefit from numerous operational advantages. One type of application where nanostructured sensors provide unique value in comparison with, for instance, conventional surface plasmon resonance, is investigations of the influence of nanoscale geometry on biomolecular binding events. In this study, we show that plasmonic "nanowells" conformally coated with a continuous lipid bilayer can be used to detect the preferential binding of the insulin receptor tyrosine kinase substrate protein (IRSp53) I-BAR domain to regions of negative surface curvature, i.e., the interior of the nanowells. Two different sensor architectures with and without an additional niobium oxide layer are compared for this purpose. In both cases, curvature preferential binding of IRSp53 (at around 0.025 nm^-1 and higher) can be detected qualitatively. The high refractive index niobium oxide influences the near field distribution and makes the signature for bilayer formation less clear, but the contrast for accumulation at regions of negative curvature is slightly higher. This work shows the first example of analyzing preferential binding of an average-sized and biologically important protein to negative membrane curvature in a label-free manner and in real-time, illustrating a unique application for nanoplasmonic sensors.

Detecting Selective Protein Binding Inside Plasmonic Nanopores: Toward a Mimic of the Nuclear Pore Complex

Biosensors based on plasmonic nanostructures offer label-free and real-time monitoring of biomolecular interactions. However, so do many other surface sensitive techniques with equal or better resolution in terms of surface coverage. Yet, plasmonic nanostructures offer unique possibilities to study effects associated with nanoscale geometry. In this work we use plasmonic nanopores with double gold films and detect binding of proteins inside them. By thiol and trietoxysilane chemistry, receptors are selectively positioned on the silicon nitride interior walls. Larger (~150 nm) nanopores are used detect binding of averaged sized proteins (~60 kg/mol) with high signal to noise (>100). Further, we fabricate pores that approach the size of the nuclear pore complex (diameter down to 50 nm) and graft disordered phenylalanine-glycine nucleoporin domains to the walls, followed by titration of karyopherinβ1 transport receptors. The interactions are shown to occur with similar affinity as determined by conventional surface plasmon resonance on planar surfaces. Our work illustrates another unique application of plasmonic nanostructures, namely the possibility to mimic the geometry of a biological nanomachine with integrated optical sensing capabilities.

Fast and Versatile Multiscale Patterning by Combining Template-Stripping with Nanotransfer Printing

Metal nanostructures are widely used in plasmonic and electronic applications due to their inherent properties. Often, the fabrication of such nanostructures is limited to small areas, as the processing is costly, low-throughput, and comprises harsh fabrication conditions. Here, we introduce a template-stripping based nanotransfer printing method to overcome these limitations. This versatile technique enables the transfer of arbitrary thin film metal structures onto a variety of substrates, including glass, Kapton, silicon, and PDMS. Structures can range from tens of nanometers to hundreds of micrometers over a wafer scale area. The process is organic solvent-free, multilayer compatible, and only takes minutes to perform. The stability of the transferred gold structures on glass exceeds by far those fabricated by e-beam evaporation. Therefore, an adhesion layer is no longer needed, enabling a faster and cheaper fabrication as well as the production of superior nanostructures. Structures can be transferred onto curved substrates, and the technique is compatible with roll-to-roll fabrication; thus, the process is suitable for flexible and stretchable electronics.

Nanoplasmonic sensors for biointerfacial science

In recent years, nanoplasmonic sensors have become widely used for the label-free detection of biomolecules across medical, biotechnology, and environmental science applications. To date, many nanoplasmonic sensing strategies have been developed with outstanding measurement capabilities, enabling detection down to the single-molecule level. One of the most promising directions has been surface-based nanoplasmonic sensors, and the potential of such technologies is still emerging. Going beyond detection, surface-based nanoplasmonic sensors open the door to enhanced, quantitative measurement capabilities across the biointerfacial sciences by taking advantage of high surface sensitivity that pairs well with the size of medically important biomacromolecules and biological particulates such as viruses and exosomes. The goal of this review is to introduce the latest advances in nanoplasmonic sensors for the biointerfacial sciences, including ongoing development of nanoparticle and nanohole arrays for exploring different classes of biomacromolecules interacting at solid-liquid interfaces. The measurement principles for nanoplasmonic sensors based on utilizing the localized surface plasmon resonance (LSPR) and extraordinary optical transmission (EOT) phenomena are first introduced. The following sections are then categorized around different themes within the biointerfacial sciences, specifically protein binding and conformational changes, lipid membrane fabrication, membrane-protein interactions, exosome and virus detection and analysis, and probing nucleic acid conformations and binding interactions. Across these themes, we discuss the growing trend to utilize nanoplasmonic sensors for advanced measurement capabilities, including positional sensing, biomacromolecular conformation analysis, and real-time kinetic monitoring of complex biological interactions. Altogether, these advances highlight the rich potential of nanoplasmonic sensors and the future growth prospects of the community as a whole. With ongoing development of commercial nanoplasmonic sensors and analytical models to interpret corresponding measurement data in the context of biologically relevant interactions, there is significant opportunity to utilize nanoplasmonic sensing strategies for not only fundamental biointerfacial science, but also translational science applications related to clinical medicine and pharmaceutical drug development among countless possibilities.

Superior LSPR substrates based on electromagnetic decoupling for on-a-chip high-throughput label-free biosensing

Localized surface plasmon resonance (LSPR) biosensing based on supported metal nanoparticles offers unparalleled possibilities for high-end miniaturization, multiplexing and high-throughput label-free molecular interaction analysis in real time when integrated within an opto-fluidic environment. However, such LSPR-sensing devices typically contain extremely large regions of dielectric materials that are open to molecular adsorption, which must be carefully blocked to avoid compromising the device readings. To address this issue, we made the support essentially invisible to the LSPR by carefully removing the dielectric material overlapping with the localized plasmonic fields through optimized wet-etching. The resulting LSPR substrate, which consists of gold nanodisks centered on narrow SiO₂ pillars, exhibits markedly reduced vulnerability to nonspecific substrate adsorption, thus allowing, in an ideal case, the implementation of thicker and more efficient passivation layers. We demonstrate that this approach is effective and fully compatible with state-of-the-art multiplexed real-time biosensing technology and thus represents the ideal substrate design for high-throughput label-free biosensing systems with minimal sample consumption.

Recent Advances in Biosensor Development for Foodborne Virus Detection

Outbreaks of foodborne diseases related to fresh produce have been increasing in North America and Europe. Viral foodborne pathogens are poorly understood, suffering from insufficient awareness and surveillance due to the limits on knowledge, availability, and costs of related technologies and devices. Current foodborne viruses are emphasized and newly emerging foodborne viruses are beginning to attract interest. To face current challenges regarding foodborne pathogens, a point-of-care (POC) concept has been introduced to food testing technology and device. POC device development involves technologies such as microfluidics, nanomaterials, biosensors and other advanced techniques. These advanced technologies, together with the challenges in developing foodborne virus detection assays and devices, are described and analysed in this critical review. Advanced technologies provide a path forward for foodborne virus detection, but more research and development will be needed to provide the level of manufacturing capacity required.

Probing the Interaction of Dielectric Nanoparticles with Supported Lipid Membrane Coatings on Nanoplasmonic Arrays

The integration of supported lipid membranes with surface-based nanoplasmonic arrays provides a powerful sensing approach to investigate biointerfacial phenomena at membrane interfaces. While a growing number of lipid vesicles, protein, and nucleic acid systems have been explored with nanoplasmonic sensors, there has been only very limited investigation of the interactions between solution-phase nanomaterials and supported lipid membranes. Herein, we established a surface-based localized surface plasmon resonance (LSPR) sensing platform for probing the interaction of dielectric nanoparticles with supported lipid bilayer (SLB)-coated, plasmonic nanodisk arrays. A key emphasis was placed on controlling membrane functionality by tuning the membrane surface charge vis-à-vis lipid composition. The optical sensing properties of the bare and SLB-coated sensor surfaces were quantitatively compared, and provided an experimental approach to evaluate nanoparticle-membrane interactions across different SLB platforms. While the interaction of negatively-charged silica nanoparticles (SiNPs) with a zwitterionic SLB resulted in monotonic adsorption, a stronger interaction with a positively-charged SLB resulted in adsorption and lipid transfer from the SLB to the SiNP surface, in turn influencing the LSPR measurement responses based on the changing spatial proximity of transferred lipids relative to the sensor surface. Precoating SiNPs with bovine serum albumin (BSA) suppressed lipid transfer, resulting in monotonic adsorption onto both zwitterionic and positively-charged SLBs. Collectively, our findings contribute a quantitative understanding of how supported lipid membrane coatings influence the sensing performance of nanoplasmonic arrays, and demonstrate how the high surface sensitivity of nanoplasmonic sensors is well-suited for detecting the complex interactions between nanoparticles and lipid membranes.

Fabrication and Characterization of Plasmonic Nanopores with Cavities in the Solid Support

Plasmonic nanostructures are widely used for various sensing applications by monitoring changes in refractive index through optical spectroscopy or as substrates for surface enhanced Raman spectroscopy. However, in most practical situations conventional surface plasmon resonance is preferred for biomolecular interaction analysis because of its high resolution in surface coverage and the simple single-material planar interface. Still, plasmonic nanostructures may find unique sensing applications, for instance when the nanoscale geometry itself is of interest. This calls for new methods to prepare nanoscale particles and cavities with controllable dimensions and curvature. In this work, we present two types of plasmonic nanopores where the solid support underneath a nanohole array has been etched, thereby creating cavities denoted as ‘nanowells’ or ‘nanocaves’ depending on the degree of anisotropy (dry or wet etch). The refractometric sensitivity is shown to be enhanced upon removing the solid support because of an increased probing volume and a shift of the asymmetric plasmonic field towards the liquid side of the finite gold film. Furthermore, the structures exhibit different spectral changes upon binding inside the cavities compared to the gold surface, which means that the structures can be used for location-specific detection. Other sensing applications are also suggested.

Topographically Flat Nanoplasmonic Sensor Chips for Biosensing and Materials Science

Nanoplasmonic sensors typically comprise arrangements of noble metal nanoparticles on a dielectric support. Thus, they are intrinsically characterized by surface topography with corrugations at the 10-100 nm length scale. While irrelevant in some bio- and chemosensing applications, it is also to be expected that the surface topography significantly influences the interaction between solids, fluids, nanoparticles and (bio)molecules, and the nanoplasmonic sensor surface. To address this issue, we present a wafer-scale nanolithography-based fabrication approach for high-temperature compatible, chemically inert, topographically flat, and laterally homogeneous nanoplasmonic sensor chips. We demonstrate their sensing performance on three different examples, for which we also carry out a direct comparison with a traditional nanoplasmonic sensor with representative surface corrugation. Specifically, we (i) quantify the film-thickness dependence of the glass transition temperature in poly(methyl metacrylate) thin films, (ii) characterize the adsorption and specific binding kinetics of the avidin-biotinylated bovine serum albumin protein system, and (iii) analyze supported lipid bilayer formation on SiO₂ surfaces.

Ultrasensitive Plasmonic Platform for Label-Free Detection of Membrane-Associated Species

Lipid membranes and membrane proteins are important biosensing targets, motivating the development of label-free methods with improved sensitivity. Silica-coated metal nanoparticles allow these systems to be combined with supported lipid bilayers for sensing membrane proteins through localized surface plasmon resonance (LSPR). However, the small sensing volume of LSPR makes the thickness of the silica layer critical for performance. Here, we develop a simple, inexpensive, and rapid sol-gel method for preparing thin conformal, continuous silica films and demonstrate its applicability using gold nanodisk arrays with LSPRs in the near-infrared range. Silica layers as thin as ∼5 nm are observed using cross-sectional scanning transmission electron microscopy. The loss in sensitivity due to the thin silica coating was found to be only 16%, and the biosensing capabilities of the substrates were assessed through the binding of cholera toxin B to GM1 lipids. This sensor platform should prove useful in the rapid, multiplexed detection and screening of membrane-associated biological targets.

Biosensing using plasmonic nanohole arrays with small, homogenous and tunable aperture diameters

Plasmonic nanohole arrays are widely used for optical label-free molecular detection. An important factor for many applications is the diameter of the apertures. So far nanohole arrays with controllable diameters below 100 nm have not been demonstrated and it has not been systematically investigated how the diameter influences the optical properties. In this work we fine-tune the diameter in short range ordered nanohole arrays down to 50 nm. The experimental far field spectra show how the wavelength of maximum extinction remains unaffected while the transmission maximum blue shifts with smaller diameters. The near field is visualized by numerical simulations, showing a homogenous enhancement throughout the cylindrical void at the transmission maximum for diameters between 50 and 100 nm. For diameters below 50 nm plasmon excitation is no longer possible experimentally or by simulations. Further, we investigate the refractive index sensing capabilities of the smaller holes. As the diameter was reduced, the sensitivity in terms of resonance shift with bulk liquid refractive index was found to be unaltered. However, for the transmission maximum the sensitivity becomes more strongly localized to the hole interior. By directing molecular binding to the bottom of the holes we demonstrate how smaller holes enhance the sensitivity in terms of signal per molecule. A real-time detection limit well below one protein per nanohole is demonstrated. The smaller plasmonic nanoholes should be suitable for studies of molecules confined in small volumes and as mimics of biological nanopores.

Nanohole Array-Directed Trapping of Mammalian Mitochondria Enabling Single Organelle Analysis

We present periodic nanohole arrays fabricated in free-standing metal-coated nitride films as a platform for trapping and analyzing single organelles. When a microliter-scale droplet containing mitochondria is dispensed above the nanohole array, the combination of evaporation and capillary flow directs individual mitochondria to the nanoholes. Mammalian mitochondria arrays were rapidly formed on chip using this technique without any surface modification steps, microfluidic interconnects, or external power sources. The trapped mitochondria were depolarized on chip using an ionophore with results showing that the organelle viability and behavior were preserved during the on-chip assembly process. Fluorescence signal related to mitochondrial membrane potential was obtained from single mitochondria trapped in individual nanoholes revealing statistical differences between the behavior of polarized vs depolarized mammalian mitochondria. This technique provides a fast and stable route for droplet-based directed localization of organelles-on-a-chip with minimal limitations and complexity, as well as promotes integration with other optical or electrochemical detection techniques.