A conformation- and ion-sensitive plasmonic biosensor

Combining plasmonic and electrochemical biosensing methods

The idea of combining electrochemical (EC) and plasmonic biosensor methods was introduced almost thirty years ago and the potential of electrochemical-plasmonic (EC-P) biosensors has been highlighted ever since. Despite that, the use of EC-P biosensors in analytics has been rather limited so far and the search for unique applications of the EC-P method continues. In this paper, we review the advances in the field of EC-P biosensors and discuss the features and benefits they can provide. In addition, we identify the main challenges for the development of EC-P biosensors and the limitations that prevent EC-P biosensors from more widespread use. Finally, we review applications of EC-P biosensors for the investigation and quantification of biomolecules, and for the study of biomolecular and cellular processes.

Do conformational changes contribute to the surface plasmon resonance signal?

Surface plasmon resonance (SPR)-based biosensors are widely used instruments for characterizing molecular interactions. In theory the SPR signal depends only on mass changes for interacting molecules of same chemical nature. Whether conformational changes of interacting molecules also contribute to the SPR signal is still a subject of lively debates. Works have been published claiming that conformational changes were detected but all factors contributing to the SPR signal were not carefully considered, in addition to often using no or improper controls. In the present work we used a very well-characterized oligonucleotide, the thrombin-binding DNA aptamer (TBA), which upon binding of potassium ions folds into a two G-tetrad antiparallel G-quadruplex structure. All terms contributing to the maximal expected SPR response, R_max, in particular the refractive index increment, RII, of both partners and the fraction of immobilized TBA target available, c_a, were experimentally assessed. The resulting R_max was then compared to the maximal experimental SPR response for potassium ions binding to TBA using appropriate controls. Regardless how the RIIs were measured, by SPR or refractometry, and how much TBA available for interacting with potassium ions was considered, the theoretical and the experimental SPR responses never matched, the former being always lower than the latter. Using a straightforward experimental model system and by thoroughly taking into account all contributing factors we therefore conclude that conformational changes can indeed contribute to the measured SPR signal.

Influence of the crystallographic texture of ITO on the electrodeposition of silver nanoparticles

The electrochemical control over nucleation and growth of metal nanoparticles on foreign substrates is an active field of research, where the surface properties of the substrate have a key role in nucleation dynamics. Polycrystalline indium tin oxide (ITO) films are highly desired substrates for many optoelectronic applications, for which the only parameter that is often specified is the sheet resistance. As a result, growth on ITO is highly irreproducible. Here, we show that ITO substrates with same technical specifications (i.e. sheet resistance, light transmittance and roughness) and supplier may still have different crystalline texture, which we find it has a strong impact on the nucleation and growth of silver nanoparticles during electrodeposition. We find that the preferential presence of lower index surfaces leads to few orders of magnitude lower island density, which is strongly dependent on the nucleation pulse potential. By contrast, the island density on ITO with preferential 〈111〉 orientation is barely affected by the nucleation pulse potential. This work highlights the importance of reporting the surface properties of polycrystalline substrates when presenting nucleation studies and metal nanoparticle electrochemical growth.

Biosensing Applications Using Nanostructure-Based Localized Surface Plasmon Resonance Sensors

Localized surface plasmon resonance (LSPR)-based biosensors have recently garnered increasing attention due to their potential to allow label-free, portable, low-cost, and real-time monitoring of diverse analytes. Recent developments in this technology have focused on biochemical markers in clinical and environmental settings coupled with advances in nanostructure technology. Therefore, this review focuses on the recent advances in LSPR-based biosensor technology for the detection of diverse chemicals and biomolecules. Moreover, we also provide recent examples of sensing strategies based on diverse nanostructure platforms, in addition to their advantages and limitations. Finally, this review discusses potential strategies for the development of biosensors with enhanced sensing performance.

Optical imaging of single-protein size, charge, mobility, and binding

Detection and identification of proteins are typically achieved by analyzing protein size, charge, mobility and binding to antibodies, which are critical for biomedical research and disease diagnosis and treatment. Despite the importance, measuring these quantities with one technology and at the single-molecule level has not been possible. Here we tether a protein to a surface with a flexible polymer, drive it into oscillation with an electric field, and image the oscillation with a near field optical imaging method, from which we determine the size, charge, and mobility of the protein. We also measure antibody binding and conformation changes in the protein. The work demonstrates a capability for comprehensive protein analysis and precision protein biomarker detection at the single molecule level.

Protein identification at the single-molecule level is the ultimate goal for biological research and disease diagnosis. Here, the authors identify the size, charge, mobility, and binding of individual protein molecules by measuring the optical and electrical responses of each protein molecule tethered to a surface.

Plasmonic biosensors relying on biomolecular conformational changes: Case of odorant binding proteins

Plasmonic nanostructures serve in a range of analytical techniques that were developed for the analysis of chemical and biological species. Among others, they have been pursued for the investigation of odorant binding proteins (OBP) and their interaction with odorant molecules. These compounds are low molecular weight agents, which makes their direct detection with conventional surface plasmon resonance (SPR) challenging. Therefore, other plasmonic sensor modalities need to be implemented for the detection and interaction analysis of OBPs. This chapter provides a guide for carrying out such experiments based on two techniques that take advantage of conformation changes of OBPs occurring upon specific interaction with their affinity partners. First, there is discussed SPR monitoring of conformation changes of biomolecules that are not accompanied by a strong increase in the surface mass density but rather with its re-distribution perpendicular to the surface. Second, the implementation of surface plasmon-enhanced fluorescence energy transfer is presented for the sensitive monitoring of conformational changes of biomolecules tagged with a fluorophore at its defined part. Examples from our and other laboratories illustrate the performance of these concepts and their applicability for the detection of low molecular weight odorant molecules by the use of OBPs attached to the sensor surface is discussed.

Determination of the Distance Between the Cytochrome and Dehydrogenase Domains of Immobilized Cellobiose Dehydrogenase by Using Surface Plasmon Resonance with a Center of Mass Based Model

Changes in the tertiary conformation of adsorbed biomolecules can induce detectable shifts (Δθ_r) in the surface plasmon resonance (SPR) angle. Here it is shown how to calculate the corresponding shifts in the adsorbate’s center of mass (Δz_avg) along the sensing surface normal from the measured Δθ_r. The novel developed model was used for determining the mean distance between the cytochrome (CYT) and flavodehydrogenase (DH) domains of the enzyme cellobiose dehydrogenase (CDH) isolated from the fungi Neurospora crassa, Corynascus thermophilus, and Myriococcum thermophilum as a function of pH, [Ca²⁺], and substrate concentration. SPR confirmed the results from earlier electrochemical and SAXS studies stating that the closed conformation, where the two domains are in close vicinity, is stabilized by a lower pH and an increased [Ca²⁺]. Interestingly, an increasing substrate concentration in the absence of any electron acceptors stabilizes the open conformation as the electrostatic repulsion due to the reaped electrons pushes the DH and CYT domains apart. The accuracy of distance determination was limited mostly by the random fluctuations between replicate measurements, and it was possible to detect movements <1 nm of the domains with respect to each other. The results agreed with calculations using already established models treating conformational changes as contraction or expansion of the thickness of the adsorbate layer (t_protein). Although the models yielded equivalent results, in this case, the Δz_avg-based method also works in situations, where the adsorbate’s mass is not evenly distributed within the layer.

Computational nanoplasmonics in the quasistatic limit for biosensing applications

The phenomenon of localized surface plasmon resonance (LSPR) provides high sensitivity in detecting biomolecules through shifts in resonance frequency when a target is present. Computational studies in this field have used the full Maxwell equations with simplified models of a sensor-analyte system, or they neglected the analyte altogether. In the long-wavelength limit, one can simplify the theory via an electrostatics approximation while adding geometrical detail in the sensor and analytes (at moderate computational cost). This work uses the latter approach, expanding the open-source PyGBe code to compute the extinction cross section of metallic nanoparticles in the presence of any target for sensing. The target molecule is represented by a surface mesh, based on its crystal structure. PyGBe is research software for continuum electrostatics, written in python with computationally expensive parts accelerated on GPU hardware, via PyCUDA. It is also accelerated algorithmically via a treecode that offers O(NlogN) computational complexity. These features allow PyGBe to handle problems with half a million boundary elements or more. In this work, we demonstrate the suitability of PyGBe, extended to compute LSPR response in the electrostatic limit, for biosensing applications. Using a model problem consisting of an isolated silver nanosphere in an electric field, our results show grid convergence as 1/N, and accurate computation of the extinction cross section as a function of wavelength (compared with an analytical solution). For a model of a sensor-analyte system, consisting of a spherical silver nanoparticle and a set of bovine serum albumin (BSA) proteins, our results again obtain grid convergence as 1/N (with respect to the Richardson extrapolated value). Computing the LSPR response as a function of wavelength in the presence of BSA proteins captures a redshift of 0.5 nm in the resonance frequency due to the presence of the analytes at 1-nm distance. The final result is a sensitivity study of the biosensor model, obtaining the shift in resonance frequency for various distances between the proteins and the nanoparticle. All results in this paper are fully reproducible, and we have deposited in archival data repositories all the materials needed to run the computations again and recreate the figures. PyGBe is open source under a permissive license and openly developed. Documentation is available at http://pygbe.github.io/pygbe/docs/.

Metadevices with Potential Practical Applications

Metamaterials are "new materials" with different superior physical properties, which have generated great interest and become popular in scientific research. Various designs and functional devices using metamaterials have formed a new academic world. The application concept of metamaterial is based on designing diverse physical structures that can break through the limitations of traditional optical materials and composites to achieve extraordinary material functions. Therefore, metadevices have been widely studied by the academic community recently. Using the properties of metamaterials, many functional metadevices have been well investigated and further optimized. In this article, different metamaterial structures with varying functions are reviewed, and their working mechanisms and applications are summarized, which are near-field energy transfer devices, metamaterial mirrors, metamaterial biosensors, and quantum-cascade detectors. The development of metamaterials indicates that new materials will become an important breakthrough point and building blocks for new research domains, and therefore they will trigger more practical and wide applications in the future.

Gold nanorods as a high-pressure sensor of phase transitions and refractive-index gauge

Gold nanorods (Au NRs), nanospheres and other nanoparticles display numerous superior physicochemical properties, such as resistance to oxidation and aggressive agents, strong enhancement of local electric field and a high absorption coefficient in the visible and near-infrared (NIR) range. The absorption peaks of surface plasmon resonance (SPR) in Au NRs are highly sensitive to their surrounding medium and to its refractive index (RI) changes. However, no applications of NRs for detecting phase transitions have been reported. Here, we show that Au NRs effectively detect phase transitions of compressed compounds, liquid and solid, by measuring their RI. Owing to the direct interaction of the NRs with their surrounding medium, its subtle RI changes can be observed by the use of high-pressure absorption vis-NIR spectroscopy. We have applied a Au NR-based sensor in a diamond anvil cell (DAC) for monitoring the phase transitions of compressed water, its freezing to ice VI and at the subsequent solid-solid phase transition to ice VII, and the monotonic compression and solid-solid phase transitions in urea and thiourea.

Microscale and Nanoscale Electrophotonic Diagnostic Devices

Detecting and identifying infectious agents and potential pathogens in complex environments and characterizing their mode of action is a critical need. Traditional diagnostics have targeted a single characteristic (e.g., spectral response, surface receptor, mass, intrinsic conductivity, etc.). However, advances in detection technologies have identified emerging approaches in which multiple modes of action are combined to obtain enhanced performance characteristics. Particularly appealing in this regard, electrophotonic devices capable of coupling light to electron translocation have experienced rapid recent growth and offer significant advantages for diagnostics. In this review, we explore three specific promising approaches that combine electronics and photonics: (1) assays based on closed bipolar electrochemistry coupling electron transfer to color or fluorescence, (2) sensors based on localized surface plasmon resonances, and (3) emerging nanophotonics approaches, such as those based on zero-mode waveguides and metamaterials.

Temperature-Induced Denaturation of BSA Protein Molecules for Improved Surface Passivation Coatings

Bovine serum albumin (BSA) is the most widely used protein for surface passivation applications, although it has relatively weak, nonsticky interactions with hydrophilic surfaces such as silica-based materials. Herein, we report a simple and versatile method to increase the stickiness of BSA protein molecules adsorbing onto silica surfaces, resulting in up to a 10-fold improvement in blocking efficiency against serum biofouling. Circular dichroism spectroscopy, dynamic light scattering, and nanoparticle tracking analysis showed that temperature-induced denaturation of BSA proteins in bulk solution resulted in irreversible unfolding and protein oligomerization, thereby converting weakly adhesive protein monomers into a more adhesive oligomeric form. The heat-treated, denatured BSA oligomers remained stable after cooling. Room-temperature quartz crystal microbalance-dissipation and localized surface plasmon resonance experiments revealed that denatured BSA oligomers adsorbed more quickly and in larger mass quantities onto silica surfaces than native BSA monomers. We also determined that the larger surface contact area of denatured BSA oligomers is an important factor contributing to their more adhesive character. Importantly, denatured BSA oligomers were a superior passivating agent to inhibit biofouling on silica surfaces and also improved Western blot application performance. Taken together, the findings demonstrate how temperature-induced denaturation of BSA protein molecules can lead to improved protein-based coatings for surface passivation applications.

Quantitative Comparison of Protein Adsorption and Conformational Changes on Dielectric-Coated Nanoplasmonic Sensing Arrays

Nanoplasmonic sensors are a popular, surface-sensitive measurement tool to investigate biomacromolecular interactions at solid-liquid interfaces, opening the door to a wide range of applications. In addition to high surface sensitivity, nanoplasmonic sensors have versatile surface chemistry options as plasmonic metal nanoparticles can be coated with thin dielectric layers. Within this scope, nanoplasmonic sensors have demonstrated promise for tracking protein adsorption and substrate-induced conformational changes on oxide film-coated arrays, although existing studies have been limited to single substrates. Herein, we investigated human serum albumin (HSA) adsorption onto silica- and titania-coated arrays of plasmonic gold nanodisks by localized surface plasmon resonance (LSPR) measurements and established an analytical framework to compare responses across multiple substrates with different sensitivities. While similar responses were recorded on the two substrates for HSA adsorption under physiologically-relevant ionic strength conditions, distinct substrate-specific behavior was observed at lower ionic strength conditions. With decreasing ionic strength, larger measurement responses occurred for HSA adsorption onto silica surfaces, whereas HSA adsorption onto titania surfaces occurred independently of ionic strength condition. Complementary quartz crystal microbalance-dissipation (QCM-D) measurements were also performed, and the trend in adsorption behavior was similar. Of note, the magnitudes of the ionic strength-dependent LSPR and QCM-D measurement responses varied, and are discussed with respect to the measurement principle and surface sensitivity of each technique. Taken together, our findings demonstrate how the high surface sensitivity of nanoplasmonic sensors can be applied to quantitatively characterize protein adsorption across multiple surfaces, and outline broadly-applicable measurement strategies for biointerfacial science applications.

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.

An optical fiber-based LSPR aptasensor for simple and rapid in-situ detection of ochratoxin A

Label-free biosensing methods that rely on the use of localized surface plasmon resonance (LSPR) have attracted great attention as a result of their simplicity, high sensitivity, and relatively low cost. However, in-situ analysis of real samples using these techniques has remained challenging because colloidal nanoparticles (NPs) can be unstable at certain levels of pH and salt concentration. Even in the case of a chip-type LSPR sensor that can resolve the instability problem by employing NPs immobilized on the substrate, loading of a sample to sensor chip with exact volume control can be difficult for unskilled users. Herein, we report an optical-fiber-based LSPR aptasensor that can avoid these problems and serve as a portable and simple system for sensitive detection of a small mycotoxin, ochratoxin A (OTA), in real samples. The optical fiber coated with aptamer-modified gold nanorods (GNRs) is simply dipped into a solution containing OTA and subjected to LSPR analysis. Quantitative analysis of OTA is performed by measuring the spectral red shift of the LSPR peak of GNRs. Under optimized conditions, the LSPR peak shift displays a linear response (R² = 0.9887) to OTA in the concentration range from 10pM to 100nM, with a limit of detection of 12.0pM (3S). The developed sensor shows a high selectivity for OTA over other mycotoxins such as zearalenone (ZEN) and ochratoxin B (OTB), and shows an accurate detection capability for OTA in real grape juice samples.

Effect of size and curvature on the enzyme activity of bionanoconjugates

Biotic-abiotic hybrids comprised of globular proteins and functional nanostructures with complementary and synergistic properties are central to a number of bionanotechnological applications. A comprehensive understanding of the effect of physicochemical properties of abiotic nanostructures on the biological activity of the bionanoconjugates is critical in the design of these bio-nano hybrids. In this study, using size and curvature-controlled gold nanoparticles as a model abiotic system, we investigated the effect of hydrodynamic diameter and surface curvature on the activity of a model enzyme, horseradish peroxidase (HRP), adsorbed on the surface of the nanostructures. In contrast with the previous studies, we have employed a novel class of gold superstructures (gold nanoparticles on spheres) to deconvolute the effects of size and curvature on the catalytic activity of the bionanoconjugates. This study improves our understanding of the bio/nano interface and the design of bioinorganic hybrids with potential applications in biomimetic and bioenabled sensors, energy harvesting, optoelectronic components and devices, responsive and autonomous materials.

Rapid, Point-of-Care, Paper-Based Plasmonic Biosensor for Zika Virus Diagnosis

Zika virus (ZIKV) is an increasing global health challenge. There is an urgent need for rapid, low-cost, and accurate diagnostic tests that can be broadly distributed and applied in pandemic regions. Here, an innovative, adaptable, and rapidly deployable bioplasmonic paper-based device (BPD) is demonstrated for the detection of ZIKV infection, via quantification of serum anti-ZIKV-nonstructural protein 1 (NS1) IgG and IgM. BPD is based on ZIKV-NS1 protein as a capture element and gold nanorods as plasmonic nanotransducers. The BPD displays excellent sensitivity and selectivity to both anti-ZIKV-NS1 IgG and IgM in human serum. In addition, excellent stability of BPDs at room and even elevated temperature for one month is achieved by metal-organic framework (MOF)-based biopreservation. MOF-based preservation obviates the need for device refrigeration during transport and storage, thus enabling their use in point-of-care and resource-limited settings for ZIKV surveillance. Furthermore, the versatile design (interchangeable recognition element) of BPDs more generally enables their ready adaptation to diagnose other emerging infectious diseases.

Influence of Surface Charge of the Nanostructures on the Biocatalytic Activity

The physicochemical properties of abiotic nanostructures determine the structure and function of biological counterparts in biotic-abiotic nanohybrids. A comprehensive understanding of the interfacial interactions and the predictive capability of their structure and function is paramount for virtually all fields of bionanotechnology. In this study, using plasmonic nanostructures as a model abiotic system, we investigate the effect of the surface charge of nanostructures on the biocatalytic reaction kinetics of a bound enzyme. We found that the surface charge of nanostructures profoundly influences the structure, orientation, and activity of the bound enzyme. Furthermore, the interactions of the enzyme with nanoparticles result in stable conjugates that retain their functionality at elevated temperatures, unlike their free counterparts that lose their secondary structure and biocatalytic activity.

Computational Sensing Using Low-Cost and Mobile Plasmonic Readers Designed by Machine Learning

Plasmonic sensors have been used for a wide range of biological and chemical sensing applications. Emerging nanofabrication techniques have enabled these sensors to be cost-effectively mass manufactured onto various types of substrates. To accompany these advances, major improvements in sensor read-out devices must also be achieved to fully realize the broad impact of plasmonic nanosensors. Here, we propose a machine learning framework which can be used to design low-cost and mobile multispectral plasmonic readers that do not use traditionally employed bulky and expensive stabilized light sources or high-resolution spectrometers. By training a feature selection model over a large set of fabricated plasmonic nanosensors, we select the optimal set of illumination light-emitting diodes needed to create a minimum-error refractive index prediction model, which statistically takes into account the varied spectral responses and fabrication-induced variability of a given sensor design. This computational sensing approach was experimentally validated using a modular mobile plasmonic reader. We tested different plasmonic sensors with hexagonal and square periodicity nanohole arrays and revealed that the optimal illumination bands differ from those that are "intuitively" selected based on the spectral features of the sensor, e.g., transmission peaks or valleys. This framework provides a universal tool for the plasmonics community to design low-cost and mobile multispectral readers, helping the translation of nanosensing technologies to various emerging applications such as wearable sensing, personalized medicine, and point-of-care diagnostics. Beyond plasmonics, other types of sensors that operate based on spectral changes can broadly benefit from this approach, including e.g., aptamer-enabled nanoparticle assays and graphene-based sensors, among others.

Collagen-Gold Nanoparticle Conjugates for Versatile Biosensing

Integration of noble metal nanoparticles with proteins offers promising potential to create a wide variety of biosensors that possess both improved selectivity and versatility. The multitude of functionalities that proteins offer coupled with the unique optical properties of noble metal nanoparticles can allow for the realization of simple, colorimetric sensors for a significantly larger range of targets. Herein, we integrate the structural protein collagen with 10 nm gold nanoparticles to develop a protein-nanoparticle conjugate which possess the functionality of the protein with the desired colorimetric properties of the nanoparticles. Applying the many interactions that collagen undergoes in the extracellular matrix, we are able to selectively detect both glucose and heparin with the same collagen-nanoparticle conjugate. Glucose is directly detected through the cross-linking of the collagen fibrils, which brings the attached nanoparticles into closer proximity, leading to a red-shift in the LSPR frequency. Conversely, heparin is detected through a competition assay in which heparin-gold nanoparticles are added to solution and compete with heparin in the solution for the binding sites on the collagen fibrils. The collagen-nanoparticle conjugates are shown to detect both glucose and heparin in the physiological range. Lastly, glucose is selectively detected in 50% mouse serum with the collagen-nanoparticle devices possessing a linear range of 3-25 mM, which is also within the physiologically relevant range.

Immobilized enzymes: understanding enzyme – surface interactions at the molecular level

Interactions between immobilized enzymes and supporting surfaces are complex and context-dependent and can significantly alter enzyme structure, stability and activity.

Quantitative Profiling of Nanoscale Liposome Deformation by a Localized Surface Plasmon Resonance Sensor

Characterizing the shape of sub-100 nm, biological soft-matter particulates (e.g., liposomes and exosomes) adsorbed at a solid-liquid interface remains a challenging task. Here, we introduce a localized surface plasmon resonance (LSPR) sensing approach to quantitatively profile the deformation of nanoscale, fluid-phase 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) liposomes contacting a titanium dioxide substrate. Experimental and theoretical results validate that, due to its high sensitivity to the spatial proximity of phospholipid molecules near the sensor surface, the LSPR sensor can discriminate fine differences in the extent of ionic strength-modulated liposome deformation at both low and high surface coverages. By contrast, quartz crystal microbalance-dissipation (QCM-D) measurements performed with equivalent samples were qualitatively sensitive to liposome deformation only at saturation coverage. Control experiments with stiffer, gel-phase 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) liposomes verified that the LSPR measurement discrimination arises from the extent of liposome deformation, while the QCM-D measurements yield a more complex response that is also sensitive to the motion of adsorbed liposomes and coupled solvent along with lateral interactions between liposomes. Collectively, our findings demonstrate the unique measurement capabilities of LSPR sensors in the area of biological surface science, including competitive advantages for probing the shape properties of adsorbed, nanoscale biological particulates.

Fingerprints of Calcium-Binding Protein Conformational Dynamics Monitored by Surface Plasmon Resonance

Surface plasmon resonance (SPR) spectroscopy is widely used to probe interactions involving biological macromolecules by detecting changes in the refractive index in a metal/dielectric interface following the dynamic formation of a molecular complex. In past years, SPR-based experimental approaches were developed to monitor conformational changes induced by the binding of small analytes to proteins coupled to the surface of commercially available sensor chips. A significant contribution to our understanding of the phenomenon came from the study of several Ca(2+)-sensor proteins operating in diverse cellular scenarios, in which the conformational switch is triggered by specific Ca(2+) signals. Structural and physicochemical analyses demonstrated that the SPR signal not only depends on the change in protein size upon Ca(2+)-binding but likely originates from variations in the hydration shell structure. The resulting changes in the dielectric properties of water or of the protein-water interface eventually reflect different crowding conditions on the SPR sensor chip, which mimic the cellular environment. SPR could hence be used to monitor conformational transitions in proteins, especially when a significant variation in the hydrophobicity of the solvent-exposed protein surface occurs, thus leading to changes in the dielectric milieu of the whole sensor chip surface. We review recent work in which SPR has been successfully employed to provide a fingerprint of the conformational change dynamics in proteins under native and altered conditions, which include post-translational modifications, copresence of competing analytes, and point mutations of single amino acids associated with genetic diseases.

A simple and efficient design to improve the detection of biotin-streptavidin interaction with plasmonic nanobiosensors

In this manuscript we propose a simple and efficient strategy to improve the sensitivity of localized surface plasmon resonance (LSPR) shift-based biosensors using biotin-streptavidin recognition interaction as a proof-of-concept. Specifically, biotin molecules are immobilized on a low-cost plasmonic LSPR biosensor based on annealed self-assembled spherical gold nanoparticles (AuNSs) and successively incubated with increasing concentrations of streptavidin, achieving a limit of detection (LOD) of 5nM. Interestingly, when the detection is performed by the same biotin-functionalized plasmonic AuNSs substrate but against streptavidin previously conjugated to gold nanorods, the LSPR shift is 26-fold enhanced. Moreover, we confirm these results through numerical simulations and demonstrate that the proposed sensing architecture can operate as transducer not only to confirm the adsorption of bioanalyte but also to provide the chemical identity of the capture and targeted molecules from their vibrational Raman fingerprints. Therefore, we are confident that the development of such plasmonic biosensors that use metallic labels for improving the sensitivity of detection could become highly promising for future point-of-care diagnostic assays, pushing sensitivity towards single-molecule detection limit.

Highly enhanced transverse plasmon resonance and tunable double Fano resonances in gold@titania nanorods

Gold nanorods have attracted intensive interest owing to their localized surface plasmon resonance properties and enormous potential applications. The transverse plasmon of Au nanorods is usually weaker than the longitudinal one, hampering certain plasmonic applications. Herein we report on the intensification of the transverse plasmon resonance by coating TiO2 onto Au nanorods. The transverse plasmon mode of the resultant Au@TiO2 nanorods with a sufficiently thick shell can be comparable to or even stronger than the longitudinal one in intensity. Moreover, both the transverse and longitudinal plasmon resonances of the Au@TiO2 nanorods exhibit an asymmetric line shape on their scattering spectra. Electrodynamic simulations and analyses based on a coupled oscillator model suggest that the asymmetric line shape originates from the coupling between the Au core and TiO2 shell. Apart from the shell thickness, the plasmonic properties of the Au@TiO2 nanorods can also be tuned by the dimension of the Au nanorod core. In addition, the polarization-dependent light scattering from the individual Au@TiO2 nanorods has also been investigated. These results will be of high importance for understanding the interactions between noble metals and semiconductors in plasmonic hybrid nanosystems, and for designing novel plasmonic nanostructures with desired optical properties and functions.

Increasing the spectral shifts in LSPR biosensing using DNA-functionalized gold nanorods in a competitive assay format for the detection of interferon-γ

We demonstrate an approach that utilizes DNA-functionalized gold nanorods (AuNRs) in an indirect competitive assay format to increase the spectra shift in localized surface plasmon resonance (LSPR) biosensing. We use interferon gamma (IFN-γ) as a model analyte to demonstrate the feasibility of our detection method. The LSPR chips with periodic gold nanodot arrays are fabricated using a thermal lithography process and are functionalized with IFN-γ aptamers for detection. The DNA-functionalized AuNRs and IFN-γ compete with each other to bind to the aptamers during detection, and the spectra shifts are mainly caused by the AuNRs rather than IFN-γ. When using our approach, the target molecules do not need to be captured by two capture ligands simultaneously during detection and thus do not require multiple binding sites. Both experiments and finite-difference time-domain (FDTD) simulations show that making the AuNRs as close to the chip surface as possible is very critical for increasing LSPR shifts, and the simulated results also show that the orientation of the AuNR affects the plasmon coupling between the gold nanodots on the chip surface and the nearby AuNRs. Although only the detection of IFN-γ is demonstrated in this study, we expect that the LSPR biosensing method can be applied to label-free detection of a variety of molecules as long as suitable aptamers are available.

Plasmonic Nanohole Sensor for Capturing Single Virus-Like Particles toward Virucidal Drug Evaluation

A plasmonic nanohole sensor for virus-like particle capture and virucidal drug evaluation is reported. Using a materials-selective surface functionalization scheme, passive immobilization of virus-like particles only within the nanoholes is achieved. The findings demonstrate that a low surface coverage of particles only inside the functionalized nanoholes significantly improves nanoplasmonic sensing performance over conventional nanohole arrays.

Single-crystalline aluminum film for ultraviolet plasmonic nanolasers

Significant advances have been made in the development of plasmonic devices in the past decade. Plasmonic nanolasers, which display interesting properties, have come to play an important role in biomedicine, chemical sensors, information technology, and optical integrated circuits. However, nanoscale plasmonic devices, particularly those operating in the ultraviolet regime, are extremely sensitive to the metal and interface quality. Thus, these factors have a significant bearing on the development of ultraviolet plasmonic devices. Here, by addressing these material-related issues, we demonstrate a low-threshold, high-characteristic-temperature metal-oxide-semiconductor ZnO nanolaser that operates at room temperature. The template for the ZnO nanowires consists of a flat single-crystalline Al film grown by molecular beam epitaxy and an ultrasmooth Al₂O₃ spacer layer synthesized by atomic layer deposition. By effectively reducing the surface plasmon scattering and metal intrinsic absorption losses, the high-quality metal film and the sharp interfaces formed between the layers boost the device performance. This work should pave the way for the use of ultraviolet plasmonic nanolasers and related devices in a wider range of applications.

Origin of the Avalanche-Like Photoluminescence from Metallic Nanowires

Surface plasmonic systems provide extremely efficient ways to modulate light-matter interaction in photon emission, light harvesting, energy conversion and transferring, etc. Various surface plasmon enhanced luminescent behaviors have been observed and investigated in these systems. But the origin of an avalanche-like photoluminescence, which was firstly reported in 2007 from Au and subsequently from Ag nanowire arrays/monomers, is still not clear. Here we show, based on systematic investigations including the excitation power/time related photoluminescent measurements as well as calculations, that this avalanche-like photoluminescence is in fact a result of surface plasmon assisted thermal radiation. Nearly all of the related observations could be perfectly interpreted with this concept. Our finding is crucial for understanding the surface plasmon mediated thermal and photoemission behaviors in plasmonic structures, which is of great importance in designing functional plasmonic devices.

Plasmonic paper: a porous and flexible substrate enabling nanoparticle-based combinatorial chemistry

The physical properties and manipulation of the nanomaterials immobilized on paper substrate offers tremendous potential for a variety of applications.

Peptide Functionalized Gold Nanorods for the Sensitive Detection of a Cardiac Biomarker Using Plasmonic Paper Devices

The sensitivity of localized surface plasmon resonance (LSPR) of metal nanostructures to adsorbates lends itself to a powerful class of label-free biosensors. Optical properties of plasmonic nanostructures are dependent on the geometrical features and the local dielectric environment. The exponential decay of the sensitivity from the surface of the plasmonic nanotransducer calls for the careful consideration in its design with particular attention to the size of the recognition and analyte layers. In this study, we demonstrate that short peptides as biorecognition elements (BRE) compared to larger antibodies as target capture agents offer several advantages. Using a bioplasmonic paper device (BPD), we demonstrate the selective and sensitive detection of the cardiac biomarker troponin I (cTnI). The smaller sized peptide provides higher sensitivity and a lower detection limit using a BPD. Furthermore, the excellent shelf-life and thermal stability of peptide-based LSPR sensors, which precludes the need for special storage conditions, makes it ideal for use in resource-limited settings.

Calmodulin inhibitors from natural sources: an update

Calmodulin (CaM) plays a central role in regulating a myriad of cellular functions in physiological and pathophysiological processes, thus representing an important drug target. In previous reviews, our group has reported relevant information regarding natural anti-CaM compounds up to 2009. Natural sources continue to provide a diverse and unique reservoir of CaM inhibitors for drug and research tool discovery. This review provides an update of natural products with reported CaM inhibitory properties, which includes around 70 natural products and some synthetic analogues, belonging to different structural classes. Most of these natural inhibitors were isolated from fungi and plants and belong to the stilbenoid, polyketide, alkaloid, and peptide structural classes. These products were discovered mainly using a fluorescence-based method on rationally designed biosensors, which are highly specific, low-cost, and selective and have short reaction times. The effect of several antimitotic drugs on Ca(2+)-hCaM is also described.

Detection of fibronectin conformational changes in the extracellular matrix of live cells using plasmonic nanoplates

Nanoplates enable high sensitive spectral monitoring of fibronectin conformational transitions and fibril formation within the extracellular matrix of live cells.

Highly specific plasmonic biosensors for ultrasensitive microRNA detection in plasma from pancreatic cancer patients

MicroRNAs (miRs) are small noncoding RNAs that regulate mRNA stability and/or translation. Because of their release into the circulation and their remarkable stability, miR levels in plasma and other biological fluids can serve as diagnostic and prognostic disease biomarkers. However, quantifying miRs in the circulation is challenging due to issues with sensitivity and specificity. This Letter describes for the first time the design and characterization of a regenerative, solid-state localized surface plasmon resonance (LSPR) sensor based on highly sensitive nanostructures (gold nanoprisms) that obviates the need for labels or amplification of the miRs. Our direct hybridization approach has enabled the detection of subfemtomolar concentration of miR-X (X = 21 and 10b) in human plasma in pancreatic cancer patients. Our LSPR-based measurements showed that the miR levels measured directly in patient plasma were at least 2-fold higher than following RNA extraction and quantification by reverse transcriptase-polymerase chain reaction. Through LSPR-based measurements we have shown nearly 4-fold higher concentrations of miR-10b than miR-21 in plasma of pancreatic cancer patients. We propose that our highly sensitive and selective detection approach for assaying miRs in plasma can be applied to many cancer types and disease states and should allow a rational approach for testing the utility of miRs as markers for early disease diagnosis and prognosis, which could allow for the design of effective individualized therapeutic approaches.

(Gold nanorod core)/(polyaniline shell) plasmonic switches with large plasmon shifts and modulation depths

(Gold nanorod core)/(polyaniline shell) nanostructures are prepared for functioning as active plasmonic switches. The single core/shell nanostructures exhibit a remarkable switching performance, with the modulation depth and scattering peak shift reaching 10 dB and 100 nm, respectively. The nanostructures are also deposited on substrates to form macroscale monolayers with remarkable ensemble plasmonic switching performances.

Fabrication of metallic nanopatterns with ultrasmooth surface on various substrates through lift-off and transfer process

The smooth surface of the metallic nanostructure is essential for the propagation of surface plasmon polaritons. In this paper, we present a novel method to fabricate the metallic nanopatterns with ultra-smooth surface on various substrates. By using a silica film as the sacrificial layer, we show that the prefabricated metallic nanopatterns produced by electron beam lithography and film deposition can be hydrolyzed and transferred onto a designated substrate. The ultra-smooth surface morphology of nanopatterns has been characterized and verified by scanning electron microscopy and atomic force microscopy. More importantly, we demonstrate that this method can successfully produce a variety of nanostructures with high product yield, even onto the uneven substrate. The results indicate that our proposed method is a promising and versatile means to fabricate multiplicate smooth metallic nanostructure on various substrates for the application of nanophotonic devices.

Fabrication and functionalization of periodically aligned metallic nanocup arrays using colloidal lithography with a sinusoidally wrinkled substrate

We propose a general strategy for fabricating ultrasmall attoliter-sized (10(-18) L) one-dimensional (1D) aligned nanocup arrays embedded in poly(dimethylsiloxane) (PDMS) films based on a combination of colloidal soft-lithography and wrinkle processing. The nanocup consists of a metallic shell (silver-single or double-layer silver/gold type) with a thickness of several tens of nanometers and whose diameter was ca. 500 nm and cavity depth was ca. 250 nm. First, monodisperse polystyrene (PS) colloids (d = 500 nm) were arranged onto a sinusoidally wrinkled PDMS substrate. Then, the colloid particle arrays were transferred onto another flat PDMS substrate, and a metal film was vacuum deposited over the array to form a nanostructured surface consisting of half-shell metal-coated colloid particle arrays. After the metal-coated PS array was gently transferred onto another soft PDMS substrate prepared by nonthermal curing, the attached films were thermally cured. After that, both films were carefully separated to selectively transfer the metal-coated PS particle arrays, since the metallic shell on the PS surface can adhere to the soft PDMS. Finally, the PS colloids were removed by plasma etching, leaving behind the 1D hemispherical metallic shells, called here the "metallic nanocup array structure". This structure was evaluated by performing atomic force microscopy, scanning electron microscopy, and X-ray photoelectron spectroscopy measurements. We further demonstrate chemical modification of the inner nanocup surface through construction of a self-assembled monolayer, and we also fill them with nanomaterials (silica nanoparticles) to demonstrate their application to size-selecting devices. The obtained metallic nanocup arrays could be components in a new class of chemical and/or biological nanoreactors with small reaction vessels, surface-enhanced Raman scattering (SERS)-based sensors, and size separators for nanoparticles.

Trends and challenges of refractometric nanoplasmonic biosensors: a review

Motivated by potential benefits such as sensor miniaturization, multiplexing opportunities and higher sensitivities, refractometric nanoplasmonic biosensing has profiled itself in a short time span as an interesting alternative to conventional Surface Plasmon Resonance (SPR) biosensors. This latter conventional sensing concept has been subjected during the last decades to strong commercialization, thereby strongly leaning on well-developed thin-film surface chemistry protocols. Not surprisingly, the examples found in literature based on this sensing concept are generally characterized by extensive analytical studies of relevant clinical and diagnostic problems. In contrast, the more novel Localized Surface Plasmon Resonance (LSPR) alternative finds itself in a much earlier, and especially, more fundamental stage of development. Driven by new fabrication methodologies to create nanostructured substrates, published work typically focuses on the novelty of the presented material, its optical properties and its use - generally limited to a proof-of-concept - as a label-free biosensing scheme. Given the different stages of development both SPR and LSPR sensors find themselves in, it becomes apparent that providing a comparative analysis of both concepts is not a trivial task. Nevertheless, in this review we make an effort to provide an overview that illustrates the progress booked in both fields during the last five years. First, we discuss the most relevant advances in SPR biosensing, including interesting analytical applications, together with different strategies that assure improvements in performance, throughput and/or integration. Subsequently, the remaining part of this work focuses on the use of nanoplasmonic sensors for real label-free biosensing applications. First, we discuss the motivation that serves as a driving force behind this research topic, together with a brief summary that comprises the main fabrication methodologies used in this field. Next, the sensing performance of LSPR sensors is examined by analyzing different parameters that can be invoked in order to quantitatively assess their overall sensing performance. Two aspects are highlighted that turn out to be especially important when trying to maximize their sensing performance, being (1) the targeted functionalization of the electromagnetic hotspots of the nanostructures, and (2) overcoming inherent negative influence that stem from the presence of a high refractive index substrate that supports the nanostructures. Next, although few in numbers, an overview is given of the most exhaustive and diagnostically relevant LSPR sensing assays that have been recently reported in literature, followed by examples that exploit inherent LSPR characteristics in order to create highly integrated and high-throughput optical biosensors. Finally, we discuss a series of considerations that, in our opinion, should be addressed in order to bring the realization of a stand-alone LSPR biosensor with competitive levels of sensitivity, robustness and integration (when compared to a conventional SPR sensor) much closer to reality.

Metamaterials-based label-free nanosensor for conformation and affinity biosensing

Analysis of molecular interaction and conformational dynamics of biomolecules is of paramount importance in understanding their vital functions in complex biological systems, disease detection, and new drug development. Plasmonic biosensors based upon surface plasmon resonance and localized surface plasmon resonance have become the predominant workhorse for detecting accumulated biomass caused by molecular binding events. However, unlike surface-enhanced Raman spectroscopy (SERS), the plasmonic biosensors indeed are not suitable tools to interrogate vibrational signatures of conformational transitions required for biomolecules to interact. Here, we show that highly tunable plasmonic metamaterials can offer two transducing channels for parallel acquisition of optical transmission and sensitive SERS spectra at the biointerface, simultaneously probing the conformational states and binding affinity of biomolecules, e.g., G-quadruplexes, in different environments. We further demonstrate the use of the metamaterials for fingerprinting and detection of the arginine-glycine-glycine domain of nucleolin, a cancer biomarker that specifically binds to a G-quadruplex, with the picomolar sensitivity.