Single-molecule nucleic acid interactions monitored on a label-free microcavity biosensor platform

From radioactive ligands to biosensors: binding methods with olfactory proteins

In this paper, we critically review the binding protocols currently reported in the literature to measure the affinity of odorants and pheromones to soluble olfactory proteins, such as odorant-binding proteins (OBPs), chemosensory proteins (CSPs) and Niemann-Pick class C2 (NPC2) proteins. The first part contains a brief introduction on the principles of binding and a comparison of the techniques adopted or proposed so far, discussing advantages and problems of each technique, as well as their suitable application to soluble olfactory proteins. In the second part, we focus on the fluorescent binding assay, currently the most widely used approach. We analyse advantages and drawbacks, trying to identify the causes of anomalous behaviours that have been occasionally observed, and suggest how to interpret the experimental data when such events occur. In the last part, we describe the state of the art of biosensors for odorants, using soluble olfactory proteins immobilised on biochips, and discuss the possibility of using such approach as an alternative way to measure binding events and dissociation constants.

Compound Glass Microsphere Resonator Devices

In recent years, compound glass microsphere resonator devices have attracted increasing interest and have been widely used in sensing, microsphere lasers, and nonlinear optics. Compared with traditional silica resonators, compound glass microsphere resonators have many significant and attractive properties, such as high-Q factor, an ability to achieve high rare earth ion, wide infrared transmittance, and low phonon energy. This review provides a summary and a critical assessment of the fabrication and the optical characterization of compound glasses and the related fabrication and applications of compound glass microsphere resonators.

Ultrahigh-resolution optical vector analysis using fixed low-frequency electrical phase-magnitude detection

An ultrahigh-resolution optical vector analyzer (OVA) is proposed and experimentally demonstrated based on microwave photonic frequency downconversion and fixed low-frequency electrical phase-magnitude detection. In the proposed OVA, two optical single-sideband (OSSB) signals are generated by two RF signals with a fixed frequency spacing. One propagates through an optical device under test (DUT) and is then combined with the other before entering to a low-speed photodetector. By photodetection, a low-frequency and frequency-fixed photocurrent carrying the spectral responses is achieved. Hence, a low-frequency electrical phase-magnitude detector is sufficient to extract the magnitude and phase. Sweeping the frequency of the RF signals, the spectral responses of the DUT can be obtained. As compared with the conventional OSSB- and optical double-sideband-based OVA, the proposed OVA avoids the use of high-speed photodetection and broadband electrical phase-magnitude detection. In addition, it is inherently immune to the measurement errors induced by high-order sidebands and has the capability of measuring arbitrary spectral responses. In an experiment, the proposed OVA is implemented based on an electrical phase-magnitude detector working at 10 MHz. The measurement resolution is 1 MHz, and the measurement range is larger than 45 GHz.

Light-Driven Nano-oscillators for Label-Free Single-Molecule Monitoring of MicroRNA

Here, we present a mapping tool based on individual light-driven nano-oscillators for label-free single-molecule monitoring of microRNA. This design uses microRNA as a single-molecule damper for nano-oscillators by forming a rigid dual-strand structure in the gap between nano-oscillators and the immobilized surface. The ultrasensitive detection is attributed to comparable dimensions of the gap and microRNA. A developed surface plasmon-coupled scattering imaging technology enables us to directly measure the real-time gap distance vibration of multiple nano-oscillators with high accuracy and fast dynamics. High-level and low-level states of the oscillation amplitude indicate melting and hybridization statuses of microRNA. Lifetimes of two states reveal that the hybridization rate of microRNA is determined by the three-dimensional diffusion. This imaging technique contributes application potentials in a single-molecule detection and nanomechanics study.

Amplifying fluorescence signal contrast of aptamer-modified microspheres inspired by whispering-gallery mode lasing

We propose a new sensor design that maximizes fluorescence contrast, inspired by whispering-gallery mode lasing (WGM). Aptamer-modified glass microspheres (cf. 1-38 μm) and thrombin are used as a model sensory cavity and target protein, respectively. Two types of microsphere are prepared to compare fluorescence contrast: turn-on and turn-off types by using fluorophore-labeled target protein and fluorophore-labeled DNA duplex with thrombin-binding aptamer (TBA), respectively. For the turn-on type, a fluorescence increase was detected in the presence of 100 nM thrombin, but signal amplification upon excitation power did not occur. As for the turn-off type, in the absence of thrombin, fluorophores are densely populated around the microsphere, leading to fluorescence confinement and intensity amplification upon increasing the pump intensity. By adding thrombin, a complementary strand of TBA is dissociated from the microsphere, and the G-quadruplex structure of the thrombin aptamer recognizes and binds to thrombin. As the fluorophore density around the microsphere decreases, fluorescence amplification based on WGM resonance is halted, resulting in 29-fold enhanced contrast under increased excitation power.

On-Chip Spiral Waveguides for Ultrasensitive and Rapid Detection of Nanoscale Objects

Ultrasensitive and rapid detection of nano-objects is crucial in both fundamental studies and practical applications. Optical sensors using evanescent fields in microcavities, plasmonic resonators, and nanofibers allow label-free detection down to single molecules, but practical applications are severely hindered by long response time and device reproducibility. Here, an on-chip dense waveguide sensor to monitor single unlabeled nanoparticles in a strong optical evanescent field is demonstrated. The spiral nanowaveguide design enables two orders of magnitude enhancement in sensing area compared to a straight waveguide, significantly improving the particle capture ability and shortening the target analysis time. In addition, the measurement noise is suppressed to a level of 10^-4 in the transmitted power, pushing the detection limit of single particles down to the size of 100 nm. The waveguide sensor on the silicon-on-isolator platform can be fabricated reproducibly by the conventional semiconductor processing and compatible with surface functionalization chemistries and microfluidics, which could lead to widespread use for sensing in environmental monitoring and human health.

Nanoparticle-Enhanced Plasmonic Biosensor for Digital Biomarker Detection in a Microarray

Nanoplasmonic devices have become a paradigm for biomolecular detection enabled by enhanced light-matter interactions in the fields from biological and pharmaceutical research to medical diagnostics and global health. In this work, we present a bright-field imaging plasmonic biosensor that allows visualization of single subwavelength gold nanoparticles (NPs) on large-area gold nanohole arrays (Au-NHAs). The sensor generates image heatmaps that reveal the locations of single NPs as high-contrast spikes, enabling the detection of individual NP-labeled molecules. We implemented the proposed method in a sandwich immunoassay for the detection of biotinylated bovine serum albumin (bBSA) and human C-reactive protein (CRP), a clinical biomarker of acute inflammatory diseases. Our method can detect 10 pg/mL of bBSA and 27 pg/mL CRP in 2 h, which is at least 4 orders of magnitude lower than the clinically relevant concentrations. Our sensitive and rapid detection approach paired with the robust large-area plasmonic sensor chips, which are fabricated using scalable and low-cost manufacturing, provides a powerful platform for multiplexed biomarker detection in various settings.

Combining Whispering-Gallery Mode Optical Biosensors with Microfluidics for Real-Time Detection of Protein Secretion from Living Cells in Complex Media

The noninvasive monitoring of protein secretion of cells responding to drug treatment is an effective and essential tool in latest drug development and for cytotoxicity assays. In this work, a surface functionalization method is demonstrated for specific detection of protein released from cells and a platform that integrates highly sensitive optical devices, called whispering-gallery mode biosensors, with precise microfluidics control to achieve label-free and real-time detection. Cell biomarker release is measured in real time and with nanomolar sensitivity. The surface functionalization method allows for antibodies to be immobilized on the surface for specific detection, while the microfluidics system enables detection in a continuous flow with a negligible compromise between sensitivity and flow control over stabilization and mixing. Cytochrome c detection is used to illustrate the merits of the system. Jurkat cells are treated with the toxin staurosporine to trigger cell apoptosis and cytochrome c released into the cell culture medium is monitored via the newly invented optical microfluidic platform.

Optofluidic Sensor for Inline Hemolysis Detection on Whole Blood

Hemolysis is the rupture of red blood cells and constitutes the most common reason for unsuitable blood samples in the clinic. To detect hemolysis, one has to separate the hemoglobin in blood plasma from that in red blood cells. However, current methods entail centrifugation for cell-plasma separation, which is complex, time-consuming, and not easy to integrate into point-of-care (PoC) systems. Here, we demonstrate an optofluidic sensor composed of nanofilters on an optical waveguide, which enables evanescent-wave absorption measurement of hemoglobin in plasma with the capability of real-time inline detection on whole blood without extra sample preparation like centrifugation. Long-term testing with inline integration in a modified, commercial blood gas analyzer shows high reliability and repeatability of the measurements even with the presence of interference from bilirubin. We envision that the present work has large potential in improving diagnosis quality by enabling PoC hemolysis detection in blood gas analyzers and can also lend unique sensing capabilities to other applications dealing with complex turbid media.

Advances of Optofluidic Microcavities for Microlasers and Biosensors

Optofluidic microcavities with high Q factor have made rapid progress in recent years by using various micro-structures. On one hand, they are applied to microfluidic lasers with low excitation thresholds. On the other hand, they inspire the innovation of new biosensing devices with excellent performance. In this article, the recent advances in the microlaser research and the biochemical sensing field will be reviewed. The former will be categorized based on the structures of optical resonant cavities such as the Fabry⁻Pérot cavity and whispering gallery mode, and the latter will be classified based on the working principles into active sensors and passive sensors. Moreover, the difficulty of single-chip integration and recent endeavors will be briefly discussed.

Label-Free Optical Biodetection of Pathogen Virulence Factors in Complex Media Using Microtoroids with Multifunctional Surface Functionality

Early detection of pathogens or their virulence factors in complex media has a key role in early diagnosis and treatment of many diseases. Nanomolar and selective detection of Exotoxin A, which is a virulence factor secreted from Pseudomonas aeruginosa in the sputum of Cystic Fibrosis (CF) patients, can pave the way for early diagnosis of P. aeruginosa infections. In this study, we conducted a preliminary study to demonstrate the feasibility of optical biodetection of P. aeruginosa Exotoxin A in a diluted artificial sputum mimicking the CF respiratory environment. Our surface engineering approach provides an effective biointerface enabling highly selective detection of the Exotoxin A molecules in the complex media using monoclonal anti-Exotoxin A functionalized microtoroids. The highly resilient microtoroid surface toward other constituents of the sputum provides Exotoxin A detection ability in the complex media by reproducible measurements. In this study, the limit-of-detection of Exotoxin A in the complex media is calculated as 2.45 nM.

Robust label-free biosensing using microdisk laser arrays with on-chip references

Whispering-gallery mode (WGM) microdisk lasers show great potential for highly sensitive label-free detection in large-scale sensor arrays. However, when used in practical applications under normal ambient conditions, these devices suffer from temperature fluctuations and photobleaching. Here we demonstrate that these challenges can be overcome by a novel referencing scheme that allows for simultaneous compensation of temperature drift and photobleaching. The technique relies on reference structures protected by locally dispensed passivation materials, and can be scaled to extended arrays of hundreds of devices. We prove the viability of the concept in a series of experiments, demonstrating robust and sensitive label-free detection over a wide range of constant or continuously varying temperatures. To the best of our knowledge, these measurements represent the first demonstration of biosensing in active WGM devices with simultaneous compensation of both photobleaching and temperature drift.

High-Q and highly reproducible microdisks and microlasers

High quality (Q) factor microdisks are fundamental building blocks of on-chip integrated photonic circuits and biological sensors. The resonant modes in microdisks circulate near their boundaries, making their performances strongly dependent upon surface roughness. Surface-tension-induced microspheres and microtoroids are superior to other dielectric microdisks when comparing Q factors. However, most photonic materials such as silicon and negative photoresists are hard to be reflowed and thus the realizations of high-Q microdisks are strongly dependent on electron-beam lithography. Herein, we demonstrate a robust, cost-effective, and highly reproducible technique to fabricate ultrahigh-Q microdisks. By using silica microtoroids as masks, we have successfully replicated their ultrasmooth boundaries in a photoresist via anisotropic dry etching. The experimentally recorded Q factors of passive microdisks can be as large as 1.5 × 10⁶. Similarly, ultrahigh Q microdisk lasers have also been replicated in dye-doped polymeric films. The laser linewidth is only 8 pm, which is limited by the spectrometer and is much narrower than that in previous reports. Meanwhile, high-Q deformed microdisks have also been fabricated by controlling the shape of microtoroids, making the internal ray dynamics and external directional laser emissions controllable. Interestingly, this technique also applies to other materials. Silicon microdisks with Q > 10⁶ have been experimentally demonstrated with a similar process. We believe this research will be important for the advances of high-Q micro-resonators and their applications.

Theoretical study on narrow Fano resonance of nanocrescent for the label-free detection of single molecules and single nanoparticles

This paper reports a narrow Fano resonance of 3D nanocrescent and its application in the label-free detection of single molecules. The Fano resonance depends not only on the gap size but also on the height. The Fano resonance originates from the interference between the quadrupolar mode supported by the horizontal crescent and the dipolar mode along the nanotip. When the height of 3D nanocrescent is 30 nm, the width of Fano resonance is as narrow as 10 nm. The narrow linewidth is caused by the strong narrow resonant absorption coming from the dipolar mode of nanotip overlapping with the quadrupolar mode of nanocrescent, where the absorption spectra are calculated under a horizontal incident light. The narrow Fano resonance is highly sensitive to a single nanoparticle trapped by the nanocrescent. The wavelength shift increases linearly with the refractive index with the relation of Δλ = 22.10n - 28.80, and increases with the size of trapped nanoparticle following a relation of Δλ = 0.826 × r 1.672. These results indicate that if a protein nanoparticle with radius of 2.5 nm is trapped by the nanocrescent, the shift is as large as 4.03 nm.

Whispering gallery mode resonator sensor for in situ measurements of hydrogel gelation

Whispering gallery mode (WGM) resonators are compact and ultrasensitive devices, which enable label-free sensing at the single-molecule level. Despite their high sensitivity, WGM resonators have not been thoroughly investigated for use in dynamic biochemical processes including molecular diffusion and polymerization. In this work, the first report of using WGM sensors to continuously monitor a chemical reaction (i.e. gelation) in situ in a hydrogel is described. Specifically, we monitor and quantify the gelation dynamics of polyacrylamide hydrogels using WGM resonators and compare the results to an established measurement method based on rheology. Rheology measures changes in viscoelasticity, while WGM resonators measure changes in refractive index. Different gelation conditions were studied by varying the total monomer concentration and crosslinker concentration of the hydrogel precursor solution, and the resulting similarities and differences in the signal from the WGM resonator and rheology are elucidated. This work demonstrates that WGM alone or in combination with rheology can be used to investigate the gelation dynamics of hydrogels to provide insights into their gelation mechanisms.

Recent Progress of Self-Powered Sensing Systems for Wearable Electronics

Wearable/flexible electronic sensing systems are considered to be one of the key technologies in the next generation of smart personal electronics. To realize personal portable devices with mobile electronics application, i.e., wearable electronic sensors that can work sustainably and continuously without an external power supply are highly desired. The recent progress and advantages of wearable self-powered electronic sensing systems for mobile or personal attachable health monitoring applications are presented. An overview of various types of wearable electronic sensors, including flexible tactile sensors, wearable image sensor array, biological and chemical sensor, temperature sensors, and multifunctional integrated sensing systems is provided. Self-powered sensing systems with integrated energy units are then discussed, separated as energy harvesting self-powered sensing systems, energy storage integrated sensing systems, and all-in-on integrated sensing systems. Finally, the future perspectives of self-powered sensing systems for wearable electronics are discussed.

Sculpting Fano Resonances To Control Photonic-Plasmonic Hybridization

Hybrid photonic-plasmonic systems have tremendous potential as versatile platforms for the study and control of nanoscale light-matter interactions since their respective components have either high-quality factors or low mode volumes. Individual metallic nanoparticles deposited on optical microresonators provide an excellent example where ultrahigh-quality optical whispering-gallery modes can be combined with nanoscopic plasmonic mode volumes to maximize the system's photonic performance. Such optimization, however, is difficult in practice because of the inability to easily measure and tune critical system parameters. In this Letter, we present a general and practical method to determine the coupling strength and tailor the degree of hybridization in composite optical microresonator-plasmonic nanoparticle systems based on experimentally measured absorption spectra. Specifically, we use thermal annealing to control the detuning between a metal nanoparticle's localized surface plasmon resonance and the whispering-gallery modes of an optical microresonator cavity. We demonstrate the ability to sculpt Fano resonance lineshapes in the absorption spectrum and infer system parameters critical to elucidating the underlying photonic-plasmonic hybridization. We show that including decoherence processes is necessary to capture the evolution of the lineshapes. As a result, thermal annealing allows us to directly tune the degree of hybridization and various hybrid mode quantities such as the quality factor and mode volume and ultimately maximize the Purcell factor to be 10⁴.

Broad-Range Electrically Tunable Plasmonic Resonances of a Multilayer Coaxial Nanohole Array with an Electroactive Polymer Wrapper

Plasmonic assemblies featuring high sensitivity that can be readily shifted by external fields are the key for sensitive and versatile sensing devices. In this paper, a novel fast-responsive plasmonic nanocomposite composed of a multilayer nanohole array and a responsive electrochromic polymer is proposed with the plasmonic mode appearance vigorously cycled upon orthogonal electrical stimuli. In this nanocomposite, the coaxially stacked plasmonic nanohole arrays can induce multiple intense Fano resonances, which result from the crosstalk between a broad surface plasmon resonance (SPR) and the designed discrete transmission peaks with ultrahigh sensitivity; the polymer wrapper could provide the sensitive nanohole array with real-time-varied surroundings of refractive indices upon electrical stimuli. Therefore, a pronounced pure electroplasmonic shift up to 72 nm is obtained, which is the largest pure electrotuning SPR range to our knowledge. The stacked nanohole arrays here are also directly used as a working electrode, and they ensure sufficient contact between the working electrode (plasmonic structure) and the electroactive polymer, thus providing considerably improved response speed (within 1 s) for real-time sensing and switching.

Self-Assembled Ti4+@Biospore Microspheres for Sensitive DNA Analysis

Ti⁴⁺ can be chemically adsorbed and assembled on the surface of the modified spore to form highly monodispersed Ti⁴⁺@spore microspheres. Moreover, we for the first time found that these biomicrospheres exhibit differential affinities toward ssDNA and dsDNA. As a principle-of-proof, we exploited the self-assembled Ti⁴⁺@spore microspheres for a hybridization analysis. Interestingly, in the hybridization analysis, residual ssDNA probes are selectively adsorbed on Ti⁴⁺@spore microspheres at pH 5.0 and then removed via centrifugation. By taking advantage of this property, the signal-to-noise ratio for DNA analysis was considerably increased by reducing the noise caused by the residual ssDNA probes. The proposed method features easy operation, high specificity, and sensitivity and thus exhibits potential for further applications on DNA biosensing.

A Guide to Quantitative Biomarker Assay Development using Whispering Gallery Mode Biosensors

Whispering gallery mode (WGM) sensors are a class of powerful analytical techniques defined by the measurement of changes in the local refractive index at or near the sensor surface. When functionalized with target-specific capture agents, analyte binding can be measured with very low limits of detection. There are many geometric manifestations of WGM sensors, with chip-integrated silicon photonic devices first commercialized because of the robust, wafer-scale device fabrication, facile optical interrogation, and amenability to the creation of multiplexed sensor arrays. Using these arrays, a number of biomolecular targets have been detected in both label-free and label-enhanced assay formats. For example, sub-picomolar detection limits for multiple cytokines were achieved using an enzymatically enhanced sandwich immunoassay that showed high analyte specificity suitable for detection in complex, clinical matrices. This protocol describes a generalizable approach for the development of quantitative, multiplexed immunoassays using silicon photonic microrings as an example WGM platform. © 2017 by John Wiley & Sons, Inc.

Single-Molecule Plasmon Sensing: Current Status and Future Prospects

Single-molecule detection has long relied on fluorescent labeling with high quantum-yield fluorophores. Plasmon-enhanced detection circumvents the need for labeling by allowing direct optical detection of weakly emitting and completely nonfluorescent species. This review focuses on recent advances in single molecule detection using plasmonic metal nanostructures as a sensing platform, particularly using a single particle-single molecule approach. In the past decade two mechanisms for plasmon-enhanced single-molecule detection have been demonstrated: (1) by plasmonically enhancing the emission of weakly fluorescent biomolecules, or (2) by monitoring shifts of the plasmon resonance induced by single-molecule interactions. We begin with a motivation regarding the importance of single molecule detection, and advantages plasmonic detection offers. We describe both detection mechanisms and discuss challenges and potential solutions. We finalize by highlighting the exciting possibilities in analytical chemistry and medical diagnostics.

Optical Microresonators for Sensing and Transduction: A Materials Perspective

Optical microresonators confine light to a particular microscale trajectory, are exquisitely sensitive to their microenvironment, and offer convenient readout of their optical properties. Taken together, this is an immensely attractive combination that makes optical microresonators highly effective as sensors and transducers. Meanwhile, advances in material science, fabrication techniques, and photonic sensing strategies endow optical microresonators with new functionalities, unique transduction mechanisms, and in some cases, unparalleled sensitivities. In this progress report, the operating principles of these sensors are reviewed, and different methods of signal transduction are evaluated. Examples are shown of how choice of materials must be suited to the analyte, and how innovations in fabrication and sensing are coupled together in a mutually reinforcing cycle. A tremendously broad range of capabilities of microresonator sensors is described, from electric and magnetic field sensing to mechanical sensing, from single-molecule detection to imaging and spectroscopy, from operation at high vacuum to in live cells. Emerging sensing capabilities are highlighted and put into context in the field. Future directions are imagined, where the diverse capabilities laid out are combined and advances in scalability and integration are implemented, leading to the creation of a sensor unparalleled in sensitivity and information content.

Roadmap on optical sensors

Sensors are devices or systems able to detect, measure and convert magnitudes from any domain to an electrical one. Using light as a probe for optical sensing is one of the most efficient approaches for this purpose. The history of optical sensing using some methods based on absorbance, emissive and florescence properties date back to the 16th century. The field of optical sensors evolved during the following centuries, but it did not achieve maturity until the demonstration of the first laser in 1960. The unique properties of laser light become particularly important in the case of laser-based sensors, whose operation is entirely based upon the direct detection of laser light itself, without relying on any additional mediating device. However, compared with freely propagating light beams, artificially engineered optical fields are in increasing demand for probing samples with very small sizes and/or weak light-matter interaction. Optical fiber sensors constitute a subarea of optical sensors in which fiber technologies are employed. Different types of specialty and photonic crystal fibers provide improved performance and novel sensing concepts. Actually, structurization with wavelength or subwavelength feature size appears as the most efficient way to enhance sensor sensitivity and its detection limit. This leads to the area of micro- and nano-engineered optical sensors. It is expected that the combination of better fabrication techniques and new physical effects may open new and fascinating opportunities in this area. This roadmap on optical sensors addresses different technologies and application areas of the field. Fourteen contributions authored by experts from both industry and academia provide insights into the current state-of-the-art and the challenges faced by researchers currently. Two sections of this paper provide an overview of laser-based and frequency comb-based sensors. Three sections address the area of optical fiber sensors, encompassing both conventional, specialty and photonic crystal fibers. Several other sections are dedicated to micro- and nano-engineered sensors, including whispering-gallery mode and plasmonic sensors. The uses of optical sensors in chemical, biological and biomedical areas are described in other sections. Different approaches required to satisfy applications at visible, infrared and THz spectral regions are also discussed. Advances in science and technology required to meet challenges faced in each of these areas are addressed, together with suggestions on how the field could evolve in the near future.

Gold-silver alloy semi-nanoshell arrays for label-free plasmonic biosensors

Nanosphere lithography coupled with reactive ion etching has been used to synthesize hexagonal ordered arrays of Au-Ag bimetallic semi-nanoshells to be used as plasmonic biosensors. The degree of lateral interaction between adjacent semi-nanoshells can be controlled by tailoring the reactive ion etching time in order to boost the global plasmonic properties through the formation of near-field hot-spots, which in turn can improve the sensitivity of the biosensors. To test the efficiency of the proposed system as a biosensor, we used an established protocol for the detection of biomolecules (local sensitivity), based on the receptor-ligand approach and using the biotin-streptavidin model system. We also tested the sensitivity to a homogeneous change in the refractive index of the buffer over the sensor (bulk sensitivity). Comparing the obtained results to those of an array of nanoprisms, chosen as a benchmark, significantly higher performances both in local and bulk sensitivities have been found, in agreement with electrodynamics simulations based on finite-element methods.

Optics-Integrated Microfluidic Platforms for Biomolecular Analyses

Compared with conventional optical methods, optics implemented on microfluidic chips provide small, and often much cheaper ways to interrogate biological systems from the level of single molecules up to small model organisms. The optical probing of single molecules has been used to investigate the mechanical properties of individual biological molecules; however, multiplexing of these measurements through microfluidics and nanofluidics confers many analytical advantages. Optics-integrated microfluidic systems can significantly simplify sample processing and allow a more user-friendly experience; alignments of on-chip optical components are predetermined during fabrication and many purely optical techniques are passively controlled. Furthermore, sample loss from complicated preparation and fluid transfer steps can be virtually eliminated, a particularly important attribute for biological molecules at very low concentrations. Excellent fluid handling and high surface area/volume ratios also contribute to faster detection times for low abundance molecules in small sample volumes. Although integration of optical systems with classical microfluidic analysis techniques has been limited, microfluidics offers a ready platform for interrogation of biophysical properties. By exploiting the ease with which fluids and particles can be precisely and dynamically controlled in microfluidic devices, optical sensors capable of unique imaging modes, single molecule manipulation, and detection of minute changes in concentration of an analyte are possible.

Photonic-plasmonic hybrid single-molecule nanosensor measures the effect of fluorescent labels on DNA-protein dynamics

Current methods to study molecular interactions require labeling the subject molecules with fluorescent reporters. However, the effect of the fluorescent reporters on molecular dynamics has not been quantified because of a lack of alternative methods. We develop a hybrid photonic-plasmonic antenna-in-a-nanocavity single-molecule biosensor to study DNA-protein dynamics without using fluorescent labels. Our results indicate that the fluorescein and fluorescent protein labels decrease the interaction between a single DNA and a protein due to weakened electrostatic interaction. Although the study is performed on the DNA-XPA system, the conclusion has a general implication that the traditional fluorescent labeling methods might be misestimating the molecular interactions.

Nanophotonic label-free biosensors for environmental monitoring

The field of environmental monitoring has experienced a substantial progress in the last years but still the on-site control of contaminants is an elusive problem. In addition, the growing number of pollutant sources is accompanied by an increasing need of having efficient early warning systems. Several years ago biosensor devices emerged as promising environmental monitoring tools, but their level of miniaturization and their fully operation outside the laboratory prevented their use on-site. In the last period, nanophotonic biosensors based on evanescent sensing have emerged as an outstanding choice for portable point-of-care diagnosis thanks to their capability, among others, of miniaturization, multiplexing, label-free detection and integration in lab-on-chip platforms. This review covers the most relevant nanophotonic biosensors which have been proposed (including interferometric waveguides, grating-couplers, microcavity resonators, photonic crystals and localized surface plasmon resonance sensors) and their recent application for environmental surveillance.

Size-optimized polymeric whispering gallery mode lasers with enhanced sensing performance

Integration of optically active materials into whispering gallery mode (WGM) cavities enables low-threshold laser emission. In contrast to their passive counterparts, the WGMs of these microlasers can be pumped and read out easily via free-space optics. The WGMs interact with the cavity environment via their evanescent field, and thus lend themselves to label-free bio-sensing. The detection limit of such sensors, given as the ratio of the resolution of the whole measurement system to the sensitivity of the WGMs, is an important figure of merit. In this work we show that the detection limit of polymeric microdisk lasers can be improved by more than a factor of seven by optimizing their radius and thickness. We use the bulk refractive index sensitivity, the magnitude of the sensor reaction towards refractive index changes of the bulk environment, to quantify the sensing performance and show that it can be enhanced while the spectral resolution is maintained. Furthermore, we investigate the effect of the size of the cavity on the quality factor and the lasing threshold in an aqueous environment, hence allowing optimization of the cavity size for enhanced sensor performance. For all considered quantities, numerically computed expectations are verified by experimental results.

Towards next-generation label-free biosensors: recent advances in whispering gallery mode sensors

Whispering gallery mode biosensors have been widely exploited over the past decade to study molecular interactions by virtue of their high sensitivity and applicability in real-time kinetic analysis without the requirement to label. There have been immense research efforts made for advancing the instrumentation as well as the design of detection assays, with the common goal of progressing towards real-world sensing applications. We therefore review a set of recent developments made in this field and discuss the requirements that whispering gallery mode label-free sensors need to fulfill for making a real world impact outside of the laboratory. These requirements are directly related to the challenges that these sensors face, and the methods proposed to overcome them are discussed. Moving forward, we provide the future prospects and the potential impact of this technology.

Sandwich-structure-modulated photoluminescence enhancement of wide bandgap semiconductors capping with dielectric microsphere arrays

Here we investigated the effect of substrate and film thickness on photoluminescence (PL) enhancement of wide bandgap semiconductor (i.e. ZnO) by dielectric microsphere array/luminescence film/substrate (MLS) sandwich structures. The PL enhancement channels in the sandwich structure were revealed, for the first time, including the focusing property of microsphere array (MSA) distinctly enhancing free-exciton recombination, anti-reflection effect of MSA increasing excitation cross-section area, MLS-supported TW-/SW-WGMs inducing ASE and Purcell's effect, and optical directional antenna effect for high equivalent NA of objective lens as well as out-coupling efficiency. The enhancement ratio of intensity (ERI) for ZnO UV-PL from free-exciton recombination in the sandwich structure was found to be strongly dependent upon the refractive index of substrate and luminescence film thickness. In order to achieve high ERI for PL emission, the refractive index of substrate should differ from luminescence film and the film thickness needs to be chosen to support WGMs in the sandwich structure. The maximum ERI beyond one order of magnitude for ZnO UV-PL was therefore predicted theoretically and validated experimentally, where 11.25-fold UV PL enhancement ratio was achieved in ~650-nm-thick ZnO film grown on SiC substrate and capped with 5.06-μm-diameter MSA. The ERI could further be increased by improving above-mentioned enhancement channels. The present work provides a novel platform to manipulate light by low-loss dielectric microstructures for enhancing photon-matter interaction, which would be employed for other semiconductors achieving energy-saving luminescence and high-sensitivity photoelectric detection in future.

Wafer-scale arrays of high-Q silica optical microcavities

On-chip high-Q microcavities possess significant potential in terms of integration of optical microresonators into functional optoelectronic devices that could be used in various applications, including biosensors, photonic-integrated circuits, or quantum optics experiments. Yet, despite the convenience of fabricating wafer-scale integrated microresonators with moderate Q values using standard microfabrication techniques, surface-tension-induced microcavities (STIMs), which have atomic-level surface roughness enabling the observation of Q values larger than 10⁶, could only be produced using individual thermal treatment of every single microresonator within the devised area. Here, we demonstrate a facile method for large-scale fabrication of silica STIMs of various morphologies. Q values exceeding 10⁶ are readily obtained using this technique. This study represents a significant advancement toward fabrication of wafer-scale optoelectronic circuitries.

Biological sensing and control of emission dynamics of quantum dot bioconjugates using arrays of long metallic nanorods

We study biological sensing using plasmonic and photonic-plasmonic resonances of arrays of ultralong metallic nanorods and analyze the impact of these resonances on emission dynamics of quantum dot bioconjugates. We demonstrate that the LSPRs and plasmonic lattice modes of such array can be used to detect a single self-assembled monolayer of alkanethiol at the visible (550 nm) and near infrared (770 nm) range with well resolved shifts. We study adsorption of streptavidin-quantum dot conjugates to this monolayer, demonstrating that formation of nearly two dimensional arrays of quantum dots with limited emission blinking can lead to extra well-defined wavelength shifts in these modes. Using spectrally-resolved lifetime measurements we study the emission dynamics of such quantum dot bioconjugates within their monodispersed size distribution. We show that, despite their close vicinity to the nanorods, the rate of energy transfer from these quantum dots to nanorods is rather weak, while the plasmon field enhancement can be strong. Our results reveal that the nanorods present a strongly wavelength or size-dependent non-radiative decay channel to the quantum dot bioconjugates.

Label-Free Biological and Chemical Sensing Using Whispering Gallery Mode Optical Resonators: Past, Present, and Future

Sensitive and rapid label-free biological and chemical sensors are needed for a wide variety of applications including early disease diagnosis and prognosis, the monitoring of food and water quality, as well as the detection of bacteria and viruses for public health concerns and chemical threat sensing. Whispering gallery mode optical resonator based sensing is a rapidly developing field due to the high sensitivity and speed of these devices as well as their label-free nature. Here, we describe the history of whispering gallery mode optical resonator sensors, the principles behind detection, the latest developments in the fields of biological and chemical sensing, current challenges toward widespread adoption of these devices, and an outlook for the future. In addition, we evaluate the performance capabilities of these sensors across three key parameters: sensitivity, selectivity, and speed.

Label-free optical detection of single enzyme-reactant reactions and associated conformational changes

Monitoring the kinetics and conformational dynamics of single enzymes is crucial to better understand their biological functions because these motions and structural dynamics are usually unsynchronized among the molecules. However, detecting the enzyme-reactant interactions and associated conformational changes of the enzyme on a single-molecule basis remains as a challenge to established optical techniques because of the commonly required labeling of the reactants or the enzyme itself. The labeling process is usually nontrivial, and the labels themselves might skew the physical properties of the enzyme. We demonstrate an optical, label-free method capable of observing enzymatic interactions and associated conformational changes on a single-molecule level. We monitor polymerase/DNA interactions via the strong near-field enhancement provided by plasmonic nanorods resonantly coupled to whispering gallery modes in microcavities. Specifically, we use two different recognition schemes: one in which the kinetics of polymerase/DNA interactions are probed in the vicinity of DNA-functionalized nanorods, and the other in which these interactions are probed via the magnitude of conformational changes in the polymerase molecules immobilized on nanorods. In both approaches, we find that low and high polymerase activities can be clearly discerned through their characteristic signal amplitude and signal length distributions. Furthermore, the thermodynamic study of the monitored interactions suggests the occurrence of DNA polymerization. This work constitutes a proof-of-concept study of enzymatic activities using plasmonically enhanced microcavities and establishes an alternative and label-free method capable of investigating structural changes in single molecules.

Whispering gallery mode single nanoparticle detection and sizing: the validity of the dipole approximation

Interactions between whispering gallery modes (WGMs) and small nanoparticles are commonly modeled by treating the particle as a point dipole scatterer. This approach is assumed to be accurate as long as the nanoparticle radius, a, is small compared to the WGM wavelength λ. In this Letter, however, we show that the large field gradients associated with the evanescent decay of a WGM causes the dipole theory to significantly underestimate the interaction strength and, hence, the induced WGM resonance shift, even for particles as small as a∼λ/10. To mitigate this issue, we employ a renormalized Born approximation to more accurately determine nanoparticle-induced resonance shifts and, hence, enable improved particle sizing. The domain of validity of this approximation is investigated, and supporting experimental results are presented.

Single Nanoparticle Detection Using Optical Microcavities

Detection of nanoscale objects is highly desirable in various fields such as early-stage disease diagnosis, environmental monitoring and homeland security. Optical microcavity sensors are renowned for ultrahigh sensitivities due to strongly enhanced light-matter interaction. This review focuses on single nanoparticle detection using optical whispering gallery microcavities and photonic crystal microcavities, both of which have been developing rapidly over the past few years. The reactive and dissipative sensing methods, characterized by light-analyte interactions, are explained explicitly. The sensitivity and the detection limit are essentially determined by the cavity properties, and are limited by the various noise sources in the measurements. On the one hand, recent advances include significant sensitivity enhancement using techniques to construct novel microcavity structures with reduced mode volumes, to localize the mode field, or to introduce optical gain. On the other hand, researchers attempt to lower the detection limit by improving the spectral resolution, which can be implemented by suppressing the experimental noises. We also review the methods of achieving a better temporal resolution by employing mode locking techniques or cavity ring up spectroscopy. In conclusion, outlooks on the possible ways to implement microcavity-based sensing devices and potential applications are provided.

Hybrid plasmonic–photonic whispering gallery mode resonators for sensing: a critical review

In this review we present the state of the art and the most recent advances in the field of optical sensing with hybrid plasmonic–photonic whispering gallery mode (WGM) resonators.

Plasmonic Fiber Optic Refractometric Sensors: From Conventional Architectures to Recent Design Trends

Surface Plasmon Resonance (SPR) fiber sensor research has grown since the first demonstration over 20 year ago into a rich and diverse field with a wide range of optical fiber architectures, plasmonic coatings, and excitation and interrogation methods. Yet, the large diversity of SPR fiber sensor designs has made it difficult to understand the advantages of each approach. Here, we review SPR fiber sensor architectures, covering the latest developments from optical fiber geometries to plasmonic coatings. By developing a systematic approach to fiber-based SPR designs, we identify and discuss future research opportunities based on a performance comparison of the different approaches for sensing applications.

Coupling the normal incident light into waveguide modes of DBR mirrors via a diffraction grating

Here we numerically and experimentally demonstrate the conversion of normally incident light into the guiding modes of distributed Bragg reflector (DBRs) mirror. By fabricating a gold grating onto a 7.5 pairs TiO₂/SiO₂ DBR mirror, a series of asymmetrical resonances have been formed at the bandgap range of the DBR mirror. The detailed numerical calculations show that these Fano resonances are attributed to the coupling of incident waves into guiding modes of the DBR mirror. Compared with the other resonances, this coupling mechanism can be simply realized and it has also been revealed to be quite robust to the environmental changes, making the conversion between propagating waves and guiding waves to be practically interesting for many applications.

In Situ Observation of Single-Molecule Surface Reactions from Low to High Affinities

In situ observation of single-molecule surface reactions from low to high affinities is achieved by resonant coupling between optical whispering-gallery modes and the localized surface plasmon of nanorods. Transient and permanent interactions between ligands (thiol, amine) and the gold surface are monitored without labels, allowing direct determination of the associated kinetic constants and rapid development of new functionalization protocols.

Mesoporous nanospheres functionalized optical microfiber biosensor for low concentration neurotransmitter detection

A label-free and ultrasensitive microfiber interferometer biosensor has been demonstrated for detection of neurotransmitter molecule (5-HT). The surface morphology of the silicon dioxide nanospheres acting as molecule sieve provides an effective mean of gathering 5-HT molecules by designed mesoporous structure. The slight concentration change of 5-HT molecules is translated into a dramatic wavelength shift of the interferometric fringe pattern. The experimental results show that the biosensor has a linear response in concentration range from 100 fM to 1 µM and a detection limit as low as 84 fM.

Phone-sized whispering-gallery microresonator sensing system

We develop a compact whispering-gallery-mode (WGM) sensing system by integrating multiple components, including a tunable laser, a temperature controller, a function generator, an oscilloscope, a photodiode detector, and a testing computer, into a phone-sized embedded system. We demonstrate a thermal sensing experiment by using this portable system. Such a system successfully eliminates bulky measurement equipment required for characterizing optical resonators and will open up new avenues for practical sensing applications by using ultra-high Q WGM resonators.

M-DNA/Transition Metal Dichalcogenide Hybrid Structure-based Bio-FET sensor with Ultra-high Sensitivity

Here, we report a high performance biosensor based on (i) a Cu²⁺-DNA/MoS₂ hybrid structure and (ii) a field effect transistor, which we refer to as a bio-FET, presenting a high sensitivity of 1.7 × 10³ A/A. This high sensitivity was achieved by using a DNA nanostructure with copper ions (Cu²⁺) that induced a positive polarity in the DNA (receptor). This strategy improved the detecting ability for doxorubicin-like molecules (target) that have a negative polarity. Very short distance between the biomolecules and the sensor surface was obtained without using a dielectric layer, contributing to the high sensitivity. We first investigated the effect of doxorubicin on DNA/MoS₂ and Cu²⁺-DNA/MoS₂ nanostructures using Raman spectroscopy and Kelvin force probe microscopy. Then, we analyzed the sensing mechanism and performance in DNA/MoS₂- and Cu²⁺-DNA/MoS₂-based bio-FETs by electrical measurements (I_D-V_G at various V_D) for various concentrations of doxorubicin. Finally, successful operation of the Cu²⁺-DNA/MoS₂ bio-FET was demonstrated for six cycles (each cycle consisted of four steps: 2 preparation steps, a sensing step, and an erasing step) with different doxorubicin concentrations. The bio-FET showed excellent reusability, which has not been achieved previously in 2D biosensors.

High-Q silk fibroin whispering gallery microresonator

We have experimentally demonstrated an on-chip all-silk fibroin whispering gallery mode microresonator by using a simple molding and solution-casting technique. The quality factors of the fabricated silk protein microresonators are on the order of 10⁵. A high-sensitivity thermal sensor was realized in this silk fibroin microtoroid with a sensitivity of -1.17 nm/K, that is 8 times higher than previous WGM resonator-based thermal sensors. This opens the way to fabricate biodegradable and biocompatible protein based microresonators on a flexible chip for biophotonics applications.

Performance and noise analysis of optical microresonator-based biochemical sensors using intensity detection

Optical microcavity sensors using intensity detection open up the possibility to realize fully integrated high-performance sensing devices, which are significant for both fundamental study of molecular interaction and rapid disease diagnosis. Although the performance of microresonator-based sensors has been studied focusing on the resonance-tracking method, the situation can be much different for intensity-detection sensors. Here we conducted a systematically investigation on the noises sources in intensity detection scheme and their influences on key performance parameters, e.g., signal-to-noise ratio (SNR), limit-of-detection (LOD), and detection range, for various sensors configurations. Especially, the trade-off between SNR and LOD is identified and theoretically analyzed. With experiment noises taken into consideration, our work aims to provide design guidelines for integrated microresonator sensors with optimized performance.

Integrating a DNA Strand Displacement Reaction with a Whispering Gallery Mode Sensor for Label-Free Mercury (II) Ion Detection

Mercury is an extremely toxic chemical pollutant of our environment. It has attracted the world’s attention due to its high mobility and the ease with which it accumulates in organisms. Sensitive devices and methods specific for detecting mercury ions are, hence, in great need. Here, we have integrated a DNA strand displacement reaction with a whispering gallery mode (WGM) sensor for demonstrating the detection of Hg²⁺ ions. Our approach relies on the displacement of a DNA hairpin structure, which forms after the binding of mercury ions to an aptamer DNA sequence. The strand displacement reaction of the DNA aptamer provides highly specific and quantitative means for determining the mercury ion concentration on a label-free WGM sensor platform. Our approach also shows the possibility for manipulating the kinetics of a strand displacement reaction with specific ionic species.