Integrated planar optical waveguide interferometer biosensors: A comparative review

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

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

Optical biosensors: an exhaustive and comprehensive review

Optical biosensors have exhibited worthwhile performance in detecting biological systems and promoting significant advances in clinical diagnostics, drug discovery, food process control, and environmental monitoring. Without complexity in their pretreatment and probable influence on the nature of target molecules, these biosensors have additional advantages such as high sensitivity, robustness, reliability, and potential to be integrated on a single chip. In this review, the state of the art optical biosensor technologies, including those based on surface plasmon resonance (SPR), optical waveguides, optical resonators, photonic crystals, and optical fibers, are presented. The principles for each type of biosensor are concisely introduced and particular emphasis has been placed on recent achievements. The strengths and weaknesses of each type of biosensor have been outlined as well. Concluding remarks regarding the perspectives of future developments are discussed.

Optical Biosensors for the Detection of Rheumatoid Arthritis (RA) Biomarkers: A Comprehensive Review

A comprehensive review of optical biosensors for the detection of biomarkers associated with rheumatoid arthritis (RA) is presented here, including microRNAs (miRNAs), C-reactive protein (CRP), rheumatoid factor (RF), anti-citrullinated protein antibodies (ACPA), interleukin-6 (IL-6) and histidine, which are biomarkers that enable RA detection and/or monitoring. An overview of the different optical biosensors (based on fluorescence, plasmon resonances, interferometry, surface-enhanced Raman spectroscopy (SERS) among other optical techniques) used to detect these biomarkers is given, describing their performance and main characteristics (limit of detection (LOD) and dynamic range), as well as the connection between the respective biomarker and rheumatoid arthritis. It has been observed that the relationship between the corresponding biomarker and rheumatoid arthritis tends to be obviated most of the time when explaining the mechanism of the optical biosensor, which forces the researcher to look for further information about the biomarker. This review work attempts to establish a clear association between optical sensors and rheumatoid arthritis biomarkers as well as to be an easy-to-use tool for the researchers working in this field.

Label-Free Optical Resonator-Based Biosensors

The demand for biosensor technology has grown drastically over the last few decades, mainly in disease diagnosis, drug development, and environmental health and safety. Optical resonator-based biosensors have been widely exploited to achieve highly sensitive, rapid, and label-free detection of biological analytes. The advancements in microfluidic and micro/nanofabrication technologies allow them to be miniaturized and simultaneously detect various analytes in a small sample volume. By virtue of these advantages and advancements, the optical resonator-based biosensor is considered a promising platform not only for general medical diagnostics but also for point-of-care applications. This review aims to provide an overview of recent progresses in label-free optical resonator-based biosensors published mostly over the last 5 years. We categorized them into Fabry-Perot interferometer-based and whispering gallery mode-based biosensors. The principles behind each biosensor are concisely introduced, and recent progresses in configurations, materials, test setup, and light confinement methods are described. Finally, the current challenges and future research topics of the optical resonator-based biosensor are discussed.

SPR Biosensor Based on Polymer Multi-Mode Optical Waveguide and Nanoparticle Signal Enhancement

We present a surface plasmon resonance (SPR) biosensor that is based on a planar-optical multi-mode (MM) polymer waveguide structure applied for the detection of biomolecules in the lower nano-molar (nM) range. The basic sensor shows a sensitivity of 608.6 nm/RIU when exposed to refractive index changes with a measurement resolution of 4.3 × 10-3 RIU. By combining the SPR sensor with an aptamer-functionalized, gold-nanoparticle (AuNP)-enhanced sandwich assay, the detection of C-reactive protein (CRP) in a buffer solution was achieved with a response of 0.118 nm/nM. Due to the multi-mode polymer waveguide structure and the simple concept, the reported biosensor is well suited for low-cost disposable lab-on-a-chip applications and can be used with rather simple and economic devices. In particular, the sensor offers the potential for fast and multiplexed detection of several biomarkers on a single integrated platform.

A Review on the Role of Nanosensors in Detecting Cellular miRNA Expression in Colorectal Cancer

BACKGROUND

Colorectal cancer (CRC) is one of the leading causes of death across the globe. Early diagnosis with high sensitivity can prevent CRC progression, thereby reducing the condition of metastasis.

OBJECTIVE

The purpose of this review is (i) to discuss miRNA based biomarkers responsible for CRC, (ii) to brief on the different methods used for the detection of miRNA in CRC, (iii) to discuss different nanobiosensors so far found for the accurate detection of miRNAs in CRC using spectrophotometric detection, piezoelectric detection.

METHODS

The keywords for the review like micro RNA detection in inflammation, colorectal cancer, nanotechnology, were searched in PubMed and the relevant papers on the topics of miRNA related to CRC, nanotechnology-based biosensors for miRNA detection were then sorted and used appropriately for writing the review.

RESULTS

The review comprises a general introduction explaining the current scenario of CRC, the biomarkers used for the detection of different cancers, especially CRC and the importance of nanotechnology and a general scheme of a biosensor. The further subsections discuss the mechanism of CRC progression, the role of miRNA in CRC progression and different nanotechnology-based biosensors so far investigated for miRNA detection in other diseases, cancer and CRC. A scheme depicting miRNA detection using gold nanoparticles (AuNPs) is also illustrated.

CONCLUSION

This review may give insight into the different nanostructures, like AuNPs, quantum dots, silver nanoparticles, MoS2derived nanoparticles, etc., based approaches for miRNA detection using biosensors.

Critical assessment of relevant methods in the field of biosensors with direct optical detection based on fibers and waveguides using plasmonic, resonance, and interference effects

Direct optical detection has proven to be a highly interesting tool in biomolecular interaction analysis to be used in drug discovery, ligand/receptor interactions, environmental analysis, clinical diagnostics, screening of large data volumes in immunology, cancer therapy, or personalized medicine. In this review, the fundamental optical principles and applications are reviewed. Devices are based on concepts such as refractometry, evanescent field, waveguides modes, reflectometry, resonance and/or interference. They are realized in ring resonators; prism couplers; surface plasmon resonance; resonant mirror; Bragg grating; grating couplers; photonic crystals, Mach-Zehnder, Young, Hartman interferometers; backscattering; ellipsometry; or reflectance interferometry. The physical theories of various optical principles have already been reviewed in detail elsewhere and are therefore only cited. This review provides an overall survey on the application of these methods in direct optical biosensing. The "historical" development of the main principles is given to understand the various, and sometimes only slightly modified variations published as "new" methods or the use of a new acronym and commercialization by different companies. Improvement of optics is only one way to increase the quality of biosensors. Additional essential aspects are the surface modification of transducers, immobilization strategies, selection of recognition elements, the influence of non-specific interaction, selectivity, and sensitivity. Furthermore, papers use for reporting minimal amounts of detectable analyte terms such as value of mass, moles, grams, or mol/L which are difficult to compare. Both these essential aspects (i.e., biochemistry and the presentation of LOD values) can be discussed only in brief (but references are provided) in order to prevent the paper from becoming too long. The review will concentrate on a comparison of the optical methods, their application, and the resulting bioanalytical quality.

External Cavity Quantum Cascade Laser-Based Mid-Infrared Dispersion Spectroscopy for Qualitative and Quantitative Analysis of Liquid-Phase Samples

Acquisition of classical absorption spectra of liquids in the mid-IR range with quantum cascade lasers (QCLs) is often limited in sensitivity by noise from the laser source. Alternatively, measurement of molecular dispersion (i.e., refractive index) spectra poses an experimental approach that is immune to intensity fluctuations and further offers a direct relationship between the recorded signal and the sample concentration. In this work, we present an external cavity quantum cascade laser (EC-QCL) based Mach-Zehnder interferometer setup to determine dispersion spectra of liquid samples. We present two approaches for acquisition of refractive index spectra and compare the qualitative experimental results. Furthermore, the performance for quantitative analysis is evaluated. Finally, multivariate analysis of a spectrally complex mixture comprising three different sugars is performed. The obtained figures of merit by partial least squares (PLS) regression modelling compare well with standard absorption spectroscopy, demonstrating the potential of the introduced dispersion spectroscopic method for quantitative chemical analysis.

Vertically Coupled Plasmonic Racetrack Ring Resonator for Biosensor Applications

Plasmonic chemical and biological sensors offer significant advantages such as really compact sizes and extremely high sensitivity. Biosensors based on plasmonic waveguides and resonators are some of the most attractive candidates for mobile and wearable devices. However, high losses in the metal and complicated schemes for practical implementation make it challenging to find the optimal configuration of a compact plasmon biosensor. Here, we propose a novel plasmonic refractive index sensor based on a metal strip waveguide placed under a waveguide-based racetrack ring resonator made of the same metal. This scheme guarantees effective coupling between the waveguide and resonator and low loss light transmittance through the long-range waveguide. The proposed device can be easily fabricated (e.g., using optical lithography) and integrated with materials like graphene oxide for providing adsorption of the biomolecules on the sensitive part of the optical elements. To analyze the properties of the designed sensing system, we performed numerical simulations along with some analytical estimations. There is one other interesting general feature of this sensing scheme that is worth pointing out before looking at its details. The sensitivity of the considered device can be significantly increased by surrounding the resonator with media of slightly different refractive indices, which allows sensitivity to reach a value of more than 1 μm per refractive index unit.

Label-Free MicroRNA Optical Biosensors

MicroRNAs (miRNAs) play crucial roles in regulating gene expression. Many studies show that miRNAs have been linked to almost all kinds of disease. In addition, miRNAs are well preserved in a variety of specimens, thereby making them ideal biomarkers for biosensing applications when compared to traditional protein biomarkers. Conventional biosensors for miRNA require fluorescent labeling, which is complicated, time-consuming, laborious, costly, and exhibits low sensitivity. The detection of miRNA remains a big challenge due to their intrinsic properties such as small sizes, low abundance, and high sequence similarity. A label-free biosensor can simplify the assay and enable the direct detection of miRNA. The optical approach for a label-free miRNA sensor is very promising and many assays have demonstrated ultra-sensitivity (aM) with a fast response time. Here, we review the most relevant label-free microRNA optical biosensors and the nanomaterials used to enhance the performance of the optical biosensors.

Highly sensitive label-free in vitro detection of aflatoxin B1 in an aptamer assay using optical planar waveguide operating as a polarization interferometer

This work reports on further development of an optical biosensor for the in vitro detection of mycotoxins (in particular, aflatoxin B1) using a highly sensitive planar waveguide transducer in combination with a highly specific aptamer bioreceptor. This sensor is built on a SiO2-Si3N4-SiO2 optical planar waveguide (OPW) operating as a polarization interferometer (PI), which detects a phase shift between p- and s-components of polarized light propagating through the waveguide caused by the molecular adsorption. The refractive index sensitivity (RIS) of the recently upgraded PI experimental setup has been improved and reached values of around 9600 rad per refractive index unity (RIU), the highest RIS values reported, which enables the detection of low molecular weight analytes such as mycotoxins in very low concentrations. The biosensing tests yielded remarkable results for the detection of aflatoxin B1 in a wide range of concentrations from 1 pg/mL to 1 μg/mL in direct assay with specific DNA-based aptamers. Graphical abstract Optical planar waveguide polarization interferometry biosensor for detection of aflatoxin B1 using specific aptamer.

Experimental study of subwavelength grating bimodal waveguides as ultrasensitive interferometric sensors

Over the recent years, subwavelength grating (SWG) structures have increasingly attracted attention in the area of evanescent-field photonic sensors. In this Letter, for the first time to the best of our knowledge, we demonstrate experimentally the real-time refractive index (RI) sensing using the SWG bimodal interferometric structures. Two different configurations are considered to compare the effect of the nonlinear phase shift, obtained between the two first transverse electromagnetic propagating modes, in the measured bulk sensitivity. Very high experimental values up to 2270 nm/RIU are reached, which perfectly match the numerical simulations and significantly enhance other existing SWG and spectral-based sensors. By measuring the spectral shift, the obtained experimental sensitivity does not depend on the sensor length. As a result, a highly sensitive and compact single-channel interferometer is experimentally validated for refractive index sensing, thus opening new paths in the field of optical integrated sensors.

Integrated multichannel Young's interferometer sensor based on long-range surface plasmon waveguides

Two integrated Young's interferometer (YI) sensors based on long-range surface plasmon polariton (LRSPP) waveguides are presented. The first sensor is single-channel and based on a Y-junction splitter, and the other is multi-channel and based on a corporate feed structure. The multichannel YI enables simultaneous and independent phase-based monitoring of refractive index changes in multiple channels. The diverging output beams from the waveguides are overlapped in the far field to form interference patterns which are then post-processed using the fast Fourier transform (FFT) algorithm to extract phase values. The sensing capability of these YIs was demonstrated through sequential injection of solutions with increasing refractive index into the sensing channels. A detection limit of ∼ 1 × 10^-6 RIU was obtained for both LRSPP based YIs, a significant improvement over measurements from similar structures using attenuation-based sensing.

Soft and Stretchable Polymeric Optical Waveguide-Based Sensors for Wearable and Biomedical Applications

The past decades have witnessed the rapid development in soft, stretchable, and biocompatible devices for applications in biomedical monitoring, personal healthcare, and human-machine interfaces. In particular, the design of soft devices in optics has attracted tremendous interests attributed to their distinct advantages such as inherent electrical safety, high stability in long-term operation, potential to be miniaturized, and free of electromagnetic interferences. As the alternatives to conventional rigid optical waveguides, considerable efforts have been made to develop light-guiding devices by using various transparent and elastic polymers, which offer desired physiomechanical properties and enable wearable/implantable applications in optical sensing, diagnostics, and therapy. Here, we review recent progress in soft and stretchable optical waveguides and sensors, including advanced structural design, fabrication strategies, and functionalities. Furthermore, the potential applications of those optical devices for various wearable and biomedical applications are discussed. It is expected that the newly emerged soft and stretchable optical technologies will provide a safe and reliable alternative to next-generation, smart wearables and healthcare devices.

Resonant Grating without a Planar Waveguide Layer as a Refractive Index Sensor

Dielectric grating-based sensors are usually based on the guided mode resonance (GMR) obtained using a thin planar waveguide layer (PWL) adjacent to a thin subwavelength grating layer. In this work, we present a detailed investigation of thick subwavelength dielectric grating structures that exhibit reflection resonances above a certain thickness without the need for the waveguide layer, showing great potential for applications in biosensing and tunable filtering. Analytic and numerical results are thoroughly discussed, as well as an experimental demonstration of the structure as a chemical sensor in the SWIR (short wave infrared) spectral range (1200-1800 nm). In comparison to the GMR structure with PWL, the thick grating structure has several unique properties: (i) It gives higher sensitivity when the spaces are filled, with the analyte peaking at certain space values due to an increase in the interaction volume between the analyte and the evanescent optical field between the grating lines; (ii) the TM (transverse magnetic) resonance, in certain cases, provides a better figure of merit; (iii) the sensitivity increases as the grating height increases; (iii) the prediction of the resonance locations based on the effective medium approximation does not give satisfactory results when the grating height is larger than a certain value, and the invalidity becomes more severe as the period increases; (iv) a sudden increase in the Q-factor of the resonance occurs at a specific height value accompanied by the high local field enhancement (~10³) characteristic of a nano-antenna type pattern. Rigorous numerical simulations of the field distribution are presented to explain the different observed phenomena.

Three-Dimensional Microtubular Devices for Lab-on-a-Chip Sensing Applications

The rapid advance of micro-/nanofabrication technologies opens up new opportunities for miniaturized sensing devices based on novel three-dimensional (3D) architectures. Notably, microtubular geometry exhibits natural advantages for sensing applications due to its unique properties including the hollow sensing channel, high surface-volume ratio, well-controlled shape parameters and compatibility to on-chip integration. Here the state-of-the-art sensing techniques based on microtubular devices are reviewed. The developed microtubular sensors cover microcapillaries, rolled-up nanomembranes, chemically synthesized tubular arrays, and photoresist-based tubular structures via 3D printing. Various types of microtubular sensors working in optical, electrical, and magnetic principles exhibit an extremely broad scope of sensing targets including liquids, biomolecules, micrometer-sized/nanosized objects, and gases. Moreover, they have also been applied for the detection of mechanical, acoustic, and magnetic fields as well as fluorescence signals in labeling-based analyses. At last, a comprehensive outlook of future research on microtubular sensors is discussed on pushing the detection limit, extending the functionality, and taking a step forward to a compact and integrable core module in a lab-on-a-chip analytical system for understanding fundamental biological events or performing accurate point-of-care diagnostics.

Trimodal Waveguide Demonstration and Its Implementation as a High Order Mode Interferometer for Sensing Application

This work implements and demonstrates an interferometric transducer based on a trimodal optical waveguide concept. The readout signal is generated from the interference between the fundamental and second-order modes propagating on a straight polymer waveguide. Intuitively, the higher the mode order, the larger the fraction of power (evanescent field) propagating outside the waveguide core, hence the higher the sensitivity that can be achieved when interfering against the strongly confined fundamental mode. The device is fabricated using the polymer SU-8 over a SiO₂ substrate and shows a free spectral range of 20.2 nm and signal visibility of 5.7 dB, reaching a sensitivity to temperature variations of 0.0586 dB/°C. The results indicate that the proposed interferometer is a promising candidate for highly sensitive, compact and low-cost photonic transducer for implementation in different types of sensing applications, among these, point-of-care.

Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions

The implication of RNA in multiple cellular processes beyond protein coding has revitalized interest in the development of small molecules for therapeutically targeting RNA and for further probing its cellular biology. However, the process of rationally designing such small molecule probes is hampered by the paucity of information about fundamental molecular recognition principles of RNA. In this Review, we summarize two important and often underappreciated aspects of RNA-small molecule recognition: RNA conformational dynamics and the biophysical properties of interactions of small molecules with RNA, specifically thermodynamics and kinetics. While conformational flexibility is often said to impede RNA ligand development, the ability of small molecules to influence the RNA conformational landscape can have a significant effect on the cellular functions of RNA. An analysis of the conformational landscape of RNA and the interactions of individual conformations with ligands can thus guide the development of new small molecule probes, which needs to be investigated further. Additionally, while it is common practice to quantify the binding affinities ( K_a or K_d) of small molecules for biomacromolecules as a measure of their activity, further biophysical characterization of their interaction can provide a deeper understanding. Studies that focus on the thermodynamic and kinetic parameters for interaction between RNA and ligands are next discussed. Finally, this Review provides the reader with a perspective on how such in-depth analysis of biophysical characteristics of the interaction of RNA and small molecules can impact our understanding of these interactions and how they will benefit the future design of small molecule probes.

Study of a Broadband Difference Interferometer Based on Low-Cost Polymer Slab Waveguides

A model and the waveguide parameters of a broadband, polymer-based slab waveguide difference interferometer is presented in this paper. The parameters were determined based on knowledge of the dispersion in the structure materials used to fabricate the waveguide. The impact of the waveguide layer thickness, propagation path length, and change in the waveguide cover refractive index on the output signal from the system was determined. It has been shown that the direction of the maximum shifting is determined by the thickness of the waveguide layer. A relationship describing the shift in the signal extrema for a change in the waveguide cover refractive index was derived. The results show that the use of a propagation constant simplifies the description of the interferometer. Polymer waveguides, although they have a small contrast in refractive indices, allow for large shifts in the maxima of the signal. The determined shifts in the output signal extrema for polymer waveguides are comparable, and these shifts are larger for some waveguide thicknesses compared to waveguides based on Si₃N₄.

Nanohole array plasmonic biosensors: Emerging point-of-care applications

Point-of-care (POC) applications have expanded hugely in recent years and is likely to continue, with an aim to deliver cheap, portable, and reliable devices to meet the demands of healthcare industry. POC devices are designed, prototyped, and assembled using numerous strategies but the key essential features that biosensing devices require are: (1) sensitivity, (2) selectivity, (3) specificity, (4) repeatability, and (5) good limit of detection. Overall the fabrication and commercialization of the nanohole array (NHA) setup to the outside world still remains a challenge. Here, we review the various methods of NHA fabrication, the design criteria, the geometrical features, the effects of surface plasmon resonance (SPR) on sensing as well as current state-of-the-art of existing NHA sensors. This review also provides easy-to-understand examples of NHA-based POC biosensing applications, its current status, challenges, and future prospects.

Single-channel bimodal interferometric sensor using subwavelength structures

A novel configuration of photonic sensors based on a single-channel bimodal interferometer is proposed. The design consists of a subwavelength grating (SWG) periodic structure supporting two dispersive TE-like modes that interfere at the output to create fringes in the transmission spectrum. Dispersion relations of the bimodal periodic structures have been computed in order to study the sensing performance, obtaining a theoretical bulk sensitivity of ~1300nm/RIU and a surface sensitivity of ~6.1nm/nm. Finite-Difference Time Domain (FDTD) analysis has been also carried out in order to confirm the previously obtained sensitivity results, thus showing a perfect agreement between theoretical modelling and simulation.

Graphene Oxide as an Optical Biosensing Platform: A Progress Report

A few years ago, crucial graphene oxide (GO) features such as the carbon/oxygen ratio, number of layers, and lateral size were scarcely investigated and, thus, their impact on the overall optical biosensing performance was almost unknown. Nowadays valuable insights about these features are well documented in the literature, whereas others remain controversial. Moreover, most of the biosensing systems based on GO were amenable to operating as colloidal suspensions. Currently, the literature reports conceptually new approaches obviating the need of GO colloidal suspensions, enabling the integration of GO onto a solid phase and leading to their application in new biosensing devices. Furthermore, most GO-based biosensing devices exploit photoluminescent signals. However, further progress is also achieved in powerful label-free optical techniques exploiting GO in biosensing, particularly using optical fibers, surface plasmon resonance, and surface enhanced Raman scattering. Herein, a critical overview on these topics is offered, highlighting the key role of the physicochemical properties of GO. New challenges and opportunities in this exciting field are also highlighted.

Fluorescent Aptamer Immobilization on Inverse Colloidal Crystals

In this paper, we described a versatile two steps approach for the realization of silica inverse opals functionalized with DNA-aptamers labelled with Cy3 fluorophore. The co-assembly method was successfully employed for the realization of high quality inverse silica opal, whilst the inverse network was functionalized via epoxy chemistry. Morphological and optical assessment revealed the presence of large ordered domains with a transmission band gap depth of 32%, after the functionalization procedure. Finite Difference Time-Domain (FDTD) simulations confirmed the high optical quality of the inverse opal realized. Photoluminescence measurements evidenced the effective immobilization of DNA-aptamer molecules labelled with Cy3 throughout the entire sample thickness. This assumption was verified by the inhibition of the fluorescence of Cy3 fluorophore tailoring the position of the photonic band gap of the inverse opal. The modification of the fluorescence could be justified by a variation in the density of states (DOS) calculated by the Plane Wave Expansion (PWE) method. Finally, the development of the aforementioned approach could be seen as proof of the concept experiment, suggesting that this type of system may act as a suitable platform for the realization of fluorescence-based bio-sensors.

Label-free plasmonic biosensors for point-of-care diagnostics: a review

Introduction: Optical biosensors, particularly those based on nanoplasmonics technology, have emerged in recent decades as a potential solution for disease diagnostics and therapy follow-up at the point-of-care (POC). These biosensor platforms could overcome some of the challenges faced in conventional diagnosis techniques offering label-free assays with immediate results and employing small and user-friendly devices. Areas covered: In this review, we will provide a critical overview of the recent advances in the development of nanoplasmonic biosensors for the POC diagnostics. We focus on those systems with demonstrated capabilities for integration in portable platforms, highlighting some of the most relevant diagnostics applications targeting proteins, nucleic acids, and cells as disease biomarkers. Expert commentary: Despite the attractive features of label-free nanoplasmonic sensors in terms of miniaturization and analytical robustness, the route toward an effective clinical implementation involves the integration of fully automated microfluidic systems for sample processing and analysis, and the optimization of surface biofunctionalization procedures. Additionally, the development of multiplexed sensors for high-throughput analysis and including specific neoantigens and novel biomarkers in detection panels will provide the means for delivering a powerful analytical technology for an accurate and improved medical diagnosis.

Practical guide to characterize biomolecule adsorption on solid surfaces (Review)

The control over the adsorption or grafting of biomolecules from a liquid to a solid interface is of fundamental importance in different fields, such as drug delivery, pharmaceutics, diagnostics, and tissue engineering. It is thus important to understand and characterize how biomolecules interact with surfaces and to quantitatively measure parameters such as adsorbed amount, kinetics of adsorption and desorption, conformation of the adsorbed biomolecules, orientation, and aggregation state. A better understanding of these interfacial phenomena will help optimize the engineering of biofunctional surfaces, preserving the activity of biomolecules and avoiding unwanted side effects. The characterization of molecular adsorption on a solid surface requires the use of analytical techniques, which are able to detect very low quantities of material in a liquid environment without modifying the adsorption process during acquisition. In general, the combination of different techniques will give a more complete characterization of the layers adsorbed onto a substrate. In this review, the authors will introduce the context, then the different factors influencing the adsorption of biomolecules, as well as relevant parameters that characterize their adsorption. They review surface-sensitive techniques which are able to describe different properties of proteins and polymeric films on solid two-dimensional materials and compare these techniques in terms of sensitivity, penetration depth, ease of use, and ability to perform "parallel measurements."

Silicon Photonic Biosensors Using Label-Free Detection

Thanks to advanced semiconductor microfabrication technology, chip-scale integration and miniaturization of lab-on-a-chip components, silicon-based optical biosensors have made significant progress for the purpose of point-of-care diagnosis. In this review, we provide an overview of the state-of-the-art in evanescent field biosensing technologies including interferometer, microcavity, photonic crystal, and Bragg grating waveguide-based sensors. Their sensing mechanisms and sensor performances, as well as real biomarkers for label-free detection, are exhibited and compared. We also review the development of chip-level integration for lab-on-a-chip photonic sensing platforms, which consist of the optical sensing device, flow delivery system, optical input and readout equipment. At last, some advanced system-level complementary metal-oxide semiconductor (CMOS) chip packaging examples are presented, indicating the commercialization potential for the low cost, high yield, portable biosensing platform leveraging CMOS processes.

Multifunctional waveguide interferometer sensor: simultaneous detection of refraction and absorption with size-exclusion function

A waveguide Young interferometer is presented with simultaneous detection of complex refractive index of a liquid sample. The real part of the refractive index change (refraction) is detected by tracing phase shifts of the interferogram generated by a sensing and reference waveguide. The imaginary part of the refractive index (absorption) is determined by the attenuation of the transmitted signal at certain wavelength. Furthermore, nano-filters are fabricated atop the sensing waveguide, which enables size-exclusion filtering of species to the evanescent field. It shows capability of distinguishing small and large particles from 100 nm to 500 nm in diameter, which is further confirmed by fluorescent excitation experiments. The present sensor could find broad application in optical characterization of complex turbid media with regard to their complex refractive index.

Surface sensing with integrated optical waveguides: a design guideline

Waveguide-based biochemical sensors exploit detection of target molecules that bind specifically to a functionalized waveguide surface. For optimum sensitivity, the waveguide should be designed to mediate maximum influence of the surface layer on the effective refractive index of the guided mode. In this paper, we define a surface sensitivity metric which quantifies this impact and which allows to broadly compare different waveguide types and integration platforms. Focusing on silicon nitride and silicon-on-insulator (SOI) as the most common material systems, we systematically analyze and optimize a variety of waveguide types, comprising simple strips, slot and double slot structures, as well as sub-wavelength gratings (SWG). Comparing the highest achievable surface sensitivities, we provide universal design guidelines and physically interpret the observed trends and limitations. Our findings allow to select the appropriate WG platform and to optimize sensitivity for a given measurement task.

Mycotoxin Biosensor Based on Optical Planar Waveguide

The research aim of this work is to develop a simple and highly sensitive optical biosensor for detection of mycotoxins. This sensor is built on a planar waveguide operating on the polarization interferometry principle, i.e., detecting a phase shift between p- and s-components of polarized light developed during the binding of analyte molecules. The operation of the proposed sensor is similar to that of a Mach⁻Zehnder interferometer, while its design is much simpler and it does not require splitting the waveguide into two arms. The refractive index sensitivity of the polarization interferometer sensor was in the range of 5200 radians per refractive index unit (RIU). Several tests were conducted to detect ochratoxin A (OTA) at different concentrations in direct immunoassay with specific antibodies immobilized in the sensing window. The lowest concentration of OTA of 0.01 ng/mL caused a phase shift of nearly one period. The results obtained prove high sensitivity of the sensors, which are capable of detecting even lower concentrations of mycotoxins at the ppt (part-per-trillion) level.

Surface-Enhanced Raman Scattering for Rapid Detection and Characterization of Antibiotic-Resistant Bacteria

As the prevalence of antibiotic-resistant bacteria continues to rise, biosensing technologies are needed to enable rapid diagnosis of bacterial infections. Furthermore, understanding the unique biochemistry of resistance mechanisms can facilitate the development of next generation therapeutics. Surface-enhanced Raman scattering (SERS) offers a potential solution to real-time diagnostic technologies, as well as a route to fundamental, mechanistic studies. In the current review, SERS-based approaches to the detection and characterization of antibiotic-resistant bacteria are covered. The commonly used nanomaterials (nanoparticles and nanostructured surfaces) and surface modifications (antibodies, aptamers, reporters, etc.) for SERS bacterial detection and differentiation are discussed first, and followed by a review of SERS-based detection of antibiotic-resistant bacteria from environmental/food processing and clinical sources. Antibiotic susceptibility testing and minimum inhibitory concentration testing with SERS are then summarized. Finally, recent developments of SERS-based chemical imaging/mapping of bacteria are reviewed.

Reusable thin-film all-polymer couplers for vertical light coupling to single-mode waveguides

A reusable all-polymer coupler using gratings and tapers for vertical light coupling to single-mode planar waveguides is demonstrated. Numerical simulations are performed to optimize the tapers and gratings to increase the coupling efficiency. A hot-embossing replication technique is used for the fabrication of waveguide sensors and gratings, which is adaptable to mass production, such as roll-to-roll processes. The external grating is reversibly bonded to the waveguide via van der Waals forces, and the thus realized re-usability reduces the fabrication costs. The utility of the structure is shown by using these grating couplers for testing of asymmetric Mach-Zehnder interferometers.

Recent Progress of Imprinted Polymer Photonic Waveguide Devices and Applications

Polymers are promising materials for fabricating photonic integrated waveguide devices. Versatile functional devices can be manufactured using a simple process, with low cost and potential mass-manufacturing. This paper reviews the recent progress of polymer photonic integrated devices fabricated using the UV imprinting technique. The passive polymer waveguide devices for wavelength filtering, power splitting, and light collecting, and the active polymer waveguide devices based on the thermal-optic tuning effect, are introduced. Then, the electro-optic (EO) modulators, by virtue of the high EO coefficient of polymers, are described. Finally, the photonic biosensors, which are based on low-cost and biocompatible polymer platforms, are presented.

Exploring Molecular-Biomembrane Interactions with Surface Plasmon Resonance and Dual Polarization Interferometry Technology: Expanding the Spotlight onto Biomembrane Structure

The molecular analysis of biomolecular-membrane interactions is central to understanding most cellular systems but has emerged as a complex technical challenge given the complexities of membrane structure and composition across all living cells. We present a review of the application of surface plasmon resonance and dual polarization interferometry-based biosensors to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. We first describe the optical principals and instrumentation of surface plasmon resonance, including both linear and extraordinary transmission modes and dual polarization interferometry. We then describe the wide range of model membrane systems that have been developed for deposition on the chips surfaces that include planar, polymer cushioned, tethered bilayers, and liposomes. This is followed by a description of the different chemical immobilization or physisorption techniques. The application of this broad range of engineered membrane surfaces to biomolecular-membrane interactions is then overviewed and how the information obtained using these techniques enhance our molecular understanding of membrane-mediated peptide and protein function. We first discuss experiments where SPR alone has been used to characterize membrane binding and describe how these studies yielded novel insight into the molecular events associated with membrane interactions and how they provided a significant impetus to more recent studies that focus on coincident membrane structure changes during binding of peptides and proteins. We then discuss the emerging limitations of not monitoring the effects on membrane structure and how SPR data can be combined with DPI to provide significant new information on how a membrane responds to the binding of peptides and proteins.

Optofluidics Refractometers

Refractometry is a classic analytical method in analytical chemistry and biosensing. By integrating advanced micro- and nano-optical systems with well-developed microfluidics technology, optofluidics are shown to be a powerful, smart and universal platform for refractive index sensing applications. This paper reviews recent work on optofluidic refractometers based on different sensing mechanisms and structures (e.g., photonic crystal/photonic crystal fibers, waveguides, whisper gallery modes and surface plasmon resonance), and traces the performance enhancement due to the synergistic integration of optics and microfluidics. A brief discussion of future trends in optofluidic refractometers, namely volume sensing and resolution enhancement, are also offered.

Integrated Optical Mach-Zehnder Interferometer Based on Organic-Inorganic Hybrids for Photonics-on-a-Chip Biosensing Applications

The development of portable low-cost integrated optics-based biosensors for photonics-on-a-chip devices for real-time diagnosis are of great interest, offering significant advantages over current analytical methods. We report the fabrication and characterization of an optical sensor based on a Mach-Zehnder interferometer to monitor the growing concentration of bacteria in a liquid medium. The device pattern was imprinted on transparent self-patternable organic-inorganic di-ureasil hybrid films by direct UV-laser, reducing the complexity and cost production compared with lithographic techniques or three-dimensional (3D) patterning using femtosecond lasers. The sensor performance was evaluated using, as an illustrative example, E. coli cell growth in an aqueous medium. The measured sensitivity (2 × 10^-4 RIU) and limit of detection (LOD = 2 × 10^-4) are among the best values known for low-refractive index contrast sensors. Furthermore, the di-ureasil hybrid used to produce this biosensor has additional advantages, such as mechanical flexibility, thermal stability, and low insertion losses due to fiber-device refractive index mismatch (~1.49). Therefore, the proposed sensor constitutes a direct, compact, fast, and cost-effective solution for monitoring the concentration of lived-cells.

Design Parameter Optimization of a Silicon-Based Grating Waveguide for Performance Improvement in Biochemical Sensor Application

We performed numerical analysis and design parameter optimization of a silicon-based grating waveguide refractive index (RI) sensor. The performance of the grating waveguide RI sensor was determined by the full-width at half-maximum (FWHM) and the shift in the resonance wavelength in the transmission spectrum. The transmission extinction, a major figure-of-merit of an RI sensor that reflects both FWHM and resonance shift performance, could be significantly improved by the proper determination of three major grating waveguide parameters: duty ratio, grating period, and etching depth. We analyzed the transmission characteristics of the grating waveguide under various design parameter conditions using a finite-difference time domain method. We achieved a transmission extinction improvement of >26 dB under a given bioenvironmental target change by the proper choice of the design procedure and parameters. This design procedure and choice of appropriate parameters would enable the widespread application of silicon-based grating waveguide in high-performance RI biochemical sensor.

Protein analysis by Mach-Zehnder interferometers with a hybrid plasmonic waveguide with nano-slots

Optical biosensing devices for the affinity analysis of molecular binding events could offer significant advantages over current analytical methods. However, most of those excited with a single optical mode are "blind" to the conformational change of bound molecules. We succeeded in designing Mach-Zehnder interferometers (MZI) with a hybrid plasmonic (HP) waveguide with nano-slots. By addressing the structure with dual polarizations, the optogeometrical properties (density and thickness) of protein layers have been determined without ambiguity. Differences in the hybrid mode dispersion between the transverse electric (TE) and transverse magnetic (TM) modes separately allow the determination of the thickness and the density at all stages during the molecular interaction. Moreover, nano-slots can be equated with an effective optical capacitance resulting in strong field confinement and low propagation loss. A proof of concept is conducted by analyzing the conformational change of HepV, a recombinant fragment of collagen V, during complicated molecular interaction. Instead of wavelength interrogation, a cost-effective method with output intensity variation at particular wavelengths due to "resonance phenomena" was employed to monitor the biological event.

Broad-band difference interferometer as a refractive index sensor

Integrated Optical Broad-Band Difference Interferometer (IO BB DI) is introduced as an alternative and economical measurement method to integrated optical label-free affinity sensors. A detailed theoretical analysis of the method is presented and the effects of the waveguide layer on the operation of the system are shown. A very short operating distance of less than 0.5 mm allows miniaturization of the interferometer. The analysis was performed for Si₃N₄/SiO₂ layers that can be obtained in standard microelectronics technological processes.

Focal molography is a new method for the in situ analysis of molecular interactions in biological samples

Focal molography is a next-generation biosensor that visualizes specific biomolecular interactions in real time. It transduces affinity modulation on the sensor surface into refractive index modulation caused by target molecules that are bound to a precisely assembled nanopattern of molecular recognition sites, termed the 'mologram'. The mologram is designed so that laser light is scattered at specifically bound molecules, generating a strong signal in the focus of the mologram via constructive interference, while scattering at nonspecifically bound molecules does not contribute to the effect. We present the realization of molograms on a chip by submicrometre near-field reactive immersion lithography on a light-sensitive monolithic graft copolymer layer. We demonstrate the selective and sensitive detection of biomolecules, which bind to the recognition sites of the mologram in various complex biological samples. This allows the label-free analysis of non-covalent interactions in complex biological samples, without a need for extensive sample preparation, and enables novel time- and cost-saving ways of performing and developing immunoassays for diagnostic tests.

Dual-Mode Electro-Optical Techniques for Biosensing Applications: A Review

The monitoring of biomolecular interactions is a key requirement for the study of complex biological processes and the diagnosis of disease. Technologies that are capable of providing label-free, real-time insight into these interactions are of great value for the scientific and clinical communities. Greater understanding of biomolecular interactions alongside increased detection accuracy can be achieved using technology that can provide parallel information about multiple parameters of a single biomolecular process. For example, electro-optical techniques combine optical and electrochemical information to provide more accurate and detailed measurements that provide unique insights into molecular structure and function. Here, we present a comparison of the main methods for electro-optical biosensing, namely, electrochemical surface plasmon resonance (EC-SPR), electrochemical optical waveguide lightmode spectroscopy (EC-OWLS), and the recently reported silicon-based electrophotonic approach. The comparison considers different application spaces, such as the detection of low concentrations of biomolecules, integration, the tailoring of light-matter interaction for the understanding of biomolecular processes, and 2D imaging of biointeractions on a surface.

Complex refractive index spectra of whole blood and aqueous solutions of anticoagulants, analgesics and buffers in the mid-infrared

Mid-infrared (MIR) spectroscopy is a powerful tool for characterising the vibrations of molecular bonds and is therefore ideal for label-free detection of chemical species. Recent research into thin-film deposition and etching techniques for mid-infrared materials shows potential for realising miniaturised bedside biosensors for clinical diagnostics exploiting MIR spectroscopy, to replace laboratory based-techniques. However, lack of refractive index information for commonly encountered biological media and analytes hampers optimisation of biosensor performance for maximum sensitivity, especially for devices exploiting evanescent spectroscopy. Here we present refractive index data for human whole blood and several aqueous solutions of general interest to the clinical community: anticoagulants, analgesics and buffers. The refractive indices are generally dominated by the water content of each sample and the whole blood spectra exhibit additional strong features due to protein content. Furthermore, we present a generalised method for extracting complex refractive indices of aqueous solutions in the mid-infrared region using conventional attenuated total reflection Fourier transform spectroscopy (ATR-FTIR) without the need for collimated or polarised incident light, as is required for existing methods.

Optical biosensors

Optical biosensors represent the most common type of biosensor. Here we provide a brief classification, a description of underlying principles of operation and their bioanalytical applications. The main focus is placed on the most widely used optical biosensors which are surface plasmon resonance (SPR)-based biosensors including SPR imaging and localized SPR. In addition, other optical biosensor systems are described, such as evanescent wave fluorescence and bioluminescent optical fibre biosensors, as well as interferometric, ellipsometric and reflectometric interference spectroscopy and surface-enhanced Raman scattering biosensors. The optical biosensors discussed here allow the sensitive and selective detection of a wide range of analytes including viruses, toxins, drugs, antibodies, tumour biomarkers and tumour cells.

Photonic crystal and quasi-crystals providing simultaneous light coupling and beam splitting within a low refractive-index slab waveguide

Coupling between free space components and slab waveguides is a common requirement for integrated optical devices, and is typically achieved by end-fire or grating coupling. Power splitting and distribution requires additional components. Usually grating couplers are used in combination with MMI/Y-splitters to do this task. In this paper, we present a photonic crystal device which performs both tasks simultaneously and is able to couple light at normal incidence and near normal incidence. Our approach is scalable to large channel counts with little impact on device footprint. We demonstrate in normal incidence coupling with multi-channel splitting for 785 nm light. Photonic crystals are etched into single mode low refractive index SiON film on both SiO₂/Si and borosilicate glass substrate. Triangular lattices are shown to provide coupling to 6 beams with equal included angle (60°), while a quasi-crystal lattice with 12-fold rotational symmetry yields coupling to 12 beams with equal included angle (30°). We show how to optimize the lattice constant to achieve efficient phase matching between incident and coupled mode wave vectors, and how to adjust operating wavelength from visible to infrared wavelengths.