Nanoscale porous silicon waveguide for label-free DNA sensing

Tamm Plasmon Polariton Biosensors Based on Porous Silicon: Design, Validation and Analysis

Tamm Plasmon Polariton (TPP) is a nanophotonic phenomenon that has attracted much attention due to its spatial strong field confinement, ease of mode excitation, and polarization independence. TPP has applications in sensing, storage, lasing, perfect absorber, solar cell, nonlinear optics, and many others. In this work, we demonstrate a biosensing platform based on TPP resonant mode. Both theoretical analyses based on the transfer matrix method and experimental validation through nonspecific detection of liquids of different refractive indices and specific detection of SARS-CoV-2 nucleocapsid protein (N-protein) are presented. Results show that the TPP biosensor has high sensitivity and good specificity. For N-protein detection, the sensitivity can be up to 1.5 nm/(µg/mL), and the limit of detection can reach down to 7 ng/mL with a spectrometer of 0.01 nm resolution in wavelength shift. Both nonspecific detection of R.I. liquids and specific detection of N-protein have been simulated and compared with experimental results to demonstrate consistency. This work paves the way for design, optimization, fabrication, characterization, and performance analysis of TPP based biosensors.

Rapid genetic screening with high quality factor metasurfaces

Genetic analysis methods are foundational to advancing personalized medicine, accelerating disease diagnostics, and monitoring the health of organisms and ecosystems. Current nucleic acid technologies such as polymerase chain reaction (PCR) and next-generation sequencing (NGS) rely on sample amplification and can suffer from inhibition. Here, we introduce a label-free genetic screening platform based on high quality (high-Q) factor silicon nanoantennas functionalized with nucleic acid fragments. Each high-Q nanoantenna exhibits average resonant quality factors of 2,200 in physiological buffer. We quantitatively detect two gene fragments, SARS-CoV-2 envelope (E) and open reading frame 1b (ORF1b), with high-specificity via DNA hybridization. We also demonstrate femtomolar sensitivity in buffer and nanomolar sensitivity in spiked nasopharyngeal eluates within 5 minutes. Nanoantennas are patterned at densities of 160,000 devices per cm2, enabling future work on highly-multiplexed detection. Combined with advances in complex sample processing, our work provides a foundation for rapid, compact, and amplification-free molecular assays.

A high-throughput fully automatic biosensing platform for efficient COVID-19 detection

We propose a label-free biosensor based on a porous silicon resonant microcavity and localized surface plasmon resonance. The biosensor detects SARS-CoV-2 antigen based on engineered trimeric angiotensin converting enzyme-2 binding protein, which is conserved across different variants. Robotic arms run the detection process including sample loading, incubation, sensor surface rinsing, and optical measurements using a portable spectrometer. Both the biosensor and the optical measurement system are readily scalable to accommodate testing a wide range of sample numbers. The limit of detection is 100 TCID_50/ml. The detection time is 5 min, and the throughput of one single robotic site is up to 384 specimens in 30 min. The measurement interface requires little training, has standard operation, and therefore is suitable for widespread use in rapid and onsite COVID-19 screening or surveillance.

Optical Fiber Based Mach-Zehnder Interferometer for APES Detection

A 3-aminopropyl-triethoxysilane (APES) fiber-optic sensor based on a Mach–Zehnder interferometer (MZI) was demonstrated. The MZI was constructed with a core-offset fusion single mode fiber (SMF) structure with a length of 3.0 cm. As APES gradually attaches to the MZI, the external environment of the MZI changes, which in turn causes change in the MZI’s interference. That is the reason why we can obtain the relationships between the APES amount and resonance dip wavelength by measuring the transmission variations of the resonant dip wavelength of the MZI. The optimized amount of 1% APES for 3.0 cm MZI biosensors was 3 mL, whereas the optimized amount of 2% APES was 1.5 mL.

Waveguide Enhanced Raman Spectroscopy for Biosensing: A Review

Waveguide enhanced Raman spectroscopy (WERS) utilizes simple, robust, high-index contrast dielectric waveguides to generate a strong evanescent field, through which laser light interacts with analytes residing on the surface of the waveguide. It offers a powerful tool for the direct identification and reproducible quantification of biochemical species and an alternative to surface enhanced Raman spectroscopy (SERS) without reliance on fragile noble metal nanostructures. The advent of low-cost laser diodes, compact spectrometers, and recent progress in material engineering, nanofabrication techniques, and software modeling tools have made realizing portable and cheap WERS Raman systems with high sensitivity a realistic possibility. This review highlights the latest progress in WERS technology and summarizes recent demonstrations and applications. Following an introduction to the fundamentals of WERS, the theoretical framework that underpins the WERS principles is presented. The main WERS design considerations are then discussed, and a review of the available approaches for the modification of waveguide surfaces for the attachment of different biorecognition elements is provided. The review concludes by discussing and contrasting the performance of recent WERS implementations, thereby providing a future roadmap of WERS technology where the key opportunities and challenges are highlighted.

Development of a highly sensitive sensor chip using optical diagnostic based on functionalized plasmonically active AuNPs

Measuring solution concentration plays an important role in chemical, biochemical, clinical diagnosis, environmental monitoring, and biological analyses. In this work, we develop a transmission-mode localized surface plasmon resonance sensor chip system and convenient method which is highly efficient, highly sensitive for detection sensing using multimode fiber. The plasmonically active sensor's surface AuNPs with high-density NPs were decorated onto 1 cm sensing length of various clad-free fiber in the form of homogeneous monolayer utilizing a self-assembly process for immobilization of the target molecule. The carboxyl bond is formed through a functional reaction on the sensor head. Using the significance in the refractive index difference and numerical aperture, which is caused by a variation in the concentration of measuring bovine serum albumin (BSA) protein which can be accurately measured by the output signal. The refractive index variation of the medium analyte layer can be converted to signal output power change at the He-Ne wavelength of 632.8 nm. The sensor detection limit was estimated to be 0.075 ng ml^-1for BSA protein which shows high sensitivity compared to other types of label-free optical biosensors. This also leads to a possibility of finding the improvement in the sensitivity label-free biosensors. The conventional method should allow multimode fiber biosensors to become a possible replacement for conventional biosensing techniques based on fluorescence.

Detection of SARS-CoV-2 DNA Targets Using Femtoliter Optofluidic Waveguides

Chip-scale SARS-CoV-2 testing was demonstrated using silicon nitride (Si3N4) nanoslot fluidic waveguides to detect a tagged oligonucleotide with a coronavirus DNA sequence. The slot waveguides were fabricated using complementary metal-oxide-semiconductor (CMOS) fabrication processes, including multiscale lithography and selective reactive ion etching (RIE), forming femtoliter fluidic channels. Finite difference method (FDM) simulation was used to calculate the optical field distribution of the waveguide mode when the waveguide sensor was excited by transverse electric (TE) and transverse magnetic (TM) polarized light. For the TE polarization, a strong optical field was created in the slot region and its field intensity was 14× stronger than the evanescent sensing field from the TM polarization. The nanoscale confinement of the optical sensing field significantly enhanced the light-analyte interaction and improved the optical sensitivity. The sensitivity enhancement was experimentally demonstrated by measuring the polarization-dependent fluorescence emission from the tagged oligonucleotide. The photonic chips consisting of femtoliter Si3N4 waveguides provide a low-cost and high throughput platform for real-time virus identification, which is critical for point-of-care (PoC) diagnostic applications.

Optical Sensitivity of Waveguides Inscribed in Nanoporous Silicate Framework

Laser direct writing technique in glass is a powerful tool for various waveguides' fabrication that highly develop the element base for designing photonic devices. We apply this technique to fabricate waveguides in porous glass (PG). Nanoporous optical materials for the inscription can elevate the sensing ability of such waveguides to higher standards. The waveguides were fabricated by a single-scan approach with femtosecond laser pulses in the densification mode, which resulted in the formation of a core and cladding. Experimental studies revealed three types of waveguides and quantified the refractive index contrast (up to Δn = 1.2·10^-2) accompanied with ~1.2 dB/cm insertion losses. The waveguides demonstrated the sensitivity to small objects captured by the nanoporous framework. We noticed that the deposited ethanol molecules (3 µL) on the PG surface influence the waveguide optical properties indicating the penetration of the molecule to its cladding. Continuous monitoring of the output near field intensity distribution allowed us to determine the response time (6 s) of the waveguide buried at 400 µm below the glass surface. We found that the minimum distinguishable change of the refractive index contrast is 2 × 10^-4. The results obtained pave the way to consider the waveguides inscribed into PG as primary transducers for sensor applications.

Mass Transfer Limitations of Porous Silicon-Based Biosensors for Protein Detection

Porous silicon (PSi) thin films have been widely studied for biosensing applications, enabling label-free optical detection of numerous targets. The large surface area of these biosensors has been commonly recognized as one of the main advantages of the PSi nanostructure. However, in practice, without application of signal amplification strategies, PSi-based biosensors suffer from limited sensitivity, compared to planar counterparts. Using a theoretical model, which describes the complex mass transport phenomena and reaction kinetics in these porous nanomaterials, we reveal that the interrelated effect of bulk and hindered diffusion is the main limiting factor of PSi-based biosensors. Thus, without significantly accelerating the mass transport to and within the nanostructure, the target capture performance of these biosensors would be comparable, regardless of the nature of the capture probe–target pair. We use our model to investigate the effect of various structural and biosensor characteristics on the capture performance of such biosensors and suggest rules of thumb for their optimization.

Single-mode porous silicon waveguide interferometers with unity confinement factors for ultra-sensitive surface adlayer sensing

Guided wave-optics has emerged as a promising platform for label free biosensing. However, device sensitivity toward surface-bound small molecules is directly limited by the evanescent interaction and low confinement factor with the active sensing region. Here, we report a mesoporous silicon waveguide design and inverse fabrication technique that resolves the evanescent field interaction limitation while achieving maximal transverse confinement factors and preserving single-mode operation. The waveguide sensors are characterized in a Fabry-Perot interferometer configuration and the ultra-high sensitivity to small molecule adlayers is demonstrated. We also identify dispersion to be a promising degree of freedom for exceeding the sensitivity limits predicted by the conventional non-dispersive effective medium theory.

Label-free discrimination of single nucleotide changes in DNA by reflectometric interference Fourier transform spectroscopy

Phenotypic variation - such as disease susceptibility and differential drug response - has a strong genetic component. Substantial effort has therefore been made to identify causal genomic variants explaining such variation among humans. Point mutations (PMs), which are single nucleotide changes in the genome, have been identified to be the most abundant form of causal genomic variants, making them useful, reliable diagnostic markers. Methods developed to genotype PMs have moved towards solid-phase assays, which not only show greater sensitivity and specificity, but also enable scalability and faster processing time. Most current assays are, however, based on fluorescent probes, which makes them relatively expensive. To develop a more cost-effective label-free genotyping method, we used a porous silicon (PSi) base as an efficient support for DNA biosensing and coupled it with reflectometric interference Fourier transform spectroscopy (RIFTS). To assess the versatility of this approach, we tested both a single nucleotide substitution in VKORC1 (-1639G > A; rs9923231) and a single nucleotide insertion in BRCA1 (5382insC; rs80357906). We demonstrate that the PSi-RIFTS method can efficiently detect both PM types with high sensitivity where hybridization of complementary DNA can be quantifiably differentiated from mismatch and non-complementary hybridization events. In addition, we show that the PSi base with immobilized DNA not only can be re-used to type further samples, but it also remains stable for 14 days, suggesting its potential for high-throughput applications.

Photonic crystal nanobeam biosensors based on porous silicon

Photonic crystal (PhC) nanobeams (NB) patterned on porous silicon (PSi) waveguide substrates are demonstrated for the specific, label-free detection of oligonucleotides. These photonic structures combine the large active sensing area intrinsic to PSi sensors with the high-quality (Q) factor and low-mode volume characteristic of compact resonant silicon-on-insulator (SOI) PhC NB devices. The PSi PhC NB can achieve a Q-factor near 9,000 and has an approximately 40-fold increased active sensing area for molecular attachment, compared to traditional SOI PhC NB sensors. The PSi PhC NB exhibits a resonance shift that is more than one order of magnitude larger than that of a similarly designed SOI PhC NB for the detection of small chemical molecules and 16-base peptide nucleic acids. The design and fabrication of PSi PhC NB sensors are compatible with CMOS processing, sensor arrays, and integration with lab-on-chip systems.

Screening of Transgenic Cotton Based on a Porous Silicon Biosensor

Label-free porous silicon (PSi)-based biosensor enables the detection and identification of the protein in transgenic cotton. Changes in optical response signal in the presence of the target protein can be detected by Fourier transform infrared (FTIR) spectromicroscopy when binding of the target protein with its antibody is selectively captured on the PSi biosensor. Here we describe the transgenic protein (antifreeze protein, AFP), and compare with non-transgenic plants. Significant red shifts are observed for transgenic antifreeze protein cotton lines.

Comparative study of macroporous silicon-based photovoltaic characteristics using indium tin oxide-silicon and pn-silicon junction based devices

We report highly ordered macroporous silicon (Si)-based photovoltaic characteristics using indium tin oxide (ITO)/n-Si and pn-Si junction-based devices. The detailed fabrication processes including new controlled ITO etching are presented. Theoretical device simulations are performed to understand the presented device structures and propose an optimum device design based on processing limitations. The performance of ITO/n-Si junction devices directly depends on the conformal ITO coating along the pore surface. While pn-Si junction device requires additional doping step, the device can overcome the limitation of ITO conformal coating, especially for a device with high-aspect-ratio macropore structures. Experimental results also support the simulation analysis. The three-dimensional structural properties of well-defined macroporous Si coupled with the formation of photovoltaic devices are attractive for multi-functional applications.

Porous silicon-poly(ε-caprolactone) film composites: evaluation of drug release and degradation behavior

This work focuses on an evaluation of novel composites of porous silicon (pSi) with the biocompatible polymer ε-polycaprolactone (PCL) for drug delivery and tissue engineering applications. The degradation behavior of the composites in terms of their morphology along with the effect of pSi on polymer degradation was monitored. PSi particles loaded with the drug camptothecin (CPT) were physically embedded into PCL films formed from electrospun PCL fiber sheets. PSi/PCL composites revealed a release profile of CPT (monitored via fluorescence spectroscopy) in accordance with the Higuchi release model, with significantly lower burst release percentage compared to pSi microparticles alone. Degradation studies of the composites, using gravimetric analysis, differential scanning calorimetry (DSC), and field emission scanning electron microscopy (FESEM), carried out in phosphate-buffered saline (PBS) under simulated physiological conditions, indicated a modest mass loss (15%) over 5 weeks due to pSi dissolution and minor polymer hydrolysis. DSC results showed that, relative to PCL-only controls, pSi suppressed crystallization of the polymer film during PBS exposure. This suppression affects the evolution of surface morphology during this exposure that, in turn, influences the degradation behavior of the polymer. The implications of the above properties of these composites as a possible therapeutic device are discussed.

Room-Temperature Low-Threshold Lasing from Monolithically Integrated Nanostructured Porous Silicon Hybrid Microcavities

Silicon photonics would strongly benefit from monolithically integrated low-threshold silicon-based laser operating at room temperature, representing today the main challenge toward low-cost and power-efficient electronic-photonic integrated circuits. Here we demonstrate low-threshold lasing from fully transparent nanostructured porous silicon (PSi) monolithic microcavities (MCs) infiltrated with a polyfluorene derivative, namely, poly(9,9-di- n-octylfluorenyl-2,7-diyl) (PFO). The PFO-infiltrated PSiMCs support single-mode blue lasing at the resonance wavelength of 466 nm, with a line width of ∼1.3 nm and lasing threshold of 5 nJ (15 μJ/cm²), a value that is at the state of the art of PFO lasers. Furthermore, time-resolved photoluminescence shows a significant shortening (∼57%) of PFO emission lifetime in the PSiMCs, with respect to nonresonant PSi reference structures, confirming a dramatic variation of the radiative decay rate due to a Purcell effect. Our results, given also that blue lasing is a worst case for silicon photonics, are highly appealing for the development of low-cost, low-threshold silicon-based lasers with wavelengths tunable from visible to the near-infrared region by simple infiltration of suitable emitting polymers in monolithically integrated nanostructured PSiMCs.

Image Processing of Porous Silicon Microarray in Refractive Index Change Detection

A new method for extracting the dots is proposed by the reflected light image of porous silicon (PSi) microarray utilization in this paper. The method consists of three parts: pretreatment, tilt correction and spot segmentation. First, based on the characteristics of different components in HSV (Hue, Saturation, Value) space, a special pretreatment is proposed for the reflected light image to obtain the contour edges of the array cells in the image. Second, through the geometric relationship of the target object between the initial external rectangle and the minimum bounding rectangle (MBR), a new tilt correction algorithm based on the MBR is proposed to adjust the image. Third, based on the specific requirements of the reflected light image segmentation, the array cells are segmented into dots as large as possible and the distance between the dots is equal in the corrected image. Experimental results show that the pretreatment part of this method can effectively avoid the influence of complex background and complete the binarization processing of the image. The tilt correction algorithm has a shorter computation time, which makes it highly suitable for tilt correction of reflected light images. The segmentation algorithm makes the dots in a regular arrangement, excludes the edges and the bright spots. This method could be utilized in the fast, accurate and automatic dots extraction of the PSi microarray reflected light image.

Porous Silicon Gradient Refractive Index Micro-Optics

The emergence and growth of transformation optics over the past decade has revitalized interest in how a gradient refractive index (GRIN) can be used to control light propagation. Two-dimensional demonstrations with lithographically defined silicon (Si) have displayed the power of GRIN optics and also represent a promising opportunity for integrating compact optical elements within Si photonic integrated circuits. Here, we demonstrate the fabrication of three-dimensional Si-based GRIN micro-optics through the shape-defined formation of porous Si (PSi). Conventional microfabrication creates Si square microcolumns (SMCs) that can be electrochemically etched into PSi elements with nanoscale porosity along the shape-defined etching pathway, which imparts the geometry with structural birefringence. Free-space characterization of the transmitted intensity distribution through a homogeneously etched PSi SMC exhibits polarization splitting behavior resembling that of dielectric metasurfaces that require considerably more laborious fabrication. Coupled birefringence/GRIN effects are studied by way of PSi SMCs etched with a linear (increasing from edge to center) GRIN profile. The transmitted intensity distribution shows polarization-selective focusing behavior with one polarization focused to a diffraction-limited spot and the orthogonal polarization focused into two laterally displaced foci. Optical thickness-based analysis readily predicts the experimentally observed phenomena, which strongly match finite-element electromagnetic simulations.

Porous Silicon-Based Biosensors: Towards Real-Time Optical Detection of Target Bacteria in the Food Industry

Rapid detection of target bacteria is crucial to provide a safe food supply and to prevent foodborne diseases. Herein, we present an optical biosensor for identification and quantification of Escherichia coli (E. coli, used as a model indicator bacteria species) in complex food industry process water. The biosensor is based on a nanostructured, oxidized porous silicon (PSi) thin film which is functionalized with specific antibodies against E. coli. The biosensors were exposed to water samples collected directly from process lines of fresh-cut produce and their reflectivity spectra were collected in real time. Process water were characterized by complex natural micro-flora (microbial load of >10⁷ cell/mL), in addition to soil particles and plant cell debris. We show that process water spiked with culture-grown E. coli, induces robust and predictable changes in the thin-film optical interference spectrum of the biosensor. The latter is ascribed to highly specific capture of the target cells onto the biosensor surface, as confirmed by real-time polymerase chain reaction (PCR). The biosensors were capable of selectively identifying and quantifying the target cells, while the target cell concentration is orders of magnitude lower than that of other bacterial species, without any pre-enrichment or prior processing steps.

A regenerative label-free fiber optic sensor using surface plasmon resonance for clinical diagnosis of fibrinogen

Purpose

We present the regenerative label-free fiber optical biosensor that exploits surface plasmon resonance for quantitative detection of fibrinogen (Fbg) extracted from human blood plasma.

Materials and methods

The sensor head was made up of a multimode optical fiber with its polymer cladding replaced by metal composite of nanometer thickness made of silver, aluminum, and nickel. The Ni layer coated allowed a direct immobilization of histidine-tagged peptide (HP) on its metal surface without an additional cross-linker in between. On the coated HP layer, immunoglobulin G was then immobilized for specific capturing of Fbg.

Results

We demonstrated a real-time quantitative detection of Fbg concentrations with limit of detection of ~10 ng/mL. The fact that the HP layer could be removed by imidazole with acid also permitted us to demonstrate the regeneration of the outermost metal surface of the sensor head for the sensor reusability.

Conclusion

The sensor detection limit was estimated to be ~10 pM, which was believed to be sensitive enough for detecting Fbg during the clinical diagnosis of cardiovascular diseases, myocardial infarction, strokes, and Alzheimer’s diseases.

Detection of trace heavy metal ions in water by nanostructured porous Si biosensors

Specific and sensitive detection and quantification of heavy metals in real water using label-free optical biosensors.

Nanostructured porous Si optical biosensors: effect of thermal oxidation on their performance and properties

The influence of thermal oxidation conditions on the performance of porous Si optical biosensors used for label-free and real-time monitoring of enzymatic activity is studied. We compare three oxidation temperatures (400, 600, and 800 °C) and their effect on the enzyme immobilization efficiency and the intrinsic stability of the resulting oxidized porous Si (PSiO2), Fabry-Pérot thin films. Importantly, we show that the thermal oxidation profoundly affects the biosensing performance in terms of greater optical sensitivity, by monitoring the catalytic activity of horseradish peroxidase and trypsin-immobilized PSiO2. Despite the significant decrease in porous volume and specific surface area (confirmed by nitrogen gas adsorption-desorption studies) with elevating the oxidation temperature, higher content and surface coverage of the immobilized enzymes is attained. This in turn leads to greater optical stability and sensitivity of PSiO2 nanostructures. Specifically, films produced at 800 °C exhibit stable optical readout in aqueous buffers combined with superior biosensing performance. Thus, by proper control of the oxide layer formation, we can eliminate the aging effect, thus achieving efficient immobilization of different biomolecules, optical signal stability, and sensitivity.

Effect of DNA-induced corrosion on passivated porous silicon biosensors

This work examines the influence of charge density and surface passivation on the DNA-induced corrosion of porous silicon (PSi) waveguides in order to improve PSi biosensor sensitivity, reliability, and reproducibility when exposed to negatively charged DNA molecules. Increasing the concentration of either DNA probes or targets enhances the corrosion process and masks binding events. While passivation of the PSi surface by oxidation and silanization is shown to diminish the corrosion rate and lead to a saturation in the changes by corrosion after about 2 h, complete mitigation can be achieved by replacing the DNA probe molecules with charge-neutral PNA probe molecules. A model to explain the DNA-induced corrosion behavior, consistent with experimental characterization of the PSi through Fourier transform infrared spectroscopy and prism coupling optical measurements, is also introduced.

Selective optical response of hydrolytically stable stratified Si rugate mirrors to liquid infiltration

Stratified optical filters with distinct spectral features and layered surface chemistry were prepared on silicon substrates with stepwise anodic porosification and thermal carbonization. The use of differing parameters for successive carbonization treatments enabled the production of hydrolytically stable porous silicon-based layered optical structures where the adsorption of water to the lower layer is inhibited. This enables selective shifting of reflectance bands by means of liquid infiltration. The merit of using thermal carbonization for creating layered functionality was demonstrated by comparing the hydrolytic stability resulting from this approach to other surface chemistries available for Si. The functionality of the stratified optical structures was demonstrated under water and ethanol infiltration, and changes in the adsorption properties after 9 months of storage were evaluated. The changes observed in the structure were explained using simulations based on the transfer matrix method and the Bruggeman effective medium approximation. Scanning electron microscopy was used for imaging the morphology of the porous structure. Finally, the adaptability of the method for preparing complex structures was demonstrated by stacking superimposed rugate structures with several reflective bands.

Porous silicon Bloch surface and sub-surface wave structure for simultaneous detection of small and large molecules

A porous silicon (PSi) Bloch surface wave (BSW) and Bloch sub-surface wave (BSSW) composite biosensor is designed and used for the size-selective detection of both small and large molecules. The BSW/BSSW structure consists of a periodic stack of high and low refractive index PSi layers and a reduced optical thickness surface layer that gives rise to a BSW with an evanescent tail that extends above the surface to enable the detection of large surface-bound molecules. Small molecules were detected in the sensor by the BSSW, which is a large electric field intensity spatially localized to a desired region of the Bragg mirror and is generated by the implementation of a step or gradient refractive index profile within the Bragg mirror. The step and gradient BSW/BSSW sensors are designed to maximize both resonance reflectance intensity and sensitivity to large molecules. Size-selective detection of large molecules including latex nanospheres and the M13KO7 bacteriophage as well as small chemical linker molecules is reported.

A label-free electrochemistry biosensor based flower-like 3-dimensional ZnO superstructures for detection of DNA arrays

A highly sensitive electrochemical DNA sensor was constructed by homogenously distributing Au nanoparticles (AuNPs) on a flower-like 3D ZnO superstructure–chitosan (CS) matrix.

Investigation of cascaded SiN microring resonators at 1.3 µm and 1.5 µm

An optical device operating at wavelengths around 1.3 µm and 1.5 µm is demonstrated experimentally. It is based on cascaded microring resonators (CMRRs) and the Vernier effect (VE). The architecture consists of two microring resonators (MRRs) connected via a common waveguide; two waveguides were added for the interrogation of CMRRs. The free spectral ranges of both MRRs are slightly different in order to activate the VE, which is known to enhance the sensitivity in optical sensors. CMRRs were fabricated on a silicon nitride (SiN) platform. Two types of buffer layers-benzocyclobutene (BCB) polymer and thermal silicon oxide (SiOx)-were tested. A study of CMRRs was carried out with three structures of different structural parameters. The experimental results show good agreement with the theoretical analysis. This approach is promising for the fabrication of highly sensitive optical sensors in wide operating wavelength range.

Observations of immuno-gold conjugates on influenza viruses using waveguide-mode sensors

Gold nanoparticles were conjugated to an antibody (immuno-AuNP) against A/Udorn/307/1972 (H3N2) influenza virus to detect viruses on a sensing plate designed for an evanescent field-coupled waveguide-mode sensor. Experiments were conducted using human influenza A/H3N2 strains, and immuno-AuNP could detect 8×10(5) PFU/ml (40 pg/µl) intact A/Udorn/307/1972 and 120 pg/µl A/Brisbane/10/2007. Furthermore, increased signal magnitude was achieved in the presence of non-ionic detergent, as the virtual detection level was increased to 8×10(4) PFU/ml A/Udorn/307/1972. Immuno-AuNPs were then complexed with viruses to permit direct observation, and they formed a ring of confined nanodots on the membrane of both intact and detergent-treated viruses as directly visualized by scanning electron microscopy. With this complex the detection limit was improved further to 8×10(3) PFU/ml on anti-rabbit IgG immobilized sensing plate. These strategies introduce methods for observing trapped intact viruses on the sensing plates generated for optical systems.

Chemical surface modifications for the development of silicon-based label-free integrated optical (IO) biosensors: a review

Increasing interest has been paid to label-free biosensors in recent years. Among them, refractive index (RI) optical biosensors enable high density and the chip-scale integration of optical components. This makes them more appealing to help develop lab-on-a-chip devices. Today, many RI integrated optical (IO) devices are made using silicon-based materials. A key issue in their development is the biofunctionalization of sensing surfaces because they provide a specific, sensitive response to the analyte of interest. This review critically discusses the biofunctionalization procedures, assay formats and characterization techniques employed in setting up IO biosensors. In addition, it provides the most relevant results obtained from using these devices for real sample biosensing. Finally, an overview of the most promising future developments in the fields of chemical surface modification and capture agent attachment for IO biosensors follows.

Mass transport effects in suspended waveguide biosensors integrated in microfluidic channels

Label-free optical biosensors based on integrated photonic devices have demonstrated sensitive and selective detection of biological analytes. Integrating these sensor platforms into microfluidic devices reduces the required sample volume and enables rapid delivery of sample to the sensor surface, thereby improving response times. Conventionally, these devices are embedded in or adjacent to the substrate; therefore, the effective sensing area lies within the slow-flow region at the floor of the channel, reducing the efficiency of sample delivery. Recently, a suspended waveguide sensor was developed in which the device is elevated off of the substrate and the sensing region does not rest on the substrate. This geometry places the sensing region in the middle of the parabolic velocity profile, reduces the distance that a particle must travel by diffusion to be detected, and allows binding to both surfaces of the sensor. We use a finite element model to simulate advection, diffusion, and specific binding of interleukin 6, a signaling protein, to this waveguide-based biosensor at a range of elevations within a microfluidic channel. We compare the transient performance of these suspended waveguide sensors with that of traditional planar devices, studying both the detection threshold response time and the time to reach equilibrium. We also develop a theoretical framework for predicting the behavior of these suspended sensors. These simulation and theoretical results provide a roadmap for improving sensor performance and minimizing the amount of sample required to make measurements.

DNA-directed immobilization of horseradish peroxidase onto porous SiO2 optical transducers

Multifunctional porous Si nanostructure is designed to optically monitor enzymatic activity of horseradish peroxidase. First, an oxidized PSi optical nanostructure, a Fabry-Pérot thin film, is synthesized and is used as the optical transducer element. Immobilization of the enzyme onto the nanostructure is performed through DNA-directed immobilization. Preliminary studies demonstrate high enzymatic activity levels of the immobilized horseradish peroxidase, while maintaining its specificity. The catalytic activity of the enzymes immobilized within the porous nanostructure is monitored in real time by reflective interferometric Fourier transform spectroscopy. We show that we can easily regenerate the surface for consecutive biosensing analysis by mild dehybridization conditions.

Chemical stabilization of porous silicon for enhanced biofunctionalization with immunoglobulin

Porous silicon (PSi) is widely used in biological experiments, owing to its biocompatibility and well-established fabrication methods that allow tailoring its surface. Nevertheless, there are some unresolved issues such as deciding whether the stabilization of PSi is necessary for its biological applications and evaluating the effects of PSi stabilization on the surface biofunctionalization with proteins. In this work we demonstrate that non-stabilized PSi is prone to detachment owing to the stress induced upon biomolecular adsorption. Biofunctionalized non-stabilized PSi loses the interference properties characteristic of a thin film, and groove-like structures resulting from a final layer collapse were observed by scanning electron microscopy. Likewise, direct PSi derivatization with 3-aminopropyl-triethoxysilane (APTS) does not stabilize PSi against immunoglobulin biofunctionalization. To overcome this problem, we developed a simple chemical process of stabilizing PSi (CoxPSi) for biological applications, which has several advantages over thermal stabilization (ToxPSi). The process consists of chemical oxidation in H2O2, surface derivatization with APTS and a curing step at 120 °C. This process offers integral homogeneous PSi morphology, hydrophilic surface termination (contact angle θ = 26°) and highly efficient derivatized and biofunctionalized PSi surfaces (six times more efficient than ToxPSi). All these features are highly desirable for biological applications, such as biosensing, where our results can be used for the design and optimization of the biomolecular immobilization cascade on PSi surfaces.

Surface functionalization chemistries on highly sensitive silica-based sensor chips

The surfaces of silica-based sensor chips, designed for evanescent-field-coupled waveguide-mode sensors, were functionalized using various surface chemistries. The immobilization of molecular entities on the functionalized silica surfaces was monitored using various microscopic techniques (scanning electron, fluorescence, and atomic force microscopies). Further, gold nanoparticle-based signal enhancement analyses were performed with protein conjugation on different functionalized surfaces using a waveguide-mode sensor. Based on these analyses, the sensor surfaces modified with glutaraldehyde (Glu) and carbonyldiimidazole were found to be good for molecules of different sizes. In addition, it can be inferred that the Glu-modified surface may be suitable for small molecules with diameters around 5 nm owing to its surface roughness. The modified surface with carbonyldiimidazole is suitable for the direct immobilization of larger molecules especially for biomolecular assemblies without intermediate chemical modifications.

Waveguide-mode sensors as aptasensors

Aptamers are artificial nucleic acid ligands that can be generated by in vitro selection through partition and amplification. Aptamers can be generated against a wide range of biomolecules through the formation of versatile stem-loop structures. Because aptamers are potential substitutes for antibodies and drugs, the development of an aptamer-based sensor (aptasensor) is mandatory for diagnosis. We previously reported that waveguide-mode sensors are useful in the analysis of a wide range of biomolecular interactions, including aptamers. The advantages of the waveguide-mode sensor that we developed include physical and chemical stability and that higher sensitivity can be achieved with ease by perforating the waveguide layer or using colored materials such as dyes or metal nanoparticles as labels. Herein, we provide an overview of the strategies and applications for aptamer-based analyses using waveguide-mode sensors.