Selective chemical modification of silicon nitride/silicon oxide nanostructures to develop label-free biosensors

Biofunctionalization of Multiplexed Silicon Photonic Biosensors

Silicon photonic (SiP) sensors offer a promising platform for robust and low-cost decentralized diagnostics due to their high scalability, low limit of detection, and ability to integrate multiple sensors for multiplexed analyte detection. Their CMOS-compatible fabrication enables chip-scale miniaturization, high scalability, and low-cost mass production. Sensitive, specific detection with silicon photonic sensors is afforded through biofunctionalization of the sensor surface; consequently, this functionalization chemistry is inextricably linked to sensor performance. In this review, we first highlight the biofunctionalization needs for SiP biosensors, including sensitivity, specificity, cost, shelf-stability, and replicability and establish a set of performance criteria. We then benchmark biofunctionalization strategies for SiP biosensors against these criteria, organizing the review around three key aspects: bioreceptor selection, immobilization strategies, and patterning techniques. First, we evaluate bioreceptors, including antibodies, aptamers, nucleic acid probes, molecularly imprinted polymers, peptides, glycans, and lectins. We then compare adsorption, bioaffinity, and covalent chemistries for immobilizing bioreceptors on SiP surfaces. Finally, we compare biopatterning techniques for spatially controlling and multiplexing the biofunctionalization of SiP sensors, including microcontact printing, pin- and pipette-based spotting, microfluidic patterning in channels, inkjet printing, and microfluidic probes.

Directly immersible silicon photonic probes: Application to rapid SARS-CoV-2 serological testing

Silicon photonic probes based on broad-band Mach-Zehnder interferometry are explored for the first time as directly immersible immunosensors alleviating the need for microfluidics and pumps. Each probe includes two U-shaped waveguides allowing light in- and out-coupling from the same chip side through a bifurcated fiber and a mechanical coupler. At the opposite chip side, two Mach-Zehnder interferometers (MZI) are located enabling real-time monitoring of binding reactions by immersion of this chip side into a sample. The sensing arm windows of the two MZIs have different length resulting in two distinct peaks in the Fourier domain, the phase shift of which can be monitored independently through Fast Fourier Transform of the output spectrum. The photonic probes analytical potential was demonstrated through detection of antibodies against SARS-CoV-2 in human serum samples. For this, one MZI was functionalized with the Receptor Binding Domain (RBD) of SARS-CoV-2 Spike 1 protein, and the other with bovine serum albumin to serve as reference. The biofunctionalized probes were immersed for 10 min in human serum sample and then for 5 min in goat anti-human IgG Fc specific antibody solution. Using a humanized rat antibody against SARS-CoV-2 RBD, a detection limit of 20 ng/mL was determined. Analysis of human serum samples indicated that the proposed sensor discriminated completely non-infected/non-vaccinated from vaccinated individuals, and the antibodies levels determined correlated well with those determined in the same samples by ELISA. These results demonstrated the potential of the proposed sensor to serve as an efficient tool for expeditious point-of-care testing.

Fabrication of Multiscale 1-Octadecene Monolayer Patterned Arrays Based on a Chemomechanical Method

A controlled and self-assembled micromachining system was built to fabricate a mico/nanoscale monolayer patterned array on a silicon surface using a diamond tip. The process was as follows: (1) we preprocessed a silicon wafer to obtain a hydrogen-terminated silicon surface; (2) we scratched three rectangular arrays of 10 μm × 3 μm with a spacing of 2 μm on the silicon surface with a diamond tip in 1-octadecene solution; the Si-H bonds were broken, and silicon free radicals were formed; (3) the 1-octadecene molecules were connected with silicon atoms based on Si-C covalent bonds, and the 1-octadecene nano monolayer was self-assembled on the patterned arrays of the silicon surface. Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Sessile water contact angles were used to detect and characterize the self-assembled monolayers (SAMs). The XPS results showed that the Si2p peak and the O1s peak were significantly decreased after self-assembly; however, the C1s peak was successively significantly increased. Sessile water contact angles showed that the hydrophilicity was weakened after the formation of 1-octenecene SAMs on the silicon substrate. The nanofriction of the sample was measured with AFM. The change in nanofriction also demonstrated that the SAMs were formed in accordance with the patterned array. We demonstrated that, by using this method, self-assembled multiscale structures on silicon substrate can be formed quickly and conveniently.

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.

Selective Gas-Phase Functionalization of SiO2 and SiNx Surfaces with Hydrocarbons

Selective functionalization of dielectric surfaces is required for area-selective atomic layer deposition and etching. We have identified precursors for the selective gas-phase functionalization of plasma-deposited SiO₂ and SiN_x surfaces with hydrocarbons. The corresponding reaction mechanism of the precursor molecules with the two surfaces was studied using in situ surface infrared spectroscopy. We show that at a substrate temperature of 70 °C, cyclic azasilanes preferentially react with an -OH-terminated SiO₂ surface over a -NH_x-terminated SiN_x surface with an attachment selectivity of ∼5.4, which is limited by the partial oxidation of the SiN_x surface. The cyclic azasilane undergoes a ring-opening reaction where the Si-N bond cleaves upon the reaction with surface -OH groups forming a Si-O-Si linkage. After ring opening, the backbone of the grafted hydrocarbon is terminated with a secondary amine, -NHCH₃, which can react with water to form an -OH-terminated surface and release CH₃NH₂ as the product. The surface coverage of the grafted cyclic azasilane is calculated as ∼3.3 × 10¹⁴ cm^-2, assuming that each reacted -OH group contributes to one hydrocarbon linkage. For selective attachment to SiN_x over SiO₂ surfaces, we determined the reaction selectivity of aldehydes. We demonstrate that aldehydes selectively attach to SiN_x over SiO₂ surfaces, and for the specific branched aliphatic aldehyde used in this work, almost no reaction was detected with the SiO₂ surface. A fraction of the aldehyde molecules reacts with surface -NH₂ groups to form an imine (Si-N═C) surface linker with H₂O released as the byproduct. The other fraction of the aldehydes also reacts with surface -NH₂ groups but do not undergo the water-elimination step and remains attached to the surface as an aminoalcohol (Si-NH-COH-). The surface coverage of the grafted aldehyde is calculated as ∼9.8 × 10¹⁴ cm^-2 using a known infrared absorbance cross-section for the -C(CH₃)₃ groups.

Sensitive detection of cardiac troponin-I protein using fabricated piezoresistive microcantilevers by a novel method of asymmetric biofunctionalization

Microcantilever-based sensor platform has attracted a lot of attention over the time in detection of a variety of molecules due to their miniaturized dimensions. Sensitivity enhancement is an important aspect of such sensors, especially when used for point-of-care diagnostic purpose. However, the major concern while operating these sensors in deflection mode is their sensitivity which mainly relies on selective chemical modification protocols employed on these sensor surfaces. One of the ways of getting better sensitivity is through asymmetric (one side) biofunctionalization of the sensor surface. In the presented work here, we have demonstrated a novel approach of asymmetric biofunctionalization of proteins in overall sensitivity enhancement of piezoresistive silicon nitride-oxide microcantilever sensor platform inside a flow chamber. Herein, using our developed surface chemistry, asymmetrically biofunctionalized microcantilevers first exhibited a greater electrical response in terms of piezoresistance change than their symmetric counterpart in the detection of human immunoglobulins (HIgGs) protein. Finally, these microcantilevers were employed to exhibit the enhanced sensitivity towards the detection of a crucial cardiac marker protein, i.e. Troponin-I (cTnI) down to 250 ng ml^-1 using asymmetric biofunctionalization process. This study shows that the developed asymmetric biofunctionalization methodology may be used as a general protocol to detect other important biomarkers of clinical applications with improved sensitivity.

Development of a methodology for reversible chemical modification of silicon surfaces with application in nanomechanical biosensors

Hypervalent tellurium compounds have a particular reactivity towards thiol compounds which are related to their biological properties. In this work, this property was assembled to tellurium-functionalized surfaces. These compounds were used as linkers in the immobilization process of thiolated biomolecules (such as DNA) on microcantilever surfaces. The telluride derivatives acted as reversible binding agents due to their redox properties, providing the regeneration of microcantilever surfaces and allowing their reuse for further biomolecules immobilizations, recycling the functional surface. Initially, we started from the synthesis of 4-((3-((4-methoxyphenyl) tellanyl) phenyl) amino)-4-oxobutanoic acid, a new compound, which was immobilized on a silicon surface. In nanomechanical systems, the detection involved a hybridization study of thiolated DNA sequences. Fluorescence microscopy technique was used to confirm the immobilization and removal of the telluride-DNA system and provided revealing results about the potentiality of applying redox properties to chalcogen derivatives at surfaces.

Experimental study of the evanescent-wave photonic sensors response in presence of molecular beacon conformational changes

An experimental study of the influence of the conformational change suffered by molecular beacon (MB) probes-upon the biorecognition of nucleic acid target oligonucleotides over evanescent wave photonic sensors-is reported. To this end, high sensitivity photonic sensors based on silicon photonic bandgap (PBG) structures were used, where the MB probes were immobilized via their 5' termination. Those MBs incorporate a biotin moiety close to their 3' termination in order to selectively bind a streptavidin molecule to them. The different photonic sensing responses obtained toward the target oligonucleotide detection, when the streptavidin molecule was bound to the MB probes or not, demonstrate the conformational change suffered by the MB upon hybridization, which promotes the displacement of the streptavidin molecule away from the surface of the photonic sensing structure.

Emerging Cytokine Biosensors with Optical Detection Modalities and Nanomaterial-Enabled Signal Enhancement

Protein biomarkers, especially cytokines, play a pivotal role in the diagnosis and treatment of a wide spectrum of diseases. Therefore, a critical need for advanced cytokine sensors has been rapidly growing and will continue to expand to promote clinical testing, new biomarker development, and disease studies. In particular, sensors employing transduction principles of various optical modalities have emerged as the most common means of detection. In typical cytokine assays which are based on the binding affinities between the analytes of cytokines and their specific antibodies, optical schemes represent the most widely used mechanisms, with some serving as the gold standard against which all existing and new sensors are benchmarked. With recent advancements in nanoscience and nanotechnology, many of the recently emerging technologies for cytokine detection exploit various forms of nanomaterials for improved sensing capabilities. Nanomaterials have been demonstrated to exhibit exceptional optical properties unique to their reduced dimensionality. Novel sensing approaches based on the newly identified properties of nanomaterials have shown drastically improved performances in both the qualitative and quantitative analyses of cytokines. This article brings together the fundamentals in the literature that are central to different optical modalities developed for cytokine detection. Recent advancements in the applications of novel technologies are also discussed in terms of those that enable highly sensitive and multiplexed cytokine quantification spanning a wide dynamic range. For each highlighted optical technique, its current detection capabilities as well as associated challenges are discussed. Lastly, an outlook for nanomaterial-based cytokine sensors is provided from the perspective of optimizing the technologies for sensitivity and multiplexity as well as promoting widespread adaptations of the emerging optical techniques by lowering high thresholds currently present in the new approaches.

3D-printed microfluidic magnetic preconcentrator for the detection of bacterial pathogen using an ATP luminometer and antibody-conjugated magnetic nanoparticles

Various types of microfluidic systems have been developed to detect bacterial pathogens. However, most of these require enrichment steps that take at least several hours when detecting bacteria that are present with a low number of cells and, in addition, fabrication requires complicated assembly steps. In this study, we report the development of 3D microfluidic magnetic preconcentrator (3DμFMP) made of plastic via 3D printing without the need for any assembly. 3DμFMP could selectively preconcentrate enterohemorrhagic Escherichia coli O157:H7 in 100mL by a factor of 700 within 1h using antibody-conjugated magnetic nanoparticles (Ab-MNPs). With the combined use of an ATP luminometer, as low as 10 E. coli O157:H7 CFU (colony forming unit)/mL could be detected in blood. These results demonstrate the feasibility of 3DμFMP as a preconcentrator to improve the detection limit of existing bacterial detection systems.

Surface etching, chemical modification and characterization of silicon nitride and silicon oxide--selective functionalization of Si3N4 and SiO2

The ability to selectively chemically functionalize silicon nitride (Si3N4) or silicon dioxide (SiO2) surfaces after cleaning would open interesting technological applications. In order to achieve this goal, the chemical composition of surfaces needs to be carefully characterized so that target chemical reactions can proceed on only one surface at a time. While wet-chemically cleaned silicon dioxide surfaces have been shown to be terminated with surficial Si-OH sites, chemical composition of the HF-etched silicon nitride surfaces is more controversial. In this work, we removed the native oxide under various aqueous HF-etching conditions and studied the chemical nature of the resulting Si3N4 surfaces using infrared absorption spectroscopy (IRAS), x-ray photoelectron spectroscopy (XPS), low energy ion scattering (LEIS), and contact angle measurements. We find that HF-etched silicon nitride surfaces are terminated by surficial Si-F and Si-OH bonds, with slightly subsurface Si-OH, Si-O-Si, and Si-NH2 groups. The concentration of surficial Si-F sites is not dependent on HF concentration, but the distribution of oxygen and Si-NH2 displays a weak dependence. The Si-OH groups of the etched nitride surface are shown to react in a similar manner to the Si-OH sites on SiO2, and therefore no selectivity was found. Chemical selectivity was, however, demonstrated by first reacting the -NH2 groups on the etched nitride surface with aldehyde molecules, which do not react with the Si-OH sites on a SiO2 surface, and then using trichloro-organosilanes for selective reaction only on the SiO2 surface (no reactivity on the aldehyde-terminated Si3N4 surface).

Asymmetric immobilization of antibodies on a piezo-resistive micro-cantilever surface

For cantilever-based MEMS sensors, selective chemical modification of the sensing surface is used for the detection of chemical and biological analytes.

Optimization of high-Q coupled nanobeam cavity for label-free sensing

We numerically and experimentally investigated the lateral coupling between photonic crystal (PhC) nanobeam (NB) cavities, pursuing high sensitivity and figure of merit (FOM) label-free biosensor. We numerically carried out 3D finite-difference time-domain (3D-FDTD) and the finite element method (FEM) simulations. We showed that when two PhC NB cavities separated by a small gap are evanescently coupled, the variation in the gap width significantly changes the coupling efficiency between the two coupled NB cavities and the resulting resonant frequencies split. Experimentally, we fabricated laterally-coupled PhC NB cavities using (InGaAsP) layer on the InP substrate. For sensing, we showed that the laterally coupled PhC NB cavities sensor exhibits higher sensitivity than the single PhC NB cavity. The higher sensitivity of laterally coupled PhC NB cavities is due to the strong evanescent coupling between nearby PhC NB cavities, which depends on the gap width and it is attributed to the large confinement of the electromagnetic field in the gap (air or liquid). As a result of the lateral coupling, both even (symmetric) and odd (asymmetric) modes exist. We show that even modes are more sensitive than odd modes. In addition, higher-order modes exhibit higher sensitivity. Hence, we characterized and examined the fabricated PhC NB cavity as a label-free biosensor, and it exhibits high figure of merit due to its high Q-factor. This illustrates a potentially useful method for optical sensing at nanoscale.

Description of an advantageous optical label-free biosensing interferometric read-out method to measure biological species

In this article we report a new, simple, and reliable optical read-out detection method able to assess Rotavirus present in human sera as well as in the viral pollution sources. It is based on the interference of two interferometers used as biophotonic transducers. The method significantly improves the optical label-free biosensing response measuring both, the concentration of the AgR and its corresponding size. Two different immunoassays were carried out: Bovine Serum Albumin (BSA), and the recognition by its antibody (anti-BSA); and Rotavirus (AgR) and the recognition by its antibody (anti-AgR). In the cases studied, and using as model interferometer a simple Fabry-Perot transducer, we demonstrate a biosensing enhancement of two orders of magnitude in the Limit of Detection (LoD). In fact, this read-out optical method may have significant implications to enhance other optical label-free photonic transducers reported in the scientific literature.

Slotted photonic crystal sensors

Optical biosensors are increasingly being considered for lab-on-a-chip applications due to their benefits such as small size, biocompatibility, passive behaviour and lack of the need for fluorescent labels. The light guiding mechanisms used by many of them results in poor overlap of the optical field with the target molecules, reducing the maximum sensitivity achievable. This review article presents a new platform for optical biosensors, namely slotted photonic crystals, which provide higher sensitivities due to their ability to confine, spatially and temporally, the optical mode peak within the analyte itself. Loss measurements showed values comparable to standard photonic crystals, confirming their ability to be used in real devices. A novel resonant coupler was designed, simulated, and experimentally tested, and was found to perform better than other solutions within the literature. Combining with cavities, microfluidics and biological functionalization allowed proof-of-principle demonstrations of protein binding to be carried out. Higher sensitivities were observed in smaller structures than possible with most competing devices reported in the literature. This body of work presents slotted photonic crystals as a realistic platform for complete on-chip biosensing; addressing key design, performance and application issues, whilst also opening up exciting new ideas for future study.

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.

Copper-free click biofunctionalization of silicon nitride surfaces via strain-promoted alkyne-azide cycloaddition reactions

Cu-free "click" chemistry is explored on silicon nitride (Si(3)N(4)) surfaces as an effective way for oriented immobilization of biomolecules. An ω-unsaturated ester was grafted onto Si(3)N(4) using UV irradiation. Hydrolysis followed by carbodiimide-mediated activation yielded surface-bound active succinimidyl and pentafluorophenyl ester groups. These reactive surfaces were employed for the attachment of bicyclononyne with an amine spacer, which subsequently enabled room temperature strain-promoted azide-alkyne cycloaddition (SPAAC). This stepwise approach was characterized by means of static water contact angle, X-ray photoelectron spectroscopy, and fluorescence microscopy. The surface-bound SPAAC reaction was studied with both a fluorine-tagged azide and an azide-linked lactose, yielding hydrophobic and bioactive surfaces for which the presence of trace amounts of Cu ions would have been problematic. Additionally, patterning of the Si(3)N(4) surface using this metal-free click reaction with a fluorescent azide is shown. These results demonstrate the ability of the SPAAC as a generic tool for anchoring complex molecules onto a surface under extremely mild, namely ambient and metal-free, conditions in a clean and relatively fast manner.

Photonic-crystal membranes for optical detection of single nano-particles, designed for biosensor application

A sensor designed to detect bio-molecules is presented. The sensor exploits a planar 2D photonic crystal (PC) membrane with sub-micron thickness and through holes, to induce high optical fields that allow detection of nano-particles smaller than the diffraction limit of an optical microscope. We report on our design and fabrication of a PC membrane with a nano-particle trapped inside. We have also designed and built an imaging system where an optical microscope and a CCD camera are used to take images of the PC membrane. Results show how the trapped nano-particle appears as a bright spot in the image. In a first experimental realization of the imaging system, single particles with a radius of 75 nm can be detected.

Surface self-assembly of N-fluorenyl-9-methoxycarbonyl diphenylalanine on silica wafer

N-Fluorenyl-9-methoxycarbonyl diphenylalanine (Fmoc-FF-OH) was chemically immobilized to the surface of silica wafer as the "seed". When immersing this peptide attached silica wafer into the dipeptide aqueous solution, the occurrence of a pH triggered surface self-assembly resulted in the formation of peptide nanorods on the surface of silica wafer. This surface self-assembly exhibited a dependence on the concentration of the dipeptide aqueous solution. It was proposed that the self-assembly of this dipeptide on the surface of silica wafer was similar to that in aqueous solution. In comparison with the conventional physical adsorption on the substrates, the chemically attached self-assembled nanorods exhibited much improved adsorption capacity on the substrate surface.

Single-strand DNA detection using a planar photonic-crystal-waveguide-based sensor

We report an experimental demonstration of single-strand DNA (ssDNA) detection at room temperature using a photonic-crystal-waveguide-based optical sensor. The sensor surface was previously biofunctionalized with ssDNA probes to be used as specific target receptors. Our experiments showed that it is possible to detect these hybridization events using planar photonic-crystal structures, reaching an estimated detection limit as low as 19.8 nM for the detection of the complementary DNA strand.

Experimental determination of the sensitivity of Bloch surface waves based sensors

Detection of glucose in water solution for several different concentrations has been performed with the purpose to determine the sensitivity of Near Infrared Bloch Surface Waves (lambda = 1.55microm) upon refractive index variations of the outer medium. TE-polarized electromagnetic surface waves are excited by a prism on a silicon nitride multilayer, according to the Kretschmann configuration. The real-time reflectance changes induced by discrete variations in glucose concentration has been revealed and analyzed. Without using any particular averaging strategy during the measurements, we pushed the device detection limit down to a glucose concentration of 2.5mg/dL, corresponding to a minimum detectable refractive index variation of the water solution as low as 3.8.10(-6).