Optical Nanobiosensor Based on Surface-Enhanced Raman Spectroscopy and Catalytic Hairpin Assembly for Early-Stage Lung Cancer Detection via Blood Circular RNA

Lung cancer has become the leading cause of cancer-related deaths globally. However, early detection of lung cancer remains challenging, resulting in poor outcomes for the patients. Herein, we developed an optical biosensor integrating surface-enhanced Raman spectroscopy (SERS) with a catalyzed hairpin assembly (CHA) to detect circular RNA (circRNA) associated with tumor formation and progression (circSATB2). The signals of the Raman reporter were considerably enhanced by generating abundant SERS "hot spots" with a core-shell nanoprobe and 2D SERS substrate with calibration capabilities. This approach enabled the sensitive (limit of detection: 0.766 fM) and reliable quantitative detection of the target circRNA. Further, we used the developed biosensor to detect the circRNA in human serum samples, revealing that patients with lung cancer had higher circRNA concentrations than healthy subjects. Moreover, we characterized the unique circRNA concentration profiles of the early stages (IA and IB) and subtypes (IA1, IA2, and IA3) of lung cancer. These results demonstrate the potential of the proposed optical sensing nanoplatform as a liquid biopsy and prognostic tool for the early screening of lung cancer.

Handheld Biosensor System Based on a Gradient Grating Period Guided-Mode Resonance Device

Handheld biosensors have attracted substantial attention for numerous applications, including disease diagnosis, drug dosage monitoring, and environmental sensing. This study presents a novel handheld biosensor based on a gradient grating period guided-mode resonance (GGP-GMR) sensor. Unlike conventional GMR sensors, the proposed sensor's grating period varies along the device length; hence, the resonant wavelength varies linearly along the device length. If a GGP-GMR sensor is illuminated with a narrow band of light at normal incidence, the light resonates and reflects at a specific period but transmits at other periods; this can be observed as a dark band by using a complementary metal oxide semiconductor (CMOS) underneath the sensor. The concentration of a target analyte can be determined by monitoring the shift of this dark band. We designed and fabricated a handheld device incorporating a light-emitting diode (LED) light source, the necessary optics, an optofluidic chip with an embedded GGP-GMR sensor, and a CMOS. LEDs with different beam angles and bandpass filters with different full width at half maximum values were investigated to optimize the dark band quality and improve the accuracy of the subsequent image analysis. Substrate materials with different refractive indices and waveguide thicknesses were also investigated to maximize the GGP-GMR sensor's figure of merit. Experiments were performed to validate the proposed handheld biosensor, which achieved a limit of detection (LOD) of 1.09 × 10-3 RIU for bulk solution measurement. The sensor's performance in the multiplexed detection of albumin and creatinine solutions at concentrations of 0-500 μg/mL and 0-10 mg/mL, respectively, was investigated; the corresponding LODs were 0.66 and 0.61 μg/mL.

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.

Cancer Marker Immunosensing through Surface-Enhanced Photoluminescence on Nanostructured Silver Substrates

Nanostructured noble metal surfaces enhance the photoluminescence emitted by fluorescent molecules, permitting the development of highly sensitive fluorescence immunoassays. To this end, surfaces with silicon nanowires decorated with silver nanoparticles in the form of dendrites or aggregates were evaluated as substrates for the immunochemical detection of two ovarian cancer indicators, carbohydrate antigen 125 (CA125) and human epididymis protein 4 (HE4). The substrates were prepared by metal-enhanced chemical etching of silicon wafers to create, in one step, silicon nanowires and silver nanoparticles on top of them. For both analytes, non-competitive immunoassays were developed using pairs of highly specific monoclonal antibodies, one for analyte capture on the substrate and the other for detection. In order to facilitate the identification of the immunocomplexes through a reaction with streptavidin labeled with Rhodamine Red-X, the detection antibodies were biotinylated. An in-house-developed optical set-up was used for photoluminescence signal measurements after assay completion. The detection limits achieved were 2.5 U/mL and 3.12 pM for CA125 and HE4, respectively, with linear dynamic ranges extending up to 500 U/mL for CA125 and up to 500 pM for HE4, covering the concentration ranges of both healthy and ovarian cancer patients. Thus, the proposed method could be implemented for the early diagnosis and/or prognosis and monitoring of ovarian cancer.

Gradient Guided-Mode Resonance Biosensor with Smartphone Readout

Integrating biosensors with smartphones is becoming an increasingly popular method for detecting various biomolecules and could replace expensive laboratory-based instruments. In this work, we demonstrate a novel smartphone-based biosensor system with a gradient grating period guided-mode resonance (GGP-GMR) sensor. The sensor comprises numerous gratings which each correspond to and block the light of a specific resonant wavelength. This results in a dark band, which is observed using a CCD underneath the GGP-GMR sensor. By monitoring the shift in the dark band, the concentration of a molecule in a sample can be determined. The sensor is illuminated by a light-emitting diode, and the light transmitted through the GGP-GMR sensor is directly captured by a smartphone, which then displays the results. Experiments were performed to validate the proposed smartphone biosensor and a limit of detection (LOD) of 1.50 × 10-3 RIU was achieved for sucrose solutions. Additionally, multiplexed detection was demonstrated for albumin and creatinine solutions at concentrations of 0-500 and 0-1 mg/mL, respectively; the corresponding LODs were 1.18 and 20.56 μg/mL.

Sensitive and Compact Evanescent-Waveguide Optical Detector for Sugar Sensing in Commercial Beverages

This work presents a compact and sensitive refractive index sensor able to evaluate the concentration of an analyte in a sample. Its working principle leverages on the changes in the optical absorption features introduced by the sample itself on the evanescent waves of a light beam. The device's high compactness is achieved by embedding the sample-light interaction site and the detector in a 1 cm2 glass substrate, thanks to microelectronics technologies. High sensitivity is obtained by employing a low-noise p-i-n hydrogenated amorphous silicon junction, whose manufacture process requires only four UV lithographic steps on a glass substrate, thus ensuring low production costs. The system's capabilities are investigated by sensing the sugar content in three commercial beverages. Sensitivities of 32, 53 and 80 pA/% and limits of detection of 47, 29 and 18 ppm are achieved. The above performance is comparable with state-of-the-art results available in the literature, where more complex optical setups, expensive instrumentation and bulky devices are used.

Recent Progresses in Optical Biosensors for Interleukin 6 Detection

Interleukin 6 (IL-6) is pleiotropic cytokine with pathological pro-inflammatory effects in various acute, chronic and infectious diseases. It is involved in a variety of biological processes including immune regulation, hematopoiesis, tissue repair, inflammation, oncogenesis, metabolic control, and sleep. Due to its important role as a biomarker of many types of diseases, its detection in small amounts and with high selectivity is of particular importance in medical and biological fields. Laboratory methods including enzyme-linked immunoassays (ELISAs) and chemiluminescent immunoassays (CLIAs) are the most common conventional methods for IL-6 detection. However, these techniques suffer from the complexity of the method, the expensiveness, and the time-consuming process of obtaining the results. In recent years, too many attempts have been conducted to provide simple, rapid, economical, and user-friendly analytical approaches to monitor IL-6. In this regard, biosensors are considered desirable tools for IL-6 detection because of their special features such as high sensitivity, rapid detection time, ease of use, and ease of miniaturization. In this review, current progresses in different types of optical biosensors as the most favorable types of biosensors for the detection of IL-6 are discussed, evaluated, and compared.

A New Optical Interferometric Biosensing System Enhanced with Nanoparticles for Alzheimer's Disease in Serum

In this scientific work, we demonstrate, for the first time, a new biosensing system and procedure to measure specifically the total Tau (T-Tau) protein in serum, one of the most relevant biomarkers of Alzheimer's disease (AD). AD is a progressive brain disorder that produces neuronal and cognitive dysfunction and affects a high percentage of people worldwide. For this reason, diagnosing AD at the earliest possible stage involves improving diagnostic systems. We report on the use of interferometric bio-transducers integrated with 65 microwells forming diagnostic KITs read-out by using the Interferometric Optical Detection Method (IODM). Moreover, biofunctionalized silicon dioxide (SiO₂) nanoparticles (NPs) acting as interferometric enhancers of the bio-transducers signal allow for the improvement of both the optical read-out signal and its ability to work with less-invasive biological samples such as serum instead of cerebrospinal fluid (CSF). As a result, in this paper, we describe for the first time a relevant diagnostic alternative to detect Tau protein at demanding concentrations of 10 pg/mL or even better, opening the opportunity to be used for detecting other relevant AD-related biomarkers in serum, such as β-amyloid and phosphorylated Tau (P-Tau), neurofilaments, among others that can be considered relevant for AD.

Nucleic acid aptamer-based biosensors and their application in thrombin analysis

Thrombin is a multifunctional serine protease that plays an important role in coagulation and anticoagulation processes. Aptamers have been widely applied in biosensors due to their high specificity, low cost and good biocompatibility. This review summarizes recent advances in thrombin quantification using aptamer-based biosensors. The primary focus is optical sensors and electrochemical sensors, along with their applications in thrombin analysis and disease diagnosis.

Detecting GPCR Signals With Optical Biosensors of Gα-GTP in Cell Lines and Primary Cell Cultures

G protein-coupled receptors (GPCRs) are the largest class of transmembrane receptors and mediate a wide variety of physiological processes. GPCRs respond to a plethora of extracellular ligands and initiate signaling pathways inside cells via heterotrimeric G proteins (Gαβγ). Because of the critical role GPCRs play in regulating biological processes and as pharmacological targets, the availability of tools to measure their signaling activity are of high interest. Live-cell biosensors that detect the activity of G proteins in response to GPCR stimulation have emerged as a powerful approach to investigate GPCR/G protein signaling. Here, we detail methods to monitor G protein activity through direct measurement of GTP-bound Gα subunits using optical biosensors based on bioluminescence resonance energy transfer (BRET). More specifically, this article describes the use of two types of complementary biosensors. The first protocol explains how to use a multicomponent BRET biosensor that relies on expression of exogenous G proteins in cell lines. This protocol yields robust responses that are compatible with endpoint measurements of dose-dependent ligand effects or with kinetic measurements of subsecond resolution. The second protocol describes the implementation of unimolecular biosensors that detect the activation of endogenous G proteins in cell lines expressing exogenous GPCRs or in primary cells upon stimulation of endogenous GPCRs. Overall, using the biosensors as described in this article will help users characterize the mechanisms of action of many pharmacological agents and natural ligands that modulate GPCR and G protein signaling with high precision. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Using bimolecular BRET biosensors to monitor Gα-GTP formation of tagged Gα in live cells Alternate Protocol 1: Measuring GPCR dose-dependent Gα-GTP responses in endpoint format Basic Protocol 2: Using unimolecular BRET biosensors to study endogenous G protein activity Alternate Protocol 2: Using unimolecular BRET biosensors to study endogenous G protein activity in mouse cortical neurons.

Surface plasmon resonance based-optical biosensor: Emerging diagnostic tool for early detection of diseases

The development of diagnostic tools remains at the center of the health care system. In recent times optical biosensors have been widely applied in the scientific community, especially for monitoring protein-protein or nucleic acid hybridization interactions. Optical biosensors-derived surface plasmon resonance (SPR) technology has appeared as a revolutionary technology at the current times. This review focuses on the research work in molecular biomarker evaluation using the technique based on SPR for translational clinical diagnosis. The review has covered both communicable and noncommunicable diseases by using different bio-fluids of the patient's sample for diagnosis of the diseases. An increasing number of SPR approaches have been developed in healthcare research and fundamental biological studies. The utility of SPR in the area of biosensing basically lies in its noninvasive diagnostic and prognostic feature due to its label-free high sensitivity and specificity properties. This makes SPR an invaluable tool with precise application in the recognition of different stages of the disease.

Optical Glucose Sensors Based on Chitosan-Capped ZnS-Doped Mn Nanomaterials

The primary goal of glucose sensing at the point of care is to identify glucose concentrations within the diabetes range. However, lower glucose levels also pose a severe health risk. In this paper, we propose quick, simple, and reliable glucose sensors based on the absorption and photoluminescence spectra of chitosan-capped ZnS-doped Mn nanomaterials in the range of 0.125 to 0.636 mM glucose corresponding to 2.3 mg/dL to 11.4 mg/dL. The detection limit was 0.125 mM (or 2.3 mg/dL), much lower than the hypoglycemia level of 70 mg/dL (or 3.9 mM). Chitosan-capped ZnS-doped Mn nanomaterials retain their optical properties while improving sensor stability. This study reports for the first time how the sensors' efficacy was affected by chitosan content from 0.75 to 1.5 wt.%. The results showed that 1 %wt chitosan-capped ZnS-doped Mn is the most-sensitive, -selective, and -stable material. We also put the biosensor through its paces with glucose in phosphate-buffered saline. In the same range of 0.125 to 0.636 mM, the sensors-based chitosan-coated ZnS-doped Mn had a better sensitivity than the working water environment.

Experimental Verification for Numerical Simulation of Thalamic Stimulation-Evoked Calcium-Sensitive Fluorescence and Electrophysiology with Self-Assembled Multifunctional Optrode

Owing to its capacity to eliminate a long-standing methodological limitation, fiber photometry can assist research gaining novel insight into neural systems. Fiber photometry can reveal artifact-free neural activity under deep brain stimulation (DBS). Although evoking neural potential with DBS is an effective method for mediating neural activity and neural function, the relationship between DBS-evoked neural Ca²⁺ change and DBS-evoked neural electrophysiology remains unknown. Therefore, in this study, a self-assembled optrode was demonstrated as a DBS stimulator and an optical biosensor capable of concurrently recording Ca²⁺ fluorescence and electrophysiological signals. Before the in vivo experiment, the volume of tissue activated (VTA) was estimated, and the simulated Ca²⁺ signals were presented using Monte Carlo (MC) simulation to approach the realistic in vivo environment. When VTA and the simulated Ca²⁺ signals were combined, the distribution of simulated Ca²⁺ fluorescence signals matched the VTA region. In addition, the in vivo experiment revealed a correlation between the local field potential (LFP) and the Ca²⁺ fluorescence signal in the evoked region, revealing the relationship between electrophysiology and the performance of neural Ca²⁺ concentration behavior. Concurrent with the VTA volume, simulated Ca²⁺ intensity, and the in vivo experiment, these data suggested that the behavior of neural electrophysiology was consistent with the phenomenon of Ca²⁺ influx to neurons.

Recent Progress on Optical Biosensors Developed for Nucleic Acid Detection Related to Infectious Viral Diseases

Optical biosensors have many advantages over traditional analytical methods. They enable the identification of several biological and chemical compounds directly, instantly, and without the need of labels. Their benefits include excellent specificity, sensitivity, compact size, and low cost. In this review, the main focus is placed on the nucleic acid-based optical biosensor technologies, including colorimetric, fluorescence, surface plasmon resonance (SPR), Evanescent-Wave Optical, Fiber optic and bioluminescent optical fibre. The fundamentals of each type of biosensor are briefly explained, and particular emphasis has been placed on the achievements which have been gained in the last decade on the field of diagnosis of infectious viral diseases. Concluding remarks concerning the perspectives of further developments are discussed.

Recent Developments in DNA-Nanotechnology-Powered Biosensors for Zika/Dengue Virus Molecular Diagnostics

Zika virus (ZIKV) and dengue virus (DENV) are highly contagious and lethal mosquito-borne viruses. Global warming is steadily increasing the probability of ZIKV and DENV infection, and accurate diagnosis is required to control viral infections worldwide. Recently, research on biosensors for the accurate diagnosis of ZIKV and DENV has been actively conducted. Moreover, biosensor research using DNA nanotechnology is also increasing, and has many advantages compared to the existing diagnostic methods, such as polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA). As a bioreceptor, DNA can easily introduce a functional group at the 5' or 3' end, and can also be used as a folded structure, such as a DNA aptamer and DNAzyme. Instead of using ZIKV and DENV antibodies, a bioreceptor that specifically binds to viral proteins or nucleic acids has been fabricated and introduced using DNA nanotechnology. Technologies for detecting ZIKV and DENV can be broadly divided into electrochemical, electrical, and optical. In this review, advances in DNA-nanotechnology-based ZIKV and DENV detection biosensors are discussed.

Refractive Index Measurement Using SOI Photodiode with SP Antenna toward SOI CMOS-Compatible Integrated Optical Biosensor

This paper proposes a new optical biosensor composed of a silicon-on-insulator (SOI) p-n junction photodiode (PD) with a surface plasmon (SP) antenna. When the phase-matching condition between two lateral wavelengths of the diffracted light from the SP antenna and the waveguiding mode in the SOI PD is satisfied, we observe sharp peaks in the spectroscopic light sensitivity. Since the peak wavelength depends on the RI change around the SP antenna corresponding to the phase-matching condition, the SOI PDs with an SP antenna can be applied to the optical biosensor. The RI detection limit is evaluated in the measurements with bulk solutions, and 1.11 × 10^-5 RIU (refractive index unit) can be obtained, which is comparable to that of a surface plasmon resonance (SPR) sensor, which is well known as a representative optical biosensor. In addition, the response for intermolecular bonds is estimated by the electromagnetic simulations using the finite-difference time-domain (FDTD) method to clarify its ability to detect biomolecular interactions. The results of this paper will provide new ground for high-throughput label-free biosensing, since a large number of SOI PDs with an SP antenna can be easily integrated on a single chip via an SOI complementary metal-oxide-semiconductor (CMOS) fabrication process.

Development and Application of an SPR Nanobiosensor Based on AuNPs for the Detection of SARS-CoV-2 on Food Surfaces

A new transmission route of SARS-CoV-2 through food was recently considered by the World Health Organization (WHO), and, given the pandemic scenario, the search for fast, sensitive, and low-cost methods is necessary. Biosensors have become a viable alternative for large-scale testing because they overcome the limitations of standard techniques. Herein, we investigated the ability of gold spherical nanoparticles (AuNPs) functionalized with oligonucleotides to detect SARS-CoV-2 and demonstrated their potential to be used as plasmonic nanobiosensors. The loop-mediated isothermal amplification (LAMP) technique was used to amplify the viral genetic material from the raw virus-containing solution without any preparation. The detection of virus presence or absence was performed by ultraviolet-visible (UV-Vis) absorption spectroscopy, by monitoring the absorption band of the surface plasmonic resonance (SPR) of the AuNPs. The displacement of the peak by 525 nm from the functionalized AuNPs indicated the absence of the virus (particular region of gold). On the other hand, the region ~300 nm indicated the presence of the virus when RNA bound to the functionalized AuNPs. The nanobiosensor system was designed to detect a region of the N gene in a dynamic concentration range from 0.1 to 50 × 10³ ng·mL^-1 with a limit of detection (LOD) of 1 ng·mL^-1 (2.7 × 10³ copy per µL), indicating excellent sensitivity. The nanobiosensor was applied to detect the SARS-CoV-2 virus on the surfaces of vegetables and showed 100% accuracy compared to the standard quantitative reverse transcription polymerase chain reaction (RT-qPCR) technique. Therefore, the nanobiosensor is sensitive, selective, and simple, providing a viable alternative for the rapid detection of SARS-CoV-2 in ready-to-eat vegetables.

Optical Biosensor Based on Graphene and Its Derivatives for Detecting Biomolecules

Graphene and its derivatives show great potential for biosensing due to their extraordinary optical, electrical and physical properties. In particular, graphene and its derivatives have excellent optical properties such as broadband and tunable absorption, fluorescence bursts, and strong polarization-related effects. Optical biosensors based on graphene and its derivatives make nondestructive detection of biomolecules possible. The focus of this paper is to review the preparation of graphene and its derivatives, as well as recent advances in optical biosensors based on graphene and its derivatives. The working principle of face plasmon resonance (SPR), surface-enhanced Raman spectroscopy (SERS), fluorescence resonance energy transfer (FRET) and colorimetric sensors are summarized, and the advantages and disadvantages of graphene and its derivatives applicable to various types of sensors are analyzed, and the methods of surface functionalization of graphene and its derivatives are introduced; these optical biosensors can be used for the detection of a range of biomolecules such as single cells, cellular secretions, proteins, nucleic acids, and antigen-antibodies; these new high-performance optical sensors are capable of detecting changes in surface structure and biomolecular interactions with the advantages of ultra-fast detection, high sensitivity, label-free, specific recognition, and the ability to respond in real-time. Problems in the current stage of application are discussed, as well as future prospects for graphene and its biosensors. Achieving the applicability, reusability and low cost of novel optical biosensors for a variety of complex environments and achieving scale-up production, which still faces serious challenges.

2D Material-Based Optical Biosensor: Status and Prospect

The combination of 2D materials and optical biosensors has become a hot research topic in recent years. Graphene, transition metal dichalcogenides, black phosphorus, MXenes, and other 2D materials (metal oxides and degenerate semiconductors) have unique optical properties and play a unique role in the detection of different biomolecules. Through the modification of 2D materials, optical biosensor has the advantages that traditional sensors (such as electrical sensing) do not have, and the sensitivity and detection limit are greatly improved. Here, optical biosensors based on different 2D materials are reviewed. First, various detection methods of biomolecules, including surface plasmon resonance (SPR), fluorescence resonance energy transfer (FRET), and evanescent wave and properties, preparation and integration strategies of 2D material, are introduced in detail. Second, various biosensors based on 2D materials are summarized. Furthermore, the applications of these optical biosensors in biological imaging, food safety, pollution prevention/control, and biological medicine are discussed. Finally, the future development of optical biosensors is prospected. It is believed that with their in-depth research in the laboratory, optical biosensors will gradually become commercialized and improve people's quality of life in many aspects.

Molecular Modelling of Optical Biosensor Phosphorene-Thioguanine for Optimal Drug Delivery in Leukemia Treatment

Simple Summary

Nanocarriers have been used to solve the problems associated with conventional antitumor drug delivery systems, including no specificity, severe side effects, burst release and damaging the normal cells. It improves the bioavailability and therapeutic efficiency of antitumor drugs, while providing preferential accumulation at the target site. Various 2D nanomaterials such as graphene, MoS2, and WSe2 have been used as nanocarrier. The recent discovery of phosphorene has introduced new possibilities in designing a sensible drug delivery system, due to low cytotoxicity, biocompatibility, high surface to volume ratio, which can increase its drug loading capacity. The biodegradation of phosphorene inside the human body produces non-toxic intermediates, like phosphate. Phosphate is necessary for the formation of bone and teeth. Phosphate is also used by the cell for energy, cell membranes, and DNA (deoxyribonucleic acid). Therefore, phosphorene nanocarrier is not harmful, especially for the treatment of cancer in vivo applications.

Abstract

Thioguanine is an anti-cancer drug used for the treatment of leukemia. However, thioguanine has weak aqueous solubility and low biocompatibility, which limits its performance in the treatment of cancer. In the present work, these inadequacies were targeted using density functional theory-based simulations. Three stable configurations were obtained for the adsorption of thioguanine molecules on the phosphorene surface, with adsorption energies in the range of −76.99 to −38.69 kJ/mol, indicating physisorption of the drug on the phosphorene surface. The calculated bandgap energies of the individual and combined geometries of phosphorene and thioguanine were 0.97 eV, 2.81 eV and 0.91 eV, respectively. Owing to the physisorption of the drug molecule on the phosphorene surface, the bandgap energy of the material had a direct impact on optical conductivity, which was significantly altered. All parameters that determine the potential ability for drug delivery were calculated, such as the dipole moment, chemical hardness, chemical softness, chemical potential, and electrophilicity index. The higher dipole moment (1.74 D) of the phosphorene–thioguanine complex reflects its higher biodegradability, with no adverse physiological effects.

Recent Efforts and Milestones for Simulating Nucleic Acid FRET Experiments through Computational Methods

Computational methods can greatly aid nucleic acid fluorescence experiments by either offering fully detailed atomic insights into the conformations and interactions present in the studied system or by providing accurate simulations of the fundamental parameters. Fluorescence-based optical biosensors show great potential for clinical diagnosis of life-altering diseases with a very high specificity. Many of the designs for such rely on the concept of Förster resonance energy transfer (FRET). Currently, the methods used experimentally make use of theoretical assumptions which fundamentally affect the results. Having a detailed atomistic overview or significant simulated parameters could improve the understanding of the calculations and provide much more accurate outcomes. However, there are many challenges that need to be addressed before standardized computational protocols can be employed. This review is meant to highlight the progress made for computational methods used to simulate FRET experiments for nucleic acid probes. Recent advances have been made in computational tools, such as force field parametrizations and improved protocols. Complementary simulations to experimental data are also comprised in the this review.

Disposable Polymeric Nanostructured Plasmonic Biosensors for Cell Culture Adhesion Monitoring

Over the last years, optical biosensors based on plasmonic nanomaterials have gained great scientific interest due to their unquestionable advantages compared to other biosensing technologies. They can achieve sensitive, direct, and label-free analysis with exceptional potential for multiplexing and miniaturization. Recently, it has been demonstrated the potential of using optical discs as high throughput nanotemplates for the development of plasmonic biosensors in a cost-effective way. This work is a pilot study focused on the development of an integrated plasmonic biosensor for the monitoring of cell adhesion and growth of human retinal pigmented cell line (ARPE-19) under different media conditions (0 and 2% of FBS). We observed an increase of the plasmonic band displacement under 2% FBS compared to 0% conditions over time (1, 3, and 5 h). These preliminary results show that the proposed plasmonic biosensing approach is a direct, non-destructive, and real-time tool that could be employed in the study of living cells behavior and culture conditions. Furthermore, this setup could assess the viability of the cells and their growth over time with low variability between the technical replicates improving the experimental replicability.

Peptide-Based Capture of Chikungunya Virus E2 Protein Using Porous Silicon Biosensor

The detection of pathogens presents specific challenges in ensuring that biosensors remain operable despite exposure to elevated temperatures or other extreme conditions. The most vulnerable component of a biosensor is typically the bioreceptor. Accordingly, the robustness of peptides as bioreceptors offers improved stability and reliability toward harsh environments compared to monoclonal antibodies that may lose their ability to bind target molecules after such exposures. Here, we demonstrate peptide-based capture of the Chikungunya virus E2 protein in a porous silicon microcavity biosensor at room temperature and after exposure of the peptide-functionalized biosensor to high temperature. Contact angle measurements, attenuated total reflectance-Fourier transform infrared spectra, and optical reflectance measurements confirm peptide functionalization and selective E2 protein capture. This work opens the door for other pathogenic biomarker detection using peptide-based capture agents on porous silicon and other surface-based sensor platforms.

Progress in Nanomaterials-Based Optical and Electrochemical Methods for the Assays of Exosomes

Exosomes with diameters of 30-150 nm are small membrane-bound vesicles secreted by a variety of cells. They play an important role in many biological processes, such as tumor-related immune response and intercellular signal transduction. Exosomes have been considered as emerging and noninvasive biomarkers for cancer diagnosis. Recently, a large number of optical and electrochemical biosensors have been proposed for sensitive detection of exosomes. To meet the increasing demands for ultrasensitive detection, nanomaterials have been integrated with various techniques as powerful components. Because of their intrinsic merits of biological compatibility, excellent physicochemical features and unique catalytic ability, nanomaterials have significantly improved the analytical performances of exosome biosensors. In this review, we summarized the recent progress in nanomaterials-based biosensors for the detection of cancer-derived exosomes, including fluorescence, colorimetry, surface plasmon resonance spectroscopy, surface enhanced Raman scattering spectroscopy, electrochemistry, electrochemiluminescence and so on.

Porous Silicon-Based Aptasensors: Toward Cancer Protein Biomarker Detection

The anterior gradient homologue-2 (AGR2) protein is an attractive biomarker for various types of cancer. In pancreatic cancer, it is secreted to the pancreatic juice by premalignant lesions, which would be an ideal stage for diagnosis. Thus, designing assays for the sensitive detection of AGR2 would be highly valuable for the potential early diagnosis of pancreatic and other types of cancer. Herein, we present a biosensor for label-free AGR2 detection and investigate approaches for enhancing the aptasensor sensitivity by accelerating the target mass transfer rate and reducing the system noise. The biosensor is based on a nanostructured porous silicon thin film that is decorated with anti-AGR2 aptamers, where real-time monitoring of the reflectance changes enables the detection and quantification of AGR2, as well as the study of the diffusion and target-aptamer binding kinetics. The aptasensor is highly selective for AGR2 and can detect the protein in simulated pancreatic juice, where its concentration is outnumbered by orders of magnitude by numerous proteins. The aptasensor's analytical performance is characterized with a linear detection range of 0.05-2 mg mL^-1, an apparent dissociation constant of 21 ± 1 μM, and a limit of detection of 9.2 μg mL^-1 (0.2 μM), which is attributed to mass transfer limitations. To improve the latter, we applied different strategies to increase the diffusion flux to and within the nanostructure, such as the application of isotachophoresis for the preconcentration of AGR2 on the aptasensor, mixing, or integration with microchannels. By combining these approaches with a new signal processing technique that employs Morlet wavelet filtering and phase analysis, we achieve a limit of detection of 15 nM without compromising the biosensor's selectivity and specificity.

Label-Free Detection and Spectrometrically Quantitative Analysis of the Cancer Biomarker CA125 Based on Lyotropic Chromonic Liquid Crystal

Compared with thermotropic liquid crystals (LCs), the biosensing potential of lyotropic chromonic liquid crystals (LCLCs), which are more biocompatible because of their hydrophilic nature, has scarcely been investigated. In this study, the nematic phase, a mesophase shared by both thermotropic LCs and LCLCs, of disodium cromoglycate (DSCG) was employed as the sensing mesogen in the LCLC-based biosensor. The biosensing platform was constructed so that the LCLC was homogeneously aligned by the planar anchoring strength of polyimide, but was disrupted in the presence of proteins such as bovine serum albumin (BSA) or the cancer biomarker CA125 captured by the anti-CA125 antibody, with the level of disturbance (and the optical signal thus produced) predominated by the amount of the analyte. The concentration- and wavelength-dependent optical response was analyzed by transmission spectrometry in the visible light spectrum with parallel or crossed polarizers. The concentration of CA125 can be quantified with spectrometrically derived parameters in a linear calibration curve. The limit of detection for both BSA and CA125 of the LCLC-based biosensor was superior or comparable to that of thermotropic LC-based biosensing techniques. Our results provide, to the best of our knowledge, the first evidence that LCLCs can be applied in spectrometrically quantitative biosensing.

Recent advances in Surface Plasmon Resonance (SPR) biosensors for food analysis: a review

Food safety is the prime area of concern that builds trust. With the prevailing advancements, it has become facile to ensure safety in almost all aspects. Technology has grown from tedious lab techniques to modern chromatographic techniques and immunoassays, progressed with more precise and rapid sensing through the advent of Biosensors. Biosensors provide an automated technology by presenting superfast, nondestructive and cost-effective detection in food analysis. SPR biosensor is an optical biosensor known for its versatility and has wider applications in food testing and analysis. It has an optical system for excitation and interrogation of surface plasmons, and a biomolecular recognition element to detect and seize the target analyte present in a sample. The optical signal detects the binding analyte, on the recognition element, which results in a change in refractive index at the surface and modifies the surface plasmons' propagation constant. SPR aids in label-free detection of various components such as adulterants, antibiotics, biomolecules, genetically modified foods, pesticides, insecticides, herbicides, microorganisms and microbial toxins in food and assures safety. The distinct advancements of SPR in food analysis have been found and discussed. The review also provides knowledge on the advantages and the key challenges encountered by SPR.

Plasmonic Interferometers as TREM2 Sensors for Alzheimer's Disease

We report an effective surface immobilization protocol for capture of Triggering Receptor Expressed on Myeloid Cells 2 (TREM2), a receptor whose elevated concentration in cerebrospinal fluid has recently been associated with Alzheimer's disease (AD). We employ the proposed surface functionalization scheme to design, fabricate, and assess a biochemical sensing platform based on plasmonic interferometry that is able to detect physiological concentrations of TREM2 in solution. These findings open up opportunities for label-free biosensing of TREM2 in its soluble form in various bodily fluids as an early indicator of the onset of clinical dementia in AD. We also show that plasmonic interferometry can be a powerful tool to monitor and optimize surface immobilization schemes, which could be applied to develop other relevant antibody tests.

Detection of COVID-19 Virus on Surfaces Using Photonics: Challenges and Perspectives

The propagation of viruses has become a global threat as proven through the coronavirus disease (COVID-19) pandemic. Therefore, the quick detection of viral diseases and infections could be necessary. This study aims to develop a framework for virus diagnoses based on integrating photonics technology with artificial intelligence to enhance healthcare in public areas, marketplaces, hospitals, and airfields due to the distinct spectral signatures from lasers' effectiveness in the classification and monitoring of viruses. However, providing insights into the technical aspect also helps researchers identify the possibilities and difficulties in this field. The contents of this study were collected from six authoritative databases: Web of Science, IEEE Xplore, Science Direct, Scopus, PubMed Central, and Google Scholar. This review includes an analysis and summary of laser techniques to diagnose COVID-19 such as fluorescence methods, surface-enhanced Raman scattering, surface plasmon resonance, and integration of Raman scattering with SPR techniques. Finally, we select the best strategies that could potentially be the most effective methods of reducing epidemic spreading and improving healthcare in the environment.

Detection of COVID-19 Virus on Surfaces Using Photonics: Challenges and Perspectives

The propagation of viruses has become a global threat as proven through the coronavirus disease (COVID-19) pandemic. Therefore, the quick detection of viral diseases and infections could be necessary. This study aims to develop a framework for virus diagnoses based on integrating photonics technology with artificial intelligence to enhance healthcare in public areas, marketplaces, hospitals, and airfields due to the distinct spectral signatures from lasers’ effectiveness in the classification and monitoring of viruses. However, providing insights into the technical aspect also helps researchers identify the possibilities and difficulties in this field. The contents of this study were collected from six authoritative databases: Web of Science, IEEE Xplore, Science Direct, Scopus, PubMed Central, and Google Scholar. This review includes an analysis and summary of laser techniques to diagnose COVID-19 such as fluorescence methods, surface-enhanced Raman scattering, surface plasmon resonance, and integration of Raman scattering with SPR techniques. Finally, we select the best strategies that could potentially be the most effective methods of reducing epidemic spreading and improving healthcare in the environment.

ASSURED Point-of-Need Food Safety Screening: A Critical Assessment of Portable Food Analyzers

Standard methods for chemical food safety testing in official laboratories rely largely on liquid or gas chromatography coupled with mass spectrometry. Although these methods are considered the gold standard for quantitative confirmatory analysis, they require sampling, transferring the samples to a central laboratory to be tested by highly trained personnel, and the use of expensive equipment. Therefore, there is an increasing demand for portable and handheld devices to provide rapid, efficient, and on-site screening of food contaminants. Recent technological advancements in the field include smartphone-based, microfluidic chip-based, and paper-based devices integrated with electrochemical and optical biosensing platforms. Furthermore, the potential application of portable mass spectrometers in food testing might bring the confirmatory analysis from the laboratory to the field in the future. Although such systems open new promising possibilities for portable food testing, few of these devices are commercially available. To understand why barriers remain, portable food analyzers reported in the literature over the last ten years were reviewed. To this end, the analytical performance of these devices and the extent they match the World Health Organization benchmark for diagnostic tests, i.e., the Affordable, Sensitive, Specific, User-friendly, Rapid and Robust, Equipment-free, and Deliverable to end-users (ASSURED) criteria, was evaluated critically. A five-star scoring system was used to assess their potential to be implemented as food safety testing systems. The main findings highlight the need for concentrated efforts towards combining the best features of different technologies, to bridge technological gaps and meet commercialization requirements.

Noble Metal Nanomaterial-Based Biosensors for Electrochemical and Optical Detection of Viruses Causing Respiratory Illnesses

Noble metal nanomaterials, such as gold, silver, and platinum, have been studied extensively in broad scientific fields because of their unique properties, including superior conductivity, plasmonic property, and biocompatibility. Due to their unique properties, researchers have used them to fabricate biosensors. Recently, biosensors for detecting respiratory illness-inducing viruses have gained attention after the global outbreak of coronavirus disease (COVID-19). In this mini-review, we discuss noble metal nanomaterials and associated biosensors for detecting respiratory illness-causing viruses, including SARS-CoV-2, using electrochemical and optical detection techniques. this review will provide interdisciplinary knowledge about the application of noble metal nanomaterials to the biomedical field.

Clinical Utility of Biosensing Platforms for Confirmation of SARS-CoV-2 Infection

Despite collaborative efforts from all countries, coronavirus disease 2019 (COVID-19) pandemic has been continuing to spread globally, forcing the world into social distancing period, making a special challenge for public healthcare system. Before vaccine widely available, the best approach to manage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is to achieve highest diagnostic accuracy by improving biosensor efficacy. For SARS-CoV-2 diagnostics, intensive attempts have been made by many scientists to ameliorate the drawback of current biosensors of SARS-CoV-2 in clinical diagnosis to offer benefits related to platform proposal, systematic analytical methods, system combination, and miniaturization. This review assesses ongoing research efforts aimed at developing integrated diagnostic tools to detect RNA viruses and their biomarkers for clinical diagnostics of SARS-CoV-2 infection and further highlights promising technology for SARS-CoV-2 specific diagnosis. The comparisons of SARS-CoV-2 biomarkers as well as their applicable biosensors in the field of clinical diagnosis were summarized to give scientists an advantage to develop superior diagnostic platforms. Furthermore, this review describes the prospects for this rapidly growing field of diagnostic research, raising further interest in analytical technology and strategic plan for future pandemics.

Nanomaterial-based Optical and Electrochemical Biosensors for Amyloid beta and Tau: Potential for early diagnosis of Alzheimer's Disease

INTRODUCTION

Alzheimer's disease (AD), a heterogeneous pathological process representing the most common causes of dementia worldwide, has required early and accurate diagnostic tools. Neuropathological hallmarks of AD involve the aberrant accumulation of Amyloid beta (Aβ) into Amyloid plaques and hyperphosphorylated Tau into neurofibrillary tangles, occurring long before the onset of brain dysfunction.Areas covered:Considering the significance of Aβ and Tau in AD pathogenesis, these proteins have been adopted as core biomarkers of AD, and their quantification has provided precise diagnostic information to develop next-generation AD therapeutic approaches. However, conventional diagnostic methods may not suffice to achieve clinical criteria that are acceptable for proper diagnosis and treatment. The advantages of nanomaterial-based biosensors including facile miniaturization, mass fabrication, ultra-sensitivity, make them useful to be promising tools to measure Aβ and Tau simultaneously for accurate validation of low-abundance yet potentially informative biomarkers of AD..

EXPERT OPINION

The study has identified the potential application of advanced biosensors as standardized clinical diagnostic tools for AD, evolving the way for new and efficient AD control with minimum economic and social burden. After clinical trial, nanobiosensors for measuring Aβ and Tau simultaneously possess innovative diagnosis of AD to provide significant contributions to primary Alzheimer's care intervention.

Porous Silicon Optical Devices: Recent Advances in Biosensing Applications

This review summarizes the leading advancements in porous silicon (PSi) optical-biosensors, achieved over the past five years. The cost-effective fabrication process, the high internal surface area, the tunable pore size, and the photonic properties made the PSi an appealing transducing substrate for biosensing purposes, with applications in different research fields. Different optical PSi biosensors are reviewed and classified into four classes, based on the different biorecognition elements immobilized on the surface of the transducing material. The PL signal modulation and the effective refractive index changes of the porous matrix are the main optical transduction mechanisms discussed herein. The approaches that are commonly employed to chemically stabilize and functionalize the PSi surface are described.

Cultivation of Saccharomyces cerevisiae with Feedback Regulation of Glucose Concentration Controlled by Optical Fiber Glucose Sensor

Glucose belongs among the most important substances in both physiology and industry. Current food and biotechnology praxis emphasizes its on-line continuous monitoring and regulation. These provoke increasing demand for systems, which enable fast detection and regulation of deviations from desired glucose concentration. We demonstrated control of glucose concentration by feedback regulation equipped with in situ optical fiber glucose sensor. The sensitive layer of the sensor comprises oxygen-dependent ruthenium complex and preimmobilized glucose oxidase both entrapped in organic–inorganic polymer ORMOCER^®. The sensor was placed in the laboratory bioreactor (volume 5 L) to demonstrate both regulations: the control of low levels of glucose concentrations (0.4 and 0.1 mM) and maintenance of the glucose concentration (between 2 and 3.5 mM) during stationary phase of cultivation of Saccharomyces cerevisiae. Response times did not exceed 6 min (average 4 min) with average deviation of 4%. Due to these regulation characteristics together with durable and long-lasting (≥2 month) sensitive layer, this feedback regulation system might find applications in various biotechnological processes such as production of low glucose content beverages.

Multiplex Immunoassay Techniques for On-Site Detection of Security Sensitive Toxins

Biological toxins are a heterogeneous group of high molecular as well as low molecular weight toxins produced by living organisms. Due to their physical and logistical properties, biological toxins are very attractive to terrorists for use in acts of bioterrorism. Therefore, among the group of biological toxins, several are categorized as security relevant, e.g., botulinum neurotoxins, staphylococcal enterotoxins, abrin, ricin or saxitoxin. Additionally, several security sensitive toxins also play a major role in natural food poisoning outbreaks. For a prompt response to a potential bioterrorist attack using biological toxins, first responders need reliable, easy-to-use and highly sensitive methodologies for on-site detection of the causative agent. Therefore, the aim of this review is to present on-site immunoassay platforms for multiplex detection of biological toxins. Furthermore, we introduce several commercially available detection technologies specialized for mobile or on-site identification of security sensitive toxins.

Rapid, Cost-Effective Peptide/Nucleic Acid-Based Platform for Therapeutic Antibody Monitoring in Clinical Samples

We demonstrate here a homogeneous assay, named NanoHybrid, for monoclonal antibody quantification directly in serum samples in a single-step format. NanoHybrid is composed of both synthetic peptide nucleic acids (PNAs) and nucleic acid strands conjugated to recognition elements and optical labels and is designed to allow fast fluorescence quantification of a therapeutic antibody. More specifically, we have characterized our analytical assay for the detection of trastuzumab (Herceptin), a monoclonal antibody (mAb) drug used for breast cancer treatment and for tumors overexpressing the HER2/neu protein. We show here that NanoHybrid is capable of performing fast drug quantification directly in blood serum. The results obtained with a pool of samples from breast cancer patients under trastuzumab treatment are compared with CE-IVD ELISA (enzyme-linked immunosorbent assay) showing a good agreement (Cohen's K = 0.729). Due to the modular nature of the NanoHybrid platform, this technology can be programmed to potentially detect and quantify any antibody for which a high-affinity recognition element has been characterized. We envision the application of NanoHybrid in a point-of-care (POC) drug monitoring system based on disposable kits for therapeutic drug management.

Plasmonic Optical Biosensors for Detecting C-Reactive Protein: A Review

C-reactive protein (CRP), a potent acute-phase reactant that increases rapidly in response to inflammation, tissue damage or infections, is also considered an indicator of the risk of cardiovascular diseases and neurological disorders. Recent advances in nanofabrication and nanophotonic technologies have prompted the optical plasmonic phenomena to be tailored for specific detection of human serum CRP into label-free devices. We review the CRP-specific detection platforms with high sensitivity, which feature the thin metal films for surface plasmon resonance, nano-enhancers of zero dimensional nanostructures, and metal nanoparticles for localized surface plasmon resonance. The protocols used for various types of assay reported in literature are also outlines with surface chemical pretreatment required for specific detection of CRPs on a plasmonic surface. Properties including sensitivity and detection range are described for each sensor device reviewed, while challenges faced by plasmonic CRP sensors are discussed in the conclusion, with future directions towards which research efforts need to be made.

A Paper-Based Near-Infrared Optical Biosensor for Quantitative Detection of Protease Activity Using Peptide-Encapsulated SWCNTs

A protease is an enzyme that catalyzes proteolysis of proteins into smaller polypeptides or single amino acids. As crucial elements in many biological processes, proteases have been shown to be informative biomarkers for several pathological conditions in humans, animals, and plants. Therefore, fast, reliable, and cost-effective protease biosensors suitable for point-of-care (POC) sensing may aid in diagnostics, treatment, and drug discovery for various diseases. This work presents an affordable and simple paper-based dipstick biosensor that utilizes peptide-encapsulated single-wall carbon nanotubes (SWCNTs) for protease detection. Upon enzymatic digestion of the peptide, a significant drop in the photoluminescence (PL) of the SWCNTs was detected. As the emitted PL is in the near-infrared region, the developed biosensor has a good signal to noise ratio in biological fluids. One of the diseases associated with abnormal protease activity is pancreatitis. In acute pancreatitis, trypsin concentration could reach up to 84 µg/mL in the urine. For proof of concept, we demonstrate the feasibility of the proposed biosensor for the detection of the abnormal levels of trypsin activity in urine samples.

Screening method for the detection of residues of amphenicol antibiotics in bovine milk by optical biosensor

An immunobiosensor assay was developed for multi-residue screening in bovine milk of the parent amphenicols, thiamphenicol and florfenicol, along with the metabolite florfenicol amine. A polyclonal antibody raised in a rabbit after immunisation with a florfenicol amine-protein conjugate was employed in the assay. Milk samples were subjected to acetonitrile extraction, reconstituted in buffer and diluted prior to biosensor analysis. Validation data obtained from the analysis of fortified samples has shown that the method has a detection capability of less than 0.25 µg kg^-1 for florfenicol and less than 0.5 µg kg^-1 for florfenicol amine and thiamphenicol. The cross-reactivity profile and validation data for the detection of these amphenicols is presented together with results obtained following the analysis of florfenicol incurred samples using the developed screening method along with a comparison of results obtained from the analysis of the same incurred samples using an MRM³ UPLC-MS/MS confirmatory method. Results are also presented obtained from the analysis of samples from both treated and non-treated animals which were co-housed and which show the potential for cross-contamination.

Advances in Optical Biosensors and Sensors Using Nanoporous Anodic Alumina

This review paper focuses on recent progress in optical biosensors using self-ordered nanoporous anodic alumina. We present the fabrication of self-ordered nanoporous anodic alumina, surface functionalization, and optical sensor applications. We show that self-ordered nanoporous anodic alumina has good potential for use in the fabrication of antibody-based (immunosensor), aptamer-based (aptasensor), gene-based (genosensor), peptide-based, and enzyme-based optical biosensors. The fabricated optical biosensors presented high sensitivity and selectivity. In addition, we also showed that the performance of the biosensors and the self-ordered nanoporous anodic alumina can be used for assessing biomolecules, heavy ions, and gas molecules.

Porous Silicon Fabry-Pérot Interferometer for N-Acetyl-β-d-Glucosaminidase Biomarker Monitoring

Bovine mastitis (BM) is a prominent inflammatory disease affecting the dairy industry worldwide, originated by pathogenic agent invasion onto the mammary gland. Early detection of new BM cases is of high importance for infection control within the herd. Conventional analytical techniques lack the ability to detect BM-predicting biomarkers, used as analytical indicators for health status evaluation, in real time or outside the laboratory boundaries. Herein, we describe a biosensing platform for label-free detection and identification of BM onset through targeting N-acetyl-β-d-glucosaminidase (NAGase) for potential evidence-based therapy. The lysosomal activity in dissimilar milk qualities was monitored by a gelatin-functionalized porous Si Fabry-Pérot interferometer, while estimating the biochemical reaction precipitating products within the nanostructure. The optical response was proportional to the inherent NAGase concentration found in real milk samples, influenced by two dominant BM causative pathogens (i.e., Escherichia coli and Streptococcus dysgalactiae) at various somatic cell counts. Quantitative analysis of NAGase levels within the entire inflammatory spectrum (healthy, subclinical, and clinical BM) was obtained within the range of 1.0-4.2 μM/min (enzymatic activity per volume unit), while presenting a detection limit of 0.51 μM/min. The optical performances correspond with standardized biochemical activity assay in dissimilar milk qualities. Overall, the presented sensing concept exhibits the potential of BM-predicting biomarker detection using a simple and portable experimental setup for convenient early biodiagnostics and health status evaluation.

Fast and Accurate Pneumocystis Pneumonia Diagnosis in Human Samples Using a Label-Free Plasmonic Biosensor

Pneumocystis jirovecii is a fungus responsible for human Pneumocystis pneumonia, one of the most severe infections encountered in immunodepressed individuals. The diagnosis of Pneumocystis pneumonia continues to be challenging due to the absence of specific symptoms in infected patients. Moreover, the standard diagnostic method employed for its diagnosis involves mainly PCR-based techniques, which besides being highly specific and sensitive, require specialized personnel and equipment and are time-consuming. Our aim is to demonstrate an optical biosensor methodology based on surface plasmon resonance to perform such diagnostics in an efficient and decentralized scheme. The biosensor methodology employs poly-purine reverse-Hoogsteen hairpin probes for the detection of the mitochondrial large subunit ribosomal RNA (mtLSU rRNA) gene, related to P. jirovecii detection. The biosensor device performs a real-time and label-free identification of the mtLSU rRNA gene with excellent selectivity and reproducibility, achieving limits of detection of around 2.11 nM. A preliminary evaluation of clinical samples showed rapid, label-free and specific identification of P. jirovecii in human lung fluids such as bronchoalveolar lavages or nasopharyngeal aspirates. These results offer a door for the future deployment of a sensitive diagnostic tool for fast, direct and selective detection of Pneumocystis pneumonia disease.

An Analysis of a Compact Label-Free Guiding-Wave Biosensor Based on a Semiconductor-Clad Dielectric Strip Waveguide

In this paper, a compact, integrated, semiconductor-clad strip waveguide label-free biosensor is proposed and analyzed. The device is based on CMOS-compatible materials such as amorphous-Si and silicon oxynitride. The optical sensor performance has been modeled by a three-dimensional beam propagation method. The simulations indicate that a 20-μm-long device can exhibit a surface limit of detection of 3 ng/cm² for avidin molecules in aqueous solution. The sensor performance compares well to those displayed by other photonic biosensors with much larger footprints. The fabrication tolerances have been also studied in order to analyze the feasibility of the practical implementation of the biosensor.

Continuous Detection of Increasing Concentrations of Thrombin Employing a Label-Free Photonic Crystal Aptasensor

Thrombin generation is a complex and finely regulated pathway that provokes dynamical changes of thrombin concentration in blood when a vascular injury occurs. In order to characterize the initiation phase of such process, when thrombin concentration is in the nM range, a label-free optical aptasensor is proposed here. This aptasensor combines a 1D photonic crystal structure consisting of a silicon corrugated waveguide with thrombin binding aptamers on its surface as bioreceptors. As a result, this aptasensor has been demonstrated to specifically detect thrombin concentrations ranging from 270 pM to 27 nM with an estimated detection limit of 33.5 pM and a response time of ~2 min. Furthermore, it has also been demonstrated that this aptasensor is able to continuously respond to consecutive increasing concentrations of thrombin and to detect binding events as they occur. All these features make this aptasensor a good candidate to continuously study how thrombin concentration progressively increases during the initiation phase of the coagulation cascade.

Sandwich-Type DNA Micro-Optode Based on Gold-Latex Spheres Label for Reflectance Dengue Virus Detection

A DNA micro-optode for dengue virus detection was developed based on the sandwich hybridization strategy of DNAs on succinimide-functionalized poly(n-butyl acrylate) (poly(nBA-NAS)) microspheres. Gold nanoparticles (AuNPs) with an average diameter of ~20 nm were synthesized using a centrifugation-based method and adsorbed on the submicrometer-sized polyelectrolyte-coated poly(styrene-co-acrylic acid) (PSA) latex particles via an electrostatic method. The AuNP–latex spheres were attached to the thiolated reporter probe (rDNA) by Au–thiol binding to functionalize as an optical gold–latex–rDNA label. The one-step sandwich hybridization recognition involved a pair of a DNA probe, i.e., capture probe (pDNA), and AuNP–PSA reporter label that flanked the target DNA (complementary DNA (cDNA)). The concentration of dengue virus cDNA was optically transduced by immobilized AuNP–PSA–rDNA conjugates as the DNA micro-optode exhibited a violet hue upon the DNA sandwich hybridization reaction, which could be monitored by a fiber-optic reflectance spectrophotometer at 637 nm. The optical genosensor showed a linear reflectance response over a wide cDNA concentration range from 1.0 × 10⁻²¹ M to 1.0 × 10⁻¹² M cDNA (R² = 0.9807) with a limit of detection (LOD) of 1 × 10⁻²⁹ M. The DNA biosensor was reusable for three consecutive applications after regeneration with mild sodium hydroxide. The sandwich-type optical biosensor was well validated with a molecular reverse transcription polymerase chain reaction (RT-PCR) technique for screening of dengue virus in clinical samples, e.g., serum, urine, and saliva from dengue virus-infected patients under informed consent.

Optical Biosensor for Rapid Detection of Salmonella typhimurium Based on Porous Gold@Platinum Nanocatalysts and a 3D Fluidic Chip

Screening of pathogenic bacteria is a key to avoid food poisoning. The major drawbacks of existing assays for foodborne bacteria detection include long time for culture, complex DNA extraction for the polymerase chain reaction (PCR), and low sensitivity for enzyme-linked immunosorbent assay (ELISA), greatly limiting their practical applications. Here, we developed a sensitive optical biosensor based on porous gold@platinum nanocatalysts (Au@PtNCs) and a passive three-dimensional (3D) micromixer for fast detection of Salmonella typhimurium. The target Salmonella cells were first separated using immunomagnetic nanoparticles and the passive 3D micromixer. Then, immune Au@PtNCs were labeled onto the target cells as signal output to catalyze hydrogen peroxide-3,3',5,5'-tetramethylbenzidine. Finally, the absorbance was measured at 652 nm to calculate the bacterial amount. This optical biosensor could detect Salmonella at concentrations from 1.8 × 10¹ to 1.8 × 10⁷ CFU/mL in 1 h. Its detection limit was calculated to be 17 CFU/mL. Besides, this passive 3D micromixer could magnetically separate 99% of target bacteria from the sample in 10 min. This biosensor has the potential to be extended to detect other bacteria by changing the antibodies.

Quantification of Neuropeptide Y with Picomolar Sensitivity Enabled by Guided-Mode Resonance Biosensors

Assessing levels of neuropeptide Y (NPY) in the human body has many medical uses. Accordingly, we report the quantitative detection of NPY biomarkers applying guided-mode resonance (GMR) biosensor methodology. The label-free sensor operates in the near-infrared spectral region exhibiting distinctive resonance signatures. The interaction of NPY with bioselective molecules on the sensor surface causes spectral shifts that directly identify the binding event without additional processing. In the experiments described here, NPY antibodies are attached to the sensor surface to impart specificity during operation. For the low concentrations of NPY of interest, we apply a sandwich NPY assay in which the sensor-linked anti-NPY molecule binds with NPY that subsequently binds with anti-NPY to close the sandwich. The sandwich assay achieves a detection limit of ~0.1 pM NPY. The photonic sensor methodology applied here enables expeditious high-throughput data acquisition with high sensitivity and specificity. The entire bioreaction is recorded as a function of time, in contrast to label-based methods with single-point detection. The convenient methodology and results reported are significant, as the NPY detection range of 0.1–10 pM demonstrated is useful in important medical circumstances.