Sensitive detection of protein and miRNA cancer biomarkers using silicon-based photonic crystals and a resonance coupling laser scanning platform

Highly-accurate solvent identification using dynamic evaporation reflection spectra from an inverse opal sensor combined with a deep learning model

Developing a low-cost, rapid, and highly accurate method for detecting solvents with similar structures and properties is highly demanded. In recent years, methods based on dynamic reflection spectroscopy have been developed to distinguish isomers and homologues. However, these methods heavily rely on responsive photonic crystals that can interact intricately with the solvent. In this work, we propose a deep learning approach for direct solvent identification from dynamic evaporative reflection spectra (DERS) obtained on a simple inverse opal (IO) sensor. The sensor was prepared using co-assembly and sacrificial template methods. Then, a dataset was constructed with 985 DERS obtained from 14 different solvents. Different classical machine learning and deep learning algorithms were employed for classifying these DERS. The results showed that ResNet18-CBAM, an improved convolutional neural network, outperformed all other algorithms, achieving 97.7 ± 0.9% on the 5-fold cross-validation set and 100% accuracy on the test set. This strategy presents not only a simple, efficient, and repeatable method for solvent detection but also, more importantly, by integrating the deep learning model, it allows an automatic, rapid, and accurate analysis of DERS data without the need for human intervention. It holds great application prospects in the field of solvent detection.

Multiplex microdisk biosensor based on simultaneous intensity and phase detection

Future healthcare and precision medicine require multiplex and reliable biosensors. Here we present a compact photonic crystal based microdisk biosensor that is designed for simultaneous intensity and phase measurements of multiple biomarkers in parallel. The combination of two different measurement approaches has a range of advantages. Phase detection has higher signal to noise ratios, while intensity measurement helps to align the sensor to high phase sensitivities and increase the reliability. The performance of the microdisk biosensor system is examined by simulations and measurements. For proof of concept, parallel intensity and phase shifts are measured upon binding of human-alpha-thrombin and streptavidin.

Lossy Mode Resonance Based Microfluidic Platform Developed on Planar Waveguide for Biosensing Applications

The development of resonance phenomena-based optical biosensors has gained relevance in recent years due to the excellent optical fiber properties and progress in the research on materials and techniques that allow resonance generation. However, for lossy mode resonance (LMR)-based sensors, the optical fiber presents disadvantages, such as the need for splicing the sensor head and the complex polarization control. To avoid these issues, planar waveguides such as coverslips are easier to handle, cost-effective, and more robust structures. In this work, a microfluidic LMR-based planar waveguide platform was proposed, and its use for biosensing applications was evaluated by detecting anti-immunoglobulin G (anti-IgG). In order to generate the wavelength resonance, the sensor surface was coated with a titanium dioxide (TiO2) thin-film. IgG antibodies were immobilized by covalent binding, and the detection assay was carried out by injecting anti-IgG in PBS buffer solutions from 5 to 20 μg/mL. The LMR wavelength shifted to higher values when increasing the analyte concentration, which means that the proposed system was able to detect the IgG/anti-IgG binding. The calibration curve was built from the experimental data obtained in three repetitions of the assay. In this way, a prototype of an LMR-based biosensing microfluidic platform developed on planar substrates was obtained for the first time.

Laser-Induced Patterned Photonic Crystal Heterostructure for Multimetal Ion Recognition

In this work, a new method of direct laser writing patterned photonic crystal heterostructure on a glass surface is proposed. A multi-heterostructure photonic crystal (MHPC) is predeposited on the glass surface and then the laser spot is focused on it and moves according to the set program, leading to the formation of patterned MHPC. Scanning electron microscopy (SEM) and finite element simulation show that the patterning is caused by the local thermal annealing of the polymer colloidal spheres through the thermal conduction effect of the substrate on the laser energy. The patterned area presents a function of the water confinement effect and can be used as a high-performance droplet analysis chip. By integrating the patterned MHPC array and seven fluorescent dyes, nine metal ions can be successfully recognized and discriminated. This approach is quite facile and fast for designing colloidal photonic crystals with controllable patterns. Moreover, it is of considerable significance for the practical application of photonic crystal heterostructure in the detection, sensing, anti-counterfeiting, and display fields.

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

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

Dual-amplified strategy for ultrasensitive electrochemical biosensor based on click chemistry-mediated enzyme-assisted target recycling and functionalized fullerene nanoparticles in the detection of microRNA-141

Rapid and efficient detection of tumor marker at the early stages is one of the crucial challenges in cancer diagnostics and therapy. In this study, an ultrasensitive electrochemical biosensor was fabricated by dual-amplified strategy for the detection of ultra-trace microRNA-141 (miRNA-141). Firstly, two split sequences contained G-quadruplex were connected by click chemistry-mediated nucleic acid strands self-assembly and the obtained complete G-quadruplex was complementary with miRNA-141 to formed DNA-RNA hybrid duplexes. Subsequently, the formed DNA-RNA hybrid duplexes were specifically recognized by duplex-specific nuclease (DSN), and the DNA part of the duplexes were cleaved and the miRNA-141 were released to trigger next cycle, which acquired a primal signal amplification by enzyme-assisted target recycling (EATR). Moreover, amino and thiol group multi-labeled functionalized fullerene nanoparticles (FC60) with a larger surface active sites and better biocompatibility, were designed rationally to modify the Au electrodes, which produced multiply-enhanced amplified signal. This dual-amplified sensing system exhibited a remarkable analytical performance for the detection of miRNA-141 in concentrations ranging from 0.1 pM to 100 nM and the detection limit of 7.78 fM was obtained. Compared with the biosensor with single amplification strategy such as EATR, this electrochemical biosensor based on dual-amplified strategy exhibited an excellent discrimination capability and higher analytical performance. Therefore, this electrochemical biosensor might hold a great potential for further applications in biomedical research and early clinical diagnosis.

Activate capture and digital counting (AC + DC) assay for protein biomarker detection integrated with a self-powered microfluidic cartridge

We demonstrate a rapid, 2-step, and ultrasensitive assay approach for quantification of target protein molecules from a single droplet test sample. The assay is comprised of antibody-conjugated gold nanoparticles (AuNPs) that are "activated" when they are mixed with the test sample and bind their targets. The resulting liquid is passed through a microfluidic channel with a photonic crystal (PC) biosensor that is functionalized with secondary antibodies to the target biomarker, so that only activated AuNPs are captured. Utilizing recently demonstrated hybrid optical coupling between the plasmon resonance of the AuNP and the resonance of the PC, each captured AuNP efficiently quenches the resonant reflection of the PC, thus enabling the captured AuNPs to be digitally counted with high signal-to-noise. To achieve a 2-step assay process that is performed on a single droplet test sample without washing steps or active pump elements, controlled single-pass flow rate is obtained with an absorbing paper pad waste reservoir embedded in a microfluidic cartridge. We use the activate capture and digital counting (AC + DC) approach to demonstrate HIV-1 capsid antigen p24 detection from a 40 μL spiked-in human serum sample at a one thousand-fold dynamic range (1-10³ pg mL^-1) with only a 35-minute process that is compatible with point-of-care (POC) analysis. The AC + DC approach allows for ultrasensitive and ultrafast biomolecule detection, with potential applications in infectious disease diagnostics and early stage disease monitoring.

Graphene oxide-based fluorometric determination of microRNA-141 using rolling circle amplification and exonuclease III-aided recycling amplification

A graphene oxide-based method has been developed for ultrasensitive and selective determination of microRNA-141 by means of rolling circle amplification (RCA) and exonuclease III (Exo III)-assisted recycling amplification. The method uses (a) a padlock probe with a hybrid sequence that is complementary to the target microRNA-141 at both the 5'- and the 3'-end, and (b) a long binding region of a signalling reporter strand. On addition of microRNA-141, it acts as the primer for triggering the RCA reaction following ligation. This results in the formation of a repeatedly concatenated sequence of the padlock probe. Subsequently, the RCA product hybridizes with the fluorescein-labelled signal strand to form the duplex DNA containing the blunt 3'-termini of signal strand. Addition of Exo III causes signal strand digestion and leads to RCA product recycling and liberation of fluorescein. Added graphene oxide does not absorb the fluorescein liberated because of the poor mutual interaction. Therefore, microRNA-141 can be quantified by measurement of the green fluorescence under excitation/emission wavelengths of 470/520 nm. The method has a 100 aM detection limit towards microRNA-141 and works in the wide range from 1 fM to 1 nM. It can discriminate even single-mismatched microRNA and shows good selectivity and sensitivity when applied to spiked human serum. Graphical abstract Schematic representation of a graphene oxide (GO)-based method for fluorometric determination of microRNA by using rolling circle amplification and exonuclease III (Exo III)-aided recycling amplification. With microRNA, the fluorescein-labelled signal strand becomes digested, and this genererates a fluorescent signal.

Recent advances in microfluidic methods in cancer liquid biopsy

Early cancer detection, its monitoring, and therapeutical prediction are highly valuable, though extremely challenging targets in oncology. Significant progress has been made recently, resulting in a group of devices and techniques that are now capable of successfully detecting, interpreting, and monitoring cancer biomarkers in body fluids. Precise information about malignancies can be obtained from liquid biopsies by isolating and analyzing circulating tumor cells (CTCs) or nucleic acids, tumor-derived vesicles or proteins, and metabolites. The current work provides a general overview of the latest on-chip technological developments for cancer liquid biopsy. Current challenges for their translation and their application in various clinical settings are discussed. Microfluidic solutions for each set of biomarkers are compared, and a global overview of the major trends and ongoing research challenges is given. A detailed analysis of the microfluidic isolation of CTCs with recent efforts that aimed at increasing purity and capture efficiency is provided as well. Although CTCs have been the focus of a vast microfluidic research effort as the key element for obtaining relevant information, important clinical insights can also be achieved from alternative biomarkers, such as classical protein biomarkers, exosomes, or circulating-free nucleic acids. Finally, while most work has been devoted to the analysis of blood-based biomarkers, we highlight the less explored potential of urine as an ideal source of molecular cancer biomarkers for point-of-care lab-on-chip devices.

Recent advances in merging photonic crystals and plasmonics for bioanalytical applications

Photonic crystals (PhCs) and plasmonic nanostructures offer the unprecedented capability to control the interaction of light and biomolecules at the nanoscale. Based on PhC and plasmonic phenomena, a variety of analytical techniques have been demonstrated and successfully implemented in many fields, such as biological sciences, clinical diagnosis, drug discovery, and environmental monitoring. During the past decades, PhC and plasmonic technologies have progressed in parallel with their pros and cons. The merging of photonic crystals with plasmonics will significantly improve biosensor performances and enlarge the linear detection range of analytical targets. Here, we review the state-of-the-art biosensors that combine PhC and plasmonic nanomaterials for quantitative analysis. The optical mechanisms of PhCs, plasmonic crystals, and metal nanoparticles (NPs) are presented, along with their integration and potential applications. By explaining the optical coupling of photonic crystals and plasmonics, the review manifests how PhC-plasmonic hybrid biosensors can achieve the advantages, including high sensitivity, low cost, and short assay time as well. The review also discusses the challenges and future opportunities in this fascinating field.

Graphene Oxide Signal Reporter Based Multifunctional Immunosensing Platform for Amperometric Profiling of Multiple Cytokines in Serum

Cytokines are small proteins and form complicated cytokine networks to report the status of our health. Thus, accurate profiling and sensitive quantification of multiple cytokines is essential to have a comprehensive and accurate understanding of the complex physiological and pathological conditions in the body. In this study, we demonstrated a robust electrochemical immunosensor for the simultaneous detection of three cytokines IL-6, IL-1β, and TNF-α. First, graphene oxides (GO) were loaded with redox probes nile blue (NB), methyl blue (MB), and ferrocene (Fc), followed by covalent attachment of anti-cytokine antibodies for IL-6, IL-1β, and TNF-α, respectively, to obtain Ab₂-GO-NB, Ab₂-GO-MB, and Ab₂-GO-Fc, acting as the signal reporters. The sensing interface was fabricated by attachment of mixed layers of 4-carboxylic phenyl and 4-aminophenyl phosphorylcholine (PPC) to glassy carbon surfaces. After that, the capture monoclonal antibody for IL-6, IL-1β, and TNF-α was modified to the carboxylic acid terminated sensing interface. And finally a sandwich assay was developed. The quantitative detection of three cytokines was achieved by observing the change in electrochemical signal from signal reporters Ab₂-GO-NB, Ab₂-GO-MB, and Ab₂-GO-Fc. The designed system has been successfully used for detection of three cytokines (IL-6, IL-1β, and TNF-α) simultaneously with desirable performance in sensitivity, selectivity, and stability, and recovery of 93.6%-105.5% was achieved for determining cytokines spiked in the whole mouse serum.

An Ultrasensitive Diagnostic Biochip Based on Biomimetic Periodic Nanostructure-Assisted Rolling Circle Amplification

Developing portable and sensitive devices for point of care detection of low abundance bioactive molecules is highly valuable in early diagnosis of disease. Herein, an ultrasensitive photonic crystals-assisted rolling circle amplification (PCs-RCA) biochip was constructed and further applied to circulating microRNAs (miRNAs) detection in serum. The biochip integrated the optical signal enhancement capability of biomimetic PCs surface with the thousand-fold signal amplification feature of RCA. The biomimetic PCs displayed periodic dielectric nanostructure and significantly enhanced the signal intensity of RCA reaction, leading to efficient improvement of detection sensitivity. A limit of detection (LOD) as low as 0.7 aM was obtained on the PCs-RCA biochip, and the LOD was 7 orders of magnitude lower than that of standard RCA. Moreover, the PCs-RCA biochip could discriminate a single base variation in miRNAs. Accurate quantification of ultralow-abundance circulating miRNAs in clinical serum samples was further achieved with the PCs-RCA biochip, and patients with the nonsmall cell lung carcinoma were successfully distinguished from healthy donors. The PCs-RCA biochip can detect bioactive molecules with ultrahigh sensitivity and good specificity, making it valuable in clinical disease diagnosis and health assessment.

An Automated Microfluidic Assay for Photonic Crystal Enhanced Detection and Analysis of an Antiviral Antibody Cancer Biomarker in Serum

We report on the implementation of an automated platform for detecting the presence of an antibody biomarker for human papillomavirus-associated oropharyngeal cancer from a single droplet of serum, in which a nanostructured photonic crystal surface is used to amplify the output of a fluorescence-linked immunosorbent assay. The platform is comprised of a microfluidic cartridge with integrated photonic crystal chips that interfaces with an assay instrument that automates the introduction of reagents, wash steps, and surface drying. Upon assay completion, the cartridge interfaces with a custom laser-scanning instrument that couples light into the photonic crystal at the optimal resonance condition for fluorescence enhancement. The instrument is used to measure the fluorescence intensity values of microarray spots corresponding to the biomarkers of interest, in addition to several experimental controls that verify correct functioning of the assay protocol. In this work, we report both dose-response characterization of the system using anti-E7 antibody introduced at known concentrations into serum and characterization of a set of clinical samples from which results were compared with a conventional enzyme-linked immunosorbent assay (ELISA) performed in microplate format. The demonstrated capability represents a simple, rapid, automated, and high-sensitivity method for multiplexed detection of protein biomarkers from a low-volume test sample.

Nanoantenna-Microcavity Hybrids with Highly Cooperative Plasmonic-Photonic Coupling

Nanoantennas offer the ultimate spatial control over light by concentrating optical energy well below the diffraction limit, whereas their quality factor (Q) is constrained by large radiative and dissipative losses. Dielectric microcavities, on the other hand, are capable of generating a high Q-factor through an extended photon storage time but have a diffraction-limited optical mode volume. Here we bridge the two worlds, by studying an exemplary hybrid system integrating plasmonic gold nanorods acting as nanoantennas with an on-resonance dielectric photonic crystal (PC) slab acting as a low-loss microcavity and, more importantly, by synergistically combining their advantages to produce a much stronger local field enhancement than that of the separate entities. To achieve this synergy between the two polar opposite types of nanophotonic resonant elements, we show that it is crucial to coordinate both the dissipative loss of the nanoantenna and the Q-factor of the low-loss cavity. In comparison to the antenna-cavity coupling approach using a Fabry-Perot resonator, which has proved successful for resonant amplification of the antenna's local field intensity, we theoretically and experimentally show that coupling to a modest-Q PC guided resonance can produce a greater amplification by at least an order of magnitude. The synergistic nanoantenna-microcavity hybrid strategy opens new opportunities for further enhancing nanoscale light-matter interactions to benefit numerous areas such as nonlinear optics, nanolasers, plasmonic hot carrier technology, and surface-enhanced Raman and infrared absorption spectroscopies.

Photonic crystals: emerging biosensors and their promise for point-of-care applications

Biosensors are extensively employed for diagnosing a broad array of diseases and disorders in clinical settings worldwide. The implementation of biosensors at the point-of-care (POC), such as at primary clinics or the bedside, faces impediments because they may require highly trained personnel, have long assay times, large sizes, and high instrumental cost. Thus, there exists a need to develop inexpensive, reliable, user-friendly, and compact biosensing systems at the POC. Biosensors incorporated with photonic crystal (PC) structures hold promise to address many of the aforementioned challenges facing the development of new POC diagnostics. Currently, PC-based biosensors have been employed for detecting a variety of biotargets, such as cells, pathogens, proteins, antibodies, and nucleic acids, with high efficiency and selectivity. In this review, we provide a broad overview of PCs by explaining their structures, fabrication techniques, and sensing principles. Furthermore, we discuss recent applications of PC-based biosensors incorporated with emerging technologies, including telemedicine, flexible and wearable sensing, smart materials and metamaterials. Finally, we discuss current challenges associated with existing biosensors, and provide an outlook for PC-based biosensors and their promise at the POC.

Ligating Dopamine as Signal Trigger onto the Substrate via Metal-Catalyst-Free Click Chemistry for "Signal-On" Photoelectrochemical Sensing of Ultralow MicroRNA Levels

The efficiency of photon-to-electron conversion is extremely restricted by the electron-hole recombinant. Here, a new photoelectrochemical (PEC) sensing platform has been established based on the signal amplification of click chemistry (CC) via hybridization chain reaction (HCR) for highly sensitive microRNA (miRNA) assay. In this proposal, a preferred electron donor dopamine (DA) was first assembled with designed ligation probe (probe-N₃) via amidation reaction to achieve DA-coordinated signal probe (P_DA-N₃). The P_DA-N₃ served as a flexible trigger to signal amplification through efficiently suppressing the electron-hole recombinant. Specifically, the P_DA-N₃ can be successfully ligated into the trapped hairpins (H1 and H2) via the superior ligation method of metal-catalyst-free CC, in which the electron donor DA was introduced into the assay system. Moreover, the enzyme-free HCR, employed as a versatile amplification way, ensures that lots of P_DA-N₃ can be attached to the substrate. This PEC sensing for miRNA-141 detection illustrated the outstanding linear response to a concentration variation from 0.1 fM to 0.5 nM and a detection limit down to 27 aM, without additional electron donors. The sensor is further employed to monitor miRNA-141 from prostate carcinoma cell (22Rv1), showing good quantitative detection capability. This strategy exquisitely influences the analytical performance and offers a new PEC route to highly selective and sensitive detection of biological molecules.

Recent Advances in Biosensing With Photonic Crystal Surfaces: A Review

Photonic crystal surfaces that are designed to function as wavelength-selective optical resonators have become a widely adopted platform for label-free biosensing, and for enhancement of the output of photon-emitting tags used throughout life science research and in vitro diagnostics. While some applications, such as analysis of drug-protein interactions, require extremely high resolution and the ability to accurately correct for measurement artifacts, others require sensitivity that is high enough for detection of disease biomarkers in serum with concentrations less than 1 pg/ml. As the analysis of cells becomes increasingly important for studying the behavior of stem cells, cancer cells, and biofilms under a variety of conditions, approaches that enable high resolution imaging of live cells without cytotoxic stains or photobleachable fluorescent dyes are providing new tools to biologists who seek to observe individual cells over extended time periods. This paper will review several recent advances in photonic crystal biosensor detection instrumentation and device structures that are being applied towards direct detection of small molecules in the context of high throughput drug screening, photonic crystal fluorescence enhancement as utilized for high sensitivity multiplexed cancer biomarker detection, and label-free high resolution imaging of cells and individual nanoparticles as a new tool for life science research and single-molecule diagnostics.

Enhanced fluorescence detection of miRNA-16 on a photonic crystal

We report a novel sensing method for fluorescence-labelled microRNAs (miRNAs) spotted on an all-dielectric photonic structure. Such a photonic structure provides an enhanced excitation and a directional beaming of the emitted fluorescence, resulting in a significant improvement of the overall signal collected. As a result, the Limit of Detection (LoD) is demonstrated to decrease by a factor of about 50. A compact read-out system allows a wide-field imaging-based detection, with little or no optical alignment issues, which makes this approach particularly interesting for further development for example in microarray-type bioassays.

Recent advances in cytokine detection by immunosensing

The detection of cytokines in body fluids, cells, tissues and organisms continues to attract considerable attention due to the importance of these key cell signaling molecules in biology and medicine. In this review, we describe recent advances in cytokine detection in the course of ongoing pursuit of new analytical approaches for these trace analytes with specific focus on immunosensing. We discuss recent elegant designs of sensing interface with improved performance with respect to sensitivity, selectivity, stability, simplicity, and the absence of sample matrix effects. Various immunosensing approaches based on multifunctional nanomaterials open novel opportunities for ultrasensitive detection of cytokines in body fluids in vitro and in vivo. Methodologies such as suspension arrays also known as bead assays together with optical fiber-based sensors, on their own or in combination with microfluidic devices will continue to have an important role to address the grand challenge of real-time in vivo multiplex cytokine detection.

Application of photonic crystal enhanced fluorescence to detection of low serum concentrations of human IgE antibodies specific for a purified cat allergen (Fel D1)

We demonstrate the detection of low concentrations of allergen-specific Immunoglobulin E (IgE) in human sera using a Photonic Crystal Enhanced Fluorescence (PCEF) microarray platform. The Photonic Crystal (PC) surface, designed to provide optical resonances for the excitation wavelength and emission wavelength of Cy5, was used to amplify the fluorescence signal intensity measured from a multiplexed allergen microarray. Surface-based sandwich immunoassays were used to detect and quantify specific IgE antibodies against a highly purified cat allergen (Fel d1). A comparison of the lowest detectable concentration of IgE measured by the PC microarray system and a commercially available clinical analyzer demonstrated that the PCEF microarray system provides higher sensitivity. The PCEF system was able to detect low concentrations of specific IgE (~0.02 kU/L), which is 5-17-fold more sensitive than the commercially available FDA-approved analyzers. In preliminary experiments using multi-allergen arrays, we demonstrate selective simultaneous detection of IgE antibodies to multiple allergens.

Mechanisms, Capabilities, and Applications of High-Resolution Electrohydrodynamic Jet Printing

This review gives an overview of techniques used for high-resolution jet printing that rely on electrohydrodynamically induced flows. Such methods enable the direct, additive patterning of materials with a resolution that can extend below 100 nm to provide unique opportunities not only in scientific studies but also in a range of applications that includes printed electronics, tissue engineering, and photonic and plasmonic devices. Following a brief historical perspective, this review presents descriptions of the underlying processes involved in the formation of liquid cones and jets to establish critical factors in the printing process. Different printing systems that share similar principles are then described, along with key advances that have been made in the last decade. Capabilities in terms of printable materials and levels of resolution are reviewed, with a strong emphasis on areas of potential application.

Label-Free Biosensor Imaging on Photonic Crystal Surfaces

We review the development and application of nanostructured photonic crystal surfaces and a hyperspectral reflectance imaging detection instrument which, when used together, represent a new form of optical microscopy that enables label-free, quantitative, and kinetic monitoring of biomaterial interaction with substrate surfaces. Photonic Crystal Enhanced Microscopy (PCEM) has been used to detect broad classes of materials which include dielectric nanoparticles, metal plasmonic nanoparticles, biomolecular layers, and live cells. Because PCEM does not require cytotoxic stains or photobleachable fluorescent dyes, it is especially useful for monitoring the long-term interactions of cells with extracellular matrix surfaces. PCEM is only sensitive to the attachment of cell components within ~200 nm of the photonic crystal surface, which may correspond to the region of most interest for adhesion processes that involve stem cell differentiation, chemotaxis, and metastasis. PCEM has also demonstrated sufficient sensitivity for sensing nanoparticle contrast agents that are roughly the same size as protein molecules, which may enable applications in "digital" diagnostics with single molecule sensing resolution. We will review PCEM's development history, operating principles, nanostructure design, and imaging modalities that enable tracking of optical scatterers, emitters, absorbers, and centers of dielectric permittivity.

Enhanced live cell imaging via photonic crystal enhanced fluorescence microscopy

We demonstrate photonic crystal enhanced fluorescence (PCEF) microscopy as a surface-specific fluorescence imaging technique to study the adhesion of live cells by visualizing variations in cell-substrate gap distance. This approach utilizes a photonic crystal surface incorporated into a standard microscope slide as the substrate for cell adhesion, and a microscope integrated with a custom illumination source as the detection instrument. When illuminated with a monochromatic light source, angle-specific optical resonances supported by the photonic crystal enable efficient excitation of surface-confined and amplified electromagnetic fields when excited at an on-resonance condition, while no field enhancement occurs when the same photonic crystal is illuminated in an off-resonance state. By mapping the fluorescence enhancement factor for fluorophore-tagged cellular components between on- and off-resonance states and comparing the results to numerical calculations, the vertical distance of labelled cellular components from the photonic crystal substrate can be estimated, providing critical and quantitative information regarding the spatial distribution of the specific components of cells attaching to a surface. As an initial demonstration of the concept, 3T3 fibroblast cells were grown on fibronectin-coated photonic crystals with fluorophore-labelled plasma membrane or nucleus. We demonstrate that PCEF microscopy is capable of providing information about the spatial distribution of cell-surface interactions at the single-cell level that is not available from other existing forms of microscopy, and that the approach is amenable to large fields of view, without the need for coupling prisms, coupling fluids, or special microscope objectives.

High sensitivity automated multiplexed immunoassays using photonic crystal enhanced fluorescence microfluidic system

We demonstrate a platform that integrates photonic crystal enhanced fluorescence (PCEF) detection of a surface-based microspot fluorescent assay with a microfluidic cartridge to achieve simultaneous goals of high analytic sensitivity (single digit pg/mL), high selectivity, low sample volume, and assay automation. The PC surface, designed to provide optical resonances for the excitation wavelength and emission wavelength of Cyanines 5 (Cy5), was used to amplify the fluorescence signal intensity measured from a multiplexed biomarker microarray. The assay system is comprised of a plastic microfluidic cartridge for holding the PC and an assay automation system that provides a leak-free fluid interface during introduction of a sequence of fluids under computer control. Through the use of the assay automation system and the PC embedded within the microfluidic cartridge, we demonstrate pg/mL-level limits of detection by performing representative biomarker assays for interleukin 3 (IL3) and Tumor Necrosis Factor (TNF-α). The results are consistent with limits of detection achieved without the use of the microfluidic device with the exception that coefficients of variability from spot-to-spot are substantially lower than those obtained by performing assays with manual manipulation of assay liquids. The system's capabilities are compatible with the goal of diagnostic instruments for point-of-care settings.

High-throughput imaging assay of multiple proteins via target-induced DNA assembly and cleavage

This work integrates target-induced DNA assembly and cleavage on a DNA chip to design a versatile imaging strategy as an assay for multiple proteins. The DNA assembly is achieved via immunological recognition to trigger the proximity hybridization for releasing a DNA sequence, which then hybridizes with FITC-DNA1 immobilized on the chip to induce the enzymatic cleavage of DNA1 and thus decrease the signals. The signal readout is performed with both fluorescent imaging of the left FITC and chemiluminescent (CL) imaging, by adding peroxidase labelled anti-FITC in assembly solution and CL substrates to produce CL emission. This one-step incubation can be completed in 30 min. The imaging method shows wide detection ranges and detection limits down to pg mL-1 for the simultaneous detection of 4 protein biomarkers. This high-throughput strategy with good practicability can be easily extended to other protein analytes, providing a powerful protocol for protein analysis and clinical diagnosis.

Direct detection of transcription factors in cotyledons during seedling development using sensitive silicon-substrate photonic crystal protein arrays

Transcription factors control important gene networks, altering the expression of a wide variety of genes, including those of agronomic importance, despite often being expressed at low levels. Detecting transcription factor proteins is difficult, because current high-throughput methods may not be sensitive enough. One-dimensional, silicon-substrate photonic crystal (PC) arrays provide an alternative substrate for printing multiplexed protein microarrays that have greater sensitivity through an increased signal-to-noise ratio of the fluorescent signal compared with performing the same assay upon a traditional aminosilanized glass surface. As a model system to test proof of concept of the silicon-substrate PC arrays to directly detect rare proteins in crude plant extracts, we selected representatives of four different transcription factor families (zinc finger GATA, basic helix-loop-helix, BTF3/NAC [for basic transcription factor of the NAC family], and YABBY) that have increasing transcript levels during the stages of seedling cotyledon development. Antibodies to synthetic peptides representing the transcription factors were printed on both glass slides and silicon-substrate PC slides along with antibodies to abundant cotyledon proteins, seed lectin, and Kunitz trypsin inhibitor. The silicon-substrate PC arrays proved more sensitive than those performed on glass slides, detecting rare proteins that were below background on the glass slides. The zinc finger transcription factor was detected on the PC arrays in crude extracts of all stages of the seedling cotyledons, whereas YABBY seemed to be at the lower limit of their sensitivity. Interestingly, the basic helix-loop-helix and NAC proteins showed developmental profiles consistent with their transcript patterns, indicating proof of concept for detecting these low-abundance proteins in crude extracts.

Nanotechnology-based strategies for the detection and quantification of microRNA

MicroRNAs (miRNAs) are important regulators of gene expression, and many pathological conditions, including cancer, are characterized by altered miRNA expression levels. Therefore, accurate and sensitive quantification of miRNAs may result in correct disease diagnosis establishing these small noncoding RNA transcripts as valuable biomarkers. Aiming at overcoming some limitations of conventional quantification strategies, nanotechnology is currently providing numerous significant alternatives to miRNA sensing. In this review an up-to-date account of nanotechnology-based strategies for miRNA detection and quantification is given. The topics covered are: nanoparticle-based approaches in solution, sensing based on nanostructured surfaces, combined nanoparticle/surface sensing approaches, and single-molecule approaches.

Photonic crystal enhancement of a homogeneous fluorescent assay using submicron fluid channels fabricated by E-jet patterning

We demonstrate the enhancement of a liquid-based homogenous fluorescence assay using the resonant electric fields from a photonic crystal (PC) surface. Because evanescent fields are confined to the liquid volume nearest to the photonic crystal, we developed a simple approach for integrating a PC fabricated on a silicon substrate within a fluid channel with submicron height, using electrohydrodynamic jet (e-jet) printing of a light-curable epoxy adhesive to define the fluid channel pattern. The PC is excited by a custom-designed compact instrument that illuminates the PC with collimated light that precisely matches the resonant coupling condition when the PC is covered with aqueous media. Using a molecular beacon nucleic acid fluorescence resonant energy transfer (FRET) probe for a specific miRNA sequence, we demonstrate an 8× enhancement of the fluorescence emission signal, compared to performing the same assay without exciting resonance in the PC detecting a miRNA sequence at a concentration of 62 nM from a liquid volume of only ∼20 nL. The approach may be utilized for any liquid-based fluorescence assay for applications in point-of-care diagnostics, environmental monitoring, or pathogen detection.