Multiplexed detection and label-free quantitation of microRNAs using arrays of silicon photonic microring resonators

Ultrasensitive and Multiple Disease-Related MicroRNA Detection Based on Tetrahedral DNA Nanostructures and Duplex-Specific Nuclease-Assisted Signal Amplification

A highly sensitive and multiple microRNA (miRNA) detection method by combining three-dimensional (3D) DNA tetrahedron-structured probes (TSPs) to increase the probe reactivity and accessibility with duplex-specific nuclease (DSN) for signal amplification for sensitive miRNA detection was proposed. Briefly, 3D DNA TSPs labeled with different fluorescent dyes for specific target miRNA recognition were modified on a gold nanoparticle (GNP) surface to increase the reactivity and accessibility. Upon hybridization with a specific target, the TSPs immobilized on the GNP surface hybridized with the corresponding target miRNA to form DNA-RNA heteroduplexes, and the DSN can recognize the formed DNA-RNA heteroduplexes to hydrolyze the DNA in the heteroduplexes to produce a specific fluorescent signal corresponding to a specific miRNA, while the released target miRNA strands can initiate another cycle, resulting in a significant signal amplification for sensitive miRNA detection. Different targets can produce different fluorescent signals, leading to the development of a sensitive detection for multiple miRNAs in a homogeneous solution. Under optimized conditions, the proposed assay can simultaneously detect three different miRNAs in a homogeneous solution with a logarithmic linear range spanning 5 magnitudes (10^-12-10^-16) and achieving a limit of detection down to attomolar concentrations. Meanwhile, the proposed miRNA assay exhibited the capability of discriminating single bases (three bases mismatched miRNAs) and showed good eligibility in the analysis of miRNAs extracted from cell lysates and miRNAs in cell incubation media, which indicates its potential use in biomedical research and clinical analysis.

PCR-Free, Multiplexed Expression Profiling of microRNAs Using Silicon Photonic Microring Resonators

We describe an approach for multiplexed microRNA analysis using silicon photonic microring resonators to detect cDNA reverse transcription products via a subsequent enzymatic signal enhancement strategy. Key to this method is a modified stem loop primer that facilitates downstream signal amplification via enzymatic turnover and improves the sensor signal 20-fold when compared to traditional stem loop primers. This approach facilitates targeted microRNA quantification in only 2.5 h and without requiring target amplification via the polymerase chain reaction (PCR). Primers for 7 miRNA targets were orthogonally designed to avoid cross-hybridization between capture probes. This approach was applied to the detection of total RNA from human tissues and found to display differential expression profiles consistent with literature precedent. This development holds promise as an alternative to single-plex RT-qPCR methods and more expensive RNA-seq by offering a cost-effective method to analyze targeted miRNA panels in emerging diagnostic applications.

Integrating a DNA Strand Displacement Reaction with a Whispering Gallery Mode Sensor for Label-Free Mercury (II) Ion Detection

Mercury is an extremely toxic chemical pollutant of our environment. It has attracted the world’s attention due to its high mobility and the ease with which it accumulates in organisms. Sensitive devices and methods specific for detecting mercury ions are, hence, in great need. Here, we have integrated a DNA strand displacement reaction with a whispering gallery mode (WGM) sensor for demonstrating the detection of Hg²⁺ ions. Our approach relies on the displacement of a DNA hairpin structure, which forms after the binding of mercury ions to an aptamer DNA sequence. The strand displacement reaction of the DNA aptamer provides highly specific and quantitative means for determining the mercury ion concentration on a label-free WGM sensor platform. Our approach also shows the possibility for manipulating the kinetics of a strand displacement reaction with specific ionic species.

Oligonucleotide-based label-free detection with optical microresonators: strategies and challenges

This review targets diversified oligonucleotide-based biodetection techniques, focusing on the use of microresonators of whispering gallery mode (WGM) type as optical biosensors mostly integrated with lab-on-a-chip systems. On-chip and microfluidics combined devices along with optical microresonators provide rapid, robust, reproducible and multiplexed biodetection abilities in considerably small volumes. We present a detailed overview of the studies conducted so far, including biodetection of various oligonucleotide biomarkers as well as deoxyribonucleic acids (DNAs), ribonucleic acids (RNAs) and proteins. We particularly advert to chemical surface modifications for specific and selective biosensing.

Effect of the Concentration Difference between Magnesium Ions and Total Ribonucleotide Triphosphates in Governing the Specificity of T7 RNA Polymerase-Based Rolling Circle Transcription for Quantitative Detection

T7 RNA polymerase-based rolling circle transcription (RCT) is a more powerful tool than universal runoff transcription and traditional DNA polymerase-based rolling circle amplification (RCA). However, RCT is rarely employed in quantitative detection due to its poor specificity for small single-stranded DNA (ssDNA), which can be transcribed efficiently by T7 RNA polymerase even without a promoter. Herein we show that the concentration difference between Mg(2+) and total ribonucleotide triphosphates (rNTPs) radically governs the specificity of T7 RNA polymerase. Only when the total rNTP concentration is 9 mM greater than the Mg(2+) concentration can T7 RNA polymerase transcribe ssDNA specifically and efficiently. This knowledge improves our traditional understanding of T7 RNA polymerase and makes convenient application of RCT in quantitative detection possible. Subsequently, an RCT-based label-free chemiluminescence method for microRNA detection was designed to test the capability of this sensing platform. Using this simple method, microRNA as low as 20 amol could be quantitatively detected. The results reveal that the developed sensing platform holds great potential for further applications in the quantitative detection of a variety of targets.

Reprogrammable multiplexed detection of circulating oncomiRs using hybridization chain reaction

Coupling the DNA polymerization capability of HCR with the plasmonic properties of AuNP for reprogrammable, multiplexed and visual detection of three different circulating oncomiRs in seven different combinations.

Label-Free Nanoplasmonic-Based Short Noncoding RNA Sensing at Attomolar Concentrations Allows for Quantitative and Highly Specific Assay of MicroRNA-10b in Biological Fluids and Circulating Exosomes

MicroRNAs are short noncoding RNAs consisting of 18-25 nucleotides that target specific mRNA moieties for translational repression or degradation, thereby modulating numerous biological processes. Although microRNAs have the ability to behave like oncogenes or tumor suppressors in a cell-autonomous manner, their exact roles following release into the circulation are only now being unraveled and it is important to establish sensitive assays to measure their levels in different compartments in the circulation. Here, an ultrasensitive localized surface plasmon resonance (LSPR)-based microRNA sensor with single nucleotide specificity was developed using chemically synthesized gold nanoprisms attached onto a solid substrate with unprecedented long-term stability and reversibility. The sensor was used to specifically detect microRNA-10b at the attomolar (10(-18) M) concentration in pancreatic cancer cell lines, derived tissue culture media, human plasma, and media and plasma exosomes. In addition, for the first time, our label-free and nondestructive sensing technique was used to quantify microRNA-10b in highly purified exosomes isolated from patients with pancreatic cancer or chronic pancreatitis, and from normal controls. We show that microRNA-10b levels were significantly higher in plasma-derived exosomes from pancreatic ductal adenocarcinoma patients when compared with patients with chronic pancreatitis or normal controls. Our findings suggest that this unique technique can be used to design novel diagnostic strategies for pancreatic and other cancers based on the direct quantitative measurement of plasma and exosome microRNAs, and can be readily extended to other diseases with identifiable microRNA signatures.

Magnetically-actuated, bead-enhanced silicon photonic immunosensor

Magnetic actuation has been introduced to an optical immunosensor technology resulting in improvements in both rapidity and limit of detection for an assay quantitating low concentrations of a representative protein biomarker. For purposes of demonstration, an assay was designed for monocyte chemotactic protein 1 (MCP-1), a small cytokine which regulates migration and infiltration of monocytes and macrophages, and is an emerging biomarker for several diseases. The immunosensor is based on arrays of highly multiplexed silicon photonic microring resonators. A one-step sandwich immunoassay was performed and the signal was further enhanced through a tertiary recognition event between biotinylated tracer antibodies and streptavidin-coated magnetic beads. By integrating a magnet under the sensor chip, magnetic beads were rapidly directed towards the sensor surface resulting in improved assay performance metrics. Notably, the time required in the bead binding step was reduced by a factor of 11 (4 vs 45 min), leading to an overall decrease in assay time from 73 min to 32 min. The magnetically-actuated assay also lowered the limit of detection (LOD) for MCP-1 from 124 pg mL^-1 down to 57 pg mL^-1. In sum, the addition of magnetic actuation into bead-enhanced sandwich assays on a silicon photonic biosensor platform might facilitate improved detection of biomarkers in point-of-care diagnostics settings.

Development and validation of an immunosensor for monocyte chemotactic protein 1 using a silicon photonic microring resonator biosensing platform

OBJECTIVES

We report the development of an optical immunosensor for the detection of monocyte chemotactic protein 1 (MCP-1) in serum samples. MCP-1 is a cytokine that is an emerging biomarker for several diseases/disorders, including ischemic cardiomyopathy, fibromyalgia, and some cancers.

DESIGN AND METHODS

The detection of MCP-1 was achieved by performing a sandwich immunoassay on a silicon photonic microring resonator sensor platform. The resonance wavelengths supported by microring sensors are responsive to local changes in the environment accompanying biomarker binding. This technology offers a modularly multiplexable approach to detecting analyte localization in an antibody-antigen complex at the sensor surface.

RESULTS

The immunosensor allowed the rapid detection of MCP-1 in buffer and spiked human serum samples. An almost 2 order of magnitude linear range was observed, between 84.3 and 1582.1pg/mL and the limits of blank and detection were determined to be 0.3 and 0.5pg/mL, respectively. The platform's ability to analyze MCP-1 concentrations across a clinically-relevant concentration range was demonstrated.

CONCLUSIONS

A silicon photonic immunosensor technology was applied to the detection of clinically-relevant concentrations of MCP-1. The performance of the sensor was validated through a broad dynamic range and across a number of suggested clinical cut-off values. Importantly, the intrinsic scalability and rapidity of the technology makes it readily amenable to the simultaneous detection of multiplexed biomarker panels, which is particularly needed for the clinical realization of inflammatory diagnostics.

Contact Transfer Printing of Side Edge Prefunctionalized Nanoplasmonic Arrays for Flexible microRNA Biosensor

For a nanoplasmonic approach of wearable biochip platform, understanding correlation between near-field enhancement on nanostructures and sensing capability is a crucial step to improve the sensitivity in biosensing. A novel and effective method is demonstrated to increase sensitivity with the enhanced electric fields and to reduce noise with targeted functionalization enabled by transferring side edge prefunctionalized (SEPF) nanostructure arrays onto flexible substrates. Nanostructure sidewalls have selective biochemically functional terminals for the hybridization of microRNAs (miRNAs) and the immobilization of resonant nanoparticles, thus forming hetero assemblies of the nanostructure and the nanoparticles. The unique configuration has shown ultrasensitive biosensing of miRNA-21 in a 10 × 10^-15 m level by a red-shift in scattering spectra induced by a plasmon coupling. This ultrasensitive SEPF nanostructure arrays are fabricated on a flexible substrate using a contact transfer printing with a release layer of trichloro(1H, 1H, 2H, 2H-perfluorooctyl)silane. The introduction of the release layer at a prefunctionalizing step has proven to provide selective functionalization only on the sidewalls of the nanostructures. This reduces a background noise caused by the scattering from nonspecifically bound nanoparticles on the substrate, thus enabling reliable and precise detection.

Whispering gallery mode sensors

We present a comprehensive overview of sensor technology exploiting optical whispering gallery mode (WGM) resonances. After a short introduction we begin by detailing the fundamental principles and theory of WGMs in optical microcavities and the transduction mechanisms frequently employed for sensing purposes. Key recent theoretical contributions to the modeling and analysis of WGM systems are highlighted. Subsequently we review the state of the art of WGM sensors by outlining efforts made to date to improve current detection limits. Proposals in this vein are numerous and range, for example, from plasmonic enhancements and active cavities to hybrid optomechanical sensors, which are already working in the shot noise limited regime. In parallel to furthering WGM sensitivity, efforts to improve the time resolution are beginning to emerge. We therefore summarize the techniques being pursued in this vein. Ultimately WGM sensors aim for real-world applications, such as measurements of force and temperature, or alternatively gas and biosensing. Each such application is thus reviewed in turn, and important achievements are discussed. Finally, we adopt a more forward-looking perspective and discuss the outlook of WGM sensors within both a physical and biological context and consider how they may yet push the detection envelope further.

Mach-Zehnder interferometer (MZI) point-of-care system for rapid multiplexed detection of microRNAs in human urine specimens

MicroRNAs have been identified as promising biomarkers for human diseases. The development of a point-of-care (POC) test for the disease-associated miRNAs would be especially beneficial, since miRNAs are unexpectedly well preserved in various human specimens, including urine. Here, we present the Mach-Zehnder interferometer-miRNA detection system capable of detecting multiple miRNAs in clinical urine samples rapidly and simultaneously in a label-free and real-time manner. Through measurement of the light phase change, the MZI sensor provides an optical platform for fast profiling of small molecules with improved accuracy. We demonstrate that this system could specifically detect target miRNAs (miR-21, and let-7a), and even identify the single nucleotide polymorphism of the let-7 family of miRNAs from synthetic and cell line samples. The clinical applicability of this system is confirmed by simultaneously detecting two types of miRNAs in urine samples of bladder cancer patients in a single reaction, with a detection time of 15 min. The POC system can be expanded to detect a number of miRNAs of different species and should be useful for a variety of clinical applications requiring at or near the site of patient care.

Highly specific plasmonic biosensors for ultrasensitive microRNA detection in plasma from pancreatic cancer patients

MicroRNAs (miRs) are small noncoding RNAs that regulate mRNA stability and/or translation. Because of their release into the circulation and their remarkable stability, miR levels in plasma and other biological fluids can serve as diagnostic and prognostic disease biomarkers. However, quantifying miRs in the circulation is challenging due to issues with sensitivity and specificity. This Letter describes for the first time the design and characterization of a regenerative, solid-state localized surface plasmon resonance (LSPR) sensor based on highly sensitive nanostructures (gold nanoprisms) that obviates the need for labels or amplification of the miRs. Our direct hybridization approach has enabled the detection of subfemtomolar concentration of miR-X (X = 21 and 10b) in human plasma in pancreatic cancer patients. Our LSPR-based measurements showed that the miR levels measured directly in patient plasma were at least 2-fold higher than following RNA extraction and quantification by reverse transcriptase-polymerase chain reaction. Through LSPR-based measurements we have shown nearly 4-fold higher concentrations of miR-10b than miR-21 in plasma of pancreatic cancer patients. We propose that our highly sensitive and selective detection approach for assaying miRs in plasma can be applied to many cancer types and disease states and should allow a rational approach for testing the utility of miRs as markers for early disease diagnosis and prognosis, which could allow for the design of effective individualized therapeutic approaches.

Diffusion-based microfluidic PCR for "one-pot" analysis of cells

Genetic analysis starting with cell samples often requires multi-step processing including cell lysis, DNA isolation/purification, and polymerase chain reaction (PCR) based assays. When conducted on a microfluidic platform, the compatibility among various steps often demands a complicated procedure and a complex device structure. Here we present a microfluidic device that permits a "one-pot" strategy for multi-step PCR analysis starting from cells. Taking advantage of the diffusivity difference, we replace the smaller molecules in the reaction chamber by diffusion while retaining DNA molecules inside. This simple scheme effectively removes reagents from the previous step to avoid interference and thus permits multi-step processing in the same reaction chamber. Our approach shows high efficiency for PCR and potential for a wide range of genetic analysis including assays based on single cells.

Nanomaterials-Based Sensing Strategies for Electrochemical Detection of MicroRNAs

MicroRNAs (miRNAs) play important functions in post-transcriptional regulation of gene expression. They have been regarded as reliable molecular biomarkers for many diseases including cancer. However, the content of miRNAs in cells can be low down to a few molecules per cell. Thus, highly sensitive analytical methods for miRNAs detection are desired. Recently, electrochemical biosensors have held great promise as devices suitable for point-of-care diagnostics and multiplexed platforms for fast, simple and low-cost nucleic acid analysis. Signal amplification by nanomaterials is one of the most popular strategies for developing ultrasensitive assay methods. This review surveys the latest achievements in the use of nanomaterials to detect miRNAs with a focus on electrochemical techniques.

Antibodies specific for nucleic acids and applications in genomic detection and clinical diagnostics

Detection of nucleic acids using antibodies is uncommon. This is in part because nucleic acids are poor immunogens and it is difficult to elicit antibodies having high affinity to each type of nucleic acid while lacking cross-reactivity to others. We describe the origins and applications of a variety of anti-nucleic acid antibodies, including ones reacting with modified nucleosides and nucleotides, single-stranded DNA, double-stranded DNA, RNA, DNA:RNA hybrids, locked-nucleic acids or peptide nucleic acid:nucleic acid hybrids. Carefully selected antibodies can be excellent reagents for detecting bacteria, viruses, small RNAs, microRNAs, R-loops, cancer cells, stem cells, apoptotic cells and so on. The detection may be sensitive, simple, rapid, specific, reproducible, quantitative and cost-effective. Current microarray and diagnostic methods that depend on cDNA or cRNA can be replaced by using antibody detection of nucleic acids. Therefore, development should be encouraged to explore new utilities and create a robust arsenal of new anti-nucleic acid antibodies.

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.

Ultraspecific and highly sensitive nucleic acid detection by integrating a DNA catalytic network with a label-free microcavity

Nucleic acid detection with label-free biosensors circumvents costly fluorophore functionalization steps associated with conventional assays by utilizing transducers of impressive ultimate detection limits. Despite this technological prowess, molecular recognition at a surface limits the biosensors' sensitivity, specificity, and reusability. It is therefore imperative to integrate novel molecular approaches with existing label-free transducers to overcome those limitations. Here, we demonstrate this concept by integrating a DNA strand displacement circuit with a micron-scale whispering gallery mode (WGM) microsphere biosensor. The integrated biosensor exhibits at least 25-fold improved nucleic acid sensitivity, and sets a new record for label-free microcavity biosensors by detecting 80 pM (32 fmol) of a 22nt oligomer; this improvement results from the catalytic behavior of the circuit. Furthermore, the integrated sensor exhibits extremely high specificity; single nucleotide variants yield 40- to 100-fold lower signal. Finally, the same physical sensor was demonstrated to alternatingly detect 2 different nucleic acid sequences through 5 cycles of detection, showcasing both its reusability and its versatility.

Multiplex ligation-dependent probe amplification (MLPA) for ultrasensitive multiplexed microRNA detection using ribonucleotide-modified DNA probes

Using the ribonucleotide-modified DNA probes, multiple microRNAs can be simultaneously detected in one ligation-based PCR reaction. As low as 0.2 fM microRNA can be accurately detected with high specificity.

Programming nanopore ion flow for encoded multiplex microRNA detection

Many efforts are being made in translating the nanopore into an ultrasensitive single-molecule platform for various genetic and epigenetic detections. However, compared with current approaches including PCR, the low throughput limits the nanopore applications in biological research and clinical settings, which usually requires simultaneous detection of multiple biomarkers for accurate disease diagnostics. Herein we report a barcode probe approach for multiple nucleic acid detection in one nanopore. Instead of directly identifying different targets in a nanopore, we designed a series of barcode probes to encode different targets. When the probe is bound with the target, the barcode group polyethylene glycol attached on the probe through click chemistry can specifically modulate nanopore ion flow. The resulting signature serves as a marker for the encoded target. Therefore counting different signatures in a current recording allows simultaneous analysis of multiple targets in one nanopore. The principle of this approach was verified by using a panel of cancer-derived microRNAs as the target, a type of biomarker for cancer detection.

Refractive index-based detection of gradient elution liquid chromatography using chip-integrated microring resonator arrays

Refractive index-based sensors offer attractive characteristics as nondestructive and universal detectors for liquid chromatographic separations, but a small dynamic range and sensitivity to minor thermal perturbations limit the utility of commercial RI detectors for many potential applications, especially those requiring the use of gradient elutions. As such, RI detectors find use almost exclusively in sample abundant, isocratic separations when interfaced with high-performance liquid chromatography. Silicon photonic microring resonators are refractive index-sensitive optical devices that feature good sensitivity and tremendous dynamic range. The large dynamic range of microring resonators allows the sensors to function across a wide spectrum of refractive indices, such as that encountered when moving from an aqueous to organic mobile phase during a gradient elution, a key analytical advantage not supported in commercial RI detectors. Microrings are easily configured into sensor arrays, and chip-integrated control microrings enable real-time corrections of thermal drift. Thermal controls allow for analyses at any temperature and, in the absence of rigorous temperature control, obviates extended detector equilibration wait times. Herein, proof of concept isocratic and gradient elution separations were performed using well-characterized model analytes (e.g., caffeine, ibuprofen) in both neat buffer and more complex sample matrices. These experiments demonstrate the ability of microring arrays to perform isocratic and gradient elutions under ambient conditions, avoiding two major limitations of commercial RI-based detectors and maintaining comparable bulk RI sensitivity. Further benefit may be realized in the future through selective surface functionalization to impart degrees of postcolumn (bio)molecular specificity at the detection phase of a separation. The chip-based and microscale nature of microring resonators also make it an attractive potential detection technology that could be integrated within lab-on-a-chip and microfluidic separation devices.

Subpicogram per milliliter detection of interleukins using silicon photonic microring resonators and an enzymatic signal enhancement strategy

The detection of biomolecules at ultralow (low to subpicogram per milliliter) concentrations and within complex, clinically relevant matrices is a formidable challenge that is complicated by limitations imposed by the Langmuir binding isotherm and mass transport, for surface-based affinity biosensors. Here we report the integration of an enzymatic signal enhancement scheme onto a multiplexable silicon photonic microring resonator detection platform. To demonstrate the analytical value of this combination, we simultaneously quantitated levels of the interleukins IL-2, IL-6, and IL-8 in undiluted cerebrospinal fluid in an assay format that is multiplexable, relatively rapid (90 min), and features a 3 order of magnitude dynamic range and a limit of detection ≤1 pg/mL. The modular nature of this assay and technology should lend itself broadly amenable to different analyte classes, making it a versatile tool for biomarker analysis in clinically relevant settings.

Electronic detection of microRNA at attomolar level with high specificity

Small RNA (19-23 nucleotides) molecules play an important role in gene regulation, embryonic differentiation, hematopoiesis, and a variety of cancers. Here, we present an ultrasensitive, extremely specific, label-free, and rapid electronic detection of microRNAs (miRNAs) using a carbon nanotubes field-effect transistor functionalized with the Carnation Italian ringspot virus p19 protein biosensor. miRNA-122a was chosen as the target, which was first hybridized to a probe molecule. The probe-miRNA duplex was then quantified by measuring the change in resistance of biosensor resulting from its binding to p19, which selects 21-23 bp RNA duplexes in a size-dependent but sequence-independent manner. The biosensor displayed a wide dynamic range up to 10(-14) M and was able to detect as low as 1 aM miRNA in the presence of a million-fold excess of total RNA, paving the way for simple, point-of-care, low-cost early detection of miRNA as a biomarker in diagnosis of many diseases, including cancer.

Biomolecular analysis with microring resonators: applications in multiplexed diagnostics and interaction screening

Microring optical resonators are a promising class of sensor whose value in bioanalytical applications has only begun to be explored. Utilized in the telecommunication industry for signal processing applications, microring resonators have more recently been re-tasked for biosensing because of their scalability, sensitivity, and versatility. Their sensing modality arises from light/matter interactions--light propagating through the microring and the resultant evanescent field extending beyond the structure is sensitive to the refractive index of the local environment, which modulates resonant wavelength of light supported by the cavity. This sensing capability has recently been utilized for the detection of numerous biological targets including proteins, nucleic acids, viruses, and small molecules. Herein we highlight some of the most exciting recent uses of this technology for biosensing applications, with an eye towards future developments in the field.

Integration of microsphere resonators with bioassay fluidics for whispering gallery mode imaging

Whispering gallery mode resonators are small, radially symmetric dielectrics that trap light through continuous total internal reflection. The resonant condition at which light is efficiently confined within the structure is linked with refractive index, which has led to the development of sensitive label-free sensing schemes based on whispering gallery mode resonators. One resonator design uses inexpensive high index glass microspheres that offer intrinsically superior optical characteristics, but have proven difficult to multiplex and integrate with the fluidics for sample delivery and fluid exchange necessary for assay development. Recently, we introduced a fluorescence imaging approach that enables large scale multiplexing with microsphere resonators, thus removing one obstacle for assay development. Here we report an approach for microsphere immobilization that overcomes limitations arising from their integration with fluidic delivery. The approach is an adaptation of a calcium-assisted glass bonding method originally developed for microfluidic glass chip fabrication. Microspheres bonded to glass using this technique are shown to be stable with respect to fluid flow and show no detectable loss in optical performance. Measured Q-factors, for example, remain unchanged following sphere bonding to the substrate. The stability of the immobilized resonators is further demonstrated by transferring lipid films onto the immobilized spheres using the Langmuir-Blodgett technique. Bilayers of DOPC doped with GM1 were transferred onto immobilized resonators to detect the binding of cholera toxin to GM1. Binding curves generated from shifts in the whispering gallery mode resonance result in a measured Kd of 1.5 × 10(-11) with a limit of detection of 3.3 pM. These results are discussed in terms of future assay development using microsphere resonators.

Interfacing lipid bilayer nanodiscs and silicon photonic sensor arrays for multiplexed protein-lipid and protein-membrane protein interaction screening

Soluble proteins are key mediators of many biochemical signaling pathways via direct interaction with the lipid bilayer and via membrane-bound receptors. Components of the cell membrane are involved in many important biological processes, including viral infection, blood clotting, and signal transduction, and as such, they are common targets of therapeutic agents. Therefore, the development of analytical approaches to study interactions at the cell membrane is of critical importance. Herein, we integrate two key technologies, silicon photonic microring resonator arrays and phospholipid bilayer nanodiscs, which together allow multiplexed screening of soluble protein interactions with lipid and membrane-embedded targets. Microring resonator arrays are an intrinsically multiplexable, label-free analysis platform that has previously been applied to studying protein-protein, protein-nucleic acid, and nucleic acid-nucleic acid interactions. Nanodiscs are protein-stabilized lipid assemblies that represent a convenient construct to mimic the native phospholipid bilayer, investigate the effects of membrane composition, and solubilize membrane-embedded targets. Exploiting the natural affinity of nanodisc-supported lipid bilayers for oxide-passivated silicon, we assembled single and multiplex sensor arrays via direct physisorption, characterizing electrostatic effects on the nanodisc attachment. Using model systems, we demonstrate the applicability of this platform for the parallel screening of protein interactions with nanodisc-embedded lipids, glycolipids, and membrane proteins.

Label-free biosensor based on an electrical tracing-assisted silicon microring resonator with a low-cost broadband source

We present a novel biosensor based on an electrical tracing-assisted silicon dual-microring resonator sensor system. The dual-microring system comprises one microring resonator as a sensing element and the other microring resonator integrated with an electrical controller as a tracing element. The resonance wavelength shift of the sensing microring induced by the refractive index change due to antigen-ligand bindings is traced and determined by direct voltage applied to the electrical tunable tracing microring. The sensor system enables the use of a low-cost broadband light source instead of a bulky and expensive tunable laser, which allows the development of cost-effective point-of-care diagnostic devices by significantly reducing the device cost and increasing its portability. The sensing capability of the developed dual-microring sensor was investigated using biotin-streptavidin binding as a model system. We have demonstrated the quantitative detection of streptavidin over a broad range of concentrations down to 190 pM by monitoring the electrical power applied to the tracing ring. We have also validated the sensing principle of the dual-microring system by a direct comparison between the calculated and measured values for the resonance wavelength shift of the sensing microring. Furthermore, we have shown the quantitative and specific detection of a well-known breast cancer biomarker, human epidermal growth factor receptor 2 (HER2), in a bovine serum albumin solution using the antibody-modified dual-microring sensor system.

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

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

Label-free detection with high-Q microcavities: a review of biosensing mechanisms for integrated devices

Optical microcavities that confine light in high-Q resonance promise all of the capabilities required for a successful next-generation microsystem biodetection technology. Label-free detection down to single molecules as well as operation in aqueous environments can be integrated cost-effectively on microchips, together with other photonic components, as well as electronic ones. We provide a comprehensive review of the sensing mechanisms utilized in this emerging field, their physics, engineering and material science aspects, and their application to nanoparticle analysis and biomolecular detection. We survey the most recent developments such as the use of mode splitting for self-referenced measurements, plasmonic nanoantennas for signal enhancements, the use of optical force for nanoparticle manipulation as well as the design of active devices for ultra-sensitive detection. Furthermore, we provide an outlook on the exciting capabilities of functionalized high-Q microcavities in the life sciences.

Zwitterionic polymer-modified silicon microring resonators for label-free biosensing in undiluted human plasma

A widely acknowledged goal in personalized medicine is to radically reduce the costs of highly parallelized, small fluid volume, point-of-care and home-based diagnostics. Recently, there has been a surge of interest in using complementary metal-oxide-semiconductor (CMOS)-compatible silicon photonic circuits for biosensing, with the promise of producing chip-scale integrated devices containing thousands of orthogonal sensors, at minimal cost on a per-chip basis. A central challenge in biosensor translation is to engineer devices that are both sensitive and specific to a target analyte within unprocessed biological fluids. Despite advances in the sensitivity of silicon photonic biosensors, poor biological specificity at the sensor surface remains a significant factor limiting assay performance in complex media (i.e. whole blood, plasma, serum) due to the non-specific adsorption of proteins and other biomolecules. Here, we chemically modify the surface of silicon microring resonator biosensors for the label-free detection of an analyte in undiluted human plasma. This work highlights the first application of a non-fouling zwitterionic surface coating to enable silicon photonic-based label-free detection of a protein analyte at clinically relevant sensitivities in undiluted human plasma.

Real-time observation of antigen-antibody association using a low-cost biosensing system based on photonic bandgap structures

In this letter, we present experimental results of antibody detection using a biosensor based on photonic bandgap structures, which are interrogated using a power-based readout technique. This interrogation method allows a real-time monitoring of the association process between the antigen probes and the target antibodies, allowing the instantaneous observation of any interaction event between molecules. because etunable lasers and optical spectrum analyzers are avoided for the readout, a drastic reduction of the final cost of the platform is obtained. Furthermore, the performance of the biosensing system is significantly enhanced due to the large number of data values obtained per second.

Chaperone probes and bead-based enhancement to improve the direct detection of mRNA using silicon photonic sensor arrays

Herein, we describe the utility of chaperone probes and a bead-based signal enhancement strategy for the analysis of full length mRNA transcripts using arrays of silicon photonic microring resonators. Changes in the local refractive index near microring sensors associated with biomolecular binding events are transduced as a shift in the resonant wavelength supported by the cavity, enabling the sensitive analysis of numerous analytes of interest. We employ the sensing platform for both the direct and bead-enhanced detection of three different mRNA transcripts, achieving a dynamic range spanning over 4 orders of magnitude and demonstrating expression profiling capabilities in total RNA extracts from the HL-60 cell line. Small, dual-use DNA chaperone molecules were developed and found to both enhance the binding kinetics of mRNA transcripts by disrupting complex secondary structure and serve as sequence-specific linkers for subsequent bead amplification. Importantly, this approach does not require amplification of the mRNA transcript, thereby allowing for simplified analyses that do not require expensive enzymatic reagents or temperature ramping capabilities associated with RT-PCR-based methods.

Chemical silicon surface modification and bioreceptor attachment to develop competitive integrated photonic biosensors

Methodology for the functionalization of silicon-based materials employed for the development of photonic label-free nanobiosensors is reported. The studied functionalization based on organosilane chemistry allowed the direct attachment of biomolecules in a single step, maintaining their bioavailability. Using this immobilization approach in probe microarrays, successful specific detection of bacterial DNA is achieved, reaching hybridization sensitivities of 10 pM. The utility of the immobilization approach for the functionalization of label-free nanobiosensors based on photonic crystals and ring resonators was demonstrated using bovine serum albumin (BSA)/anti-BSA as a model system.

Ultrasensitive detection of a protein by optical trapping in a photonic-plasmonic microcavity

Microcavity and whispering gallery mode (WGM) biosensors derive their sensitivity from monitoring frequency shifts induced by protein binding at sites of highly confined field intensities, where field strengths can be further amplified by excitation of plasmon resonances in nanoparticle layers. Here, we propose a mechanism based on optical trapping of a protein at the site of plasmonic field enhancements for achieving ultra sensitive detection in only microliter-scale sample volumes, and in real-time. We demonstrate femto-Molar sensitivity corresponding to a few 1000 s of macromolecules. Simulations based on Mie theory agree well with the optical trapping concept at plasmonic 'hotspots' locations.

miRNA therapeutics: delivery and biological activity of peptide nucleic acids targeting miRNAs

Peptide nucleic acids (PNAs) are DNA/RNA mimics extensively used for pharmacological regulation of gene expression in a variety of cellular and molecular systems, and they have been described as excellent candidates for antisense and antigene therapies. At present, very few data are available on the use of PNAs as molecules targeting miRNAs. miRNAs are a family of small nc RNAs that regulate gene expression by sequence-selective targeting of mRNAs, leading to a translational repression or mRNA degradation to the control of highly regulated biological functions, such as differentiation, cell cycle and apoptosis. The aim of this article is to present the state-of-the-art concerning the possible use of PNAs to target miRNAs and modify their biological metabolism within the cells. The results present in the literature allow to propose PNA-based molecules as very promising reagents to modulate the biological activity of miRNAs. In consideration of the involvement of miRNAs in human pathologies, PNA-mediated targeting of miRNAs has been proposed as a potential novel therapeutic approach.

Label-free, multiplexed detection of bacterial tmRNA using silicon photonic microring resonators

A label-free biosensing method for the sensitive detection and identification of bacterial transfer-messenger RNA (tmRNA) is presented employing arrays of silicon photonic microring resonators. Species specific tmRNA molecules are targeted by complementary DNA capture probes that are covalently attached to the sensor surface. Specific hybridization is monitored in near real-time by observing the resonance wavelength shift of each individual microring. The sensitivity of the biosensing platform allowed for detection down to 53 fmol of Streptococcus pneumoniae tmRNA, equivalent to approximately 3.16×10(7) CFU of bacteria. The simplicity and scalability of this biosensing approach makes it a promising tool for the rapid identification of different bacteria via tmRNA profiling.

Label-free virus detection using silicon photonic microring resonators

Viruses represent a continual threat to humans through a number of mechanisms, which include disease, bioterrorism, and destruction of both plant and animal food resources. Many contemporary techniques used for the detection of viruses and viral infections suffer from limitations such as the need for extensive sample preparation or the lengthy window between infection and measurable immune response, for serological methods. In order to develop a method that is fast, cost-effective, and features reduced sample preparation compared to many other virus detection methods, we report the application of silicon photonic microring resonators for the direct, label-free detection of intact viruses in both purified samples as well as in a complex, real-world analytical matrix. As a model system, we demonstrate the quantitative detection of Bean pod mottle virus, a pathogen of great agricultural importance, with a limit of detection of 10 ng/mL. By simply grinding a small amount of leaf sample in buffer with a mortar and pestle, infected leaves can be identified over a healthy control with a total analysis time of less than 45 min. Given the inherent scalability and multiplexing capability of the semiconductor-based technology, we feel that silicon photonic microring resonators are well-positioned as a promising analytical tool for a number of viral detection applications.