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

Biofunctionalization of Multiplexed Silicon Photonic Biosensors

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

Functional Micro-/Nanomaterials for Multiplexed Biodetection

When analyzing biological phenomena and processes, multiplexed biodetection has many advantages over single-factor biodetection and is highly relevant to both human health issues and advancements in the life sciences. However, many key problems with current multiplexed biodetection strategies remain unresolved. Herein, the main issues are analyzed and summarized: 1) generating sufficient signal to label targets, 2) improving the signal-to-noise ratio to ensure total detection sensitivity, and 3) simplifying the detection process to reduce the time and labor costs of multiple target detection. Then, available solutions made possible by designing and controlling the properties of micro- and nanomaterials are introduced. The aim is to emphasize the role that micro-/nanomaterials can play in the improvement of multiplexed biodetection strategies. Through analyzing existing problems, introducing state-of-the-art developments regarding relevant materials, and discussing future directions of the field, it is hopeful to help promote necessary developments in multiplexed biodetection and associated scientific research.

High resolution biosensor to test the capping level and integrity of mRNAs

5′ Cap structures are ubiquitous on eukaryotic mRNAs, essential for post-transcriptional processing, translation initiation and stability. Here we describe a biosensor designed to detect the presence of cap structures on mRNAs that is also sensitive to mRNA degradation, so uncapped or degraded mRNAs can be detected in a single step. The biosensor is based on a chimeric protein that combines the recognition and transduction roles in a single molecule. The main feature of this sensor is its simplicity, enabling semi-quantitative analyses of capping levels with minimal instrumentation. The biosensor was demonstrated to detect the capping level on several in vitro transcribed mRNAs. Its sensitivity and dynamic range remained constant with RNAs ranging in size from 250 nt to approximately 2700 nt and the biosensor was able to detect variations in the capping level in increments of at least 20%, with a limit of detection of 2.4 pmol. Remarkably, it also can be applied to more complex analytes, such mRNA vaccines and mRNAs transcribed in vivo. This biosensor is an innovative example of a technology able to detect analytically challenging structures such as mRNA caps. It could find application in a variety of scenarios, from quality analysis of mRNA-based products such as vaccines to optimization of in vitro capping reactions.

Biotoxoid Photonic Sensors with Temperature Insensitivity Using a Cascade of Ring Resonator and Mach-Zehnder Interferometer

The great advances in silicon photonic-sensing technology have made it an attractive platform for wide sensing applications. However, most silicon photonic-sensing platforms suffer from high susceptibility to the temperature fluctuation of an operating environment. Additional complex and costly chemical signal-enhancement strategies are usually required to improve the signal-to-noise ratio (SNR). Here, a biotoxoid photonic sensor that is resistant to temperature fluctuation has been demonstrated. This novel sensor consists of a ring resonator coupled to a Mach-Zehnder interferometer (MZI) readout unit. Instead of using costly wavelength interrogation, our photonic sensor directly measures the light intensity ratio between the two output ports of MZI. The temperature dependence (TD)-controlling section of the MZI is used to eliminate the adverse effects of ambient temperature fluctuation. The simulation and experimental results show a linear relationship between the interrogation function and the concentration of an analyte under operation conditions. The thermal drift of the proposed sensor is just 0.18%, which is a reduction of 567-fold for chemical sensing and 28-fold for immuno-biosensing compared to the conventional single-ring resonator. The SNR increases from 6.85 to 19.88 dB within a 2 °C temperature variation. The high SNR optical sensor promises great potential for amplification-free detection of nucleic acids and other biomarkers.

Multiplexed microRNA Expression Profiling by Combined Asymmetric PCR and Label-Free Detection using Silicon Photonic Sensor Arrays

Analysis methods based upon the quantitative, real-time polymerase chain reaction are extremely powerful; however, they face intrinsic limitations in terms of target multiplexing. In contrast, silicon photonic microring resonators represent a modularly multiplexable sensor array technology that is well-suited to the analysis of targeted biomarker panels. In this manuscript we employ an asymmetric polymerase chain reaction approach to selectively amplify copies of cDNAs generated from targeted miRNAs before multiplexed, label-free quantitation through hybridization to microring resonator arrays pre-functionalized with capture sequences. This method, which shows applicability to low input amounts and a large dynamic range, was demonstrated for the simultaneous detection of eight microRNA targets from twenty primary brain tumor samples with expression profiles in good agreement with literature precedent.

Combining asymmetric PCR-based enzymatic amplification with silicon photonic microring resonators for the detection of lncRNAs from low input human RNA samples

A method for quantifying biologically relevant long-non-coding RNAs by combining nucleic acid amplification via asymmetric polymerase chain reaction (PCR) with label-free PCR product detection using silicon photonic microring resonator arrays is described. This approach eliminates the need for fluorophores, which presents a limit for spectral multiplexing in conventional qPCR methods, and rather offers potential for much higher levels of plexity by spatially arraying capture probes. Here, we demonstrate the potential of this technique to detect two differentially expressed lncRNA transcripts and an internal control mRNA transcript in different commercial human tissue specimens, as well as in a glioblastoma cell line using only nanogram input amounts of total RNA. The obtained results were validated using single-plex RT-qPCR and found to be in good agreement, demonstrating the potential of this technique for lncRNA quantification applications.

Label-Free Optical Biodetection of Pathogen Virulence Factors in Complex Media Using Microtoroids with Multifunctional Surface Functionality

Early detection of pathogens or their virulence factors in complex media has a key role in early diagnosis and treatment of many diseases. Nanomolar and selective detection of Exotoxin A, which is a virulence factor secreted from Pseudomonas aeruginosa in the sputum of Cystic Fibrosis (CF) patients, can pave the way for early diagnosis of P. aeruginosa infections. In this study, we conducted a preliminary study to demonstrate the feasibility of optical biodetection of P. aeruginosa Exotoxin A in a diluted artificial sputum mimicking the CF respiratory environment. Our surface engineering approach provides an effective biointerface enabling highly selective detection of the Exotoxin A molecules in the complex media using monoclonal anti-Exotoxin A functionalized microtoroids. The highly resilient microtoroid surface toward other constituents of the sputum provides Exotoxin A detection ability in the complex media by reproducible measurements. In this study, the limit-of-detection of Exotoxin A in the complex media is calculated as 2.45 nM.

A Guide to Quantitative Biomarker Assay Development using Whispering Gallery Mode Biosensors

Whispering gallery mode (WGM) sensors are a class of powerful analytical techniques defined by the measurement of changes in the local refractive index at or near the sensor surface. When functionalized with target-specific capture agents, analyte binding can be measured with very low limits of detection. There are many geometric manifestations of WGM sensors, with chip-integrated silicon photonic devices first commercialized because of the robust, wafer-scale device fabrication, facile optical interrogation, and amenability to the creation of multiplexed sensor arrays. Using these arrays, a number of biomolecular targets have been detected in both label-free and label-enhanced assay formats. For example, sub-picomolar detection limits for multiple cytokines were achieved using an enzymatically enhanced sandwich immunoassay that showed high analyte specificity suitable for detection in complex, clinical matrices. This protocol describes a generalizable approach for the development of quantitative, multiplexed immunoassays using silicon photonic microrings as an example WGM platform. © 2017 by John Wiley & Sons, Inc.

Multiplexed silicon photonic sensor arrays enable facile characterization of coagulation protein binding to nanodiscs with variable lipid content

Interactions of soluble proteins with the cell membrane are critical within the blood coagulation cascade. Of particular interest are the interactions of γ-carboxyglutamic acid-rich domain-containing clotting proteins with lipids. Variability among conventional analytical methods presents challenges for comparing clotting protein-lipid interactions. Most previous studies have investigated only a single clotting protein and lipid composition and have yielded widely different binding constants. Herein, we demonstrate that a combination of lipid bilayer nanodiscs and a multiplexed silicon photonic analysis technology enables high-throughput probing of many protein-lipid interactions among blood-clotting proteins. This approach allowed direct comparison of the binding constants of prothrombin, factor X, activated factor VII, and activated protein C to seven different binary lipid compositions. In a single experiment, the binding constants of one protein interacting with all lipid compositions were simultaneously determined. A simple surface regeneration then facilitated similar binding measurements for three other coagulation proteins. As expected, our results indicated that all proteins exhibit tighter binding (lower K_d ) as the proportion of anionic lipid increases. Interestingly, at high proportions of phosphatidylserine, the K_d values of all four proteins began to converge. We also found that although k_off values for all four proteins followed trends similar to those observed for the K_d values, the variation among the proteins was much lower, indicating that much of the variation came from the kinetic binding (k_on) of the proteins. These findings indicate that the combination of silicon photonic microring resonator arrays and nanodiscs enables rapid interrogation of biomolecular binding interactions at model cell membrane interfaces.

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.

Targeted Treatment for Bacterial Infections: Prospects for Pathogen-Specific Antibiotics Coupled with Rapid Diagnostics

Antibiotics are a cornerstone of modern medicine and have significantly reduced the burden of infectious diseases. However, commonly used broad-spectrum antibiotics can cause major collateral damage to the human microbiome, causing complications ranging from antibiotic-associated colitis to the rapid spread of resistance. Employing narrower spectrum antibiotics targeting specific pathogens may alleviate this predicament as well as provide additional tools to expand an antibiotic repertoire threatened by the inevitability of resistance. Improvements in clinical diagnosis will be required to effectively utilize pathogen-specific antibiotics and new molecular diagnostics are poised to fulfill this need. Here we review recent trends and the future prospects of deploying narrower spectrum antibiotics coupled with rapid diagnostics. Further, we discuss the theoretical advantages and limitations of this emerging approach to controlling bacterial infectious diseases.

Applications of Optical Microcavity Resonators in Analytical Chemistry

Optical resonator sensors are an emerging class of analytical technologies that use recirculating light confined within a microcavity to sensitively measure the surrounding environment. Bolstered by advances in microfabrication, these devices can be configured for a wide variety of chemical or biomolecular sensing applications. We begin with a brief description of optical resonator sensor operation, followed by discussions regarding sensor design, including different geometries, choices of material systems, methods of sensor interrogation, and new approaches to sensor operation. Throughout, key developments are highlighted, including advancements in biosensing and other applications of optical sensors. We discuss the potential of alternative sensing mechanisms and hybrid sensing devices for more sensitive and rapid analyses. We conclude with our perspective on the future of optical microcavity sensors and their promise as versatile detection elements within analytical chemistry.

A dual-amplified electrochemical detection of mRNA based on duplex-specific nuclease and bio-bar-code conjugates

On the basis of strong preference for cleaving double-stranded DNA or DNA in DNA:RNA heteroduplexes of duplex-specific nuclease (DSN), a dual-amplified electrochemical detection of mRNA was developed in this article, by coupling the enhancement of DSN and bio-bar-code conjugates. Capture probe was linked with magnetic nanoparticles (MNPs) at its 5' end and bio-bar-code at its 3' end. In the presence of target surviving mRNA, all hybridized S1 strands were cleaved off the biosensor by the DSN, and the bio-bar-code probe with CdS nanoparticles (CdS NPs) was released into the solution. The metal sulfide nanoparticles were measured by anodic stripping voltammetry (ASV) subsequently. This assay exhibited high sensitivity and selectivity with a detection limit of 0.48fM. In addition, we proved that this simple and cost-effective strategy is capable of detecting the target in complicated biological samples and holds great potential application in biomedical research and clinical diagnostics.

Next generation ligand binding assays-review of emerging real-time measurement technologies

Over the last few years, numerous ligand binding assay technologies that utilize real-time measurement have been introduced; however, an assemblage and evaluation of these technologies has not previously been published. Herein, we describe six emerging real-time measurement technologies: Maverick™, MX96 SPR™, NanoDLSay™, AMMP®/ViBE®, SoPrano™, and two Lab-on-a-Chip (LoC) microfluidic devices. The development stage gate of these technologies ranges from pre-commercial to commercially available. Due to the novelty, the application and utility of some of the technologies regarding bioanalysis are likely to evolve but it is our hope that this review will provide insight into the direction the development of real-time measurement technologies is moving and the vision of those that are taking us there. Following the technology discussions, a comprehensive summary table is presented.

Molecular inversion probe-based SPR biosensing for specific, label-free and real-time detection of regional DNA methylation

DNA regional methylation can be detected in real-time and label-free using surface plasmon resonance biosensing coupled to molecular inversion probe based amplification.

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.

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.

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.

Single domain antibodies for the detection of ricin using silicon photonic microring resonator arrays

Ricin is a lethal protein toxin derived from the castor bean plant. Given its notorious history as a biowarfare agent and homicidal weapon, ricin has been classified as a category B bioterrorism agent. Current ricin detection methods based on immunoassays lack the required sensitivity and specificity for many homeland security surveillance applications. Importantly, many conventional antibody-based methodologies are unable to distinguish ricin from RCA 120, a nontoxic protein also found in the castor bean plant. Single domain antibodies (sdAbs), which are recombinantly derived from immunized llamas, are known to have high affinities for ricin A or B chains and low cross-reactivity with RCA 120. Herein, we demonstrate the use of silicon photonic microring resonators for antibody affinity profiling and one-step ricin detection at concentrations down to 300 pM using a 15 min, label-free assay format. These sdAbs were also simultaneously compared with a commercial anti-RCA IgG antibody in a multicapture agent, single target immunoassay using arrays of microrings, which allowed direct comparison of sensitivity and specificity. A selected sdAb was also found to exhibit outstanding specificity against another biotoxin, saporin, which has mechanism of action similar to ricin. Given the rapidity, scalability, and multiplexing capability of this silicon-based technology, this work represents a step toward using microring resonator arrays for the sensitive and specific detection of biowarfare agents.