Microphotonic control of single molecule fluorescence correlation spectroscopy using planar optofluidics

Optofluidic Particle Manipulation Platform with Nanomembrane

We demonstrate a method for fabricating and utilizing an optofluidic particle manipulator on a silicon chip that features a 300 nm thick silicon dioxide membrane as part of a microfluidic channel. The fabrication method is based on etching silicon channels and converting the walls to silicon dioxide through thermal oxidation. Channels are encapsulated by a sacrificial polymer which fills the length of the fluid channel by way of spontaneous capillary action. The sacrificial material is then used as a mold for the formation of a nanoscale, solid-state, silicon dioxide membrane. The hollow channel is primarily used for fluid and particle transport but is capable of transmitting light over short distances and utilizes radiation pressure for particle trapping applications. The optofluidic platform features solid-core ridge waveguides which can direct light on and off of the silicon chip and intersect liquid channels. Optical loss values are characterized for liquid and solid-core structures and at interfaces. Estimates are provided for the optical power needed to trap particles of various sizes.

Label-Free Physical Techniques and Methodologies for Proteins Detection in Microfluidic Biosensor Structures

Proteins in biological fluids (blood, urine, cerebrospinal fluid) are important biomarkers of various pathological conditions. Protein biomarkers detection and quantification have been proven to be an indispensable diagnostic tool in clinical practice. There is a growing tendency towards using portable diagnostic biosensor devices for point-of-care (POC) analysis based on microfluidic technology as an alternative to conventional laboratory protein assays. In contrast to universally accepted analytical methods involving protein labeling, label-free approaches often allow the development of biosensors with minimal requirements for sample preparation by omitting expensive labelling reagents. The aim of the present work is to review the variety of physical label-free techniques of protein detection and characterization which are suitable for application in micro-fluidic structures and analyze the technological and material aspects of label-free biosensors that implement these methods. The most widely used optical and impedance spectroscopy techniques: absorption, fluorescence, surface plasmon resonance, Raman scattering, and interferometry, as well as new trends in photonics are reviewed. The challenges of materials selection, surfaces tailoring in microfluidic structures, and enhancement of the sensitivity and miniaturization of biosensor systems are discussed. The review provides an overview for current advances and future trends in microfluidics integrated technologies for label-free protein biomarkers detection and discusses existing challenges and a way towards novel solutions.

Optofluidic multiplex detection of single SARS-CoV-2 and influenza A antigens using a novel bright fluorescent probe assay

This work introduces an ultrasensitive single protein capture and detection technique based on a bright fluorescent reporter probe that is sensed on a photonic chip with integrated microfluidics. We perform differentiated detection of single SARS-CoV-2 and influenza A antigens at clinically relevant concentrations from clinical nasal swab materials. This ultrasensitive capture and detection technique could one day be realized as a tool for molecular diagnostics at the point of care.

The urgency for the development of a sensitive, specific, and rapid point-of-care diagnostic test has deepened during the ongoing COVID-19 pandemic. Here, we introduce an ultrasensitive chip-based antigen test with single protein biomarker sensitivity for the differentiated detection of both severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A antigens in nasopharyngeal swab samples at diagnostically relevant concentrations. The single-antigen assay is enabled by synthesizing a brightly fluorescent reporter probe, which is incorporated into a bead-based solid-phase extraction assay centered on an antibody sandwich protocol for the capture of target antigens. After optimization of the probe release for detection using ultraviolet light, the full assay is validated with both SARS-CoV-2 and influenza A antigens from clinical nasopharyngeal swab samples (PCR-negative spiked with target antigens). Spectrally multiplexed detection of both targets is implemented by multispot excitation on a multimode interference waveguide platform, and detection at 30 ng/mL with single-antigen sensitivity is reported.

Enhanced Detection of Single Viruses On-Chip via Hydrodynamic Focusing

Planar optofluidics provide a powerful tool for facilitating chip-scale light-matter interactions. Silicon-based liquid core waveguides have been shown to offer single molecule sensitivity for efficient detection of bioparticles. Recently, a PDMS based planar optofluidic platform was introduced that opens the way to rapid development and prototyping of unique structures, taking advantage of the positive attributes of silicon dioxide-based optofluidics and PDMS based microfluidics. Here, hydrodynamic focusing is integrated into a PDMS based optofluidic chip to enhance the detection of single H1N1 viruses on-chip. Chip-plane focusing is provided by a system of microfluidic channels to force the particles towards a region of high optical collection efficiency. Focusing is demonstrated and enhanced detection is quantified using fluorescent polystyrene beads where the coefficient of variation is found to decrease by a factor of 4 with the addition of hydrodynamic focusing. The mean signal amplitude of fluorescently tagged single H1N1 viruses is found to increase with the addition of focusing by a factor of 1.64.

Fiber Light-Coupled Optofluidic Waveguide (FLOW) Immunosensor for Highly Sensitive Detection of p53 Protein

Highly sensitive detection of molecular tumor markers is essential for biomarker-based cancer diagnostics. In this work, we showcase the implementation of fiber light-coupled optofluidic waveguide (FLOW) immunosensor for the detection of p53 protein, a typical tumor marker. The FLOW consists of a liquid-core capillary and an accompanying optical fiber, which allows evanescent interaction between light and microfluidic sample. Molecular binding at internal surface of the capillary induces a response in wavelength shift of the transmission spectrum in the optical fiber. To enable highly sensitive molecular detection, the evanescent-wave interaction has been strengthened by enlarging shape factor R via fine geometry control. The proposed FLOW immunosensor works with flowing microfluid, which increases the surface molecular coverage and improves the detection limit. As a result, the FLOW immunosensor presents a log-linear response to the tumor protein at concentrations ranging from 10 fg/mL up to 10 ng/mL. In addition, the nonspecifically adsorbed molecules can be effectively removed by the fluid at an optimal flow rate, which benefits the accuracy of the measurement. Tested in serum samples, the FLOW successfully maintains its sensitivity and specificity on p53 protein, making it suitable for diagnostics applications.

Scalable Spatial-Spectral Multiplexing of Single-Virus Detection Using Multimode Interference Waveguides

Simultaneous detection of multiple pathogens and samples (multiplexing) is one of the key requirements for diagnostic tests in order to enable fast, accurate and differentiated diagnoses. Here, we introduce a novel, highly scalable, photonic approach to multiplex analysis with single virus sensitivity. A solid-core multimode interference (MMI) waveguide crosses multiple fluidic waveguide channels on an optofluidic chip to create multi-spot excitation patterns that depend on both the wavelength and location of the channel along the length of the MMI waveguide. In this way, joint spectral and spatial multiplexing is implemented that encodes both spatial and spectral information in the time dependent fluorescence signal. We demonstrate this principle by using two excitation wavelengths and three fluidic channels to implement a 6x multiplex assay with single virus sensitivity. High fidelity detection and identification of six different viruses from a standard influenza panel is reported. This multimodal multiplexing strategy scales favorably to large numbers of targets or large numbers of clinical samples. Further, since single particles are detected unbound in flow, the technique can be broadly applied to direct detection of any fluorescent target, including nucleic acids and proteins.

Optofluidic bioanalysis: fundamentals and applications

Over the past decade, optofluidics has established itself as a new and dynamic research field for exciting developments at the interface of photonics, microfluidics, and the life sciences. The strong desire for developing miniaturized bioanalytic devices and instruments, in particular, has led to novel and powerful approaches to integrating optical elements and biological fluids on the same chip-scale system. Here, we review the state-of-the-art in optofluidic research with emphasis on applications in bioanalysis and a focus on waveguide-based approaches that represent the most advanced level of integration between optics and fluidics. We discuss recent work in photonically reconfigurable devices and various application areas. We show how optofluidic approaches have been pushing the performance limits in bioanalysis, e.g. in terms of sensitivity and portability, satisfying many of the key requirements for point-of-care devices. This illustrates how the requirements for bianalysis instruments are increasingly being met by the symbiotic integration of novel photonic capabilities in a miniaturized system.

Signal-to-noise Enhancement in Optical Detection of Single Viruses with Multi-spot Excitation

We present fluorescence detection of single H1N1 viruses with enhanced signal to noise ratio (SNR) achieved by multi-spot excitation in liquid-core anti-resonant reflecting optical waveguides (ARROWs). Solid-core Y-splitting ARROW waveguides are fabricated orthogonal to the liquid-core section of the chip, creating multiple excitation spots for the analyte. We derive expressions for the SNR increase after signal processing, and analyze its dependence on signal levels and spot number. Very good agreement between theoretical calculations and experimental results is found. SNR enhancements up to 5x10⁴ are demonstrated.

Optofluidic devices with integrated solid-state nanopores

This review (with 90 refs.) covers the state of the art in optofluidic devices with integrated solid-state nanopores for use in detection and sensing. Following an introduction into principles of optofluidics and solid-state nanopore technology, we discuss features of solid-state nanopore based assays using optofluidics. This includes the incorporation of solid-state nanopores into optofluidic platforms based on liquid-core anti-resonant reflecting optical waveguides (ARROWs), methods for their fabrication, aspects of single particle detection and particle manipulation. We then describe the new functionalities provided by solid-state nanopores integrated into optofluidic chips, in particular acting as smart gates for correlated electro-optical detection and discrimination of nanoparticles. This enables the identification of viruses and λ-DNA, particle trajectory simulations, enhancing sensitivity by tuning the shape of nanopores. The review concludes with a summary and an outlook.

Optofluidic analysis system for amplification-free, direct detection of Ebola infection

The massive outbreak of highly lethal Ebola hemorrhagic fever in West Africa illustrates the urgent need for diagnostic instruments that can identify and quantify infections rapidly, accurately, and with low complexity. Here, we report on-chip sample preparation, amplification-free detection and quantification of Ebola virus on clinical samples using hybrid optofluidic integration. Sample preparation and target preconcentration are implemented on a PDMS-based microfluidic chip (automaton), followed by single nucleic acid fluorescence detection in liquid-core optical waveguides on a silicon chip in under ten minutes. We demonstrate excellent specificity, a limit of detection of 0.2 pfu/mL and a dynamic range of thirteen orders of magnitude, far outperforming other amplification-free methods. This chip-scale approach and reduced complexity compared to gold standard RT-PCR methods is ideal for portable instruments that can provide immediate diagnosis and continued monitoring of infectious diseases at the point-of-care.

Dual-core optofluidic chip for independent particle detection and tunable spectral filtering

We present the first integration of fluidically tunable filters with a separate particle detection channel on a single planar, optofluidic chip. Two optically connected, but fluidically isolated liquid-core antiresonant reflecting optical waveguide (ARROW) segments serve as analyte and spectral filter sections, respectively. Ultrasensitive detection of fluorescent nanobeads with high signal-to-noise ratio provided by a fluidically tuned excitation notch filter is demonstrated. In addition, reconfigurable filter response is demonstrated using both core index tuning and bulk liquid tuning. Notch filters with 43 dB rejection ratio and a record 90 nm tuning range are implemented by using different mixtures of ethylene glycol and water in the filter section. Moreover, absorber dyes and liquids with pH-dependent transmission in the filter channel provide additional spectral control independent of the waveguide response. Using both core index and pH control, independent filter tuning at multiple wavelengths is demonstrated for the first time. This extensive on-chip control over spectral filtering as one of the fundamental components of optical particle detection techniques offers significant advantages in terms of compactness, cost, and simplicity, and opens new opportunities for waveguide-based optofluidic analysis systems.

Dual-color fluorescence cross-correlation spectroscopy on a planar optofluidic chip

Fluorescence cross-correlation spectroscopy (FCCS) is a highly sensitive fluorescence technique with distinct advantages in many bioanalytical applications involving interaction and binding of multiple components. Due to the use of multiple beams, bulk optical FCCS setups require delicate and complex alignment procedures. We demonstrate the first implementation of dual-color FCCS on a planar, integrated optofluidic chip based on liquid-core waveguides that can guide liquid and light simultaneously. In this configuration, the excitation beams are delivered in predefined locations and automatically aligned within the excitation waveguides. We implement two canonical applications of FCCS in the optofluidic lab-on-chip environment: particle colocalization and binding/dissociation dynamics. Colocalization is demonstrated in the detection and discrimination of single-color and double-color fluorescently labeled nanobeads. FCCS in combination with fluorescence resonance energy transfer (FRET) is used to detect the denaturation process of double-stranded DNA at nanomolar concentration.

Hollow waveguides with low intrinsic photoluminescence fabricated with Ta(2)O(5) and SiO(2) films

A type of integrated hollow core waveguide with low intrinsic photoluminescence fabricated with Ta(2)O(5) and SiO(2) films is demonstrated. Hollow core waveguides made with a combination of plasma-enhanced chemical vapor deposition SiO(2) and sputtered Ta(2)O(5) provide a nearly optimal structure for optofluidic biofluorescence measurements with low optical loss, high fabrication yield, and low background photoluminescence. Compared to earlier structures made using Si(3)N(4), the photoluminescence background of Ta(2)O(5) based hollow core waveguides is decreased by a factor of 10 and the signal-to-noise ratio for fluorescent nanobead detection is improved by a factor of 12.

Optimized piranha etching process for SU8-based MEMS and MOEMS construction

We demonstrate the optimization of the concentration, temperature and cycling of a piranha (H(2)O(2):H(2)SO(4)) mixture that produces high yields while quickly etching hollow structures made using a highly crosslinked SU8 polymer sacrificial core. The effects of the piranha mixture on the thickness, refractive index and roughness of common micro-electromechanical systems and micro-opto-electromechanical systems fabrication materials (SiN, SiO(2) and Si) were determined. The effectiveness of the optimal piranha mixture was demonstrated in the construction of hollow anti-resonant reflecting optical waveguides.

Photonic methods to enhance fluorescence correlation spectroscopy and single molecule fluorescence detection

Recent advances in nanophotonics open the way for promising applications towards efficient single molecule fluorescence analysis. In this review, we discuss how photonic methods bring innovative solutions for two essential questions: how to detect a single molecule in a highly concentrated solution, and how to enhance the faint optical signal emitted per molecule? The focus is set primarily on the widely used technique of fluorescence correlation spectroscopy (FCS), yet the discussion can be extended to other single molecule detection methods.

Micropore and nanopore fabrication in hollow antiresonant reflecting optical waveguides

We demonstrate the fabrication of micropore and nanopore features in hollow antiresonant reflecting optical waveguides to create an electrical and optical analysis platform that can size select and detect a single nanoparticle. Micropores (4 μm diameter) are reactive-ion etched through the top SiO(2) and SiN layers of the waveguides, leaving a thin SiN membrane above the hollow core. Nanopores are formed in the SiN membranes using a focused ion-beam etch process that provides control over the pore size. Openings as small as 20 nm in diameter are created. Optical loss measurements indicate that micropores did not significantly alter the loss along the waveguide.

Loss-based optical trap for on-chip particle analysis

Optical traps have become widespread tools for studying biological objects on the micro and nanoscale. However, conventional laser tweezers and traps rely on bulk optics and are not compatible with current trends in optofluidic miniaturization. Here, we report a new type of particle trap that relies on propagation loss in confined modes in liquid-core optical waveguides to trap particles. Using silica beads and E. coli bacteria, we demonstrate unique key capabilities of this trap. These include single particle trapping with micron-scale accuracy at arbitrary positions over waveguide lengths of several millimeters, definition of multiple independent particle traps in a single waveguide, and combination of optical trapping with single particle fluorescence analysis. The exclusive use of a two-dimensional network of planar waveguides strongly reduces experimental complexity and defines a new paradigm for on-chip particle control and analysis.

Ultrasensitive Qbeta phage analysis using fluorescence correlation spectroscopy on an optofluidic chip

We demonstrate detection and analysis of the Qbeta bacteriophage on the single virus level using an integrated optofluidic biosensor. Individual Qbeta phages with masses on the order of attograms were sensed and analyzed on a silicon chip in their natural liquid environment without the need for virus immobilization. The diffusion coefficient of the viruses was extracted from the fluorescence signal by means of fluorescence correlation spectroscopy (FCS) and found to be 15.90+/-1.50 microm(2)/s in excellent agreement with previously published values. The aggregation and disintegration of the phage were also observed. Virus flow velocities determined by FCS were in the 60-300 microm/s range. This study suggests considerable potential for an inexpensive and portable sensor capable of discrimination between viruses of different sizes.

Anisotropic diffusion of fluorescently labeled ATP in rat cardiomyocytes determined by raster image correlation spectroscopy

A series of experimental data points to the existence of profound diffusion restrictions of ADP/ATP in rat cardiomyocytes. This assumption is required to explain the measurements of kinetics of respiration, sarcoplasmic reticulum loading with calcium, and kinetics of ATP-sensitive potassium channels. To be able to analyze and estimate the role of intracellular diffusion restrictions on bioenergetics, the intracellular diffusion coefficients of metabolites have to be determined. The aim of this work was to develop a practical method for determining diffusion coefficients in anisotropic medium and to estimate the overall diffusion coefficients of fluorescently labeled ATP in rat cardiomyocytes. For that, we have extended raster image correlation spectroscopy (RICS) protocols to be able to discriminate the anisotropy in the diffusion coefficient tensor. Using this extended protocol, we estimated diffusion coefficients of ATP labeled with the fluorescent conjugate Alexa Fluor 647 (Alexa-ATP). In the analysis, we assumed that the diffusion tensor can be described by two values: diffusion coefficient along the myofibril and that across it. The average diffusion coefficients found for Alexa-ATP were as follows: 83 ± 14 μm²/s in the longitudinal and 52 ± 16 μm²/s in the transverse directions (n = 8, mean ± SD). Those values are ∼2 (longitudinal) and ∼3.5 (transverse) times smaller than the diffusion coefficient value estimated for the surrounding solution. Such uneven reduction of average diffusion coefficient leads to anisotropic diffusion in rat cardiomyocytes. Although the source for such anisotropy is uncertain, we speculate that it may be induced by the ordered pattern of intracellular structures in rat cardiomyocytes.

Fluorescent liquid-core/air-cladding waveguides towards integrated optofluidic light sources

We have demonstrated fluorescent liquid-core/air-cladding (LA) waveguides suitable for use as integrated optofluidic light sources. These waveguides were fabricated by conventional soft lithography using poly(dimethylsiloxane) (PDMS). Two-phase stratified flows of air and ethylene glycol with fluorescent dye were generated along the PDMS channel. Compared to the liquid-core/liquid-cladding (L(2)) waveguide, the larger refractive index contrast of the LA waveguide resulted in stronger optical confinement. Specifically, the larger refractive index contrast led to experimentally achievable captured fractions (the amount of light to be coupled into the liquid core) as high as 22.8% and the measured propagation losses as low as 0.14 dB cm(-1). Furthermore, in our LA waveguides, diffusional mixing of the core and cladding fluids did not occur and the size of the core stream could be reversibly tuned simply by adjusting the flow rates of the two contiguous phases.

Optofluidic waveguides: I. Concepts and implementations

We review recent developments and current status of liquid-core optical waveguides in optofluidics with emphasis on suitability for creating fully planar optofluidic labs-on-a-chip. In this first of two contributions, we give an overview of the different waveguide types that are being considered for effectively combining micro and nanofluidics with integrated optics. The large number of approaches is separated into conventional index-guided waveguides and more recent implementations using wave interference. The underlying principle for waveguiding and the current status are described for each type. We then focus on reviewing recent work on microfabricated liquid-core antiresonant reflecting optical (ARROW) waveguides, including the development of intersecting 2D waveguide networks and optical fluorescence and Raman detection with planar beam geometry. Single molecule detection capability and addition of electrical control for electrokinetic manipulation and analysis of single bioparticles are demonstrated. The demonstrated performance of liquid-core ARROWs is representative of the potential of integrated waveguides for on-chip detection with ultrahigh sensitivity, and points the way towards the next generation of high-performance, low-cost and portable biomedical instruments.