An integrated optics microfluidic device for detecting single DNA molecules

Optimization of flow-focusing devices for homogeneous extensional flow

We present a methodology for the shape optimization of flow-focusing devices with the purpose of creating a wide region of homogeneous extensional flow, characterized by a uniform strain-rate along the centerline of the devices. The numerical routines employed include an optimizer, a finite-volume solver, and a mesh generator operating on geometries with the walls parameterized by Bézier curves. The optimizations are carried out for devices with different geometric characteristics (channel aspect ratio and length). The performance of the optimized devices is assessed for varying Reynolds numbers, velocity ratio between streams, and fluid rheology. Brownian dynamics simulations are also performed to evaluate the stretching and relaxation of λ-DNA molecules in the devices. Overall, the optimized flow-focusing devices generate a homogeneous extensional flow over a range of conditions typically found in microfluidics. At high Weissenberg numbers, the extension of λ-DNA molecules in the optimized flow-focusing devices is close to that obtained in an ideal planar extensional flow with an equivalent Hencky strain. The devices presented in this study can be useful in microfluidic applications taking advantage of homogeneous extensional flows and easy control of the Hencky strain and strain-rate.

Design and microfabrication of a miniature fiber optic probe with integrated lenses and mirrors for Raman and fluorescence measurements

Fiber optics coupled to components such as lenses and mirrors have seen extensive use as probes for Raman and fluorescence measurements. Probes can be placed directly on or into a sample to allow for simplified and remote application of these optical techniques. The size and complexity of such probes however limits their application. We have used microfabrication in polydimethylsiloxane (PDMS) to create compact probes that are 0.5 mm thick by 1 mm wide. The miniature probes incorporate pre-aligned mirrors, lenses, and two fiber optic guides to allow separate input and output optical paths suitable for Raman and fluorescence spectroscopy measurements. The fabricated probe has 70 % unidirectional optical throughput and generates no spectral artifacts in the wavelength range of 200 to 800 nm. The probe is demonstrated for measurement of fluorescence within microfluidic devices and collection of Raman spectra from a pharmaceutical tablet. The fluorescence limit of detection was 6 nM when using the probe to measure resorufin inside a 150-μm inner diameter glass capillary, 100 nM for resorufin in a 60-μm-deep × 100-μm-wide PDMS channel, and 11 nM for fluorescein in a 25-μm-deep × 80-μm-wide glass channel. It is demonstrated that the same probe can be used on different sample types, e.g., microfluidic chips and tablets. Compared to existing Raman and fluorescence probes, the microfabricated probes enable measurement in smaller spaces and have lower fabrication cost. Graphical abstract A microfabricated spectroscopic probe with integrated optics was developed for chemical detection in small spaces and in remote applications.

Chemical-assisted femtosecond laser writing of lab-in-fibers

The lab-on-chip (LOC) platform has presented a powerful opportunity to improve functionalization, parallelization, and miniaturization on planar or multilevel geometries that has not been possible with fiber optic technology. A migration of such LOC devices into the optical fiber platform would therefore open the revolutionary prospect of creating novel lab-in-fiber (LIF) systems on the basis of an efficient optical transport highway for multifunctional sensing. For the LIF, the core optical waveguide inherently offers a facile means to interconnect numerous types of sensing elements along the optical fiber, presenting a radical opportunity for optimizing the packaging and densification of diverse components in convenient geometries beyond that available with conventional LOCs. In this paper, three-dimensional patterning inside the optical fiber by femtosecond laser writing, together with selective chemical etching, is presented as a powerful tool to form refractive index structures such as optical waveguides and gratings as well as to open buried microfluidic channels and optical resonators inside the flexible and robust glass fiber. In this approach, optically smooth surfaces (~12 nm rms) are introduced for the first time inside the fiber cladding that precisely conform to planar nanograting structures when formed by aberration-free focusing with an oil-immersion lens across the cylindrical fiber wall. This process has enabled optofluidic components to be precisely embedded within the fiber to be probed by either the single-mode fiber core waveguide or the laser-formed optical circuits. We establish cladding waveguides, X-couplers, fiber Bragg gratings, microholes, mirrors, optofluidic resonators, and microfluidic reservoirs that define the building blocks for facile interconnection of inline core-waveguide devices with cladding optofluidics. With these components, more advanced, integrated, and multiplexed fiber microsystems are presented demonstrating fluorescence detection, Fabry-Perot interferometric refractometry, and simultaneous sensing of refractive index, temperature, and bending strain. The flexible writing technique and multiplexed sensors described here open powerful prospects to migrate the benefits of LOCs into a more flexible and miniature LIF platform for highly functional and distributed sensing capabilities. The waveguide backbone of the LIF inherently provides an efficient exchange of information, combining sensing data that are attractive in telecom networks, smart catheters for medical procedures, compact sensors for security and defense, shape sensors, and low-cost health care products.

Lab-on-a-chip technologies for single-molecule studies

Recent developments on various lab-on-a-chip techniques allow miniaturized and integrated devices to perform on-chip single-molecule studies. Fluidic-based platforms that utilize unique microscale fluidic behavior are capable of conducting single-molecule experiments with high sensitivities and throughputs, while biomolecular systems can be studied on-chip using techniques such as DNA curtains, magnetic tweezers, and solid-state nanopores. The advances of these on-chip single-molecule techniques lead to next-generation lab-on-a-chip devices, such as DNA transistors, and single-molecule real-time (SMRT) technology for rapid and low-cost whole genome DNA sequencing. In this Focus article, we will discuss some recent successes in the development of lab-on-a-chip techniques for single-molecule studies and expound our thoughts on the near future of on-chip single-molecule studies.

Development of a generic microfluidic device for simultaneous detection of antibodies and nucleic acids in oral fluids

A prototype dual-path microfluidic device (Rheonix CARD) capable of performing simultaneously screening (antigen or antibody) and confirmatory (nucleic acid) detection of pathogens is described. The device fully integrates sample processing, antigen or antibody detection, and nucleic acid amplification and detection, demonstrating rapid and inexpensive “sample-to-result” diagnosis with performance comparable to benchtop analysis. For the chip design, a modular approach was followed allowing the optimization of individual steps in the sample processing process. This modular design provides great versatility accommodating different disease targets independently of the production method. In the detection module, a lateral flow (LF) protocol utilizing upconverting phosphor (UCP) reporters was employed. The nucleic acid (NA) module incorporates a generic microtube containing dry reagents. Lateral flow strips and PCR primers determine the target or disease that is diagnosed. Diagnosis of HIV infection was used as a model to investigate the simultaneous detection of both human antibodies against the virus and viral RNA. The serological result is available in less than 30 min, and the confirmation by RNA amplification takes another 60 min. This approach combines a core serological portable diagnostic with a nucleic acid-based confirmatory test.

Recent advances in single-molecule detection on micro- and nano-fluidic devices

Single-molecule detection (SMD) allows static and dynamic heterogeneities from seemingly equal molecules to be revealed in the studies of molecular structures and intra- and inter-molecular interactions. Micro- and nanometer-sized structures, including channels, chambers, droplets, etc., in microfluidic and nanofluidic devices allow diffusion-controlled reactions to be accelerated and provide high signal-to-noise ratio for optical signals. These two active research frontiers have been combined to provide unprecedented capabilities for chemical and biological studies. This review summarizes the advances of SMD performed on microfluidic and nanofluidic devices published in the past five years. The latest developments on optical SMD methods, microfluidic SMD platforms, and on-chip SMD applications are discussed herein and future development directions are also envisioned.

Monitoring CD4 in whole blood with an opto-fluidic detector based on spatially modulated fluorescence emission

We describe a new optical detection technique, termed "spatially modulated fluorescence emission," that delivers high signal-to-noise discrimination without precision optics to enable a flow cytometer that can combine high performance, robustness, compactness, low cost, and ease of use. The detection technique is demonstrated with measurements of absolute CD4+ and percentage CD4 counts in human blood. Benchmarking against a commonly used commercial instrument for this test yields excellent agreement for both absolute CD4 and percentage CD4.

A microfluidic chip-compatible bioassay based on single-molecule detection with high sensitivity and multiplexing

Many applications in pharmaceutical development, clinical diagnostics, and biological research demand rapid detection of multiple analytes (multiplexed detection) in a minimal volume. This need has led to the development of several novel array-based sensors. The most successful of these so far have been suspension arrays based on polystyrene beads. However, the 5 microm beads used for these assays are incompatible with most microfluidic chip technologies, mostly due to clogging problems. The challenge, then, is to design a detection particle that has high information content (for multiplexed detection), is compatible with miniaturization, and can be manufactured easily at low cost. DNA is a solid molecular wire that is easily produced and manipulated, which makes it a useful material for nanoparticles. DNA molecules are very information-rich, readily deformable, and easily propagated. We exploit these attributes in a suspension array sensor built from specialized recombinant DNA, Digital DNA, that carries both specific analyte-recognition units, and a geometrically encoded identification pattern. Here we show that this sensor combines high multiplexing with high sensitivity, is biocompatible, and has sufficiently small particle size to be used within microfluidic chips that are only 1 microm deep. We expect this technology will be the foundation of a broadly applicable technique to identify and quantitate proteins, nucleic acids, viruses, and toxins simultaneously in a minimal volume.

Microfluorimeter with disposable polymer chip for detection of coeliac disease toxic gliadin

Coeliac disease is an inflammatory disease of the upper small intestine and results from gluten ingestion in genetically susceptible individuals, and is the only life-long nutrient-induced enteropathy. The only treatment is a strict gluten-free diet and the longer the individual fails to adhere to this diet, the greater the chance of developing malnutrition and other complications. The existence of reliable gluten free food is crucial to the well-being of the population. Here we report on a microfluorimeter device for the in situ detection of gliadin in foodstuffs, which could be used for a rapid control of raw materials in food processing, as well as for process control of gliadin contamination. The microfluorimeter is based on a reflector that is used inside a microfluidic chip, exploiting various strategically placed reflective or totally metallised mirrors for efficient collection of the fluorescent light emitted in a large solid angle. The chip is capable of executing five assays in parallel and has been demonstrated to possess detection sensitivity applicable to fluoroimmunoassays. Various immunoassay formats exploiting fluorescence detection, using enzyme/fluorophore labels were developed and compared in terms of sensitivity, ease of assay, assay time and compatibility with buffer used to extract gliadin from raw and cooked foodstuffs, with the best performance observed with an indirect competition assay using a fluorophore-labelled anti-mouse antibody. This assay was exploited within the microfluorimeter device, and a very low detection limit of 4.1 ng/mL was obtained. The system was observed to be highly reproducible, with an RSD of 5.9%, for a concentration of 50 ng/mL of gliadin applied to each of the five channels of the microfluorimeter. Biofunctionalised disposable strips incorporated into the microfluorimeter were subjected to accelerated Arrhenius thermal stability studies and it was demonstrated that strips pre-coated with gliadin could be stored for approximately 2 years at 4 degrees C, with no discernable loss in sensitivity or detectability of the assay. Finally, the microfluorimeter was applied to the analysis of commercial gluten-free food samples, and an excellent correlation with routine ELISA measurements was obtained. The developed microfluorimeter should find widespread application for on-site execution of fluoroimmunoassays.

Aberration-free lithography setup for fabrication of holographic diffractive optical elements

A holographic optical lithography setup with extremely small longitudinal spherical aberration is described. The setup is used for the fabrication of holographic diffractive optical elements intended to collect light emitted from a fluorescence spot located on a biochip surface. A key feature of the optical setup is its ability to simulate a point-source-like fluorescence spot. A detailed description of the setup together with its optical properties are provided. The fluorescence light collection efficiency of the holographic diffractive optical elements produced using this setup is demonstrated.

High throughput single molecule detection for monitoring biochemical reactions

The design, performance and application of a novel optical system for high throughput single molecule detection (SMD) configured in a continuous flow format using microfluidics is reported. The system consisted of a microfabricated polymer-based multi-channel fluidic network situated within the optical path of a laser source (lambda(ex) = 660 nm) with photon transduction accomplished using an electron-multiplying charge coupled device (EMCCD) operated in a frame transfer mode that allowed tracking single molecules as they passed through a large field-of-view (FoV) illumination zone. The microfluidic device consisted of 30 microchannels possessing dimensions of 30 microm (width) x 20 microm (depth) with a 25 microm pitch. Individual molecules were electrokinetically driven through the fluidic network and excited within the wide-field illumination area with the resulting fluorescence collected via an objective and imaged onto the EMCCD camera. The detection system demonstrated sufficient sensitivity to detect single DNA molecules labeled with a fluorescent tag (AlexaFluor 660) identified through their characteristic emission wavelength and the burst of photons produced during their transit through the excitation volume. In its present configuration and fluidic architecture, the sample processing throughput was approximately 4.02 x 10(5) molecules s(-1), but could be increased dramatically through the use of narrower channels and a smaller pitch. The system was further evaluated using a single molecule-based fluorescence quenching assay for measuring the population differences between duplexed and single-stranded DNA molecules as a function of temperature for determining the duplex melting temperature, T(m).

Fabrication of holographic diffractive optical elements for enhancing light collection from fluorescence-based biochips

An approach to enhancing the light collection from fluorescence emitters bound on the surface of a biochip is presented. It is based on the integration of diffractive optical elements on the underside of the chip that are essentially thick volume holograms written into a layer of photopolymer recording material. The high diffractive efficiency and angular selectivity of these types of diffractive elements make them very effective collectors of the spatially anisotropic light emitted by surface-bound fluorophores. The holographic lithography setup used to fabricate the diffractive elements is described. Results obtained using both a focused laser and light from a fluorescence spot to characterize the performance of the diffractive optical elements are presented.

Bead-based microfluidic toxin sensor integrating evaporative signal amplification

We have devised a microfluidic platform that incorporates substrate-laden silica beads for sensing the proteolytic activity of botulinum neurotoxin type A (BoNT/A)-one of the most poisonous substances known and a significant biological threat. The sensor relies on toxin-mediated cleavage of a fluorophore-tagged peptide substrate specific for only BoNT/A. Peptide immobilized on beads is recognized and cleaved by the toxin, releasing fluorescent fragments into solution that can be concentrated at an isolated port via evaporation and detected using microscopy. Evaporative concentration in combination with a specific channel geometry provides up to a 3-fold signal amplification in 35 min, allowing for detection of low levels of fluorophore-labeled peptide-a task not easily accomplished using traditional channel designs. Our bead-based microfluidic platform can sense BoNT/A down to 10 pg of toxin per mL buffer solution in 3.5 h and can be adapted to sensing other toxins that operate via enzymatic cleavage of a known substrate.