Fabrication of microfluidic devices containing patterned microwell arrays

Microfluidic synthesis and accurate immobilization of low-density QD-encoded magnetic microbeads for multiplex immunoassay

Magnetic-fluorescent microbeads have been widely used in the multiplex detection of biological molecules. The traditional method relies on flow cytometry to decode and analyze the microbeads. Alternative strategies that employ immobilized microbeads on a plane and involve fluorescence imaging to analyze the microbeads have been proposed. Among these strategies, an integrated chip that controls magnetic field contribution using nickel powder pillars and captured microbeads has attracted great attention. Despite its unique advantages such as low manufacturing costs, reusability and high capture efficiency, existing research had been limited by the inability to precisely capture a single microbead, and the overlapping of microbeads has made multiplex immunoassays based on this strategy impossible. In this work, low-density microbeads were prepared in a microfluidic chip using IBOMA as the main monomer. The low density of the microbeads made the preparation of an aqueous suspension easier. An integration of nickel patterns, magnets and channels was carried out and demonstrated the capacity of capturing single microbeads precisely. Fluorescence coding further empowered this method with the ability of multiplex immunoassay, which was verified using three types of IgG, and a calibration curve for the detection of anti-human IgG was established using a sandwich immunoassay. These results show the promising potential of this strategy for biomedical detection.

Microfluidic synthesis of Janus-structured QD-encoded magnetic microbeads for multiplex immunoassay

Uniform and monodisperse quantum dot (QD)-encoded magnetic microbeads with Janus structure were produced in a microfluidic device via photopolymerization. UV light through a microscope objective was used to solidify the microbeads which showed sharp interfaces and excellent magnetic responses. QDs with different emission peaks (450 nm for blue and 640 nm for red) were mixed at different ratios to provide three spectral codes. The QD-encoded microbeads can be distinguished by analyzing their fluorescent images in HSV color space. After hydrolysis of the anhydride group in alkaline solution, protein was immobilized on microbeads via activation of carboxyl groups using (1-ethyl-3(3-dimethylaminoprophyl) carbodiimide/N-hydroxysuccinimide (EDC/NHS). A microhole array in polydimethylsiloxane (PDMS) substrates with a specific size was fabricated to trap individual microbeads in a single microhole. The combination of Janus-structured QD-encoded magnetic microbeads and microhole arrays facilitates both flexibility, binding kinetics, sensitivity for suspension assay, and fluorescence mapping analysis for conventional biochips, thus providing a novel platform for multiplex bioanalysis. The capability of this integration for multiplex immunoassays was verified using three kinds of IgG and their corresponding anti-IgG. A detection limit of 0.07 ng/mL was achieved for human IgG, indicating practical applications in various fields.

Tailoring Thermoplastic In-Plane Nanopore Size by Thermal Fusion Bonding for the Analysis of Single Molecules

We report a simple method for tailoring the size of in-plane nanopores fabricated in thermoplastics for single-molecule sensing. The in-plane pores were fabricated via nanoimprint lithography (NIL) from resin stamps, which were generated from Si masters. We could reduce the size of the in-plane nanopores from 30 to ∼10 nm during the thermal fusion bonding (TFB) step, which places a cover plate over the imprinted polymer substrate under a controlled pressure and temperature to form the relevant nanofluidic devices. Increased pressures during TFB caused the cross-sectional area of the in-plane pore to be reduced. The in-plane nanopores prepared with different TFB pressures were utilized to detect single-λ-DNA molecules via resistive pulse sensing, which showed a higher current amplitude in devices bonded at higher pressures. Using this method, we also show the ability to tune the pore size to detect single-stranded (ss) RNA molecules and single ribonucleotide adenosine monophosphate (rAMP). However, due to the small size of the pores required for detection of the ssRNA and rAMPs, the surface charge arising from carboxylate groups generated during O2 plasma oxidation of the surfaces of the nanopores to make them wettable had to be reduced to allow translocation of coions. This was accomplished using EDC/NHS coupling chemistry and ethanolamine. This simple modification chemistry increased the event frequency from ∼1 s-1 to >136 s-1 for an ssRNA concentration of 100 nM.

Customizable live-cell imaging chambers for multimodal and multiplex fluorescence microscopy

Using multiple imaging modalities while performing independent experiments in parallel can greatly enhance the throughput of microscopy-based research, but requires the provision of appropriate experimental conditions in a format that meets the optical requirements of the microscope. Although customized imaging chambers can meet these challenges, the difficulty of manufacturing custom chambers and the relatively high cost and design inflexibility of commercial chambers has limited the adoption of this approach. Herein, we demonstrate the use of 3D printing to produce inexpensive, customized, live-cell imaging chambers that are compatible with a range of imaging modalities, including super-resolution microscopy. In this approach, biocompatible plastics are used to print imaging chambers designed to meet the specific needs of an experiment, followed by adhesion of the printed chamber to a glass coverslip, producing a chamber that is impermeant to liquids and that supports the growth and imaging of cells over multiple days. This approach can also be used to produce moulds for casting microfluidic devices made of polydimethylsiloxane. The utility of these chambers is demonstrated using designs for multiplex microscopy, imaging under shear, chemotaxis, and general cellular imaging. Together, this approach represents an inexpensive yet highly customizable approach for producing imaging chambers that are compatible with modern microscopy techniques.

Low cost 3D microfluidic chips for multiplex protein detection based on photonic crystal beads

Point-of-care testing (POCT) devices used in multiplex bioassays are in great demand for clinical, environmental and biomedical applications. Photonic crystal beads (PCBs), as structural color self-coding carriers, can be integrated with microfluidic chips to realize convenient and highly sensitive biomarker detection. Here we developed a three dimensional (3D) microfluidic chip based on PCBs, which is low cost and easy to manufacture for mass production and application. The chip was fabricated with polyethylene terephthalate, polymethyl methacrylate sheets, a Ni square mesh grid and transparent double-sided tape. In practice, the target molecules could be captured by PCBs immobilized with probes in a flow-through manner. It was found that the as-proposed chip needed less washing and its background was effectively reduced in comparison with a flow-over chip. Besides, the limit of detection (LOD) of anti-human alpha fetoprotein (AFP) was calculated to be 18.92 ng mL^-1, which could meet the need of clinical detection of AFP. Furthermore, the chip demonstrated the feasibility of simultaneous detection of human immunoglobulin G, carcinoembryonic antigen and AFP, which suggests that it has a broad application prospect in multiplex bioassays.

Use of Ice-Nucleating Proteins To Improve the Performance of Freeze-Thaw Valves in Microfluidic Devices

Currently, reliable valving on integrated microfluidic devices fabricated from rigid materials is confined to expensive and complex methods. Freeze-thaw valves (FTVs) can provide a low cost, low complexity valving mechanism, but reliable implementation of them has been greatly hindered by the lack of ice nucleation sites within the valve body's small volume. Work to date has required very low temperatures (on the order of -40 °C or colder) to induce freezing without nucleation sites, making FTVs impractical due to instrument engineering challenges. Here, we report the use of ice-nucleating proteins (INPs) to induce ice formation at relatively warm temperatures in microfluidic devices. Microfluidic channels were filled with buffers containing femtomolar INP concentrations from Pseudomonas syringae. The channels were cooled externally with simple, small-footprint Peltier thermoelectric coolers (TECs), and the times required for channel freezing (valve closure) and thawing (valve opening) were measured. Under optimized conditions in plastic chips, INPs made sub-10 s actuations possible at TEC temperatures as warm as -13 °C. Additionally, INPs were found to have no discernible inhibitory effects in model enzyme-linked immunosorbent assays or polymerase chain reactions, indicating their compatibility with microfluidic systems that incorporate these widely used bioassays. FTVs with INPs provide a much needed reliable valving scheme for rigid plastic devices with low complexity, low cost, and no moving parts on the device or instrument. The reduction in freeze time, accessible actuation temperatures, chemical compatibility, and low complexity make the implementation of compact INP-based FTV arrays practical and attractive for the control of integrated biochemical assays.

Transport of biomolecules to binding partners displayed on the surface of microbeads arrayed in traps in a microfluidic cell

Arrays of probe molecules integrated into a microfluidic cell are utilized as analytical tools to screen the binding interactions of the displayed probes against a target molecule. These assay platforms are useful in enzyme or antibody discovery, clinical diagnostics, and biosensing, as their ultraminiaturized design allows for high sensitivity and reduced consumption of reagents and target. We study here a platform in which the probes are first grafted to microbeads which are then arrayed in the microfluidic cell by capture in a trapping course. We examine a course which consists of V-shaped, half-open enclosures, and study theoretically and experimentally target mass transfer to the surface probes. Target binding is a two step process of diffusion across streamlines which convect the target over the microbead surface, and kinetic conjugation to the surface probes. Finite element simulations are obtained to calculate the target surface concentration as a function of time. For slow convection, large diffusive gradients build around the microbead and the trap, decreasing the overall binding rate. For rapid convection, thin diffusion boundary layers develop along the microbead surface and within the trap, increasing the binding rate to the idealized limit of untrapped microbeads in a channel. Experiments are undertaken using the binding of a target, fluorescently labeled NeutrAvidin, to its binding partner biotin, on the microbead surface. With the simulations as a guide, we identify convective flow rates which minimize diffusion barriers so that the transport rate is only kinetically determined and measure the rate constant.

Mass transfer in the biomolecular binding of a target against probe molecules on the surface of microbeads sequestered in wells in a microfluidic cell

Diagnostic tools which screen the binding interactions of a protein target against a display of biomolecular probes to identify molecules which bind the target are central to cell proteomic studies, and to diagnostic assays. Here, we study a microfluidic design for screening interactions in which the probe molecules are hosted on microbeads sequestered in wells arranged at the bottom of a microfluidic flow channel. Assays are undertaken by streaming an analyte solution with a fluorescently labelled target through the cell, and identifying the fluorescing beads. Numerical simulations are first constructed for the analyte flow over the microbeads in the well array, and the increase in the target concentration on the microbead surface. The binding profile is expressed as a function of the ratio of the convective to the diffusive transport rates (Peclet number or Pe), and the ratio of the kinetic to the diffusive rates (Damkohler number, Da). For any Pe, as Da becomes small enough, the transport is determined by the intrinsic kinetic binding rate. As Pe increases, a thin concentration boundary layer develops over the top surface of the microbead because of the convective flow, and target binds more rapidly. However, the relatively stagnant layers of liquid in the well provide a diffusion barrier which slows the target transport, and for any Da and Pe the transport is slower than equivalent patches of probes arranged on the channel wall. Experiments are also undertaken at high Pe, using the binding of fluorescently labelled NeutrAvidin as a target to probes of its binding partner, biotin, on the microbead surface. The binding profile is compared to the simulations to measure the kinetic rate constant, and this comparison shows that the transport in the cell is not kinetically limited because of the diffusion barriers created by the stagnant liquid layer in the well. Simulations and experiments on microbeads which are only partially recessed in the well demonstrate an increase in the mass transfer rate as more of the microbead surface intersects the flow and the diffusion limitation due to the stagnant layer of liquid surrounding the bottom part of the microbead is minimized.

A large-area hemispherical perforated bead microarray for monitoring bead based aptamer and target protein interaction

Herein, we present a large-area 3D hemispherical perforated microwell structure for a bead based bioassay. Such a unique microstructure enables us to perform the rapid and stable localization of the beads at the single bead level and the facile manipulation of the bead capture and retrieval with high speed and efficiency. The fabrication process mainly consisted of three steps: the convex micropatterned nickel (Ni) mold production from the concave micropatterned silicon (Si) wafer, hot embossing on the polymer matrix to generate the concave micropattened acrylate sheet, and reactive ion etching to make the bottom holes. The large-area hemispherical perforated micropatterned acrylate sheet was sandwiched between two polydimethylsiloxane (PDMS) microchannel layers. The bead solution was injected and recovered in the top PDMS microchannel, while the bottom PDMS microchannel was connected with control lines to exert the hydrodynamic force in order to alter the flow direction of the bead solution for the bead capture and release operation. The streptavidin-coated microbead capture was achieved with almost 100% yield within 1 min, and all the beads were retrieved in 10 s. Lysozyme or thrombin binding aptamer labelled microbeads were trapped on the proposed bead microarray, and the in situ fluorescence signal of the bead array was monitored after aptamer-target protein interaction. The protein-aptamer conjugated microbeads were recovered, and the aptamer was isolated for matrix assisted laser desorption/ionization time-of-flight mass spectrometry analysis to confirm the identity of the aptamer.

Microfluidic antibody arrays for simultaneous cell separation and stimulus

A microfluidic chip containing stamped antibody arrays was developed for simultaneous cell separation and drug testing. Poly(dimethyl siloxane) (PDMS) stamping was used to deposit antibodies in a microfluidic channel, forming discrete cell-capture regions on the surface. Cell mixtures were then introduced, resulting in the separation of cells when specific antibodies were used. Anti-CD19 antibody regions resulted in 94 % capture purity for CD19+ Ramos cells. An antibody that captures multiple cell types, for example anti-CD71, can also be used to capture several cell types simultaneously. Cells could also be loaded onto the arrays with spatial control using laminar streams. Both Ramos B cells and HuT 78 T cells were isolated in the chip and exposed to staurosporine in the same channel. Both cell lines had similar responses to the drug, with 2-10 % of cells remaining viable after 20 h of drug treatment, depending on cell type. The chip can also be used to analyze the efficacy of antibody therapy against cancer cells. Anti-CD95 was deposited on the surface and used for simultaneous cell capture and apoptosis induction via the extrinsic pathway. Cells captured on anti-CD95 surfaces had significant viability loss (15 % viability after 24 h) when compared with a control anti-CD71 antibody (81 % viability after 24 h). This chip can be used for a variety of cell separation and/or drug testing studies, enabling researchers to isolate cells and test them against different anti-cancer compounds and to follow cell response using fluorescence or other readout methods.

An automated integrated platform for rapid and sensitive multiplexed protein profiling using human saliva samples

During the last decade, saliva has emerged as a potentially ideal diagnostic biofluid for noninvasive testing. In this paper, we present an automated, integrated platform useable by minimally trained personnel in the field for the diagnosis of respiratory diseases using human saliva as a sample specimen. In this platform, a saliva sample is loaded onto a disposable microfluidic chip containing all the necessary reagents and components required for saliva analysis. The chip is then inserted into the automated analyzer, the SDReader, where multiple potential protein biomarkers for respiratory diseases are measured simultaneously using a microsphere-based array via fluorescence sandwich immunoassays. The results are read optically, and the images are analyzed by a custom-designed algorithm. The fully automated assay requires as little as 10 μL of saliva sample, and the results are reported in 70 min. The performance of the platform was characterized by testing protein standard solutions, and the results were comparable to those from the 3.5 h lab bench assay that we have previously reported. The device was also deployed in two clinical environments where 273 human saliva samples collected from different subjects were successfully tested, demonstrating the device's potential to assist clinicians with the diagnosis of respiratory diseases by providing timely protein biomarker profiling information. This platform, which combines noninvasive sample collection and fully automated analysis, can also be utilized in point-of-care diagnostics.

Enzyme nanoarchitectonics: organization and device application

Fabrication of ultrasmall functional machines and their integration within ultrasmall areas or volumes can be useful for creation of novel technologies. The ultimate goal of the development of ultrasmall machines and device systems is to construct functional structures where independent molecules operate as independent device components. To realize exotic functions, use of enzymes in device structures is an attractive solution because enzymes can be regarded as efficient machines possessing high reaction efficiencies and specificities and can operate even under ambient conditions. In this review, recent developments in enzyme immobilization for advanced functions including device applications are summarized from the viewpoint of micro/nano-level structural control, or nanoarchitectonics. Examples are roughly classified as organic soft matter, inorganic soft materials or integrated/organized media. Soft matter such as polymers and their hybrids provide a medium appropriate for entrapment and encapsulation of enzymes. In addition, self-immobilization based on self-assembly and array formation results in enzyme nanoarchitectures with soft functions. For the confinement of enzymes in nanospaces, hard inorganic mesoporous materials containing well-defined channels play an important role. Enzymes that are confined exhibit improved stability and controllable arrangement, which are useful for formation of functional relays and for their integration into artificial devices. Layer-by-layer assemblies as well as organized lipid assemblies such as Langmuir-Blodgett films are some of the best media for architecting controllable enzyme arrangements. The ultrathin forms of these films facilitate their connection with external devices such as electrodes and transistors. Artificial enzymes and enzyme-mimicking catalysts are finally briefly described as examples of enzyme functions involving non-biological materials. These systems may compensate for the drawbacks of natural enzymes, such as their instabilities under harsh conditions. We believe that enzymes and their mimics will be freely coupled, organized and integrated upon demand in near future technologies.

Enabling systems biology approaches through microfabricated systems

With the experimental tools and knowledge that have accrued from a long history of reductionist biology, we can now start to put the pieces together and begin to understand how biological systems function as an integrated whole. Here, we describe how microfabricated tools have demonstrated promise in addressing experimental challenges in throughput, resolution, and sensitivity to support systems-based approaches to biological understanding.

A lipobead microarray assembled by particle entrapment in a microfluidic obstacle course and used for the display of cell membrane receptors

Platforms which can display cell membrane ligands and receptors as a microarray library of probes for screening against a target are essential tools in drug discovery, biomarker identification, and pathogen detection. Membrane receptors and ligands require their native bilayer environment to retain their selectivity and binding affinity, and this complicates displaying them in a microarray platform. In this study, a design is developed in which the probes are first incorporated in supported lipid bilayers formed around micron-sized particles (lipobeads), and the microbeads themselves are then arrayed on a surface by hydrodynamic capture in a microfluidic obstacle course of traps. The traps are "V" shaped open enclosures, which are arranged in a wide channel of a microfluidic device, and capture the lipobeads (slightly smaller than the channel height) as they are streamed through the course. Screening assays are undertaken directly in the device after assembly, by streaming a fluorescently labeled target through the device and detecting the bead fluorescence. Conditions are first established for which the supported bilayers on the bead surface remain intact during the capture and assay steps, using fluorescent tags in the bilayer to infer bilayer integrity. Numerical calculations of the hydrodynamic drag coefficient on the entrapped beads are presented in conjunction with the stability experiments to develop criteria for the bilayer stability as a function of the screening assay perfusion rate. Simulations of the flow streamlines are also presented to quantify the trapping efficiency of the obstacle course. Screening assays are illustrated, assaying fluorescently labeled NeutrAvidin with biotin, and labeled cholera toxin with its ganglioside binding ligand, GM1. Sequential capturing of sets of lipobeads (one at a time, and with each set bearing a different probe), followed by indexing the bead positions after each set is entrapped, allows for the construction of an indexed array of multiple probes without the need for particle encoding and is illustrated using the NeutrAvidin-biotin pair. Finally, the lipobead platform is used for quantitatively measuring the kinetic rate constants for the binding of a probe (biotin) to a target (NeutrAvidin).

Self-sorting click reactions that generate spatially controlled chemical functionality on surfaces

This Article describes the generation of a patterned surface that can be postpolymerization modified to incorporate fragile macromolecules or delicate biomolecules without the need for special equipment. Two monomers that undergo different click reactions, pentafluorophenyl acrylate (PFPA) and 4-(trimethylsilyl) ethynylstyrene (TMSES), were sequentially polymerized from a silicon surface in the presence of a shadowmask with UV light, generating 12.5 and 62 μm pitch patterns. Two different dyes, 1-aminomethylpyrene (AMP) and 5-azidofluorescein (AF), were covalently attached to the polymer brushes through aminolysis and dual desilylation/copper(I)-catalyzed alkyne/azide cycloaddition (CuAAC) in one pot. Unlike most CuAAC reactions, the terminal alkyne of TMSES was not deprotected prior to functionalization. Although a 2 nm thickness increase was observed for poly(PFPA) brushes after polymerization of TMSES, cross-contamination was not visible through fluorescence microscopy after functionalization.