Suspension arrays of hydrogel microparticles prepared by photopatterning for multiplexed protein-based bioassays

Single-Color Barcoding for Multiplexed Hydrogel Bead-Based Immunoassays

Current developments in precision medicine require the simultaneous detection of an increasing number of biomarkers in heterogeneous, complex solutions, such as blood samples. To meet this need, immunoassays on barcoded hydrogel beads have been proposed, although the encoding and decoding of these barcodes is usually complex and/or resource-intensive. Herein, an efficient method for the fabrication of barcoded, functionalized hydrogel beads is presented. The hydrogel beads are generated using droplet-based microfluidics in combination with photochemically induced C-H insertion reactions, allowing photo-crosslinking, (bio-) functionalization, and barcode integration to be performed in a single step. The generated functionalized beads carry single-color barcodes consisting of green-fluorescent particles of different sizes and concentrations, allowing simple and simultaneous readout with a standard plate reader. As a test example, the performance of barcoded hydrogel beads (3 × 3 matrix) functionalized with capture molecules of interest (e.g., antigens) is investigated for the detection of Lyme-disease-specific antibodies in patient sera. The described barcoding strategy for hydrogel beads does not interfere with the bioanalytical process and captivates by its simplicity and versatility, making it an attractive candidate for multiplex bioanalytical processes.

Fabrication of 3D concentric amphiphilic microparticles to form uniform nanoliter reaction volumes for amplified affinity assays

Reactions performed in uniform microscale volumes have enabled numerous applications in the analysis of rare entities (e.g. cells and molecules). Here, highly monodisperse aqueous droplets are formed by simply mixing microscale multi-material particles, consisting of concentric hydrophobic outer and hydrophilic inner layers, with oil and water. The particles are manufactured in batch using a 3D printed device to co-flow four concentric streams of polymer precursors which are polymerized with UV light. The cross-sectional shapes of the particles are altered by microfluidic nozzle design in the 3D printed device. Once a particle encapsulates an aqueous volume, each "dropicle" provides uniform compartmentalization and customizable shape-coding for each sample volume to enable multiplexing of uniform reactions in a scalable manner. We implement an enzymatically-amplified immunoassay using the dropicle system, yielding a detection limit of <1 pM with a dynamic range of at least 3 orders of magnitude. Multiplexing using two types of shape-coded particles was demonstrated without cross talk, laying a foundation for democratized single-entity assays.

Direct Conjugation of Streptavidin to Encoded Hydrogel Microparticles for Multiplex Biomolecule Detection with Rapid Probe-Set Modification

Encoded hydrogel microparticles synthesized via flow lithography have drawn attention for multiplex biomarker detection due to their high multiplex capability and solution-like hybridization kinetics. However, the current methods for preparing particles cannot achieve a flexible, rapid probe-set modification, which is necessary for the production of various combinations of target panels in clinical diagnosis. In order to accomplish the unmet needs, streptavidin was incorporated into the encoded hydrogel microparticles to take advantage of the rapid streptavidin–biotin interactions that can be used in probe-set modification. However, the existing methods suffer from low efficiency of streptavidin conjugation, cause undesirable deformation of particles, and impair the assay capability. Here, we present a simple and powerful method to conjugate streptavidin to the encoded hydrogel microparticles for better assay performance and rapid probe-set modification. Streptavidin was directly conjugated to the encoded hydrogel microparticles using the aza-Michael addition click reaction, which can proceed in mild, aqueous condition without catalysts. A highly flexible and sensitive assay was developed to quantify DNA and proteins using streptavidin-conjugated encoded hydrogel microparticles. We also validated the potential applications of our particles conducting multiplex detection of cancer-related miRNAs.

Separation-encoded microparticles for single-cell western blotting

Direct measurement of proteins from single cells has been realized at the microscale using microfluidic channels, capillaries, and semi-enclosed microwell arrays. Although powerful, these formats are constrained, with the enclosed geometries proving cumbersome for multistage assays, including electrophoresis followed by immunoprobing. We introduce a hybrid microfluidic format that toggles between a planar microwell array and a suspension of microparticles. The planar array is stippled in a thin sheet of polyacrylamide gel, for efficient single-cell isolation and protein electrophoresis of hundreds-to-thousands of cells. Upon mechanical release, array elements become a suspension of separation-encoded microparticles for more efficient immunoprobing due to enhanced mass transfer. Dehydrating microparticles offer improved analytical sensitivity owing to in-gel concentration of fluorescence signal for high-throughput single-cell targeted proteomics.

Current status and future developments in preparation and application of nonspherical polymer particles

Nonspherical polymer particles (NPPs) are nano/micro-particulates of macromolecules that are anisotropic in shape, and can be designed anisotropic in chemistry. Due to shape and surface anisotropies, NPPs bear many unique structures and fascinating properties which are distinctly different from those of spherical polymer particles (SPPs). In recent years, the research on NPPs has surprisingly blossomed in recent years, and many practical materials based on NPPs with potential applications in photonic device, material science and biomedical engineering have been generated. In this review, we give a systematic, balanced and comprehensive summary of the main aspects of NPPs related to their preparation and application, and propose perspectives for the future developments of NPPs.

3D material cytometry (3DMaC): a very high-replicate, high-throughput analytical method using microfabricated, shape-specific, cell-material niches

Studying cell behavior within 3D material niches is key to understanding cell biology in health and diseases, and developing biomaterials for regenerative medicine applications. Current approaches to studying these cell-material niches have low throughput and can only analyze a few replicates per experiment resulting in reduced measurement assurance and analytical power. Here, we report 3D material cytometry (3DMaC), a novel high-throughput method based on microfabricated, shape-specific 3D cell-material niches and imaging cytometry. 3DMaC achieves rapid and highly multiplexed analyses of very high replicate numbers ("n" of 10⁴-10⁶) of 3D biomaterial constructs. 3DMaC overcomes current limitations of low "n", low-throughput, and "noisy" assays, to provide rapid and simultaneous analyses of potentially hundreds of parameters in 3D biomaterial cultures. The method is demonstrated here for a set of 85 000 events containing twelve distinct cell-biomaterial micro-niches along with robust, customized computational methods for high-throughput analytics with potentially unprecedented statistical power.

Fabrication of Hydrogel Particles of Defined Shapes Using Superhydrophobic-Hydrophilic Micropatterns

High-throughput fabrication of freestanding hydrogel particles with defined geometry and size for 3D cell culture, cell screenings, and modular tissue engineering is reported. The method employs discontinuous dewetting using superhydrophobic-hydrophilic micropatterns.

Shape-Encoded Chitosan-Polyacrylamide Hybrid Hydrogel Microparticles with Controlled Macroporous Structures via Replica Molding for Programmable Biomacromolecular Conjugation

Polymeric hydrogel microparticle-based suspension arrays with shape-based encoding offer powerful alternatives to planar and bead-based arrays toward high throughput biosensing and medical diagnostics. We report a simple and robust micromolding technique for polyacrylamide- (PAAm-) based biopolymeric-synthetic hybrid microparticles with controlled 2D shapes containing a potent aminopolysaccharide chitosan as an efficient conjugation handle uniformly incorporated in PAAm matrix. A postfabrication conjugation approach utilizing amine-reactive chemistries on the chitosan shows stable incorporation and retained chemical reactivity of chitosan, readily tunable macroporous structures via simple addition of low content long-chain PEG porogens for improved conjugation capacity and kinetics, and one-pot biomacromolecular assembly via bioorthogonal click reactions with minimal nonspecific binding. We believe that the integrated fabrication-conjugation approach reported here could offer promising routes to programmable manufacture of hydrogel microparticle-based biomacromolecular conjugation and biofunctionalization platforms for a large range of applications.

Hydrogel microparticles for biosensing

Due to their hydrophilic, biocompatible, and highly tunable nature, hydrogel materials have attracted strong interest in the recent years for numerous biotechnological applications. In particular, their solution-like environment and non-fouling nature in complex biological samples render hydrogels as ideal substrates for biosensing applications. Hydrogel coatings, and later, gel dot surface microarrays, were successfully used in sensitive nucleic acid assays and immunoassays. More recently, new microfabrication techniques for synthesizing encoded particles from hydrogel materials have enabled the development of hydrogel-based suspension arrays. Lithography processes and droplet-based microfluidic techniques enable generation of libraries of particles with unique spectral or graphical codes, for multiplexed sensing in biological samples. In this review, we discuss the key questions arising when designing hydrogel particles dedicated to biosensing. How can the hydrogel material be engineered in order to tune its properties and immobilize bioprobes inside? What are the strategies to fabricate and encode gel particles, and how can particles be processed and decoded after the assay? Finally, we review the bioassays reported so far in the literature that have used hydrogel particle arrays and give an outlook of further developments of the field.

High-Throughput Contact Flow Lithography

High-throughput fabrication of graphically encoded hydrogel microparticles is achieved by combining flow contact lithography in a multichannel microfluidic device and a high capacity 25 mm LED UV source. Production rates of chemically homogeneous particles are improved by two orders of magnitude. Additionally, the custom-built contact lithography instrument provides an affordable solution for patterning complex microstructures on surfaces.

Ag@SiO2-entrapped hydrogel microarray: a new platform for a metal-enhanced fluorescence-based protein assay

We developed a novel silver-based metal-enhanced fluorescence (MEF) biosensing platform that consisted of poly(ethylene glycol)(PEG) hydrogel microstructures entrapping silica-coated silver nanoparticles (Ag@SiO₂).

Uniform core-shell photonic crystal microbeads as microcarriers for optical encoding

We demonstrate a rapid and robust method to fabricate uniform core-shell photonic crystal (PC) microbeads by the microfluidic and centrifugation-redispersion technique. Colored crystalline colloidal arrays (CCAs) were first prepared through centrifugation-redispersion approach by self-assembly of polystyrene-poly(N-isopropylacrylamide) (PS-PNIPAm) core/shell nanoparticles (NPs). Different from the conventional NPs (e.g., charged PS or PNIPAm NPs), PS-PNIPAm NPs could easily self-assemble into well-ordered CCAs by only one purification step without laborious pretreatment (e.g., dialysis or ion exchange) or slow solvent-evaporation process. The CCAs is then encapsulated into a transparent polymer shell with functional groups (e.g., copolymer of ETPTA and butyl acrylate (BA)), triggering the formation of core-shell PC microbeads which can be used as optical encoding microcarriers. Importantly, this technique allows us to produce core-shell PC microbeads in a rapid and robust way, and the optical reflections of the PC microbeads appear highly stable to various external stimuli (e.g., temperature, pH value, and ionic strength) relying on the features of the CCAs core and protection of the polymer shell. Moreover, various probe biomolecules (e.g., proteins, antibodies, and so on) can be easily linked on the surface of the core-shell PC microbeads owing to the hydrophilic modification induced by the hydrolysis of BA on the microbead surface, enabling the multiplex biomolecular detection.

Preparation of Fe₃O₄-Embedded Poly(styrene)/Poly(thiophene) Core/Shell Nanoparticles and Their Hydrogel Patterns for Sensor Applications

This research describes the preparation and sensor applications of multifunctional monodisperse, Fe₃O₄ nanoparticles-embedded poly(styrene)/poly(thiophene) (Fe₃O₄-PSt/PTh), core/shell nanoparticles. Monodisperse Fe₃O₄-PSt/PTh nanoparticles were prepared by free-radical combination (mini-emulsion/emulsion) polymerization for Fe₃O₄-PSt core and oxidative seeded emulsion polymerization for PTh shell in the presence of FeCl₃/H₂O₂ as a redox catalyst, respectively. For applicability of Fe₃O₄-PSt/PTh as sensors, Fe₃O₄-PSt/PTh-immobilized poly(ethylene glycol) (PEG)-based hydrogels were fabricated by photolithography. The hydrogel patterns showed a good sensing performance under different H₂O₂ concentrations. They also showed a quenching sensitivity of 1 µg/mL for the Pd²⁺ metal ion within 1 min. The hydrogel micropatterns not only provide a fast water uptake property but also suggest the feasibility of both H₂O₂ and Pd²⁺ detection.

Oil-isolated hydrogel microstructures for sensitive bioassays on-chip

Multiplexed, sensitive, and on-chip molecular diagnostic assays are essential in both clinical and research settings. In past work, running reactions in nanoliter- to femtoliter-sized volumes such as microwells or droplets has led to significant increases in detection sensitivities. At the same time, hydrogels have emerged as attractive scaffolds for bioassays due to their nonfouling, flexible, and aqueous properties. In this paper, we combine these concepts and develop a novel platform in which hydrogel compartments are used as individually confined reaction volumes within a fluorinated oil phase. We fabricate functional and versatile hydrogel microstructures in microfluidic channels that are physically isolated from each other using a surfactant-free fluorinated oil phase, generating picoliter- to nanoliter-sized immobilized aqueous reaction compartments that are readily functionalized with biomolecules. In doing so, we achieve monodisperse reaction volumes with an aqueous interior while exploiting the unique chemistry of a hydrogel, which provides a solid and porous binding scaffold for biomolecules and is impenetrable to oil. Furthermore, our lithographically defined reaction volumes are readily customized with respect to geometry and chemistry within the same channel, allowing rational tuning of the confined reaction volume on a post-to-post basis without needing to use surfactants to maintain stability. We design and implement a multiplexed signal amplification assay in which gel-bound enzymes turn over small molecule substrate into fluorescent product in the oil-confined gel compartment, providing significant signal enhancement. Using short (20 min) amplification times, the encapsulation scheme provides up to 2 orders of magnitude boost of signal in nucleic acid detection assays relative to direct labeling and does not suffer from any cross-talk between the posts. We ultimately demonstrate up to 57-fold increase in nucleic acid detection sensitivity compared to a direct labeling scheme.

Fabrication of chitosan-poly(ethylene glycol) hybrid hydrogel microparticles via replica molding and its application toward facile conjugation of biomolecules

We demonstrate a facile scheme to fabricate nonspherical chitosan-poly(ethylene glycol) (PEG) microparticle platforms for conjugation of biomolecules with high surface density. Specifically, we show that PEG microparticles containing short chitosan oligomers are readily fabricated via replica molding (RM). Fluorescence and FTIR microscopy results illustrate that these chitosan moieties are incorporated with PEG networks in a stable manner while retaining chemical reactivity toward amine-reactive chemistries. The chitosan-PEG particles are then conjugated with single-stranded (ss) DNAs via Cu-free click chemistry. Fluorescence and confocal microscopy results show facile conjugation of biomolecules with the chitosan-PEG particles under mild conditions with high selectivity. These ssDNA-conjugated chitosan-PEG particles are then enlisted to assemble tobacco mosaic virus (TMV) via nucleic acid hybridization as an example of orientationally controlled conjugation of supramolecular targets. Results clearly show controllable TMV assembly with high surface density, indicating high surface DNA density on the particles. Combined, these results demonstrate a facile fabrication-conjugation scheme for robust biomolecular conjugation or assembly platforms. We expect that our approach can be enlisted in a wide array of biomolecular targets and applications.

Multiplex detection platform for tumor markers and glucose in serum based on a microfluidic microparticle array

We present a multiplex detection platform based on a microfluidic microparticle array to detect proteins and glucose in serum simultaneously. Multiplex detection of proteins and glucose was performed using biofunctionalized microparticles arrayed on gel-based microstructures integrated in microfluidics. The microparticles immobilized on these microstructures showed high stability under microfluidic flow conditions. With arrays of antibody-coated microbeads, microfluidic quantitative immunoassays for two protein tumor markers, human chorionic gonadotropin (hCG) and prostate specific antigen (PSA) were performed in serum samples with detection limits bellow the cut-off values for cancer diagnosis. Parallel to the immunoassays, quantitative enzymatic assays for glucose in the physiological concentration range were performed. Multiplex detection was achieved by using a spatially encoded microarray. By patterning antibody-coated microbeads and enzyme-containing microparticles on a novel mixed structure array, we successfully demonstrated simultaneous immunoassays (binding based assay) for proteins and an enzymatic assay (reaction kinetic based assay) for glucose. Our microparticle arrays could be potentially used for the detection of multiple categories of biomolecules (proteins, small metabolites and DNA) for clinical diagnostics and other biological applications.

Multiplex immunoassay platforms based on shape-coded poly(ethylene glycol) hydrogel microparticles incorporating acrylic acid

A suspension protein microarray was developed using shape-coded poly(ethylene glycol) (PEG) hydrogel microparticles for potential applications in multiplex and high-throughput immunoassays. A simple photopatterning process produced various shapes of hydrogel micropatterns that were weakly bound to poly(dimethylsiloxane) (PDMS)-coated substrates. These micropatterns were easily detached from substrates during the washing process and were collected as non-spherical microparticles. Acrylic acids were incorporated into hydrogels, which could covalently immobilize proteins onto their surfaces due to the presence of carboxyl groups. The amount of immobilized protein increased with the amount of acrylic acid due to more available carboxyl groups. Saturation was reached at 25% v/v of acrylic acid. Immunoassays with IgG and IgM immobilized onto hydrogel microparticles were successfully performed with a linear concentration range from 0 to 500 ng/mL of anti-IgG and anti-IgM, respectively. Finally, a mixture of two different shapes of hydrogel microparticles immobilizing IgG (circle) and IgM (square) was prepared and it was demonstrated that simultaneous detection of two different target proteins was possible without cross-talk using same fluorescence indicator because each immunoassay was easily identified by the shapes of hydrogel microparticles.

Fabrication of a gel particle array in a microfluidic device for bioassays of protein and glucose in human urine samples

This paper describes a simple method for fabricating a series of poly(ethylene glycol) diacrylate (PEG-DA) hydrogel microstructures inside microfluidic channels as probe for proteins and glucose. In order to demonstrate the feasibility of this newly developed system, bovine serum albumin (BSA) was chosen as a model protein. PEG microcolumns were used for the parallel detection of multiple components. Using tetrabromophenol blue (TBPB) and the horseradish peroxidase/glucose oxidase reaction system, bovine serum albumin (BSA) and glucose in human urine were detected by color changes. The color changes for BSA within a concentration range of 1-150 μM, and glucose within a range of 50 mM-2 M could be directly distinguished by eyes or precisely identified by optical microscope. To show the practicability of the gel particle array, protein and glucose concentrations of real human urine samples were determined, resulting in a good correlation with hospital analysis. Notably, only a 5 µL sample was needed for a parallel measurement of both analytes. Conveniently, no special readout equipment or power source was required during the diagnosis process, which is promising for an application in rapid point-of-care diagnosis.

Non-positional cell microarray prepared by shape-coded polymeric microboards: A new microarray format for multiplex and high throughput cell-based assays

A non-positional (or suspension) cell microarray was developed using shape-coded SU-8 photoresist microboards for potential application in multiplex and high-throughput cell-based assays. A conventional photolithography process on glass slides produced various shapes of SU-8 micropatterns that had a lateral dimension of 200 μm and a thickness of 40 μm. The resultant micropatterns were detached from the slides by sonication and named "microboards" due to the fact that had a much larger lateral dimension than thickness. The surfaces of the SU-8 microboards were modified with collagen to promote cell adhesion, and it was confirmed that collagen-coated SU-8 microboards supported cell adhesion and proliferation. Seeding of cells into poly(ethylene glycol)(PEG) hydrogel-coated well plates containing collagen-modified microboards resulted in selective cell adhesion onto the microboards due to the non-adhesiveness of PEG hydrogel toward cells, thereby creating non-positional arrays of microboards carrying cells. Finally, two different cell types (fibroblasts and HeLa cells) were separately cultured on different shapes of microboards and subsequently mixed together to create a non-positional cell microarray consisting of multiple cell types where each cell could be easily identified by the shape of the microboard to which they had adhered. Because numerous unique shapes of microboards can be fabricated using this method by simply changing the photomask designs, high throughput and multiplex cell-based assays would be easily achieved with this system in the future.

Hydrogel microparticles from lithographic processes: novel materials for fundamental and applied colloid science

In recent years there has been a surge in methods to synthesize geometrically and chemically complex microparticles. Analogous to atoms, the concept of a "periodic table" of particles has emerged and continues to be expanded upon. Complementing the natural intellectual curiosity that drives the creation of increasingly intricate particles is the pull from applications that take advantage of such high-value materials. Complex particles are now being used in fields ranging from diagnostics and catalysis to self-assembly and rheology, where material composition and microstructure are closely linked with particle function. This is especially true of polymer hydrogels, which offer an attractive and broad class of base materials for synthesis. Lithography affords the ability to engineer particle properties a priori and leads to the production of homogenous ensembles of particles. This review summarizes recent advances in synthesizing hydrogel microparticles using lithographic processes and highlight a number of emerging applications. We discuss advantages and limitations of current strategies, and conclude with an outlook on future trends in the field.

Facile formation of dynamic hydrogel microspheres for triggered growth factor delivery

Dynamic hydrogels have emerged as an important class of biomaterials for temporal control over growth factor delivery. In this study we formed dynamic hydrogel microspheres from protein-polymer conjugates using an aqueous two-phase suspension polymerization process. This polymerization process enabled rapid microsphere formation without the use of an organic phase, surfactants, mechanical strain or toxic radical initiators. The microspheres' size distribution was modulated by varying the protein-polymer conformation in the pre-polymer solution. Notably, the protein's ligand-induced, nanometer-scale conformational change translated to maximum hydrogel volume changes of 76±10%. The magnitude of the microspheres' volume change was tuned by varying the crosslinking time and ligand identity. After characterizing the microspheres' dynamic properties, we encapsulated two important therapeutic proteins, vascular endothelial growth factor (VEGF) and bone morphogenetic protein-2 (BMP-2), in the hydrogel microspheres and characterized how the microspheres' dynamic properties controlled their release. Significantly, the aqueous two-phase suspension polymerization process enabled high encapsulation efficiencies (65.8±4.8% and 79.5±3.0% for VEGF and BMP-2, respectively). Also, the microspheres' ligand-induced volume change triggered VEGF and BMP-2 release at specific, predetermined times. There are hundreds of proteins that undergo well-characterized conformational changes that could be processed into hydrogel microspheres via aqueous two-phase suspension polymerizations. Therefore, this approach could be used to form dynamic, growth-factor-releasing hydrogel microspheres that respond to a broad range of specific biochemical ligands.

A general route for the synthesis of functional, protein-based hydrogel microspheres using tailored protein charge

pH-induced protein aggregation facilitated the formation of nucleation centers for the chain growth polymerization of hydrogel microspheres.

Multiplexed protein quantification with barcoded hydrogel microparticles

We demonstrate the use of graphically encoded hydrogel microparticles for the sensitive and high-throughput multiplexed detection of clinically relevant protein panels in complex media. Combining established antibody capture techniques with advances in both microfluidic synthesis and analysis, we detected 1-8 pg/mL amounts of three cytokines (interleuken-2, interleuken-4, and tumor necrosis factor alpha) in single and multiplexed assays without the need for filtration or blocking agents. A range of hydrogel porosities was investigated to ensure rapid diffusion of targets and reagents into the particle as well as to maintain the structural integrity of particles during rinsing procedures and high-velocity microfluidic scanning. Covalent incorporation of capture antibodies using a heterobifunctional poly(ethylene glycol) linker enabled one-step synthesis and functionalization of particles using only small amounts of valuable reagents. In addition to the use of three separate types of single-probe particles, the flexibility of the stop-flow lithography (SFL) method was leveraged to spatially segregate the three probes for the aforementioned target set on an individual encoded particle, thereby demonstrating the feasibility of single-particle diagnostic panels. This study establishes the gel-particle platform as a versatile tool for the efficient quantification of protein targets and significantly advances efforts to extend the advantages of both hydrogel substrates and particle-based arrays to the field of clinical proteomics.