Aptamer-functionalized microgel particles for protein detection

Highly Flexible Deep-Learning-Based Automatic Analysis for Graphically Encoded Hydrogel Microparticles

Graphically encoded hydrogel microparticle (HMP)-based bioassay is a diagnostic tool characterized by exceptional multiplex detectability and robust sensitivity and specificity. Specifically, deep learning enables highly fast and accurate analyses of HMPs with diverse graphical codes. However, previous related studies have found the use of plain particles as data to be disadvantageous for accurate analyses of HMPs loaded with functional nanomaterials. Furthermore, the manual data annotation method used in existing approaches is highly labor-intensive and time-consuming. In this study, we present an efficient deep-learning-based analysis of encoded HMPs with diverse graphical codes and functional nanomaterials, utilizing the auto-annotation and synthetic data mixing methods for model training. The auto-annotation enhanced the throughput of dataset preparation up to 0.11 s/image. Using synthetic data mixing, a mean average precision of 0.88 was achieved in the analysis of encoded HMPs with magnetic nanoparticles, representing an approximately twofold improvement over the standard method. To evaluate the practical applicability of the proposed automatic analysis strategy, a single-image analysis was performed after the triplex immunoassay for the preeclampsia-related protein biomarkers. Finally, we accomplished a processing throughput of 0.353 s per sample for analyzing the result image.

One-step assembly of barcoded planar microparticles for efficient readout of multiplexed immunoassay

Barcoded planar microparticles are suitable for developing cost-efficient multiplexed assays, but the robustness and efficiency of the readout process still needs improvement. Here, we designed a one-step microparticle assembling chip that produces efficient and accurate multiplex immunoassay readout results. Our design was also compatible with injection molding for mass production.

Recent Advances in Polymer Additive Engineering for Diagnostic and Therapeutic Hydrogels

Hydrogels are hydrophilic polymer materials that provide a wide range of physicochemical properties as well as are highly biocompatible. Biomedical researchers are adapting these materials for the ever-increasing range of design options and potential applications in diagnostics and therapeutics. Along with innovative hydrogel polymer backbone developments, designing polymer additives for these backbones has been a major contributor to the field, especially for expanding the functionality spectrum of hydrogels. For the past decade, researchers invented numerous hydrogel functionalities that emerge from the rational incorporation of additives such as nucleic acids, proteins, cells, and inorganic nanomaterials. Cases of successful commercialization of such functional hydrogels are being reported, thus driving more translational research with hydrogels. Among the many hydrogels, here we reviewed recently reported functional hydrogels incorporated with polymer additives. We focused on those that have potential in translational medicine applications which range from diagnostic sensors as well as assay and drug screening to therapeutic actuators as well as drug delivery and implant. We discussed the growing trend of facile point-of-care diagnostics and integrated smart platforms. Additionally, special emphasis was given to emerging bioinformatics functionalities stemming from the information technology field, such as DNA data storage and anti-counterfeiting strategies. We anticipate that these translational purpose-driven polymer additive research studies will continue to advance the field of functional hydrogel engineering.

PEG-based Cleavable Hydrogel Microparticles with controlled porosity for permiselective trafficking of biomolecular complexes in biosensing applications

In the last decade, PEG-based hydrogels have been extensively used for the production of microparticles for biosensing applications. The biomolecule accessibility and mass transport rate represent key parameters for the...

Expanding the codes: The development of density-encoded hydrogel microcarriers for suspension arrays

Although suspension array technology (SAT), which uses encoded microspheres, provides high-quality results with versatile applicability for information-intensive bioanalytic applications, current encoding strategies limit the number of codes that can be distinguished. In this paper, we introduce density-encoded hydrogel microcarriers (DMs), which employ the intrinsic density property of biomaterials as a high-capacity coding dimension. Two hydrogel monomers were employed at different ratios to synthesize microgels with distinctive densities. DMs not only can be simultaneously decoded and separated using density gradient centrifugation, but also are compatible with flow cytometry detection. The size and color of DMs have been used as extra coding parameters, to construct an 8 × 2 × 4 (density × size × color) three-dimensionally encoded hydrogel microcarrier library. With aptamer-functionalized DMs (ADMs), we developed a 4-plex protein quantification method for the label-free detection of plasma biomarkers with sub-nanomolar detection limits and good linearities. Moreover, ADMs can be used for label-free naked-eye detection of tumor-derived exosomes. We believe that the simplicity and functionality of DMs will advance the field of suspension arrays and inspire the development of DM-based diagnostic applications.

Design, Bioanalytical, and Biomedical Applications of Aptamer-Based Hydrogels

Aptamers are special types of single-stranded DNA generated by a process called systematic evolution of ligands by exponential enrichment (SELEX). Due to significant advances in the chemical synthesis and biotechnological production, aptamers have gained considerable attention as versatile building blocks for the next generation of soft materials. Hydrogels are high water-retainable materials with a three-dimensional (3D) polymeric network. Aptamers, as a vital element, have greatly expanded the applications of hydrogels. Due to their biocompatibility, selective binding, and molecular recognition, aptamer-based hydrogels can be utilized for bioanalytical and biomedical applications. In this review, we focus on the latest strategies of aptamer-based hydrogels in bioanalytical and biomedical applications. We begin this review with an overview of the underlying design principles for the construction of aptamer-based hydrogels. Next, we will discuss some bioanalytical and biomedical applications of aptamer-based hydrogel including biosensing, target capture and release, logic devices, gene and cancer therapy. Finally, the recent progress of aptamer-based hydrogels is discussed, along with challenges and future perspectives.

Hydrogel-Based Technologies for the Diagnosis of Skin Pathology

Hydrogels, swellable hydrophilic polymer networks fabricated through chemical cross-linking or physical entanglement are increasingly utilized in various biomedical applications over the past few decades. Hydrogel-based microparticles, dressings and microneedle patches have been explored to achieve safe, sustained and on-demand therapeutic purposes toward numerous skin pathologies, through incorporation of stimuli-responsive moieties and therapeutic agents. More recently, these platforms are expanded to fulfill the diagnostic and monitoring role. Herein, the development of hydrogel technology to achieve diagnosis and monitoring of pathological skin conditions are highlighted, with proteins, nucleic acids, metabolites, and reactive species employed as target biomarkers, among others. The scope of this review includes the characteristics of hydrogel materials, its fabrication procedures, examples of diagnostic studies, as well as discussion pertaining clinical translation of hydrogel systems.

Inter-particle biomolecular reactivity tuned by surface crowders

The rate at which colloidal particles can form biomolecular bonds controls the kinetics of applications such as particle-based biosensing, targeted drug delivery and directed colloidal assembly. Here we study how the reactivity of the particle surface depends on its molecular composition, quantified by the inter-particle rate of aggregation in an optomagnetic cluster experiment. Particles were functionalized with DNA or with proteins for specific binding, and with polyethylene glycol as a passive surface crowder. The data show that the inter-particle binding kinetics are dominated by specific interactions, which surprisingly can be tuned by the passive crowder molecules for both the DNA and the protein system. The experimental results are interpreted using model simulations, which show that the crowder-induced decrease of the particle surface reactivity can be described as a reduced reactivity of the specific binder molecules on the particle surface.

Toehold Length of Target ssDNA Affects Its Reaction-Diffusion Behavior in DNA-Responsive DNA-co-Acrylamide Hydrogels

In the present study, we expand on the understanding of hydrogels with embedded deoxyribonucleic acid (DNA) cross-links, from the overall swelling to characterization of processes that precede the swelling. The hydrogels respond to target DNA strands because of a toehold-mediated strand displacement reaction in which the target strand binds to and opens the dsDNA cross-link. The spatiotemporal evolution of the diffusing target ssDNA was determined using confocal laser scanning microscopy (CLSM). The concentration profiles revealed diverse partitioning of the target DNA inside the hydrogel as compared with the immersing solution: excluding a nonbinding DNA, while accumulating a binding target. The data show that a longer toehold results in faster cross-link opening but reduced diffusion of the target, thus resulting in only a moderate increase in the overall swelling rate. The parameters obtained by fitting the data using a reaction-diffusion model were discussed in view of the molecular parameters of the target ssDNA and hydrogels.

Complex microparticle architectures from stimuli-responsive intrinsically disordered proteins

The controllable production of microparticles with complex geometries is useful for a variety of applications in materials science and bioengineering. The formation of intricate microarchitectures typically requires sophisticated fabrication techniques such as flow lithography or multiple-emulsion microfluidics. By harnessing the molecular interactions of a set of artificial intrinsically disordered proteins (IDPs), we have created complex microparticle geometries, including porous particles, core-shell and hollow shell structures, and a unique ‘fruits-on-a-vine’ arrangement, by exploiting the metastable region of the phase diagram of thermally responsive IDPs within microdroplets. Through multi-site unnatural amino acid (UAA) incorporation, these protein microparticles can also be photo-crosslinked and stably extracted to an all-aqueous environment. This work expands the functional utility of artificial IDPs as well as the available microarchitectures of this class of biocompatible IDPs, with potential applications in drug delivery and tissue engineering.

The production of microparticles with complex geometries for biotechnological use historically requires sophisticated fabrication techniques. Here, the authors create complex particle geometries by exploiting the metastable region of the phase diagram of thermally responsive intrinsically disordered proteins within microdroplets.

Morpholino Target Molecular Properties Affect the Swelling Process of Oligomorpholino-Functionalized Responsive Hydrogels

Responsive hydrogels featuring DNA as a functional unit are attracting increasing interest due to combination of versatility and numerous applications. The possibility to use nucleic acid analogues opens for further customization of the hydrogels. In the present work, the commonly employed DNA oligonucleotides in DNA-co-acrylamide responsive hydrogels are replaced by Morpholino oligonucleotides. The uncharged backbone of this nucleic acid analogue makes it less susceptible to possible enzymatic degradation. In this work we address fundamental issues related to key processes in the hydrogel response; such as partitioning of the free oligonucleotides and the strand displacement process. The hydrogels were prepared at the end of optical fibers for interferometric size monitoring and imaged using confocal laser scanning microscopy of the fluorescently labeled free oligonucleotides to observe their apparent diffusion and accumulation within the hydrogels. Morpholino-based hydrogels' response to Morpholino targets was compared to DNA hydrogels' response to DNA targets of the same base-pair sequence. Non-binding targets were observed to be less depleted in Morpholino hydrogels than in DNA hydrogels, due to their electroneutrality, resulting in faster kinetics for Morpholinos. The electroneutrality, however, also led to the total swelling response of the Morpholino hydrogels being smaller than that of DNA, since their lack of charges eliminates swelling resulting from the influx of counter-ions upon oligonucleotide binding. We have shown that employing nucleic acid analogues instead of DNA in hydrogels has a profound effect on the hydrogel response.

DNA hydrogel-empowered biosensing

DNA hydrogels as special members in the DNA nanotechnology have provided crucial prerequisites to create innovative gels owing to their sufficient stability, biocompatibility, biodegradability, and tunable multifunctionality. These properties have tailored DNA hydrogels for various applications in drug delivery, tissue engineering, sensors, and cancer therapy. Recently, DNA-based materials have attracted substantial consideration for the exploration of smart hydrogels, in which their properties can change in response to chemical or physical stimuli. In other words, these gels can undergo switchable gel-to-sol or sol-to-gel transitions upon application of different triggers. Moreover, various functional motifs like i-motif structures, antisense DNAs, DNAzymes, and aptamers can be inserted into the polymer network to offer a molecular recognition capability to the complex. In this manuscript, a comprehensive discussion will be endowed with the recognition capability of different kinds of DNA hydrogels and the alternation in physicochemical behaviors upon target introducing. Finally, we offer a vision into the future landscape of DNA based hydrogels in sensing applications.

Intelligent Detection Platform for Simultaneous Detection of Multiple MiRNAs Based on Smartphone

As a marker of malignant tumors, miRNA is closely related to the occurrence and metastasis of tumors. How to achieve rapid and sensitive real-time detection is important for clinical prevention and treatment of cancer. In this study, an intelligent detection platform based on smartphone image processing technology made point-of-care testing a reality. This new smart approach could detect multiple targets simultaneously and sensitively. Hydrogel microparticles of different coding modes (shapes, numbers) were prepared by flow lithography to detect different miRNAs. After sandwich immunoassays, different shapes of hydrogels showed different fluorescence intensities depending on their targets. Images were captured by a smartphone and then analyzed by image recognition processing software installed on the smartphone. The concentration of miRNA was obtained within 10 s. The entire reaction process did not exceed 2 h. This intelligent and portable detection platform for miRNAs was reliable and the limit of detection reached the femtomole level. This work provided a demonstration of intelligent, portable, real-time detection of tumor markers.

Post-synthesis functionalized hydrogel microparticles for high performance microRNA detection

Encoded hydrogel microparticles, synthesized by Stop Flow Lithography (SFL), have shown great potential for microRNA assays for their capability to provide high multiplexing capacity and solution-like hybridization kinetics. However, due to the low conversion of copolymerization during particle synthesis, current hydrogel microparticles can only utilize ∼10% of the input probes that functionalize the particles for miRNA assay. Here, we present a novel method of functionalizing hydrogel microparticles after particle synthesis by utilizing unconverted double bonds remaining inside the hydrogel particles to maximize functional probe incorporation and increase the performance of miRNA assay. This allows covalent bonding of functional probes to the hydrogel network after particle synthesis. Because of the abundance of the unconverted double bonds and accessibility of all probes, the probe density increases about 8.2 times compared to that of particles functionalized during the synthesis. This results lead to an enhanced miRNA assay performance that improves the limit of detection from 4.9 amol to 1.5 amol. In addition, higher specificity and shorter assay time are achieved compared to the previous method. We also demonstrate a potential application of our particles by performing multiplexed miRNA detections in human plasma samples.

Shape Coding Microhydrogel for a Real-Time Mycotoxin Detection System Based on Smartphones

How to create a portable and quick way to detect multiple coexisting toxins is closely related to everyone's health. In this paper, we have established a real-time mycotoxin detection system that combined shape-encoded hydrogel particle preparation technology and image processing technology with smartphone portable devices. First, hydrogel microparticles containing a specific recognition toxin aptamer were programmable synthesized by stop-flow lithography. The hydrogel particles prepared by us had clear, variable signals and high coding capacity. Then, the indirect competitive detection based on aptamers was simple and rapid; the total reaction time was no more than 1 h 45 min and the image processing process was no more than 10 s. Finally, images could be captured by cameras on portable devices and smartphones. The self-built Android app that used the image recognition program installed on the smartphone would analyze the image and return the results in real time. The results showed that the detection limit reached 0.1 ng/mL, which was lower than the standard. In summary, this platform provides a fast, portable, high-throughput detection solution for real-time detection of mycotoxins, with excellent application prospects.

Linker-free antibody conjugation for sensitive hydrogel microparticle-based multiplex immunoassay

Graphically encoded hydrogel microparticles were directly conjugated with reduced antibodies without linkers for highly sensitive multiplex immunoassay.

‘Off–on’ switchable fluorescent probe for prompt and cost-efficient detection of bacteria

The rapid and straightforward detection of bacteria in food and human samples is becoming important, particularly in view of the development of point-of-care devices and lab-on-a-chip tools for prevention and treatment of bacterial infections.

Multiplexed immunoassay using post-synthesis functionalized hydrogel microparticles

In response to a growing demand for simultaneous detection of multiple proteins in a single sample, multiplex immunoassay platforms have emerged at the forefront of proteomic analysis. In particular, detections using graphically encoded hydrogel microparticles synthesized via flow lithography have received attention for integrating a hydrogel, a substrate that can provide enhanced kinetics and high loading capacity, into the bead-based multiplex platform. Currently, the method of microparticle functionalization involves copolymerization of antibodies with the gel during particle synthesis. However, its practical operation is too precarious to be adopted because antibodies are susceptible to aggregation due to incompatibility with hydrophobic photoinitiators used in the photo-induced gel polymerization. In this work, we present a multiplex immunoassay platform that uses encoded hydrogel microparticles that are functionalized after particle synthesis by conjugating antibodies with remnant active groups readily available in the hydrogels. The method not only precludes antibody aggregation but also augments the loading density of the antibodies, which translates into enhanced detection performance. In addition to multiplexing, our platform demonstrates high sensitivity, a broad assay range, and a fast detection rate that outperform the enzyme linked immunosorbent assay (ELISA).

Nonfouling, Encoded Hydrogel Microparticles for Multiplex MicroRNA Profiling Directly from Formalin-Fixed, Paraffin-Embedded Tissue

MicroRNAs (miRNA) are short, noncoding RNAs that have been implicated in many diseases, including cancers. Because miRNAs are dysregulated in disease, miRNAs show promise as highly stable biomarkers. Formalin-fixed, paraffin-embedded (FFPE) tissue is a valuable sample type to assay for biomolecules because it is a convenient storage method and is often used by pathologists for histological staining. However, extracting biomolecules from FFPE tissue is challenging because of the presence of cellular and extracellular proteins, formaldehyde cross-links, and paraffin. Moreover, most protocols to measure miRNA in FFPE tissue are time-consuming and laborious. Here, we report a simple protocol to directly measure miRNA from formalin-fixed cells, FFPE tissue sections after paraffin is removed, and FFPE tissue sections using encoded hydrogel microparticles fabricated using stop flow lithography. Measurements by these particles show agreement between formalin-fixed cells and fresh cells, and measurement of FFPE tissue with paraffin is 10% less than FFPE tissue when paraffin is removed before the assay. When normal and tumor FFPE tissue are compared using this microparticle assay, we observe differential miRNA signal for oncogenic miRNAs and tumor suppressing miRNAs. This approach reduces assay times, reduces the use of hazardous chemicals to remove paraffin, and provides a sensitive, quantitative, and multiplexed measurement of miRNA in FFPE tissue.

Magnetic force assisted electrochemical sensor for the detection of thrombin with aptamer-antibody sandwich formation

A magnetic force assisted electrochemical aptamer-antibody sandwich assay (MESA) was developed for the detection of thrombin as a model protein in serum samples. The MESA using the formation of sandwich complexes on the electrochemical sensor probe for reaction and the removal of unbound bioconjugates from the sensor surface without washing are controlled by a magnetic field. Thrombin was determined by the cathodic currents of a toluidine blue O (TBO) attached with thrombin antibody modified magnetic nanoparticle (MNP) at the sensor surface. To detect thrombin in a serum sample, we applied a thrombin-specific aptamer as the capture molecule bound to the functionalized conducting polymer layer (poly-(2,2´:5´,5″-terthiophene-3´-p-benzoic acid) (pTBA)), and streptavidin and starch coated-MNP was conjugated with biotinylated thrombin antibodies (Ab) and TBO as the bioconjugate (MNP@Ab-TBO). The characterization of MNP@Ab-TBO and sensor probe was performed using voltammetry, impedance spectroscopy, XPS, and UV-VIS spectroscopy. The experimental conditions were optimized in terms of pH, binding time, removal time of unbound bioconjugates, and applied potential. The dynamic ranges of thrombin were from 1.0 to 500 nM with detection limit of 0.49 ( ± 0.06) nM. The recovery test demonstrates the reliability of the proposed sensing system for a handheld device.

PCR-Free Colorimetric DNA Hybridization Detection Using a 3D DNA Nanostructured Reporter Probe

A "sandwich-like" biosensor was developed on the basis of the magnetic bead platform for sensitive detection of breast cancer 1 (BRCA1) DNA. In the present study, a tetrahedron-structured reporter probe (TSRP) was designed, in which 3 vertices of the tetrahedron were labeled with digoxin (Dig), and the other one was labeled with a detection probe. TSRP here provided accurate enzyme loading and well-organized spatial arrangement for optimized signal amplification. The detection limit of this biosensor was as low as 10 fM, which is at least 4 orders of magnitude lower than that of the single DNA probe (100 pM), and the signal gain was 2 times higher than the analysis using three one-dimensional (1D) reporter probes. We could distinguish DNA sequences with only 1 base mismatch, and the performance of our TSRP biosensor was proven to be equally good in both PCR products and real fetal calf serum (FCS) sample as in buffer. We believe this work provided a novel avenue for the development of signal amplification strategies.

Microparticle parking and isolation for highly sensitive microRNA detection

Isolating small objects, such as particles, cells, and molecules, in individual aqueous droplets is useful for chemical and biological assays. We have developed a simple microfluidic platform to immobilize (park) microparticles at defined locations, and isolate particles in monodisperse droplets surrounded by immiscible oil. While conventional methods can only achieve stochastic encapsulation of objects within larger droplets, our in situ method ensures that a single particle is entrapped in a similar-sized droplet, with ∼95% yield for parking and isolation. This enables time-lapse studies of reactions in confined volumes and can be used to perform enzymatic amplification of a desired signal to improve the sensitivity of diagnostic assays. To demonstrate the utility of our technique, we perform highly sensitive, multiplexed microRNA detection by isolating encoded, functional hydrogel microparticles in small aqueous droplets. Non-fouling hydrogel microparticles are attractive for microRNA detection due to favorable capture kinetics. By encapsulating these particles in droplets and employing a generalizable enzyme amplification scheme, we demonstrate an order of magnitude improvement in detection sensitivity compared to a non-amplified assay.

Nanotechnology-Enhanced No-Wash Biosensors for in Vitro Diagnostics of Cancer

In vitro biosensors have been an integral component for early diagnosis of cancer in the clinic. Among them, no-wash biosensors, which only depend on the simple mixing of the signal generating probes and the sample solution without additional washing and separation steps, have been found to be particularly attractive. The outstanding advantages of facile, convenient, and rapid response of no-wash biosensors are especially suitable for point-of-care testing (POCT). One fast-growing field of no-wash biosensor design involves the usage of nanomaterials as signal amplification carriers or direct signal generating elements. The analytical capacity of no-wash biosensors with respect to sensitivity or limit of detection, specificity, stability, and multiplexing detection capacity is largely improved because of their large surface area, excellent optical, electrical, catalytic, and magnetic properties. This review provides a comprehensive overview of various nanomaterial-enhanced no-wash biosensing technologies and focuses on the analysis of the underlying mechanism of these technologies applied for the early detection of cancer biomarkers ranging from small molecules to proteins, and even whole cancerous cells. Representative examples are selected to demonstrate the proof-of-concept with promising applications for in vitro diagnostics of cancer. Finally, a brief discussion of common unresolved issues and a perspective outlook on the field are provided.

Recent advances in engineering microparticles and their nascent utilization in biomedical delivery and diagnostic applications

Complex microparticles (MPs) bearing unique characteristics such as well-tailored sizes, various morphologies, and multi-compartments have been attempted to be produced by many researchers in the past decades. However, a conventionally used method of fabricating MPs, emulsion polymerization, has a limitation in achieving the aforementioned characteristics and several approaches such as the microfluidics-assisted (droplet-based microfluidics and flow lithography-based microfluidics), electrohydrodynamics (EHD)-based, centrifugation-based, and template-based methods have been recently suggested to overcome this limitation. The outstanding features of complex MPs engineered through these suggested methods have provided new opportunities for MPs to be applied in a wider range of applications including cell carriers, drug delivery agents, active pigments for display, microsensors, interface stabilizers, and catalyst substrates. Overall, the engineered MPs expose their potential particularly in the field of biomedical engineering as the increased complexity in the engineered MPs fulfills well the requirements of the high-end applications. This review outlines the current trends of newly developed techniques used for engineered MPs fabrication and focuses on the current state of engineered MPs in biomedical applications.

Fabrication of Highly Porous Nonspherical Particles Using Stop-Flow Lithography and the Study of Their Optical Properties

A microfluidic flow lithography approach was investigated to synthesize highly porous nonspherical particles and Janus particles in a one-step and high-throughput fashion. In this study, using common solvents as porogens, we were able to synthesize highly porous particles with different shapes using ultraviolet (UV) polymerization-induced phase separation in a microfluidic channel. We also studied the pore-forming process using operating parameters such as porogen type, porogen concentration, and UV intensity to tune the pore size and increase the pore size to submicron levels. By simply coflowing multiple streams in the microfluidic channel, we were able to create porous Janus particles; we showed that their anisotropic swelling/deswelling exhibit a unique optical shifting. The distinctive optical properties and the enlarged surface area of the highly porous particles can improve their performance in various applications such as optical sensors and drug loading.

Macroporous materials: microfluidic fabrication, functionalization and applications

This article provides an up-to-date highly comprehensive overview (594 references) on the state of the art of the synthesis and design of macroporous materials using microfluidics and their applications in different fields.

Flexible Octopus-Shaped Hydrogel Particles for Specific Cell Capture

Multiarm hydrogel microparticles with varying geometry are fabricated to specifically capture cells expressing epithelial cell adhesion molecule. Results show that particle shape influences cell-capture efficiency due to differences in surface area, hydrodynamic effects, and steric constraints. These findings can lead to improved particle design for cell separation and diagnostic applications.

Multiplexed Detection of Epigenetic Markers Using Quantum Dot (QD)-Encoded Hydrogel Microparticles

Epigenetic alterations in gene expression are influenced by experiences and environment, resulting in significant variation of epigenetic markers from individual to individual. Therefore, it is imperative to measure various epigenetic markers simultaneously from samples of individual subjects to accurately analyze the epigenetic markers in biological samples. Moreover, the individualized genome-wide analysis has become a critical technology for recent trends in clinical applications such as early diagnosis and personalized medicine screening of numerous diseases. The array-based detection of modified histones, conventionally used for multiplexed analysis of epigenetic changes, requires pooling of samples from many subjects to analyze population-wise differences in the expression of histone markers and does not permit individualized analysis. Here, we report multiplexed detection of genome-wide changes in various histone modifications at a single-residue resolution using quantum dot (QD)-encoded polyethylene glycol diacrylate (PEGDA) hydrogel microparticles. To demonstrate the potential of our methodology, we present the simultaneous detection of (1) acetylation of lysine 9 of histone 3 (Ac-H3K9), (2) dimethylation of H3K9 (2Me-H3K9), and (3) trimethylation of H3K9 (3Me-H3K9) from three distinct regions in the brain [nucleus accumbens (NAc), dorsal striatum (DSt), and cerebellum (Cbl)] of cocaine-exposed mice. Our hydrogel-based epigenetic assay enabled relative quantification of the three histone variants from only 10 μL of each brain lysate (protein content = ∼ 1 μg/μL) per mouse. We verified that the exposure to cocaine induced a significant increase of acetylation while a notable decrease in methylation in NAc.

Extensible Multiplex Real-time PCR of MicroRNA Using Microparticles

Multiplex quantitative real-time PCR (qPCR), which measures multiple DNAs in a given sample, has received significant attention as a mean of verifying the rapidly increasing genetic targets of interest in single phenotype. Here we suggest a readily extensible qPCR for the expression analysis of multiple microRNA (miRNA) targets using microparticles of primer-immobilized networks as discrete reactors. Individual particles, 200~500 μm in diameter, are identified by two-dimensional codes engraved into the particles and the non-fluorescent encoding allows high-fidelity acquisition of signal in real-time PCR. During the course of PCR, the amplicons accumulate in the volume of the particles with high reliability and amplification efficiency over 95%. In a quick assay comprising of tens of particles holding different primers, each particle brings the independent real-time amplification curve representing the quantitative information of each target. Limited amount of sample was analyzed simultaneously in single chamber through this highly multiplexed qPCR; 10 kinds of miRNAs from purified extracellular vesicles (EVs).

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

Hydrogels are crosslinked hydrophilic polymers that can absorb a large amount of water. By their hydrophilic, biocompatible and highly tunable nature, hydrogels can be tailored for applications in bioanalysis and biomedicine. Of particular interest are DNA-based hydrogels owing to the unique features of nucleic acids. Since the discovery of the DNA double helical structure, interest in DNA has expanded beyond its genetic role to applications in nanotechnology and materials science. In particular, DNA-based hydrogels present such remarkable features as stability, flexibility, precise programmability, stimuli-responsive DNA conformations, facile synthesis and modification. Moreover, functional nucleic acids (FNAs) have allowed the construction of hydrogels based on aptamers, DNAzymes, i-motif nanostructures, siRNAs and CpG oligodeoxynucleotides to provide additional molecular recognition, catalytic activities and therapeutic potential, making them key players in biological analysis and biomedical applications. To date, a variety of applications have been demonstrated with FNA-based hydrogels, including biosensing, environmental analysis, controlled drug release, cell adhesion and targeted cancer therapy. In this review, we focus on advances in the development of FNA-based hydrogels, which have fully incorporated both the unique features of FNAs and DNA-based hydrogels. We first introduce different strategies for constructing DNA-based hydrogels. Subsequently, various types of FNAs and the most recent developments of FNA-based hydrogels for bioanalytical and biomedical applications are described with some selected examples. Finally, the review provides an insight into the remaining challenges and future perspectives of FNA-based hydrogels.

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.

Microfluidic chip-based silver nanoparticles aptasensor for colorimetric detection of thrombin

In this paper, a colorimetric silver nanoparticles aptasensor (aptamer-AgNPs) was developed for simple and straightforward detection of protein in microfluidic chip. Surface-functionalized microfluidic channels were employed as the capture platform. Then the mixture of target protein and aptamer-AgNPs were injected into the microfluidic channels for colorimetric detection. To demonstrate the performance of this detection platform, thrombin was chosen as a model target protein. Introduction of thrombin could form a sandwich-type complex involving immobilized AgNPs. The amount of aptamer-AgNPs on the complex augmented along with the increase of the thrombin concentration causing different color change that can be analyzed both by naked eyes and a flatbed scanner. This method is featured with low sample consumption, simple processes of microfluidic platform and straightforward colorimetric detection with aptamer-AgNPs. Thrombin at concentrations as low as 20pM can be detected using this aptasensor without signal amplification. This work demonstrated that it had good selectivity over other proteins and it could be a useful strategy to detect other targets with two affinity binding sites for ligands as well.

Aptamer-based colorimetric biosensing of abrin using catalytic gold nanoparticles

In this study we propose a simple and sensitive colorimetric aptasensor for the quantitative analysis of abrin by using catalytic AuNPs for the first time. AuNPs possess the peroxidase-like activity that can catalyse 3,3,5,5-tetramethylbenzidine (TMB) in the presence of H2O2, leading to color change of the solution. It is interesting to find that the peroxidase-like activity of AuNPs can be improved by surface activation with a target-specific aptamer. However, with a target molecule, the aptamer is desorbed from the AuNPs surface, resulting in a decrease of the catalytic abilities of AuNPs. The color change of the solution is relevant to the target concentration, and this can be judged by the naked eye and monitored by using a UV-vis spectrometer. The linear range for the current analytical system was from 0.2 nM to 17.5 nM. The corresponding limit of detection (LOD) was 0.05 nM. Some other proteins such as thrombin (Th), glucose oxidase (GOx), and bovine serum albumin (BSA) all had a negligible effect on the determination of abrin. Furthermore, several practical samples spiked with abrin were analyzed using the proposed method with excellent recoveries. This aptamer-based colorimetric biosensor is superior to other conventional methods owing to its simplicity, low cost, and high sensitivity.

An aptamer-functionalized chemomechanically modulated biomolecule catch-and-release system

The efficient extraction of (bio)molecules from fluid mixtures is vital for applications ranging from target characterization in (bio)chemistry to environmental analysis and biomedical diagnostics. Inspired by biological processes that seamlessly synchronize the capture, transport and release of biomolecules, we designed a robust chemomechanical sorting system capable of the concerted catch and release of target biomolecules from a solution mixture. The hybrid system is composed of target-specific, reversible binding sites attached to microscopic fins embedded in a responsive hydrogel that moves the cargo between two chemically distinct environments. To demonstrate the utility of the system, we focus on the effective separation of thrombin by synchronizing the pH-dependent binding strength of a thrombin-specific aptamer with volume changes of the pH-responsive hydrogel in a biphasic microfluidic regime, and show a non-destructive separation that has a quantitative sorting efficiency, as well as the system's stability and amenability to multiple solution recycling.

Microfluidic synthesis of barcode particles for multiplex assays

The increasing use of high-throughput assays in biomedical applications, including drug discovery and clinical diagnostics, demands effective strategies for multiplexing. One promising strategy is the use of barcode particles that encode information about their specific compositions and enable simple identification. Various encoding mechanisms, including spectroscopic, graphical, electronic, and physical encoding, have been proposed for the provision of sufficient identification codes for the barcode particles. These particles are synthesized in various ways. Microfluidics is an effective approach that has created exciting avenues of scientific research in barcode particle synthesis. The resultant particles have found important application in the detection of multiple biological species as they have properties of high flexibility, fast reaction times, less reagent consumption, and good repeatability. In this paper, research progress in the microfluidic synthesis of barcode particles for multiplex assays is discussed. After introducing the general developing strategies of the barcode particles, the focus is on studies of microfluidics, including their design, fabrication, and application in the generation of barcode particles. Applications of the achieved barcode particles in multiplex assays will be described and emphasized. The prospects for future development of these barcode particles are also presented.

A facile label-free colorimetric aptasensor for ricin based on the peroxidase-like activity of gold nanoparticles

A facile colorimetric aptasensor for ricin based on the peroxidase-like activity of gold nanoparticles was demonstrated for the first time.

Synthesis of colloidal microgels using oxygen-controlled flow lithography

We report a synthesis approach based on stop-flow lithography (SFL) for fabricating colloidal microparticles with any arbitrary 2D-extruded shape. By modulating the degree of oxygen inhibition during synthesis, we achieved previously unattainable particle sizes. Brownian diffusion of colloidal discs in bulk suggests the out-of-plane dimension can be as small as 0.8 μm, which agrees with confocal microscopy measurements. We measured the hindered diffusion of microdiscs near a solid surface and compared our results to theoretical predictions. These colloidal particles can also flow through physiological microvascular networks formed by endothelial cells undergoing vasculogensis under minimal hydrostatic pressure (∼5 mm H2O). This versatile platform creates future opportunities for on-chip parametric studies of particle geometry effects on particle passage properties, distribution and cellular interactions.

Gold-nanoparticle-decorated silica nanorods for sensitive visual detection of proteins

We report a rapid and highly sensitive approach based on gold-nanoparticle-decorated silica nanorods (GNP-SiNRs) label and lateral-flow strip biosensor (LFSB) for visually detecting proteins. Owing to its biocompatibility and convenient surface modification, SiNRs were used as carriers to load numerous GNPs, and the GNP-SiNRs were used as labels for the lateral-flow assay. The LFSB detection limit was lowered 50 times compared to the traditional GNP-based lateral-flow assay. Rabbit IgG was used as a model target to demonstrate the proof-of-concept. Sandwich-type immunoreactions were performed on the immunochromatographic strips, and the accumulation of GNP-SiNRs on the test zone produced the characteristic colored bands, enabling visual detection of proteins without instrumentation. The quantitative detection was performed by reading the intensities of the colored bands with a portable strip reader. The response of the optimized device was highly linear for the range of 0.05-2 ng mL(-1), and the detection limit was estimated to be 0.01 ng mL(-1). The GNP-SiNR-based LFSB, thus, offered an ultrasensitive method for rapidly detecting trace amounts of proteins. This method has a potential application with point-of-care screening for clinical diagnostics and biomedical research.

Aptamer binding assays for proteins: the thrombin example--a review

Experimentally selected single-stranded DNA and RNA aptamers are able to bind to specific target molecules with high affinity and specificity. Many analytical methods make use of affinity binding between the specific targets and their aptamers. In the development of these methods, thrombin is the most frequently used target molecule to demonstrate the proof-of-principle. This paper critically reviews more than one hundred assays that are based on aptamer binding to thrombin. This review focuses on homogeneous binding assays, electrochemical aptasensors, and affinity separation techniques. The emphasis of this review is placed on understanding the principles and unique features of the assays. The principles of most assays for thrombin are applicable to the determination of other molecular targets.