Isolation of nucleic acids using liquid-liquid phase separation of pH-sensitive elastin-like polypeptides.

Extraction of nucleic acids (NAs) is critical for many methods in molecular biology and bioanalytical chemistry. NA extraction has been extensively studied and optimized for a wide range of applications and its importance to society has significantly increased. The COVID-19 pandemic highlighted the importance of early and efficient NA testing, for which NA extraction is a critical analytical step prior to the detection by methods like polymerase chain reaction. This study explores simple, new approaches to extraction using engineered smart nanomaterials, namely NA-binding, intrinsically disordered proteins (IDPs), that undergo triggered liquid-liquid phase separation (LLPS). Two types of NA-binding IDPs are studied, both based on genetically engineered elastin-like polypeptides (ELPs), model IDPs that exhibit a lower critical solution temperature in water and can be designed to exhibit LLPS at desired temperatures in a variety of biological solutions. We show that ELP fusion proteins with natural NA-binding domains can be used to extract DNA and RNA from physiologically relevant solutions. We further show that LLPS of pH responsive ELPs that incorporate histidine in their sequences can be used for both binding, extraction and release of NAs from biological solutions, and can be used to detect SARS-CoV-2 RNA in samples from COVID-positive patients.

Microfluidic Fabrication of Silica Microspheres Infused with Positron Emission Tomography Imaging Agents.

Selective internal radiation therapy (SIRT) is a treatment which delivers radioactive therapeutic microspheres via the hepatic artery to destroy tumorigenic tissue of the liver. However, the dose required varies significantly from patient to patient due to nuances in individual biology. Therefore, a positron emission tomography (PET) imaging surrogate, or radiotracer, is used to predict in vivo behavior of therapeutic Y-90 spheres. The ideal surrogate should closely resemble Y-90 microspheres in morphology for highest predictive accuracy. This work presents the fabrication of positron-emitting silica microspheres infused with PET radiotracers copper, fluorine, and gallium. A quick one-pot synthesis is used to create precursor sol, followed by droplet formation with flow-focusing microfluidics, and finally thermal treatment to yield 10-50 µm microspheres with narrow size distribution. Loading of the infused element is controllable in the sol synthesis, while the final sphere size is tunable based on microfluidic flow rates and device channel width. The system is then employed to make radioactive Ga-68 microspheres, which are tested for radioactivity and stability. The fabrication method can be completed within a few hours, depending on the desired microsphere quantity. A microfluidic system is applied to fabricate silica particles loaded with diverse elemental infusions, including radioactive Ga-68.

Centrifugal Generation of Droplet-Based 3D Cell Cultures.

Quickly and easily producing uniform populations of microsphere-based 3D cell cultures using droplet-based templating methods has the potential to enable widespread use of such platforms in drug discovery or cancer research. Here, we advance the design of centrifuge-based droplet generation devices, describe the use of this platform for droplet generation with controlled cell occupancy, and demonstrate weeklong culture duration. Using simple-to-construct devices and easily implemented protocols, the initial concentration of encapsulated cells is adjustable up to hundreds of cells per microsphere. This work demonstrates the first instance of using centrifugal droplet-generating devices to produce large numbers of cell-encapsulating microspheres. Applications of this versatile methodology include the rapid formation of templated 3D cell culture populations suitable for suspension culture or large batch bioreactor studies that require uniform populations.

Microcompartments for Protection and Isolation of Nanoscale DNA Computing Elements.

Physical isolation of molecular computing elements holds the potential for increasing system complexity by enabling the reuse of standardized components and by protecting the components from environmental degradation. However, once elements have been compartmentalized, methods for communicating into these compartments are needed. We report the compartmentalization of steroid-responsive DNA aptamers within giant unilamellar vesicles (GUVs) that are permeable to steroid inputs. Monodisperse GUVs are loaded with aptamers using a microfluidic platform. We demonstrate the target-specific activation of individual aptamers within the GUVs and then load two noninterfering aptamers into the same GUV and demonstrate specific responses to all possible combinations of the two input steroids. Crucially, GUVs prevent the degradation of DNA components by nucleases, providing a potential mechanism for deploying nucleic acid components in vivo. Importantly, our compartments also prevent nonspecific cross-talk between complementary strands, thereby providing a method for parallel execution of cross-reacting molecular logic components. Thus, we provide a mechanism for spatially organizing molecular computing elements, which will increase system modularity by allowing standardized components to be reused.

Oil-Free Acoustofluidic Droplet Generation for Multicellular Tumor Spheroid Culture.

We present an easy-to-assemble microfluidic system for synthesizing cell-loaded dextran/alginate (DEX/ALG) hydrogel spheres using an aqueous two-phase system (ATPS) for templated fabrication of multicellular tumor spheroids (MTSs). An audio speaker driven by an amplified output of a waveform generator or smartphone provides acoustic modulation to drive the breakup of an ATPS into MTS template droplets within microcapillary fluidic devices. We apply extensions of Plateau-Rayleigh theory to help define the flow and frequency parameter space necessary for acoustofluidic ATPS droplet formation in these devices. This method provides a simple droplet microfluidic approach using off-the-shelf acoustic components for quickly initiating MTSs and subsequent 3D cell culture.

Functional Modification of Silica through Enhanced Adsorption of Elastin-Like Polypeptide Block Copolymers.

A powerful tool for controlling interfacial properties and molecular architecture relies on the tailored adsorption of stimuli-responsive block copolymers onto surfaces. Here, we use computational and experimental approaches to investigate the adsorption behavior of thermally responsive polypeptide block copolymers (elastin-like polypeptides, ELPs) onto silica surfaces, and to explore the effects of surface affinity and micellization on the adsorption kinetics and the resultant polypeptide layers. We demonstrate that genetic incorporation of a silica-binding peptide (silaffin R5) results in enhanced adsorption of these block copolymers onto silica surfaces as measured by quartz crystal microbalance and ellipsometry. We find that the silaffin peptide can also direct micelle adsorption, leading to close-packed micellar arrangements that are distinct from the sparse, patchy arrangements observed for ELP micelles lacking a silaffin tag, as evidenced by atomic force microscopy measurements. These experimental findings are consistent with results of dissipative particle dynamics simulations. Wettability measurements suggest that surface immobilization hampers the temperature-dependent conformational change of ELP micelles, while adsorbed ELP unimers (i.e., unmicellized block copolymers) retain their thermally responsive property at interfaces. These observations provide guidance on the use of ELP block copolymers as building blocks for fabricating smart surfaces and interfaces with programmable architecture and functionality.

Dietary Modulation of Oxidative Stress in Alzheimer's Disease.

Cells generate unpaired electrons, typically via oxygen- or nitrogen-based by-products during normal cellular respiration and under stressed situations. These pro-oxidant molecules are highly unstable and may oxidize surrounding cellular macromolecules. Under normal conditions, the reactive oxygen or nitrogen species can be beneficial to cell survival and function by destroying and degrading pathogens or antigens. However, excessive generation and accumulation of the reactive pro-oxidant species over time can damage proteins, lipids, carbohydrates, and nucleic acids. Over time, this oxidative stress can contribute to a range of aging-related degenerative diseases such as cancer, diabetes, macular degeneration, and Alzheimer's, and Parkinson's diseases. It is well accepted that natural compounds, including vitamins A, C, and E, ß-carotene, and minerals found in fruits and vegetables are powerful anti-oxidants that offer health benefits against several different oxidative stress induced degenerative diseases, including Alzheimer's disease (AD). There is increasing interest in developing anti-oxidative therapeutics to prevent AD. There are contradictory and inconsistent reports on the possible benefits of anti-oxidative supplements; however, fruits and vegetables enriched with multiple anti-oxidants (e.g., flavonoids and polyphenols) and minerals may be highly effective in attenuating the harmful effects of oxidative stress. As the physiological activation of either protective or destructive pro-oxidant behavior remains relatively unclear, it is not straightforward to relate the efficacy of dietary anti-oxidants in disease prevention. Here, we review oxidative stress mediated toxicity associated with AD and highlight the modulatory roles of natural dietary anti-oxidants in preventing AD.

Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity.

Dynamic protein-rich intracellular structures that contain phase-separated intrinsically disordered proteins (IDPs) composed of sequences of low complexity (SLC) have been shown to serve a variety of important cellular functions, which include signalling, compartmentalization and stabilization. However, our understanding of these structures and our ability to synthesize models of them have been limited. We present design rules for IDPs possessing SLCs that phase separate into diverse assemblies within droplet microenvironments. Using theoretical analyses, we interpret the phase behaviour of archetypal IDP sequences and demonstrate the rational design of a vast library of multicomponent protein-rich structures that ranges from uniform nano-, meso- and microscale puncta (distinct protein droplets) to multilayered orthogonally phase-separated granular structures. The ability to predict and program IDP-rich assemblies in this fashion offers new insights into (1) genetic-to-molecular-to-macroscale relationships that encode hierarchical IDP assemblies, (2) design rules of such assemblies in cell biology and (3) molecular-level engineering of self-assembled recombinant IDP-rich materials.

Magnetically Responsive Negative Acoustic Contrast Microparticles for Bioanalytical Applications.

Smart colloidal particles are routinely used as carriers for biological molecules, fluorescent reporters, cells, and other analytes for the purposes of sample preparation and detection. However, such particles are typically engineered to respond to a single type of stimulus (e.g., commercial magnetic beads to magnetic fields). Here, we demonstrate a unique class of particles that display both positive magnetic contrast and negative acoustic contrast in water. This dual functionality allows for fine spatiotemporal control, enabling multiple separation modalities and increasing the utility of the particles in various chemical and biological assays.

Creating cellular patterns using genetically engineered, gold- and cell-binding polypeptides.

Patterning cells on material surfaces is an important tool for the study of fundamental cell biology, tissue engineering, and cell-based bioassays. Here, the authors report a simple approach to pattern cells on gold patterned silicon substrates with high precision, fidelity, and stability. Cell patterning is achieved by exploiting adsorbed biopolymer orientation to either enhance (gold regions) or impede (silicon oxide regions) cell adhesion at particular locations on the patterned surface. Genetic incorporation of gold binding domains enables C-terminal chemisorption of polypeptides onto gold regions with enhanced accessibility of N-terminal cell binding domains. In contrast, the orientation of polypeptides adsorbed on the silicon oxide regions limit the accessibility of the cell binding domains. The dissimilar accessibility of cell binding domains on the gold and silicon oxide regions directs the cell adhesion in a spatially controlled manner in serum-free medium, leading to the formation of well-defined cellular patterns. The cells are confined within the polypeptide-modified gold regions and are viable for eight weeks, suggesting that bioactive polypeptide modified surfaces are suitable for long-term maintenance of patterned cells. This study demonstrates an innovative surface-engineering approach for cell patterning by exploiting distinct ligand accessibility on heterogeneous surfaces.

Microcapsules for Enhanced Cargo Retention and Diversity.

Prevention of undesired leakage of encapsulated materials prior to triggered release presents a technological challenge for the practical application of microcapsule technologies in agriculture, drug delivery, and cosmetics. A microfluidic approach is reported to fabricate perfluoropolyether (PFPE)-based microcapsules with a high core-shell ratio that show enhanced retention of encapsulated actives. For the PFPE capsules, less than 2% leakage of encapsulated model compounds, including Allura Red and CaCl2 , over a four week trial period is observed. In addition, PFPE capsules allow cargo diversity by the fabrication of capsules with either a water-in-oil emulsion or an organic solvent as core. Capsules with a toluene-based core begin a sustained release of hydrophobic model encapsulants immediately upon immersion in an organic continuous phase. The major contribution on the release kinetics stems from the toluene in the core. Furthermore, degradable silica particles are incorporated to confer porosity and functionality to the otherwise chemically inert PFPE-based polymer shell. These results demonstrate the capability of PFPE capsules with large core-shell ratios to retain diverse sets of cargo for extended periods and make them valuable for controlled release applications that require a low residual footprint of the shell material.

Measurement of flow velocity and inference of liquid viscosity in a microfluidic channel by fluorescence photobleaching.

We present a simple, noninvasive method for simultaneous measurement of flow velocity and inference of liquid viscosity in a microfluidic channel. We track the dynamics of a sharp front of photobleached fluorescent dye using a confocal microscope and measure the intensity at a single point downstream of the initial front position. We fit an exact solution of the advection diffusion equation to the fluorescence intensity recovery curve to determine the average flow velocity and the diffusion coefficient of the tracer dye. The dye diffusivity is correlated to solute concentration to infer rheological properties of the liquid. This technique provides a simple method for simultaneous elucidation of flow velocity and liquid viscosity in microchannels.

Surface functionalized hydrophobic porous particles toward water treatment application.

A microfluidic-based approach for the fabrication of organic contaminants absorbing core-shell particles is demonstrated. The hydrophobic porous core absorbs oil while the hydrophilic surface enables the particles to be well-dispersed in aqueous solutions. These particles can uptake oil from aqueous solution saturated with oil or via direct contact with oil blobs as depicted in the figure.

Polymer microcapsules with programmable active release.

We present a new type of microcapsule programmed with a tunable active release mechanism. The capsules are triggered by a plasticizing stimulus that induces a phase change transition of the polymeric membrane from a solid to a fluidized form; thereafter, the cargo is actively driven out of the capsule through a defect at the capsule wall with controllable release kinetics. Tuning the degree of membrane fluidity by tailoring the amount of plasticizing stimulus present allows us to obtain temporal variation of the release kinetics from a subsecond abrupt burst release to a slow sustained release of encapsulant over many minutes. Moreover, we demonstrate tuning of the collective capsule triggering response by adjusting stimulus content, polymer molecular weight, and capsule membrane thickness. For this model system, we use a microfluidic approach to fabricate polystyrene capsules triggered by a toluene stimulus. However, this active release approach is general and is applicable to diverse polymeric capsule systems; this versatility is demonstrated by extension of our trigger-release scheme to capsules fabricated from a rubberlike block copolymer. The utility of our technique further enhances the potential of these active release capsules for practical application.

Microfluidic synthesis of monodisperse nanoporous oxide particles and control of hierarchical pore structure.

Particles with hierarchical porosity can be formed by templating silica microparticles with a specially designed surfactant micelle/oil nanoemulsion mixture. The nanoemulsion oil droplet and micellar dimensions determine the pore size distribution: one set of pores with diameters of tens of nanometers coexisting with a second subset of pores with diameters of single nanometers. Further practical utility of these nanoporous particles requires precise tailoring of the hierarchical pore structure. In this synthesis study, the particle nanostructure is tuned by adjusting the oil, water, and surfactant mixture composition for the controlled design of nanoemulsion-templated features. We also demonstrate control of the size distribution and surface area of the smaller micelle-templated pores as a consequence of altering the hydrophobic chain length of the molecular surfactant template. Moreover, a microfluidic system is designed to process the low interfacial system for fabrication of monodisperse porous particles. The ability to direct the assembly of template nanoemulsion and micelle structures creates new opportunities to engineer hierarchically porous particles for utility as electrocatalysts for fuel cells, chromatography separations, drug delivery vehicles, and other applications.

Elastomeric negative acoustic contrast particles for affinity capture assays.

This report describes the development of elastomeric capture microparticles (ECµPs) and their use with acoustophoretic separation to perform microparticle assays via flow cytometry.We have developed simple methods to form ECµPs by cross-linking droplets of common commercially available silicone precursors in suspension followed by surface functionalization with biomolecular recognition reagents. The ECµPs are compressible particles that exhibit negative acoustic contrast in ultrasound when suspended in aqueous media, blood serum, or diluted blood. In this study, these particles have been functionalized with antibodies to bind prostate specific antigen and immunoglobulin (IgG). Specific separation of the ECµPs from blood cells is achieved by flowing them through a microfluidic acoustophoretic device that uses an ultrasonic standing wave to align the blood cells, which exhibit positive acoustic contrast, at a node in the acoustic pressure distribution while aligning the negative acoustic contrast ECµPs at the antinodes. Laminar flow of the separated particles to downstream collection ports allows for collection of the separated negative contrast (ECµPs) and positive contrast particles (cells). Separated ECµPs were analyzed via flow cytometry to demonstrate nanomolar detection for prostate specific antigen in aqueous buffer and picomolar detection for IgG in plasma and diluted blood samples. This approach has potential applications in the development of rapid assays that detect the presence of low concentrations of biomarkers in a number of biological sample types.

The targeted delivery of multicomponent cargos to cancer cells by nanoporous particle-supported lipid bilayers.

Encapsulation of drugs within nanocarriers that selectively target malignant cells promises to mitigate side effects of conventional chemotherapy and to enable delivery of the unique drug combinations needed for personalized medicine. To realize this potential, however, targeted nanocarriers must simultaneously overcome multiple challenges, including specificity, stability and a high capacity for disparate cargos. Here we report porous nanoparticle-supported lipid bilayers (protocells) that synergistically combine properties of liposomes and nanoporous particles. Protocells modified with a targeting peptide that binds to human hepatocellular carcinoma exhibit a 10,000-fold greater affinity for human hepatocellular carcinoma than for hepatocytes, endothelial cells or immune cells. Furthermore, protocells can be loaded with combinations of therapeutic (drugs, small interfering RNA and toxins) and diagnostic (quantum dots) agents and modified to promote endosomal escape and nuclear accumulation of selected cargos. The enormous capacity of the high-surface-area nanoporous core combined with the enhanced targeting efficacy enabled by the fluid supported lipid bilayer enable a single protocell loaded with a drug cocktail to kill a drug-resistant human hepatocellular carcinoma cell, representing a 10(6)-fold improvement over comparable liposomes.

Microparticles with bimodal nanoporosity derived by microemulsion templating.

Oil, water, and surfactant liquid mixtures exhibit very complex phase behavior. Depending on the conditions, such mixtures give rise to highly organized structures. A proper selection of the type and concentration of surfactants determines the structuring at the nanoscale level. In this Article, we show that hierarchically bimodal porous structures can be obtained by templating silica microparticles with a specially designed surfactant micelle/microemulsion mixture. Tuning the phase state by adjusting the surfactant composition and concentration allows for the controlled design of a system where microemulsion droplets coexist with smaller surfactant micellar structures. The microemulsion droplet and micellar dimensions determine the two types of pore sizes. We also demonstrate the fabrication of carbon and carbon/platinum replicas of the silica microspheres using a "lost-wax" approach. Such particles have great potential for the design of electrocatalysts for fuel cells, chromatography separations, and other applications.

Droplet-based microfluidics for emulsion and solvent evaporation synthesis of monodisperse mesoporous silica microspheres.

A novel method for the fabrication of monodisperse mesoporous silica particles is suggested. It is based on the formation of well-defined equally sized emulsion droplets using a microfluidic approach. The droplets contain the silica precursor/surfactant solution and are suspended in hexadecane as the continuous oil phase. The solvent is then expelled from the droplets, leading to concentration and micellization of the surfactant. At the same time, the silica solidifies around the surfactant structures, forming equally sized mesoporous particles. The procedure can be tuned to produce well-separated particles or alternatively particles that are linked together. The latter allows us to create 2D or 3D structures with hierarchical porosity.