Fluorinated Pickering Emulsions with Nonadsorbing Interfaces for Droplet-based Enzymatic Assays

Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments

Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >10⁷-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >10⁷ variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.

Multifunctional Droplets Formed by Interfacially Self-Assembled Fluorinated Magnetic Nanoparticles for Biocompatible Single Cell Culture and Magnet-Driven Manipulation

The ability to encapsulate and manipulate droplets with a picoliter volume of samples and reagents shows great potential for practical applications in chemistry, biology, and materials science. Magnetic control is a promising approach for droplet manipulation due to its ability for wireless control and its ease of implementation. However, it is challenged by the poor biocompatibility of magnetic materials in aqueous droplets. Moreover, current droplet technology is problematic because of the molecule leakage between droplets. In the paper, we propose multifunctional droplets with the surface coated by a layer of fluorinated magnetic nanoparticles for magnetically actuated droplet manipulation. Multifunctional droplets show excellent biocompatibility for cell culture, nonleakage of molecules, and high response to a magnetic field. We developed a strategy of coating the F-MNP@SiO2 on the outer surface of droplets instead of adding magnetic material into droplets to enable droplets with a highly magnetic response. The encapsulated bacteria and cells in droplets did not need to directly contact with the magnetic materials at the outer surface, showing high biocompatibility with living cells. These droplets can be precisely manipulated based on magnet distance, the time duration of the magnetic field, the droplet size, and the MNP composition, which well match with theoretical analysis. The precise magnetically actuated droplet manipulation shows great potential for accurate and sensitive droplet-based bioassays like single cell analysis.

Pickering Emulsions Stabilized by Binary Mixtures of Colloidal Particles: Synergies between Contrasting Properties

Pickering emulsions that are stabilized by colloidal particles have attracted substantial research attention because of their potential applications in various industries. Previously, single colloidal particles have usually been used to fabricate Pickering emulsions and to investigate the stabilization mechanism. However, surface modification of the colloidal stabilizer is normally required to adjust the particle wettability, which often involves chemical modification, the adsorption of a surfactant or polymer, and the addition of an electrolyte. Such a modification is expensive, time-consuming, and thus only partially effective. In this Perspective, we describe an alternative approach that uses binary mixtures of particles as stabilizers and could be an effective solution to the above-described problems with Pickering emulsions. We introduce various types of Pickering emulsions stabilized by binary mixtures of particles with different functional groups, opposite charges, or opposite wettabilities (i.e., they are hydrophilic or hydrophobic). Examples of stabilizing mechanisms are discussed, showing that compared with emulsions stabilized by single colloidal particles, emulsions stabilized by binary mixtures of particles are generated via simpler particle-pretreatment processes and have higher stability and customizable properties and thus can enable the exploration of the next generation of Pickering emulsions.

Recent trends in biocatalysis

Biocatalysis has undergone revolutionary progress in the past century. Benefited by the integration of multidisciplinary technologies, natural enzymatic reactions are constantly being explored. Protein engineering gives birth to robust biocatalysts that are widely used in industrial production. These research achievements have gradually constructed a network containing natural enzymatic synthesis pathways and artificially designed enzymatic cascades. Nowadays, the development of artificial intelligence, automation, and ultra-high-throughput technology provides infinite possibilities for the discovery of novel enzymes, enzymatic mechanisms and enzymatic cascades, and gradually complements the lack of remaining key steps in the pathway design of enzymatic total synthesis. Therefore, the research of biocatalysis is gradually moving towards the era of novel technology integration, intelligent manufacturing and enzymatic total synthesis.

Photo-Responsive Fluorosurfactant Enabled by Plasmonic Nanoparticles for Light-Driven Droplet Manipulation

The past decade has witnessed a significant development of droplet microfluidics for applications such as directed evolution and single-cell analysis. While the stability and manipulation of droplets are part of the prerequisites to further their applications, most of the currently available surfactants serve solely as stabilizers between the interfaces of water and oil. In this study, we present a novel type of photo-responsive fluorosurfactant based on fluorinated plasmonic nanoparticles (NPs). The demonstration by fluorinated gold-silica core-shell NPs (f-Au@SiO₂) has been shown to be effective in stabilizing the water-in-fluorocarbon oil droplets. More importantly, the photothermal response enabled by the f-Au@SiO₂ has been shown to be promising for the movement of droplets as well as the alteration of interfacial stability. The unique photo-responsiveness provided by the plasmonic NPs is expected to gear up the droplet microfluidics with an "active" surfactant for reconfigurable optical manipulation.

Monodisperse drops templated by 3D-structured microparticles

The ability to create uniform subnanoliter compartments using microfluidic control has enabled new approaches for analysis of single cells and molecules. However, specialized instruments or expertise has been required, slowing the adoption of these cutting-edge applications. Here, we show that three dimensional-structured microparticles with sculpted surface chemistries template uniformly sized aqueous drops when simply mixed with two immiscible fluid phases. In contrast to traditional emulsions, particle-templated drops of a controlled volume occupy a minimum in the interfacial energy of the system, such that a stable monodisperse state results with simple and reproducible formation conditions. We describe techniques to manufacture microscale drop-carrier particles and show that emulsions created with these particles prevent molecular exchange, concentrating reactions within the drops, laying a foundation for sensitive compartmentalized molecular and cell-based assays with minimal instrumentation.

Ultrahigh throughput screening for enzyme function in droplets

Water-in-oil droplets, made and handled in microfluidic devices, provide a new experimental format, in which ultrahigh throughput experiments can be conducted faster and with minimal reagent consumption. An increasing number of studies have emerged that applied this approach to directed evolution and metagenomic screening of enzyme catalysts. Here, we review the considerations necessary to implement robust workflows, based on choices of device design, detection modes, emulsion formulations and substrates, and scope out which enzyme classes have become amenable to droplet screening.

Mass Activated Droplet Sorting (MADS) Enables High-Throughput Screening of Enzymatic Reactions at Nanoliter Scale

Microfluidic droplet sorting enables the high-throughput screening and selection of water-in-oil microreactors at speeds and volumes unparalleled by traditional well-plate approaches. Most such systems sort using fluorescent reporters on modified substrates or reactions that are rarely industrially relevant. We describe a microfluidic system for high-throughput sorting of nanoliter droplets based on direct detection using electrospray ionization mass spectrometry (ESI-MS). Droplets are split, one portion is analyzed by ESI-MS, and the second portion is sorted based on the MS result. Throughput of 0.7 samples s^-1 is achieved with 98 % accuracy using a self-correcting and adaptive sorting algorithm. We use the system to screen ≈15 000 samples in 6 h and demonstrate its utility by sorting 25 nL droplets containing transaminase expressed in vitro. Label-free ESI-MS droplet screening expands the toolbox for droplet detection and recovery, improving the applicability of droplet sorting to protein engineering, drug discovery, and diagnostic workflows.

Thermodynamic perspectives on liquid–liquid droplet reactors for biochemical applications

Liquid–liquid droplet reactors have garnered significant interest in biochemical applications by simulating thermodynamic systmes, ranging from closed systems, semi-closed/semi-open systems, to open systems.

Droplet Microfluidics-Enabled High-Throughput Screening for Protein Engineering

Protein engineering—the process of developing useful or valuable proteins—has successfully created a wide range of proteins tailored to specific agricultural, industrial, and biomedical applications. Protein engineering may rely on rational techniques informed by structural models, phylogenic information, or computational methods or it may rely upon random techniques such as chemical mutation, DNA shuffling, error prone polymerase chain reaction (PCR), etc. The increasing capabilities of rational protein design coupled to the rapid production of large variant libraries have seriously challenged the capacity of traditional screening and selection techniques. Similarly, random approaches based on directed evolution, which relies on the Darwinian principles of mutation and selection to steer proteins toward desired traits, also requires the screening of very large libraries of mutants to be truly effective. For either rational or random approaches, the highest possible screening throughput facilitates efficient protein engineering strategies. In the last decade, high-throughput screening (HTS) for protein engineering has been leveraging the emerging technologies of droplet microfluidics. Droplet microfluidics, featuring controlled formation and manipulation of nano- to femtoliter droplets of one fluid phase in another, has presented a new paradigm for screening, providing increased throughput, reduced reagent volume, and scalability. We review here the recent droplet microfluidics-based HTS systems developed for protein engineering, particularly directed evolution. The current review can also serve as a tutorial guide for protein engineers and molecular biologists who need a droplet microfluidics-based HTS system for their specific applications but may not have prior knowledge about microfluidics. In the end, several challenges and opportunities are identified to motivate the continued innovation of microfluidics with implications for protein engineering.

Before the breach: Interactions between colloidal particles and liquid interfaces at nanoscale separations

Particles bound to fluid-fluid interfaces are widely used to study self-assembly and to make materials such as Pickering emulsions. In both contexts, the lateral interactions between such particles have been studied extensively. However, much less is known about the normal interactions between a particle and the interface prior to contact. We use digital holographic microscopy to measure the dynamics of individual micrometer-size colloidal particles as they approach an interface between an aqueous phase and oil. Our measurements show that the interaction between the particle and interface changes nonmonotonically as a function of salt concentration, from repulsive at 1 mM to attractive at tens of mM to negligible at 100 mM and attractive again above 200 mM. In the attractive regimes, the particles can bind to the interface at nanometer-scale separation without breaching it. Classical Derjaguin-Landau-Verwey-Overbeek theory does not explain these observations. However, a theory that accounts for nonlinear screening and correlations between the ions does predict the nonmonotonic dependence on salt concentration and produces trajectories that agree with experimental data. We further show that the normal interactions determine the lateral interactions between particles that are bound to the interface. Because the interactions we observe occur at salt concentrations used to make Pickering emulsions and other particle-laden interfaces, our results suggest that particle arrangements at the interface are likely out of equilibrium on experimental timescales.

Quantifying phenotypes in single cells using droplet microfluidics

This book chapter describes the use of droplet microfluidics to phenotype single cells. The basic process flow includes the encapsulation of single cells with a specific probe into aqueous micro-droplets suspended in a biocompatible oil. The probe is chosen to measure the phenotype of interest. After incubation, the encapsulated cell turns the probe fluorescent and renders the entire droplet fluorescent. Enumerating drops that are fluorescent quantifies the concentration of cells possessing the phenotype of interest. Examining the distribution of fluorescence further allows one to quantify the heterogeneity among the cell population.

Synthesizing Pickering Nanoemulsions by Vapor Condensation

Nanoparticle-stabilized (Pickering) emulsions are widely used in applications such as cosmetics, drug delivery, membranes, and material synthesis. However, formulating Pickering nanoemulsions remains a significant challenge. Herein, we show that Pickering nanoemulsions can be obtained in a single step even at very low nanoparticle loadings (0.2 wt %) by condensing water vapor on a nanoparticle-infused subcooled oil that spreads on water. Droplet nuclei spontaneously submerge within the oil after nucleating at the oil-air interface, resulting in the suppression of droplet growth by diffusion, and subsequently coalesce to larger sizes until their growth is curtailed by nanoparticle adsorption. The average nanoemulsion size is governed by the competition between nanoparticle adsorption kinetics and droplet growth dynamics, which are in turn a function of nanoparticle size, concentration, and condensation time. Controlling such factors can lead to the formation of highly monodisperse nanoemulsions. Emulsion formation via condensation is a fast, scalable, energy-efficient process that can be adapted for a wide variety of emulsion-based applications in biology, chemistry, and materials science.

Preparation and Investigation of Foaming Amphiphilic Fluorinated Nanoparticles for Enhanced Oil Recovery

Amphiphilic nanoparticles have attracted increasing interest as Pickering emulsifiers owing to the combined advantages of both traditional surfactants and homogeneous particles. Here, foaming amphiphilic fluorinated nanoparticles were prepared for enhanced oil recovery by the toposelective surface modification method. The structure and properties of amphiphilic nanoparticles were characterized using Fourier transform infrared spectroscopy, scanning electron microscopy, a laser diffraction method, fluorescence microscopy, a pendant drop tensiometer, and foamscan. It was found that the amphiphilic fluorinated nanoparticles exhibited significant interfacial activity at the air-water interface and generated stabilized aqueous foams against coalescence and drainage even in the absence of surfactants. When the particle concentration reached 0.6 wt %, the adsorption of the amphiphilic nanoparticles at the interface was saturated and the equilibrium surface tension dropped to around 32.7 mN/m. When the particle concentration reached 0.4 wt %, the Gibbs stability criterion was fulfilled. The amphiphilic nanoparticles foam system has a better plugging capacity and enhanced oil recovery capacity. The results obtained provide fundamental insights into the understanding of the self-assembly behavior and foam properties of amphiphilic fluorinated nanoparticles and further demonstrate the future potential of the amphiphilic nanoparticles used as colloid surfactants for enhanced oil recovery applications.

Encapsulation of Single Nanoparticle in Fast-Evaporating Micro-droplets Prevents Particle Agglomeration in Nanocomposites

This work describes the use of fast-evaporating micro-droplets to finely disperse nanoparticles (NPs) in a polymer matrix for the fabrication of nanocomposites. Agglomeration of particles is a key obstacle for broad applications of nanocomposites. The classical approach to ensure the dispersibility of NPs is to modify the surface chemistry of NPs with ligands. The surface properties of NPs are inevitably altered, however. To overcome the trade-off between dispersibility and surface-functionality of NPs, we develop a new approach by dispersing NPs in a volatile solvent, followed by mixing with uncured polymer precursors to form micro-droplet emulsions. Most of these micro-droplets contain no more than one NP per drop, and they evaporate rapidly to prevent the agglomeration of NPs during the polymer curing process. As a proof of concept, we demonstrate the design and fabrication of TiO₂ NP@PDMS nanocomposites for solar fuel generation reactions with high photocatalytic efficiency and recyclability arising from the fine dispersion of TiO₂. Our simple method eliminates the need for surface functionalization of NPs. Our approach is applicable to prepare nanocomposites comprising a wide range of polymers embedded with NPs of different composition, sizes, and shapes. It has the potential for creating nanocomposites with novel functions.

Ultrahigh-Throughput Improvement and Discovery of Enzymes Using Droplet-Based Microfluidic Screening

Enzymes are extremely valuable tools for industrial, environmental, and biotechnological applications and there is a constant need for improving existing biological catalysts and for discovering new ones. Screening microbe or gene libraries is an efficient way of identifying new enzymes. In this view, droplet-based microfluidics appears to be one of the most powerful approaches as it allows inexpensive screenings in well-controlled conditions and an ultrahigh-throughput regime. This review aims to introduce the main microfluidic devices and concepts to be considered for such screening before presenting and discussing the latest successful applications of the technology for enzyme discovery.

High-Efficiency and High-Throughput On-Chip Exchange of the Continuous Phase in Droplet Microfluidic Systems

This article describes an integrated platform for the on-chip exchange of the continuous phase in droplet microfluidic systems. The drops used in this work are stabilized by amphiphilic nanoparticles. For some characterizations and applications of these nanoparticle-stabilized drops, including the measurement of adsorption dynamics of nanoparticles to the droplet surface, it is necessary to change the composition of the continuous phase from that used during the droplet generation process. Thus far, no work has reported the exchange of the continuous phase for a large number (>1 million) of drops in a microfluidic system. This article describes the design and characterization of a high-efficiency and high-throughput on-chip exchanger of the continuous phase in a continuous-flow droplet microfluidic system. The efficiency of exchange was higher than 97%. The throughput was greater than 1 million drops/min, and this can be increased further by increasing the number of parallel exchangers used. Because drops are injected into the exchanger in a continuous-flow manner, the method is directly compatible with automation to further increase its reliability and potential scale-up.

Controlled droplet microfluidic systems for multistep chemical and biological assays

Droplet microfluidics is a relatively new and rapidly evolving field of science focused on studying the hydrodynamics and properties of biphasic flows at the microscale, and on the development of systems for practical applications in chemistry, biology and materials science.

Confinement and viscosity ratio effect on droplet break-up in a concentrated emulsion flowing through a narrow constriction

This paper describes the dimensionless groups that determine the break-up probability of droplets in a concentrated emulsion during its flow in a tapered microchannel consisting of a narrow constriction. Such channel geometry is commonly used in droplet microfluidics to investigate the content of droplets from a concentrated emulsion. In contrast to solid wells in multi-well plates, drops are metastable, and are prone to break-up which compromises the accuracy and the throughput of the assay. Unlike single drops, the break-up process in a concentrated emulsion is stochastic. Analysis of the behavior of a large number of drops (N > 5000) shows that the probability of break-up increases with applied flow rate, the size of the drops relative to the size of the constriction, and the viscosity ratio of the emulsion. This paper shows that the break-up probability collapses into a single curve when plotted as a function of the product of capillary number, viscosity ratio, and confinement factor defined as the un-deformed radius of the drop relative to the hydraulic radius of the constriction. Fundamentally, the results represent a critical step towards the understanding of the physics governing instability in concentrated emulsions. Practically, the results provide a direct guide for the rational design of microchannels and the choice of operation parameters to increase the throughput of the droplet interrogation step while preserving droplet integrity and assay accuracy.

Droplet microfluidics for microbiology: techniques, applications and challenges

Droplet microfluidics has rapidly emerged as one of the key technologies opening up new experimental possibilities in microbiology. The ability to generate, manipulate and monitor droplets carrying single cells or small populations of bacteria in a highly parallel and high throughput manner creates new approaches for solving problems in diagnostics and for research on bacterial evolution. This review presents applications of droplet microfluidics in various fields of microbiology: i) detection and identification of pathogens, ii) antibiotic susceptibility testing, iii) studies of microbial physiology and iv) biotechnological selection and improvement of strains. We also list the challenges in the dynamically developing field and new potential uses of droplets in microbiology.

Dodecylresorufin (C12R) Outperforms Resorufin in Microdroplet Bacterial Assays

This paper proves that dodecylresorufin (C12R) outperforms resorufin (the conventional form of this dye) in droplet microfluidic bacterial assays. Resorufin is a marker dye that is widely used in different fields of microbiology and has increasingly been applied in droplet microfluidic assays and experiments. The main concern associated with resorufin in droplet-based systems is dye leakage into the oil phase and neighboring droplets. The leakage decreases the performance of assays because it causes averaging of the signal between the positive (bacteria-containing) and negative (empty) droplets. Here we show that C12R is a promising alternative to conventional resorufin because it maintains higher sensitivity, specificity, and signal-to-noise ratio over time. These characteristics make C12R a suitable reagent for droplet digital assays and for monitoring of microbial growth in droplets.

Low energy emulsion-based fermentation enabling accelerated methane mass transfer and growth of poly(3-hydroxybutyrate)-accumulating methanotrophs

Methane is a low-cost feedstock for the production of polyhydroxyalkanoate biopolymers, but methanotroph fermentations are limited by the low solubility of methane in water. To enhance mass transfer of methane to water, vigorous mixing or agitation is typically used, which inevitably increases power demand and operational costs. This work presents a method for accelerating methane mass transfer without agitation by growing methanotrophs in water-in-oil emulsions, where the oil has a higher solubility for methane than water does. In systems without agitation, the growth rate of methanotrophs in emulsions is five to six times that of methanotrophs in the medium-alone incubations. Within seven days, cells within the emulsions accumulate up to 67 times more P3HB than cells in the medium-alone incubations. This is achieved due to the increased interfacial area of the aqueous phase, and accelerated methane diffusion through the oil phase.

Surface-functionalizable amphiphilic nanoparticles for pickering emulsions with designer fluid–fluid interfaces

This work describes the synthesis of amphiphilic silica nanoparticles with functionalizable surfaces for stabilizing aqueous drops in fluorinated oils, and for enabling the generation of emulsions with tailored interfacial properties.