High aspect ratio induced spontaneous generation of monodisperse picolitre droplets for digital PCR

Establishment and Validation of an Integrated Microfluidic Step Emulsification Chip Supporting Droplet Digital Nucleic Acid Analysis

Uniform and stable droplet generation is critical for accurate and efficient digital nucleic acid analysis (dNAA). In this study, an integrated microfluidic step emulsification device with wide-range droplet generation capability, small device dimensions, convenient fabrication strategy, low contamination and high robustness was developed. A tree-shaped droplet generation nozzle distribution design was proposed to increase the uniformity of droplet generation by equating flow rates, and the flow field in the design was numerically simulated. Theoretical analysis and comparative experiments on droplet size were performed regarding the influences of nozzle dimensions and surface properties. With incubation and hydrophobic reagent treatment, droplets as small as 73.1 μm were generated with multiplex nozzles of 18 μm (h) × 80 μm (w). The droplets were then collected into a standard PCR tube and an on-chip monolayer droplet collection chamber, without manual transfer and sample contamination. The oil-to-sample volume ratio in the PCR tube was recorded during collection. In the end, the droplets generated and collected using the microfluidic device proved to be stable and uniform for nucleic acid amplification and detection. This study provides reliable characteristic information for the design and fabrication of a micro-droplet generation device, and represents a promising approach for the realization of a three-in-one dNAA device under a step emulsification method.

Simple Method to Generate Droplets Spontaneously by a Superhydrophobic Double-Layer Split Nozzle

Given the problems of traditional droplet generation devices, such as the complex structure and processing technology, difficulty in droplet separation, and low transfer accuracy, we propose a low-adhesion superhydrophobic double-layer split nozzle (SDSN). It realizes spontaneous droplet generation by using an interfacial tension force inside the micro-hole to drive the droplet snap-off. It successfully achieves stable and highly consistent droplets on the micrometer-scale circular micro-hole. Droplets with a volume in the range of 0.65-1.75 ± 0.007 μL can be precisely achieved by adjusting the hole size of the SDSN from 100 to 500 μm. The SDSN is prepared by conventional mechanical drilling, chemical etching, and low surface energy modification. Compared with traditional droplet generation devices, no photolithography process is required, and the cost is lower. Moreover, the droplets can be obtained directly without any post-processing, avoiding the problem of separating droplets from another solution. The stability of SDSN is good, and the droplet volume is not affected by the fluctuation of external conditions. The rate of droplet generation can be freely adjusted by adjusting the speed of the electronic microinjection pump without affecting the droplet volume. It enables efficient droplet transfer without liquid residue, which improves the transfer accuracy and helps to save the use of expensive reagents. This simple but effective structure will be of great help to make breakthroughs in next-generation spontaneous droplet generation, liquid transport, and digital microfluidic devices.

Recent progress in nucleic acid detection with CRISPR

Recent advances in CRISPR-based biotechnologies have greatly expanded our capabilities to repurpose CRISPR for the development of molecular diagnostic systems. The key attribute that allows CRISPR to be widely utilized is its programmable and highly specific nature. In this review, we first illustrate the principle of the class 2 CRISPR nucleases for molecular diagnostics which originates from their immunologic defence systems. Next, we present the CRISPR-based schemes in the application of diagnostics with amplification-assisted or amplification-free strategies. By highlighting some of the recent advances we interpret how general bioengineering methodologies can be integrated with CRISPR. Finally, we discuss the challenges and exciting prospects for future CRISPR-based biosensing development. We hope that this review will guide the reader to systematically learn the start-of-the-art development of CRISPR-mediated nucleic acid detection and understand how to apply the CRISPR nucleases with different design concepts to more general applications in diagnostics and beyond.

Monodisperse Micro-Droplet Generation in Microfluidic Channel with Asymmetric Cross-Sectional Shape

Micro-droplets are widely used in the fields of chemical and biological research, such as drug delivery, material synthesis, point-of-care diagnostics, and digital PCR. Droplet-based microfluidics has many advantages, such as small reagent consumption, fast reaction time, and independent control of each droplet. Therefore, various micro-droplet generation methods have been proposed, including T-junction breakup, capillary flow-focusing, planar flow-focusing, step emulsification, and high aspect (height-to-width) ratio confinement. In this study, we propose a microfluidic device for generating monodisperse micro-droplets, the microfluidic channel of which has an asymmetric cross-sectional shape and high hypotenuse-to-width ratio (HTWR). It was fabricated using basic MEMS processes, such as photolithography, anisotropic wet etching of Si, and polydimethylsiloxane (PDMS) molding. Due to the geometric similarity of a Si channel and a PDMS mold, both of which were created through the anisotropic etching process of a single crystal Si, the microfluidic channel with the asymmetric cross-sectional shape and high HTWR was easily realized. The effects of HTWR of channels on the size and uniformity of generated micro-droplets were investigated. The monodisperse micro-droplets were generated as the HTWR of the asymmetric channel was over 3.5. In addition, it was found that the flow direction of the oil solution (continuous phase) affected the size of micro-droplets due to the asymmetric channel structures. Two kinds of monodisperse droplets with different sizes were successfully generated for a wider range of flow rates using the asymmetric channel structure in the developed microfluidic device.

A home-made pipette droplet microfluidics rapid prototyping and training kit for digital PCR, microorganism/cell encapsulation and controlled microgel synthesis

Droplet microfluidics offers a platform from which new digital molecular assay, disease screening, wound healing and material synthesis technologies have been proposed. However, the current commercial droplet generation, assembly and imaging technologies are too expensive and rigid to permit rapid and broad-range tuning of droplet features/cargoes. This rapid prototyping bottleneck has limited further expansion of its application. Herein, an inexpensive home-made pipette droplet microfluidics kit is introduced. This kit includes elliptical pipette tips that can be fabricated with a simple DIY (Do-It-Yourself) tool, a unique tape-based or 3D printed shallow-center imaging chip that allows rapid monolayer droplet assembly/immobilization and imaging with a smart-phone camera or miniature microscope. The droplets are generated by manual or automatic pipetting without expensive and lab-bound microfluidic pumps. The droplet size and fluid viscosity/surface tension can be varied significantly because of our particular droplet generation, assembly and imaging designs. The versatility of this rapid prototyping kit is demonstrated with three representative applications that can benefit from a droplet microfluidic platform: (1) Droplets as microreactors for PCR reaction with reverse transcription to detect and quantify target RNAs. (2) Droplets as microcompartments for spirulina culturing and the optical color/turbidity changes in droplets with spirulina confirm successful photosynthetic culturing. (3) Droplets as templates/molds for controlled synthesis of gold-capped polyacrylamide/gold composite Janus microgels. The easily fabricated and user-friendly portable kit is hence ideally suited for design, training and educational labs.

Current commercial dPCR platforms: technology and market review

Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.

High-Aspect-Ratio Microfluidic Channel with Parallelogram Cross-Section for Monodisperse Droplet Generation

Droplet-based microfluidics has been widely used as a potent high-throughput platform due to various advantages, such as a small volume of reagent consumption, massive production of droplets, fast reaction time, and independent control of each droplet. Therefore, droplet microfluidic systems demand the reliable generation of droplets with precise and effective control over their size and distribution, which is critically important for various applications in the fields of chemical analysis, material synthesis, lab-on-a-chip, cell research, diagnostic test, and so on. In this study, we propose a microfluidic device with a high-aspect-ratio (HAR) channel, which has a parallelogram cross-section, for generating monodisperse droplets. The HAR channel was fabricated using simple and cheap MEMS processes, such as photolithography, anisotropic wet etching, and PDMS molding, without expensive equipment. In addition, the parallelogram cross-section channel structure, regarded as a difficult shape to implement in previous fabrication methods, was easily formed by the self-alignment between the silicon channel and the PDMS mold, both of which were created from a single crystal silicon through an anisotropic etching process. We investigated the effects of the cross-sectional shape (parallelogram vs. rectangle) and height-to-width ratio of microfluidic channels on the size and uniformity of generated droplets. Using the developed HAR channel with the parallelogram cross-section, we successfully obtained smaller monodisperse droplets for a wider range of flow rates, compared with a previously reported HAR channel with a rectangular cross-section.

Microfluidic formation of crystal-like structures

Crystal-like structures find application in several fields ranging from biomedical engineering to material science. For instance, droplet crystals are critical for high throughput assays and material synthesis, while particle crystals are important for particles and cell encapsulation, Drop-seq technologies, and single-cell analysis. Formation of crystal-like structures relies entirely on the possibility of manipulating with great accuracy the micrometer-size objects forming the crystal. In this context, microfluidic devices offer versatile tools for the precise manipulation of droplets and particles, thus enabling fabrication of crystal-like structures that form due to hydrodynamic interactions among droplets or particles. In this review, we aim at providing an holistic representation of crystal-like structure formation mediated by hydrodynamic interactions in microfluidic devices. We also discuss the physical origin of these hydrodynamic interactions and their relation to parameters such as device geometry, fluid properties, and flow conditions.

Elliptical Pipette Generated Large Microdroplets for POC Visual ddPCR Quantification of Low Viral Load

Rapid point-of-care (POC) quantification of low virus RNA load would significantly reduce the turn-around time for the PCR test and help contain a fast-spreading epidemic. Herein, we report a droplet digital PCR (ddPCR) platform that can achieve this sensitivity and rapidity without bulky lab-bound equipment. The key technology is a flattened pipette tip with an elliptical cross-section, which extends a high aspect-ratio microfluidic chip design to pipette scale, for rapid (<5 min) generation of several thousand monodispersed droplets ∼150 to 350 μm in size with a CV of ∼2.3%. A block copolymer surfactant (polyoxyalkylene F127) is used to stabilize these large droplets in oil during thermal cycling. At this droplet size and number, positive droplets can be counted by eye or imaged by a smartphone with appropriate illumination/filtering to accurately quantify up to 100 target copies. We demonstrate with 2019 nCoV-PCR assay LODs of 3.8 copies per 20 μL of sample and a dynamic range of 4-100 copies. The ddPCR platform is shown to be inhibitor resistant with spiked saliva samples, suggesting RNA extraction may not be necessary. It represents a rapid 1.5-h POC quantitative PCR test that requires just a pipette equipped with elliptical pipette tip, a commercial portable thermal cycler, a smartphone, and a portable trans-illuminator, without bulky and expensive micropumps and optical detectors that prevent POC application.

Massive droplet generation for digital PCR via a smart step emulsification chip integrated in a reaction tube

Step emulsification (SE) devices coupled with parallel generation nozzles are widely used in the production of large-scale monodisperse droplets, especially for droplet-based digital polymerase chain reaction (ddPCR) analysis. Although current ddPCR systems based on the SE method can provide a fully enclosed ddPCR scheme, high demands on chip fabrication and system control will increase testing costs and reduce its flexibility in ddPCR analysis. In this study, a compact SE device, integrating a smart SE chip into a reaction tube, was developed to prepare large-scale water-in-fluorinated-oil droplets for ddPCR analysis. The SE chip contained dozens of droplet-generation nozzles. By adjusting the nozzle height of the SE chip, monodisperse droplets in a picolitre to nanolitre vloume could be prepared at a production rate of tens to hundreds of microlitres per minute. Subsequently, we utilized such an integrated SE device to prepare monodisperse droplets for ddPCR experiments. The volume of PCR reagent and the number of droplets could be flexibly adjusted according to the requirements of the ddPCR analysis. The quantitative results showed that emulsions prepared by the SE device could achieve ddPCR detection with high accuracy, good repeatability, and an adaptive dynamic range, which also demonstrated the robustness and reliability of such devices in the droplet preparation. Thus, this compact SE device provides an inexpensive, flexible, and simplified droplet preparation method for digital PCR quantitative analysis.

High filling rate digital PCR through-hole array chip with double independent S-shaped flow channels

Sample digital technology is a powerful method for absolute quantification of target molecules such as nucleic acids and proteins. The excellent sample stability and mass production capability has enabled the development of microwell array-based sample digitizing methods. However, in current microwell array chips, samples are loaded by the liquid scraping method, which requires complex manual operation and results in a low filling rate and limited hole filling uniformity. Here, we perform sample loading of a through-hole array chip by a microfluidics-driven method and design a double independent S-shaped flow channels sandwiched through-hole array chip. Because of the capillary force and capillary burst pressure, the sample flowing in the channel can be trapped into through-holes, but cannot flow through the other side. Via air flow and displacement of the remaining sample in the channel, the sample can be partitioned consistently, with zero surplus sample residue in the channel. We evaluated the actual performance of the sample-loading process: the chip enables 99.10% filling rate of 18 500 through-holes, with a grayscale coefficient of variation value of 6.03% determined from fluorescence images. In performing digital polymerase chain reaction on chip, the chip demonstrates good performance for the absolute quantification of target DNA. The simple and robust design of our chip, with excellent filling rate and microsample uniformity, indicates potential for use in a variety of sample digitization applications.

Microfluidics and catalyst particles

In this review article, we discuss the latest advances and future perspectives of microfluidics for micro/nanoscale catalyst particle synthesis and analysis. In the first section, we present an overview of the different methods to synthesize catalysts making use of microfluidics and in the second section, we critically review catalyst particle characterization using microfluidics. The strengths and challenges of these approaches are highlighted with various showcases selected from the recent literature. In the third section, we give our opinion on the future perspectives of the combination of catalytic nanostructures and microfluidics. We anticipate that in the synthesis and analysis of individual catalyst particles, generation of higher throughput and better understanding of transport inside individual porous catalyst particles are some of the most important benefits of microfluidics for catalyst research.

Scalable Production of Monodisperse Functional Microspheres by Multilayer Parallelization of High Aspect Ratio Microfluidic Channels

Droplet microfluidics enables the generation of highly uniform emulsions with excellent stability, precise control over droplet volume, and morphology, which offer superior platforms over conventional technologies for material synthesis and biological assays. However, it remains a challenge to scale up the production of the microfluidic devices due to their complicated geometry and long-term reliability. In this study, we present a high-throughput droplet generator by parallelization of high aspect ratio rectangular structures, which enables facile and scalable generation of uniform droplets without the need to precisely control external flow conditions. A multilayer device is formed by stacking layer-by-layer of the polydimethylsiloxane (PDMS) replica patterned with parallelized generators. By feeding the sample fluid into the device immersed in the carrying fluid, we used the multilayer device with 1200 parallelized generators to generate monodisperse droplets (~45 μm in diameter with a coefficient of variation <3%) at a frequency of 25 kHz. We demonstrate this approach is versatile for a wide range of materials by synthesis of polyacrylamide hydrogel and Poly (l-lactide-co-glycolide) (PLGA) through water-in-oil (W/O) and oil-in-water (O/W) emulsion templates, respectively. The combined scalability and robustness of such droplet emulsion technology is promising for production of monodisperse functional materials for large-scale applications.

Centrifugal Step Emulsification: How Buoyancy Enables High Generation Rates of Monodisperse Droplets

We demonstrate that buoyancy in centrifugal step emulsification enables substantially higher generation rates of monodisperse droplets compared to pressure driven set-ups. Step emulsification in general can produce droplets in comparatively simple systems (only one moving liquid) with a low CV of <5% in droplet diameter and with a minimum dead volume. If operated below a critical capillary number, the droplet diameter is defined by geometry and surface forces only. Above that critical capillary number, however, jetting occurs, leading to an increased droplet diameter and CV. Consequently, generation rates of monodisperse droplets are limited in pressure-driven systems. In this paper, we show that centrifugal step emulsification can overcome this limitation by applying sufficient buoyancy to the system. The buoyancy, induced by the centrifugal field and a density difference of the continuous and disperse phase, supports droplet necking by pulling the forming droplet away from the nozzle. The influence of buoyancy is studied using specific microfluidic designs that allow for supplying different buoyancies to the same droplet generation rates. For a droplet diameter of 100 μm, droplet generation at rates above 2.8k droplets per second and nozzle were reached, which is an increase of more than a factor of 8 in comparison to pressure-driven systems.

Slip-driven microfluidic devices for nucleic acid analysis

Slip-driven microfluidic devices can manipulate fluid by the relative movement of microfluidic plates that are in close contact. Since the demonstration of the first SlipChip device, many slip-driven microfluidic devices with different form factors have been developed, including SlipPAD, SlipDisc, sliding stripe, and volumetric bar chart chip. Slip-driven microfluidic devices can be fabricated from glass, quartz, polydimethylsiloxane, paper, and plastic with various fabrication methods: etching, casting, wax printing, laser cutting, micromilling, injection molding, etc. The slipping operation of the devices can be performed manually, by a micrometer with a base station, or autonomously, by a clockwork mechanism. A variety of readout methods other than fluorescence microscopy have been demonstrated, including both fluorescence detection and colorimetric detection by mobile phones, direct visual detection, and real-time fluorescence imaging. This review will focus on slip-driven microfluidic devices for nucleic acid analysis, including multiplex nucleic acid detection, digital nucleic acid quantification, real-time nucleic acid amplification, and sample-in-answer-out nucleic acid analysis. Slip-driven microfluidic devices present promising approaches for both life science research and clinical molecular diagnostics.

Multistep SlipChip for the Generation of Serial Dilution Nanoliter Arrays and Hepatitis B Viral Load Quantification by Digital Loop Mediated Isothermal Amplification

Serial dilution is a commonly used technique that generates a low-concentration working sample from a high-concentration stock solution and is used to set up screening conditions over a large dynamic range for biological study, optimization of reaction conditions, drug screening, etc. Creating an array of serial dilutions usually requires cumbersome manual pipetting steps or a robotic liquid handling system. Moreover, it is very challenging to set up an array of serial dilutions in nanoliter volumes in miniaturized assays. Here, a multistep SlipChip microfluidic device is presented for generating serial dilution nanoliter arrays in high throughput with a series of simple sliding motions. The dilution ratio can be precisely predetermined by the volumes of mother microwells and daughter microwells, and this paper demonstrates devices designed to have dilution ratios of 1:1, 1:2, and 1:4. Furthermore, an eight-step serial dilution SlipChip with a dilution ratio of 1:4 is applied for digital loop-mediated isothermal amplification (LAMP) across a large dynamic range and tested for hepatitis B viral load quantification with clinical samples. With 64 wells of each dilution and fewer than 600 wells in total, the serial dilution SlipChip can achieve a theoretical quantification dynamic range of 7 orders of magnitude.