Picoliter DNA sequencing chemistry on an electrowetting-based digital microfluidic platform

Digital Microfluidics for Sample Preparation in Low-Input Proteomics

Low-input proteomics, also referred to as micro- or nanoproteomics, has become increasingly popular as it allows one to elucidate molecular processes in rare biological materials. A major prerequisite for the analytics of minute protein amounts, e.g., derived from low cell numbers, down to single cells, is the availability of efficient sample preparation methods. Digital microfluidics (DMF), a technology allowing the handling and manipulation of low liquid volumes, has recently been shown to be a powerful and versatile tool to address the challenges in low-input proteomics. Here, an overview is provided on recent advances in proteomics sample preparation using DMF. In particular, the capability of DMF to isolate proteomes from cells and small model organisms, and to perform all necessary chemical sample preparation steps, such as protein denaturation and proteolytic digestion on-chip, are highlighted. Additionally, major prerequisites to making these steps compatible with follow-up analytical methods such as liquid chromatography-mass spectrometry will be discussed.

A Deep Reinforcement Learning Approach to Droplet Routing for Erroneous Digital Microfluidic Biochips

Digital microfluidic biochips (DMFBs), which are used in various fields like DNA analysis, clinical diagnosis, and PCR testing, have made biochemical experiments more compact, efficient, and user-friendly than the previous methods. However, their reliability is often compromised by their inability to adapt to all kinds of errors. Errors in biochips can be categorized into two types: known errors, and unknown errors. Known errors are detectable before the start of the routing process using sensors or cameras. Unknown errors, in contrast, only become apparent during the routing process and remain undetected by sensors or cameras, which can unexpectedly stop the routing process and diminish the reliability of biochips. This paper introduces a deep reinforcement learning-based routing algorithm, designed to manage not only known errors but also unknown errors. Our experiments demonstrated that our algorithm outperformed the previous ones in terms of the success rate of the routing, in the scenarios including both known errors and unknown errors. Additionally, our algorithm contributed to detecting unknown errors during the routing process, identifying the most efficient routing path with a high probability.

Digital microfluidics for biological analysis and applications

Digital microfluidics (DMF) is an emerging liquid-handling technology based on arrays of microelectrodes for the precise manipulation of discrete droplets. DMF offers the benefits of automation, addressability, integration and dynamic configuration ability, and provides enclosed picoliter-to-microliter reaction space, making it suitable for lab-on-a-chip biological analysis and applications that require high integration and intricate processes. A review of DMF bioassays with a special emphasis on those actuated by electrowetting on dielectric (EWOD) force is presented here. Firstly, a brief introduction is presented on both the theory of EWOD actuation and the types of droplet motion. Subsequently, a comprehensive overview of DMF-based biological analysis and applications, including nucleic acid, protein, immunoreaction and cell assays, is provided. Finally, a discussion on the strengths, challenges, and potential applications and perspectives in this field is presented.

Combining sensors and actuators with electrowetting-on-dielectric (EWOD): advanced digital microfluidic systems for biomedical applications

The concept of digital microfluidics (DMF) enables highly flexible and precise droplet manipulation at a picoliter scale, making DMF a promising approach to realize integrated, miniaturized "lab-on-a-chip" (LOC) systems for research and clinical purposes. Owing to its simplicity and effectiveness, electrowetting-on-dielectric (EWOD) is one of the most commonly studied and applied effects to implement DMF. However, complex biomedical assays usually require more sophisticated sample handling and detection capabilities than basic EWOD manipulation. Alternatively, combined systems integrating EWOD actuators and other fluidic handling techniques are essential for bringing DMF into practical use. In this paper, we briefly review the main approaches for the integration/combination of EWOD with other microfluidic manipulation methods or additional external fields for specified biomedical applications. The form of integration ranges from independently operating sub-systems to fully coupled hybrid actuators. The corresponding biomedical applications of these works are also summarized to illustrate the significance of these innovative combination attempts.

A comprehensive review on advancements in tissue engineering and microfluidics toward kidney-on-chip

This review provides a detailed literature survey on microfluidics and its road map toward kidney-on-chip technology. The whole review has been tailored with a clear description of crucial milestones in regenerative medicine, such as bioengineering, tissue engineering, microfluidics, microfluidic applications in biomedical engineering, capabilities of microfluidics in biomimetics, organ-on-chip, kidney-on-chip for disease modeling, drug toxicity, and implantable devices. This paper also presents future scope for research in the bio-microfluidics domain and biomimetics domain.

"One-to-three" droplet generation in digital microfluidics for parallel chemiluminescence immunoassays

In digital microfluidics, droplet generation is a fundamental operation for quantitative liquid manipulation. The generation of well-defined micro-droplets on a chip with restricted device geometries has become a real obstacle for digital microfluidics platforms to be used in parallel for in vitro diagnostic applications. Here, we propose a "one-to-three" droplet splitting technique that is able to generate sub-microlitre droplets beyond the "well-known" geometry limit in electrowetting-on-dielectric digital microfluidics. Accordingly, we realized an on-chip magnetic bead chemiluminescence immunoassay for parallel detection with the "one-to-three" technique. With the help of the generated micro droplets, we were able to retain the magnetic beads by a significantly reduced magnetic force. We have shown the detection of five B-type natriuretic peptide analyte samples on a single chip for around 10 minutes. The correlation coefficient of the calibration curve was 0.9942, and the detection limit was lower than 5 pg mL^-1.

Drop-to-drop liquid-liquid extraction of DNA in an electrowetting-on-dielectric digital microfluidics

Recent advancements in microfluidics and lab-on-a-chip technologies enabled miniaturization and automation of many downstream nucleic acid analysis steps such as PCR. However, DNA extraction/isolation protocol remains a stand-alone sample preparation step. For a quick sample-to-result solution, downstream protocols and sample preparation protocols need to be seamlessly integrated into a single lab-on-a-chip platform. As a step toward such integration, this paper introduces microfluidic DNA isolation using the liquid-liquid extraction (LLE) method in the drop-to-drop (DTD) format. The electrowetting-on-dielectric digital microfluidic platform is capable of handling a two-phase liquid system easily, which enables DTD LLE. In this study, the extraction of plasmid DNA (pDNA) from an aqueous sample to an ionic liquid is demonstrated. Prior to pDNA extraction study, the DTD LLE protocol was developed and optimized using organic dyes as solutes. The selective extraction of pDNA in the presence of proteins as interfering molecules is also demonstrated. This work implies that DTD LLE can substitute for magnetic beads steps in standard DNA isolation protocols.

An efficient module-less synthesis approach for Digital Microfluidic Biochip

Digital Microfluidic Biochips (DMFBs) will require error-free synthesis techniques which can function at much higher speed while implementing on real-time systems and capable of tackling more complex assay operations. Until now various bio-assays are successfully implemented based on different mixing modules present on such lab-on-chips. In present work, the concept of such dedicated virtual modules has been eliminated and a novel module-less-synthesis (MLS) method is proposed for accomplishing high-performance bio-protocols. Various shift-patterns (movements) of the micro-droplets are identified to accomplish entire mixing in lesser time compared to earlier module-based synthesis methods. We have also computed the percentage of mixing accomplishment for each directional-shift of the mixer-droplet. However, path congestion problem and operational errors are inevitable in MLS approach. Hence, the path congestion and washing problem in MLS is addressed by tweaking the earlier MLS approach and a new modified-MLS (MMLS) method is proposed. Finally, washing optimization technique on MMLS method is also given. Different real-life bio assays like PCR, IVD are tested with the proposed technique as well as synthetic benchmarks (hard test benches) are also incorporated in the experiments. For both kind of benchmarks synthesis performance improved with bioassay completion time ( T max ) significantly reduced compared to existing synthesis approaches on DMFB platform.

Microbioreactors for Process Development and Cell-Based Screening Studies

Microbioreactors (MBRs) have emerged as potent cultivation devices enabling automated small-scale experiments in parallel while enhancing their cost efficiency. The widespread use of MBRs has contributed to recent advances in industrial and pharmaceutical biotechnology, and they have proved to be indispensable tools in the development of many modern bioprocesses. Being predominantly applied in early stage process development, they open up new fields of research and enhance the efficacy of biotechnological product development. Their reduced reaction volume is associated with numerous inherent advantages - particularly the possibility for enabling parallel screening operations that facilitate high-throughput cultivations with reduced sample consumption (or the use of rare and expensive educts). As a result, multiple variables can be examined in a shorter time and with a lower expense. This leads to a simultaneous acceleration of research and process development along with decreased costs.MBRs range from simple miniaturized cultivations vessels (i.e., in the milliliter scale with limited possibilities for process control) to highly complex and automated small-scale microreactors with integrated sensors that allow for comprehensive screenings in very short time or a precise reflection of large-scale cultivation conditions. Progressive developments and improvements in manufacturing and automation techniques are already helping researchers to make use of the advantages that MBRs offer. This overview of current MBR systems surveys the diverse application for microbial and mammalian cell cultivations that have been developed in recent years.

Micro-Electrode-Dot-Array Digital Microfluidic Biochips: Technology, Design Automation, and Test Techniques

Digital microfluidic biochips (DMFBs) are being increasingly used for DNA sequencing, point-of-care clinical diagnostics, and immunoassays. DMFBs based on a micro-electrode-dot-array (MEDA) architecture have recently been proposed, and fundamental droplet manipulations, e.g., droplet mixing and splitting, have also been experimentally demonstrated on MEDA biochips. There can be thousands of microelectrodes on a single MEDA biochip, and the fine-grained control of nanoliter volumes of biochemical samples and reagents is also enabled by this technology. MEDA biochips offer the benefits of real-time sensitivity, lower cost, easy system integration with CMOS modules, and full automation. This review paper first describes recent design tools for high-level synthesis and optimization of map bioassay protocols on a MEDA biochip. It then presents recent advances in scheduling of fluidic operations, placement of fluidic modules, droplet-size-aware routing, adaptive error recovery, sample preparation, and various testing techniques. With the help of these tools, biochip users can concentrate on the development of nanoscale bioassays, leaving details of chip optimization and implementation to software tools.

Digital Microfluidics for Nucleic Acid Amplification

Digital Microfluidics (DMF) has emerged as a disruptive methodology for the control and manipulation of low volume droplets. In DMF, each droplet acts as a single reactor, which allows for extensive multiparallelization of biological and chemical reactions at a much smaller scale. DMF devices open entirely new and promising pathways for multiplex analysis and reaction occurring in a miniaturized format, thus allowing for healthcare decentralization from major laboratories to point-of-care with accurate, robust and inexpensive molecular diagnostics. Here, we shall focus on DMF platforms specifically designed for nucleic acid amplification, which is key for molecular diagnostics of several diseases and conditions, from pathogen identification to cancer mutations detection. Particular attention will be given to the device architecture, materials and nucleic acid amplification applications in validated settings.

A review of digital microfluidics as portable platforms for lab-on a-chip applications

Following the development of microfluidic systems, there has been a high tendency towards developing lab-on-a-chip devices for biochemical applications. A great deal of effort has been devoted to improve and advance these devices with the goal of performing complete sets of biochemical assays on the device and possibly developing portable platforms for point of care applications. Among the different microfluidic systems used for such a purpose, digital microfluidics (DMF) shows high flexibility and capability of performing multiplex and parallel biochemical operations, and hence, has been considered as a suitable candidate for lab-on-a-chip applications. In this review, we discuss the most recent advances in the DMF platforms, and evaluate the feasibility of developing multifunctional packages for performing complete sets of processes of biochemical assays, particularly for point-of-care applications. The progress in the development of DMF systems is reviewed from eight different aspects, including device fabrication, basic fluidic operations, automation, manipulation of biological samples, advanced operations, detection, biological applications, and finally, packaging and portability of the DMF devices. Success in developing the lab-on-a-chip DMF devices will be concluded based on the advances achieved in each of these aspects.

Electrochemiluminescence on digital microfluidics for microRNA analysis

Electrochemiluminescence (ECL) is a sensitive analytical technique with great promise for biological applications, especially when combined with microfluidics. Here, we report the first integration of ECL with digital microfluidics (DMF). ECL detectors were fabricated into the ITO-coated top plates of DMF devices, allowing for the generation of light from electrically excited luminophores in sample droplets. The new system was characterized by making electrochemical and ECL measurements of soluble mixtures of tris(phenanthroline)ruthenium(II) and tripropylamine (TPA) solutions. The system was then validated by application to an oligonucleotide hybridization assay, using magnetic particles bearing 21-mer, deoxyribose analogues of the complement to microRNA-143 (miRNA-143). The system detects single nucleotide mismatches with high specificity, and has a limit of detection of 1.5 femtomoles. The system is capable of detecting miRNA-143 in cancer cell lysates, allowing for the discrimination between the MCF-7 (less aggressive) and MDA-MB-231 (more aggressive) cell lines. We propose that DMF-ECL represents a valuable new tool in the microfluidics toolbox for a wide variety of applications.

Synthesis and cell-free cloning of DNA libraries using programmable microfluidics

Microfluidics may revolutionize our ability to write synthetic DNA by addressing several fundamental limitations associated with generating novel genetic constructs. Here we report the first de novo synthesis and cell-free cloning of custom DNA libraries in sub-microliter reaction droplets using programmable digital microfluidics. Specifically, we developed Programmable Order Polymerization (POP), Microfluidic Combinatorial Assembly of DNA (M-CAD) and Microfluidic In-vitro Cloning (MIC) and applied them to de novo synthesis, combinatorial assembly and cell-free cloning of genes, respectively. Proof-of-concept for these methods was demonstrated by programming an autonomous microfluidic system to construct and clone libraries of yeast ribosome binding sites and bacterial Azurine, which were then retrieved in individual droplets and validated. The ability to rapidly and robustly generate designer DNA molecules in an autonomous manner should have wide application in biological research and development.

Droplet microfluidics for chip-based diagnostics

Droplet microfluidics (DMF) is a fluidic handling technology that enables precision control over dispensing and subsequent manipulation of droplets in the volume range of microliters to picoliters, on a micro-fabricated device. There are several different droplet actuation methods, all of which can generate external stimuli, to either actively or passively control the shape and positioning of fluidic droplets over patterned substrates. In this review article, we focus on the operation and utility of electro-actuation-based DMF devices, which utilize one or more micro-/nano-patterned substrates to facilitate electric field-based handling of chemical and/or biological samples. The underlying theory of DMF actuations, device fabrication methods and integration of optical and opto-electronic detectors is discussed in this review. Example applications of such electro-actuation-based DMF devices have also been included, illustrating the various actuation methods and their utility in conducting chip-based laboratory and clinical diagnostic assays.

Magnetic droplet manipulation platforms for nucleic acid detection at the point of care

This review summarizes recent developments in the use of magnetically actuated droplets in point-of-care molecular diagnostic platforms. We discuss the fundamentals of magnetic droplet manipulation and the various modes of actuation. The balance of forces acting on a droplet during transport and particle extraction, as well as the devices and instrumentation developed to perform these operations will be presented and discussed. Furthermore, we review some of the recent advances on the diagnostic applications of platforms utilizing magnetic manipulation for genetic assessment of biological samples.

Topography-assisted electromagnetic platform for blood-to-PCR in a droplet

This paper presents an electromagnetically actuated platform for automated sample preparation and detection of nucleic acids. The proposed platform integrates nucleic acid extraction using silica-coated magnetic particles with real-time polymerase chain reaction (PCR) on a single cartridge. Extraction of genomic material was automated by manipulating magnetic particles in droplets using a series of planar coil electromagnets assisted by topographical features, enabling efficient fluidic processing over a variety of buffers and reagents. The functionality of the platform was demonstrated by performing nucleic acid extraction from whole blood, followed by real-time PCR detection of KRAS oncogene. Automated sample processing from whole blood to PCR-ready droplet was performed in 15 min. We took a modular approach of decoupling the modules of magnetic manipulation and optical detection from the device itself, enabling a low-complexity cartridge that operates in tandem with simple external instruments.

Low voltage picoliter droplet manipulation utilizing electrowetting-on-dielectric platforms

Picoliter droplets actuated on an electrowetting-on-dielectric (EWD) actuator are demonstrated. In this study, the physical scaling of electrodes for 33 μm and 21 μm EWD devices resulted in droplets of 12 pl and 5 pl being dispensed respectively in conjunction with 3 μm SU8 gaskets. The stacked multi-layer insulators in the actuators consisted of 200 nm tantalum pentoxide (Ta₂O₅) and 200 nm parylene C films deposited and coated with 70 nm of CYTOP. The voltages for dispensing droplets on chips without any external pressure sources are 17.1 V_rms and 22 V_rms for these two sets of devices. A 12 pl droplet can be split into two 6 pl daughter droplets at 18.7 V_rms with 33 μm electrode devices. Droplet manipulation is also demonstrated with paramagnetic beads and buffer solutions with proteins. In addition, electrodes with interlocking protrusions and special featured reservoir gasket are designed to facilitate droplet dispensing on these scaled EWD devices. In order to improve sealing of the two-piece sandwich EWD structure, a soft material, Norland Optical Adhesive (NOA), was coated on the top plate along with pressure on top. We demonstrate that based on fundamental theories and experiments, the dimensional scaling of EWD devices has not yet met a limitation as long as the EWD device can be sealed well.

Digital microfluidics

Digital microfluidics (DMF) is an emerging liquid-handling technology that enables individual control over droplets on an open array of electrodes. These picoliter- to microliter-sized droplets, each serving as an isolated vessel for chemical processes, can be made to move, merge, split, and dispense from reservoirs. Because of its unique advantages, including simple instrumentation, flexible device geometry, and easy coupling with other technologies, DMF is being applied to a wide range of fields. In this review, we summarize the state of the art of DMF technology from the perspective of analytical chemistry in sections describing the theory of droplet actuation, device fabrication and integration, and applications.

Droplet-based pyrosequencing using digital microfluidics

The feasibility of implementing pyrosequencing chemistry within droplets using electrowetting-based digital microfluidics is reported. An array of electrodes patterned on a printed-circuit board was used to control the formation, transportation, merging, mixing, and splitting of submicroliter-sized droplets contained within an oil-filled chamber. A three-enzyme pyrosequencing protocol was implemented in which individual droplets contained enzymes, deoxyribonucleotide triphosphates (dNTPs), and DNA templates. The DNA templates were anchored to magnetic beads which enabled them to be thoroughly washed between nucleotide additions. Reagents and protocols were optimized to maximize signal over background, linearity of response, cycle efficiency, and wash efficiency. As an initial demonstration of feasibility, a portion of a 229 bp Candida parapsilosis template was sequenced using both a de novo protocol and a resequencing protocol. The resequencing protocol generated over 60 bp of sequence with 100% sequence accuracy based on raw pyrogram levels. Excellent linearity was observed for all of the homopolymers (two, three, or four nucleotides) contained in the C. parapsilosis sequence. With improvements in microfluidic design it is expected that longer reads, higher throughput, and improved process integration (i.e., "sample-to-sequence" capability) could eventually be achieved using this low-cost platform.

Applications of electrowetting-based digital microfluidics in clinical diagnostics

Digital microfluidics based on electrowetting is a type of microfluidic platform in which liquids are processed as individual unit-sized droplets that are dispensed from a source, merged together, split apart or transported between locations on demand. These devices are implemented using arrays of surface electrodes to control the shape and position of droplets through the electrowetting effect. A major thrust of digital microfluidics research has been the development of integrated lab-on-a-chip devices to perform clinical in vitro diagnostic assays. A variety of preparatory and analytical processes have been implemented and feasibility has been demonstrated for test types ranging from clinical chemistries to immunoassays, nucleic acid tests and cell-based assays. In this article, the current state and future potential of digital microfluidics for clinical diagnostic testing is reviewed and evaluated.