DNA assembly with error correction on a droplet digital microfluidics platform

DNA storage: The future direction for medical cold data storage

DNA storage, characterized by its durability, data density, and cost-effectiveness, is a promising solution for managing the increasing data volumes in healthcare. This review explores state-of-the-art DNA storage technologies, and provides insights into designing a DNA storage system tailored for medical cold data. We anticipate that a practical approach for medical cold data storage will involve establishing regional, in vitro DNA storage centers that can serve multiple hospitals. The immediacy of DNA storage for medical data hinges on the development of novel, high-density, specialized coding methods. Established commercial techniques, such as DNA chemical synthesis and next-generation sequencing (NGS), along with mixed drying with alkaline salts and refined Polymerase Chain Reaction (PCR), potentially represent the optimal options for data writing, reading, storage, and accessing, respectively. Data security could be promised by the integration of traditional digital encryption and DNA steganography. Although breakthrough developments like artificial nucleotides and DNA nanostructures show potential, they remain in the laboratory research phase. In conclusion, DNA storage is a viable preservation strategy for medical cold data in the near future.

in situ Transformation of Information Into DNA Storage With Microfluidic Very Large-Scale Integration Platform

DNA data storage offers a highly compact and efficient alternative to traditional data storage methods. However, DNA writing remains time-consuming and relies on specialized infrastructure. Here, a novel, high-throughput, in situ DNA writing strategy is introduced using microfluidic very-large-scale integration (VLSI) chips inspired by dynamic random-access memory (DRAM) architecture. This method enables rapid encoding of binary data into DNA via overlap-extension PCR (OE-PCR) and programmable microfluidic partitioning. Using a widely accessible integrated microfluidic circuit, 2304 bits of data within 4 h encoded, demonstrating scalable, parallelized DNA writing on a benchtop instrument. Next-generation sequencing confirmed high-fidelity encoding with excellent signal-to-noise ratios. Furthermore, DNA data can be quickly decoded using a microfluidic VLSI qPCR platform, reducing the write-to-read latency to under 8 h. This proof-of-concept highlights the potential of programmable microfluidic VLSI platforms for efficient, rapid, and portable DNA writing and decoding, paving the way for scalable, high-throughput, decentralized DNA data storage and gene synthesis.

Low-cost and automated magnetic bead-based DNA data writing via digital microfluidics

The rapid growth in data generation presents a significant challenge for conventional storage technologies. DNA storage has emerged as a promising solution, offering substantially greater storage density and durability. However, the current DNA data writing process is costly and labor-intensive, hindering the commercialization of DNA data storage. In this study, we present a digital microfluidics (DMF) platform integrated with E47 DNAzyme ligation chemistry to develop a programmable, cost-effective, and automated DNA data writing process. Our method utilizes pre-synthesized single-stranded DNA as building blocks, which can be assembled into diverse DNA sequences that encode desired data. By employing DNAzymes as biocatalysts, we enable an enzyme-free ligation process at room temperature, significantly reducing costs compared to traditional enzyme-based methods. Our proof-of-concept demonstrates an automated DNA writing process with the reduced reagent input, providing an alternative solution to the high costs associated with current DNA data storage methods. The high specificity of ligation using DNAzymes obviates the need for storing each unique DNA block in its own reservoir, which greatly reduces the total number of reservoirs required to store the starting material. This simplifies the overall layout, and the associated plumbing of the DMF platform. To adapt the conventional column-purification required ligation on the DMF platform, we introduce a DNAzyme-cleavage-assisted bead purification assay. This method employs 17E DNAzymes to cleave and release biotinylated DNA from streptavidin beads, followed by a one-pot ligation with E47 DNAzymes to assemble the desired DNA strands. Our study represents a significant advancement in DNA data storage technology, offering a cost-effective and automated solution that enhances scalability and practicality for commercial DNA data storage applications.

DNA-DISK: Automated end-to-end data storage via enzymatic single-nucleotide DNA synthesis and sequencing on digital microfluidics

In the age of information explosion, the exponential growth of digital data far exceeds the capacity of current mainstream storage media. DNA is emerging as a promising alternative due to its higher storage density, longer retention time, and lower power consumption. To date, commercially mature DNA synthesis and sequencing technologies allow for writing and reading of information on DNA with customization and convenience at the research level. However, under the disconnected and nonspecialized mode, DNA data storage encounters practical challenges, including susceptibility to errors, long storage latency, resource-intensive requirements, and elevated information security risks. Herein, we introduce a platform named DNA-DISK that seamlessly streamlined DNA synthesis, storage, and sequencing on digital microfluidics coupled with a tabletop device for automated end-to-end information storage. The single-nucleotide enzymatic DNA synthesis with biocapping strategy is utilized, offering an ecofriendly and cost-effective approach for data writing. A DNA encapsulation using thermo-responsive agarose is developed for on-chip solidification, not only eliminating data clutter but also preventing DNA degradation. Pyrosequencing is employed for in situ and accurate data reading. As a proof of concept, DNA-DISK successfully stored and retrieved a musical sheet file (228 bits) with lower write-to-read latency (4.4 min of latency per bit) as well as superior automation compared to other platforms, demonstrating its potential to evolve into a DNA Hard Disk Drive in the future.

Hardware, Software, and Wetware Codesign Environment for Synthetic Biology

Synthetic biology is the process of forward engineering living systems. These systems can be used to produce biobased materials, agriculture, medicine, and energy. One approach to designing these systems is to employ techniques from the design of embedded electronics. These techniques include abstraction, standards, modularity, automated design, and formal semantic models of computation. Together, these elements form the foundation of "biodesign automation," where software, robotics, and microfluidic devices combine to create exciting biological systems of the future. This paper describes a "hardware, software, wetware" codesign vision where software tools can be made to act as "genetic compilers" that transform high-level specifications into engineered "genetic circuits" (wetware). This is followed by a process where automation equipment, well-defined experimental workflows, and microfluidic devices are explicitly designed to house, execute, and test these circuits (hardware). These systems can be used as either massively parallel experimental platforms or distributed bioremediation and biosensing devices. Next, scheduling and control algorithms (software) manage these systems' actual execution and data analysis tasks. A distinguishing feature of this approach is how all three of these aspects (hardware, software, and wetware) may be derived from the same basic specification in parallel and generated to fulfill specific cost, performance, and structural requirements.

Expanding the limits towards 'one-pot' DNA assembly and transformation on a rapid-prototype microfluidic device

DNA assembly and transformation are crucial to the building process in synthetic biology. These steps are significant roadblocks when engineering increasingly complex biological systems. To address this, recent development of widespread 'biofoundry' facilities has employed automation equipment to expedite the synthetic biology workflow. Despite significant progress, there is a clear demand for lower-cost and smaller-footprint automation equipment. The field of microfluidics have emerged to provide automation capabilities to meet this demand. However, we still lack devices capable of building large multi-gene systems in a consolidated process. In response to this challenge, we have developed a digital microfluidic platform that performs "one-pot" Golden Gate DNA assembly of large plasmids and transformation of E coli. The system features a novel electrode geometry and modular design, which make these devices simple to fabricate and use, thus improving the accessibility of microfluidics. This device incorporates an impedance-based adaptive closed loop water replenishment system to compensate for droplet evaporation and maintain constant assembly reaction concentrations, which we found to be crucial to the DNA assembly efficiency. We also showcase a closed-loop temperature control system that generates precise thermodynamic profiles to optimize heat shock transformation. Moreover, we validated the system by assembling and transforming large and complex plasmids conferring a biosynthetic pathway, resulting in performance comparable to those of standard techniques. We propose that the methods described here will contribute to a new generation of accessible automation platforms aimed at speeding up the 'building' process, lowering reagent consumption and removing manual work from synthetic biology.

Role of Digital Microfluidics in Enabling Access to Laboratory Automation and Making Biology Programmable

Digital microfluidics (DMF) is a liquid handling technique that has been demonstrated to automate biological experimentation in a low-cost, rapid, and programmable manner. This review discusses the role of DMF as a "digital bioconverter"-a tool to connect the digital aspects of the design-build-learn cycle with the physical execution of experiments. Several applications are reviewed to demonstrate the utility of DMF as a digital bioconverter, namely, genetic engineering, sample preparation for sequencing and mass spectrometry, and enzyme-, immuno-, and cell-based screening assays. These applications show that DMF has great potential in the role of a centralized execution platform in a fully integrated pipeline for the production of novel organisms and biomolecules. In this paper, we discuss how the function of a DMF device within such a pipeline is highly dependent on integration with different sensing techniques and methodologies from machine learning and big data. In addition to that, we examine how the capacity of DMF can in some cases be limited by known technical and operational challenges and how consolidated efforts in overcoming these challenges will be key to the development of DMF as a major enabling technology in the computer-aided biology framework.

Efficient and Low-Cost Error Removal in DNA Synthesis by a High-Durability MutS

Enzyme-based error correction is a key step in de novo DNA synthesis, yet the inherent instability of error-correction enzymes such as MutS has hindered the throughput and efficiency of DNA synthesis workflows. Here we introduce a process called Improved MICC (iMICC), in which all error-correction steps of oligos and fragments within a complete gene-synthesis cycle are completed in a simple, efficient, and low-cost manner via a MutS protein engineered for high durability. By establishing a disulfide bond of L157C-G233C, full-activity shelf life of E. coli MutS (eMutS) was prolonged from 7 to 49 days and was further extended to 63 days via cellulose-bound 4 °C storage. In synthesis of 10 Cas9 homologues in-solution and 10 xylose reductase (XR) homologues on-chip, iMICC reduced error frequency to 0.64/Kb and 0.41/Kb, respectively, with 72.1% and 86.4% of assembled fragments being error-free. By elevating base accuracy by 37.6-fold while avoiding repetitive preparation of fresh enzymes, iMICC is more efficient and robust than the wild-type eMutS, and it is 6.6-fold more accurate and 26.7-fold cheaper than CorrectASE. These advantages promise its broad applications in industrial DNA synthesis.