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

Abstract

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.