Poster Y16 - High-Throughput DNA Storage Using Programmable Assembly in Digital Microfluidics

Introduction: DNA has emerged as a promising medium for data storage due to its potential for high-density information storage and long-term stability. In an ideal DNA data storage protocol, information is encoded into DNA sequences, which are then synthesized and stored in a designated medium for long-term preservation. However, directly synthesizing DNA sequences from encoded data can be laborious and costly. In this work, synthetic short DNA fragments are employed as building blocks to efficiently generate large datasets through ligating DNA fragments in a specific manner. To address the challenge of handling numerous short DNA fragments, we developed a programmable DNA assembly platform using digital microfluidics (DMF). This platform leverages precise control and high-throughput capabilities to facilitate the efficient manipulation and assembly of DNA fragments, thus automating the DNA data writing process. To achieve high accuracy in the DNA assembly process, we ligated DNA strands onto magnetic beads, allowing for the removal of unligated DNA and undesired buffers generated during the writing process. This work not only enhances the scalability of DNA data storage, but also paves the way for practical applications of DNA as a robust and reliable medium for digital information storage.

Materials and

Methods: Both DNA blocks and splint oligos are ordered from IDT. The PCB board was designed using SolidWorks and fabricated by JPCPCB. The ITO glass was sourced from Amazon (AmScope). Dielectric and hydrophobic coatings were applied to the PCB board, and the same hydrophobic coating was applied to the ITO glass.

Results, Conclusions, and Discussions: Figure 1(a) illustrates the principle of DNA data writing onto magnetic beads. The purple, blue, and orange DNA represent building blocks, while the red DNA denotes a splint oligo that directs the sequence of DNA block assembly. Following DNA assembly, the extended DNA containing encoded data is attached to magnetic beads. In Figure 1(b), the gel image displays the results of DNA ligation after incubation in a buffer solution. The positive sample consists of two DNA blocks and a splint oligo with a sequence complementary to the DNA blocks, resulting in the formation of a ligation product (L+R). Conversely, the control sample contains DNA blocks and a splint oligo lacking the necessary hybridization sequence, leading to the absence of a ligation product. Figure 1(c) is a photograph of the DMF platform utilized for the automated DNA data writing processes.
This work presents an innovative approach utilizing digital microfluidics and reusable DNA blocks for DNA data writing. By leveraging splint oligos to guide assembly, we have demonstrated the effectiveness of splint oligo in directing the sequence of the DNA data blocks. The incorporation of DMF further enhances the scalability of the writing process, paving the way for future advancements of DNA data storage development.

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