Automated routing of droplets for DNA storage on a digital microfluidics platform

Manicka, Ajay; Stephan, Andrew; Chari, Sriram; Mendonsa, Gemma; Okubo, Peyton; Stolzberg-Schray, John; Reddy, Anil; Riedel, Marc

doi:10.1039/d3dd00083d

Cited by 2 publications

References 57 publications

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Directed assembly of single-stranded DNA fragments for data storage via enzyme-free catalytic splint ligation

Mendonsa,

Chari,

Bao

et al. 2024

Preprint

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Oligonucleotides or gene fragments can be ligated in a specified order to create longer DNA assemblies. We present a method where DNA symbols, or oligos designed to encode information for data storage, are joined to linker sequences at either end. These linkers dictate the assembly order of the symbols; the order of the symbols can be changed by changing the sequences of the linkers attached to them. Utilizing a ligating DNAzyme as a catalytic splint, we achieve room-temperature, enzyme-free assembly, offering a cost-effective alternative to traditional enzyme-based ligation methods. We demonstrate this technique by assembling three different five-symbol constructs, with the order of the symbols determined by their linking ends. This linker directed assembly technique allows data-encoding symbols to be assembled in any desired order. Furthermore, the DNAzyme-based assembly method is versatile and can be applied to various DNA assembly applications, particularly where cost-effectiveness and efficient room-temperature ligation are required.

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Directed assembly of single-stranded DNA fragments for data storage via enzyme-free catalytic splint ligation

Mendonsa,

Chari,

Bao

et al. 2024

Preprint

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Neural network execution using nicked DNA and microfluidics

Solanki,

Griffin,

Sutradhar

et al. 2023

PLoS ONE

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DNA has been discussed as a potential medium for data storage. Potentially it could be denser, could consume less energy, and could be more durable than conventional storage media such as hard drives, solid-state storage, and optical media. However, performing computations on the data stored in DNA is a largely unexplored challenge. This paper proposes an integrated circuit (IC) based on microfluidics that can perform complex operations such as artificial neural network (ANN) computation on data stored in DNA. We envision such a system to be suitable for highly dense, throughput-demanding bio-compatible applications such as an intelligent Organ-on-Chip or other biomedical applications that may not be latency-critical. It computes entirely in the molecular domain without converting data to electrical form, making it a form of in-memory computing on DNA. The computation is achieved by topologically modifying DNA strands through the use of enzymes called nickases. A novel scheme is proposed for representing data stochastically through the concentration of the DNA molecules that are nicked at specific sites. The paper provides details of the biochemical design, as well as the design, layout, and operation of the microfluidics device. Benchmarks are reported on the performance of neural network computation.

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Automated routing of droplets for DNA storage on a digital microfluidics platform

Abstract: Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data...

Cited by 2 publications

References 57 publications

Directed assembly of single-stranded DNA fragments for data storage via enzyme-free catalytic splint ligation

Directed assembly of single-stranded DNA fragments for data storage via enzyme-free catalytic splint ligation

Neural network execution using nicked DNA and microfluidics

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