Dynamic and scalable DNA-based information storage

Kevin N Lin,Albert J Keung,James M Tuck,Kevin Volkel

doi:10.1038/s41467-020-16797-2

Kevin N Lin, Albert J Keung + Show 2 more

Open Access

https://doi.org/10.1038/s41467-020-16797-2

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Journal: Nature Communications	Publication Date: Jun 12, 2020
Citations: 54	License type: open-access

Affiliation: North Carolina State University

Abstract

The physical architectures of information storage systems often dictate how information is encoded, databases are organized, and files are accessed. Here we show that a simple architecture comprised of a T7 promoter and a single-stranded overhang domain (ss-dsDNA), can unlock dynamic DNA-based information storage with powerful capabilities and advantages. The overhang provides a physical address for accessing specific DNA strands as well as implementing a range of in-storage file operations. It increases theoretical storage densities and capacities by expanding the encodable sequence space and simplifies the computational burden in designing sets of orthogonal file addresses. Meanwhile, the T7 promoter enables repeatable information access by transcribing information from DNA without destroying it. Furthermore, saturation mutagenesis around the T7 promoter and systematic analyses of environmental conditions reveal design criteria that can be used to optimize information access. This simple but powerful ss-dsDNA architecture lays the foundation for information storage with versatile capabilities.

Highlights

The physical architectures of information storage systems often dictate how information is encoded, databases are organized, and files are accessed
A generic DNA-based information storage system is shown in Fig. 1a, where digital information is encoded into a series of DNA sequences, synthesized as a pool of DNA strands, read by DNA sequencing, and decoded back into an electronically compatible form
We optimized the ratio of single-stranded DNAs (ssDNA) to primer, the number of cycles, along with other environmental parameters (Fig. 2a, Supplementary Fig. 1) to maximize the amount of ssDNA converted to ss-double-stranded DNA (dsDNA)

Summary

Introduction

The physical architectures of information storage systems often dictate how information is encoded, databases are organized, and files are accessed. We used biotin-linked 20 nt DNA oligos to bind each ss-dsDNA (i.e., each file, A, B, and C has a distinct overhang sequence or file address) and separated them out from the mixture using magnetic beads functionalized with streptavidin.

Results

Conclusion