Robust direct digital-to-biological data storage in living cells

• Published in: Nature chemical biology Vol. 17; no. 3; pp. 246 - 253
• Main Authors: Yim, Sung Sun, McBee, Ross M., Song, Alan M., Huang, Yiming, Sheth, Ravi U., Wang, Harris H.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01-03-2021; Nature Publishing Group
• Subjects: 631/326/41; 631/553; 631/92/147; 631/92/552; Arrays; Base Sequence; Binary data; Biochemical Engineering; Biochemistry; Bioorganic Chemistry; Carbon - chemistry; Cell Biology; Cell Engineering - methods; Cells (biology); Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Chromosomes; CRISPR; CRISPR-Cas Systems; Data exchange; Data recording; Data storage; Deoxyribonucleic acid; Digital data; DNA; DNA - classification; DNA - genetics; DNA - metabolism; DNA biosynthesis; Electrical stimuli; Electricity; Electrochemical Techniques; Electrochemistry; Electrons; Escherichia coli - genetics; Escherichia coli - metabolism; Ferrocyanides - chemistry; Gene expression; Humans; Information storage; Information Storage and Retrieval - methods; Oligonucleotide Array Sequence Analysis; Oxidation-Reduction; Redox properties; Sequence Analysis, DNA; Silicon - chemistry; Stimulation
• ISSN: 1552-4450; 1552-4469
• DOI: 10.1038/s41589-020-00711-4

DNA has been the predominant information storage medium for biology and holds great promise as a next-generation high-density data medium in the digital era. Currently, the vast majority of DNA-based data storage approaches rely on in vitro DNA synthesis. As such, there are limited methods to encode digital data into the chromosomes of living cells in a single step. Here, we describe a new electrogenetic framework for direct storage of digital data in living cells. Using an engineered redox-responsive CRISPR adaptation system, we encoded binary data in 3-bit units into CRISPR arrays of bacterial cells by electrical stimulation. We demonstrate multiplex data encoding into barcoded cell populations to yield meaningful information storage and capacity up to 72 bits, which can be maintained over many generations in natural open environments. This work establishes a direct digital-to-biological data storage framework and advances our capacity for information exchange between silicon- and carbon-based entities.
A new DNA data storage technology—data recording in vivo by electrical stimulation (DRIVES)—places CRISPR-based DNA encoding activity under electrochemical control by coupling cellular redox state to CRISPR array gene expression.