Terminator-free template-independent enzymatic DNA synthesis for digital information storage

Lee, Henry H.; Kalhor, Reza; Goela, Naveen; Bolot, Jean; Church, George M.

doi:10.1038/s41467-019-10258-1

Title: Terminator-free template-independent enzymatic DNA synthesis for digital information storage

Journal Article · 03 June 2019 · Nature Communications

DOI: https://doi.org/10.1038/s41467-019-10258-1 · OSTI ID:1619517

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^[2]; Bolot, Jean ^[2];

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Harvard Medical School, Boston, MA (United States); Harvard Univ., Boston, MA (United States)
Technicolor Research & Innovation Lab, Palo Alto, CA (United States)

DNA is an emerging medium for digital data and its adoption can be accelerated by synthesis processes specialized for storage applications. Here, we describe a de novo enzymatic synthesis strategy designed for data storage which harnesses the template-independent polymerase terminal deoxynucleotidyl transferase (TdT) in kinetically controlled conditions. Information is stored in transitions between non-identical nucleotides of DNA strands. To produce strands representing user-defined content, nucleotide substrates are added iteratively, yielding short homopolymeric extensions whose lengths are controlled by apyrase-mediated substrate degradation. With this scheme, we synthesize DNA strands carrying 144 bits, including addressing, and demonstrate retrieval with streaming nanopore sequencing. We further devise a digital codec to reduce requirements for synthesis accuracy and sequencing coverage, and experimentally show robust data retrieval from imperfectly synthesized strands. This work provides distributive enzymatic synthesis and information-theoretic approaches to advance digital information storage in DNA.

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Research Organization:: Harvard Medical School, Boston, MA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; USDOE

Contributing Organization:: AWS Cloud Credits for Research program

Grant/Contract Number:: FG02-02ER63445

OSTI ID:: 1619517

Alternate ID(s):: OSTI ID: 1528896

Journal Information:: Nature Communications, Vol. 10, Issue 1; Related Information: https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-019-10258-1/MediaObjects/41467_2019_10258_MOESM1_ESM.pdf; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Synthetic biology
DNA synthesis
DNA information storage
Terminal deoxynucleotidyl transferase

Title: Terminator-free template-independent enzymatic DNA synthesis for digital information storage

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