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

Henry H. Lee (), Reza Kalhor, Naveen Goela, Jean Bolot and George M. Church ()
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Henry H. Lee: Harvard Medical School
Reza Kalhor: Harvard Medical School
Naveen Goela: Technicolor Research & Innovation Lab
Jean Bolot: Technicolor Research & Innovation Lab
George M. Church: Harvard Medical School

Nature Communications, 2019, vol. 10, issue 1, 1-12

Abstract: Abstract 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.

Date: 2019
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DOI: 10.1038/s41467-019-10258-1

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