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

Author

Listed:
  • Henry H. Lee

    (Harvard Medical School
    Wyss Institute for Biologically Inspired Engineering at Harvard University)

  • Reza Kalhor

    (Harvard Medical School
    Wyss Institute for Biologically Inspired Engineering at Harvard University)

  • Naveen Goela

    (Technicolor Research & Innovation Lab)

  • Jean Bolot

    (Technicolor Research & Innovation Lab)

  • George M. Church

    (Harvard Medical School
    Wyss Institute for Biologically Inspired Engineering at Harvard University)

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.

Suggested Citation

  • Henry H. Lee & Reza Kalhor & Naveen Goela & Jean Bolot & George M. Church, 2019. "Terminator-free template-independent enzymatic DNA synthesis for digital information storage," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10258-1
    DOI: 10.1038/s41467-019-10258-1
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    Cited by:

    1. Nicholas C. Tang & Jonathan C. Su & Yulia Shmidov & Garrett Kelly & Sonal Deshpande & Parul Sirohi & Nikhil Peterson & Ashutosh Chilkoti, 2024. "Synthetic intrinsically disordered protein fusion tags that enhance protein solubility," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Lifu Song & Feng Geng & Zi-Yi Gong & Xin Chen & Jijun Tang & Chunye Gong & Libang Zhou & Rui Xia & Ming-Zhe Han & Jing-Yi Xu & Bing-Zhi Li & Ying-Jin Yuan, 2022. "Robust data storage in DNA by de Bruijn graph-based de novo strand assembly," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    3. Punnag Padhy & Mohammad Asif Zaman & Michael Anthony Jensen & Yao-Te Cheng & Yogi Huang & Mo Wu & Ludwig Galambos & Ronald Wayne Davis & Lambertus Hesselink, 2024. "Dielectrophoretic bead-droplet reactor for solid-phase synthesis," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    4. Hinako Kawabe & Christopher A. Thomas & Shuichi Hoshika & Myong-Jung Kim & Myong-Sang Kim & Logan Miessner & Nicholas Kaplan & Jonathan M. Craig & Jens H. Gundlach & Andrew H. Laszlo & Steven A. Benne, 2023. "Enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    5. Xuyang Zhao & Junyao Li & Qingyuan Fan & Jing Dai & Yanping Long & Ronghui Liu & Jixian Zhai & Qing Pan & Yi Li, 2024. "Composite Hedges Nanopores codec system for rapid and portable DNA data readout with high INDEL-Correction," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    6. Cheng Kai Lim & Jing Wui Yeoh & Aurelius Andrew Kunartama & Wen Shan Yew & Chueh Loo Poh, 2023. "A biological camera that captures and stores images directly into DNA," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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