Terminator-free template-independent enzymatic DNA synthesis for digital information storage
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.
- Publication Date:
- Research Org.:
- Harvard Medical School, Boston, MA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- Contributing Org.:
- AWS Cloud Credits for Research program
- OSTI Identifier:
- 1619517
- Alternate Identifier(s):
- OSTI ID: 1528896
- Grant/Contract Number:
- FG02-02ER63445
- Resource Type:
- Published Article
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Name: Nature Communications Journal Volume: 10 Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Synthetic biology; DNA synthesis; DNA information storage; Terminal deoxynucleotidyl transferase
Citation Formats
Lee, Henry H., Kalhor, Reza, Goela, Naveen, Bolot, Jean, and Church, George M. Terminator-free template-independent enzymatic DNA synthesis for digital information storage. United Kingdom: N. p., 2019.
Web. doi:10.1038/s41467-019-10258-1.
Lee, Henry H., Kalhor, Reza, Goela, Naveen, Bolot, Jean, & Church, George M. Terminator-free template-independent enzymatic DNA synthesis for digital information storage. United Kingdom. https://doi.org/10.1038/s41467-019-10258-1
Lee, Henry H., Kalhor, Reza, Goela, Naveen, Bolot, Jean, and Church, George M. Mon .
"Terminator-free template-independent enzymatic DNA synthesis for digital information storage". United Kingdom. https://doi.org/10.1038/s41467-019-10258-1.
@article{osti_1619517,
title = {Terminator-free template-independent enzymatic DNA synthesis for digital information storage},
author = {Lee, Henry H. and Kalhor, Reza and Goela, Naveen and Bolot, Jean and Church, George M.},
abstractNote = {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.},
doi = {10.1038/s41467-019-10258-1},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United Kingdom},
year = {Mon Jun 03 00:00:00 EDT 2019},
month = {Mon Jun 03 00:00:00 EDT 2019}
}
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https://doi.org/10.1038/s41467-019-10258-1
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Cited by: 78 works
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