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

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.

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [2];  [2]; ORCiD logo [1]
  1. Harvard Medical School, Boston, MA (United States); Harvard Univ., Boston, MA (United States)
  2. Technicolor Research & Innovation Lab, Palo Alto, CA (United States)
Publication Date:
Research Org.:
Harvard Medical School, Boston, MA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Biological Systems Science Division
Contributing Org.:
AWS Cloud Credits for Research program
OSTI Identifier:
1528896
Grant/Contract Number:  
FG02-02ER63445
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Related Information: https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-019-10258-1/MediaObjects/41467_2019_10258_MOESM1_ESM.pdf; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
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 States: 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 States. doi: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 States. doi:10.1038/s41467-019-10258-1. https://www.osti.gov/servlets/purl/1528896.
@article{osti_1528896,
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 = {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 States},
year = {2019},
month = {6}
}

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