Free-running enzymatic oligonucleotide synthesis for data storage applications.
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Abstract Here we present preliminary results for a method of oligodeoxynucleotide synthesis using terminal deoxynucleotidyl transferase (TdT) to generate mixed base homopolymer runs of defined sequence. In a process we have termed Free-Running Synthesis (FRS), we allow TdT to freely add multiple bases of a given monomer. With this method, homopolymeric runs can be used for writing DNA in a data storage capacity, where a stretch of A’s, for example, will be read as a single base, and the transitions between successive homopolymer runs encodes information. As a proof-of-concept, we demonstrate homopolymer additions of A, C and T onto the 3’ end of a 22 base initiator strand.
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TdT-based enzymatic DNA synthesis has already been applied to data storage applications.
“Indeed, two groups of Jensen et al. (2018) and Lee et al. (2018) have already applied TdT-based enzymatic DNA synthesis method to data storage applications.”
From Large-Scale de Novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities (2021) · cites this paper as Jensen et al., 2018
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Cites
De novo DNA synthesis using polymerase-nucleotide conjugates.
Palluk, S., Arlow, D. H., de Rond, T., Barthel, S., Kang, J. S., Bector, R., Baghdassarian, H. M., Truong, A. N., Kim, P. W., Singh, A. K., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4173 · Cited by 316 · see citing works
DMSO and Betaine Greatly Improve Amplification of GC-Rich Constructs in De Novo Synthesis
Jensen, M. A., Fukushima, M., & Davis, R. W. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011024 · Cited by 156 · see citing works
Self-citationBiochemical, Structural, and Physiological Characterization of Terminal Deoxynucleotidyl Transferase
Fowler, J. D., & Suo, Z. (2006) · Chemical Reviews · doi:10.1021/cr040445w · Cited by 119 · see citing works
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High‐Molecular‐Weight Polynucleotides by Transferase‐Catalyzed Living Chain‐Growth Polycondensation
Tang, L., Navarro, L. A., Chilkoti, A., & Zauscher, S. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201700991 · Cited by 48 · see citing works
Surface-Initiated Enzymatic Polymerization of DNA
Chow, D. C., & Chilkoti, A. (2007) · Langmuir · doi:10.1021/la701630g · Cited by 37 · see citing works
Enzymatic synthesis of structure-free DNA with pseudo-complementary properties
Lahoud, G., Timoshchuk, V. A., Lebedev, A. V., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn209 · Cited by 24 · see citing works
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Enzymatic DNA synthesis for digital information storage.
Lee, H. H., Kalhor, R., Goela, N., Bolot, J., & Church, G. M. (2018) · doi:10.1101/348987 · Cited by 265 · see citing works
Song, L.-F., Deng, Z.-H., Gong, Z.-Y., Li, L.-L., & Li, B.-Z. (2021) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2021.689797 · Cited by 74 · see citing works
- Authors
- Jensen, M. A., Griffin, P. B., & Davis, R. W.
- Affiliations
- Stanford University (US)
- Venue
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Published
- 2018-06-30
- OpenAlex
- W2810310556
- Cited by
- 5
- References
- 8
- Citations by year
- 2025: 1 · 2023: 1 · 2021: 1 · 2020: 1 · 2019: 1
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Locations
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (P01HG000205)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Keywords
- oligonucleotide synthesis, terminal deoxynucleotidyl transferase, DNA data storage, enzymatic DNA synthesis, nucleotide addition
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