Skip to main content
SpringerLink
Log in

Recent Progress in High-Throughput Enzymatic DNA Synthesis for Data Storage

  • Review Article
  • Published:
BioChip Journal Aims and scope Submit manuscript

Abstract

DNA has emerged as an attractive medium for storing large amounts of data due to its high information density, long-term stability, and low energy consumption. However, in contrast to commercially available storage media, DNA-based data storage currently falls behind in terms of writing and reading speeds, waste as well as cost. To harness the full potential of DNA as a data storage medium, it is imperative to advance high-throughput DNA synthesis without compromising cost and pollution. Industry-standard phosphoramidite DNA synthesis has reached its limitation because of its short nucleotide length (< 200), overconsumption of organic solvents leading to the production of toxic wastes, and slow writing speed. Enzymatic DNA synthesis shows promise as a replacement with long nucleotides, an environmentally friendly process, and fast writing speed. In this review, we overview enzymatic DNA synthesis methods, evaluate current methods that utilize high-throughput and parallel synthesis, and conclude with comments on how enzymatic DNA synthesis can be the answer to DNA data storage.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

Data availability

Data sharing is not applicable to this article as no new data were created in this study.

References

  1. Kosuri, S., Church, G.M.: Large-scale de novo DNA synthesis: technologies and applications. Nat. Methods 11(5), 499–507 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Lee, D. G., et al.: A Controlled Transcription-Driven Light-Up Aptamer Amplification for Nucleoside Triphosphate Detection. BioChip J. 17(4), 487–495 (2023)

    Article  CAS  Google Scholar 

  3. Ståhl, P.L., et al.: Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353(6294), 78–82 (2016)

    Article  PubMed  Google Scholar 

  4. Vickovic, S., et al.: High-definition spatial transcriptomics for in situ tissue profiling. Nat. Methods 16(10), 987–990 (2019)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Yang, L.H., Ahn, D.J., Koo, E.: An ultrasensitive FRET-based DNA sensor via the accumulated QD system derivatized in the nano-beads. BioChip J. 12, 340–347 (2018)

    Article  CAS  Google Scholar 

  6. Rothemund, P.W.: Folding DNA to create nanoscale shapes and patterns. Nature 440(7082), 297–302 (2006)

    Article  CAS  PubMed  Google Scholar 

  7. Lee, W.J., Kim, K.J., Hossain, M.K., Cho, H.Y., Choi, J.W.: DNA–gold nanoparticle conjugates for intracellular miRNA detection using surface-enhanced Raman spectroscopy. BioChip J. 16(1), 33–40 (2022)

    Article  CAS  Google Scholar 

  8. Zhu, Y., Zhong, N., Xiong, Y.: Data explosion, data nature and dataology. In Brain Informatics: International Conference, BI 2009 Beijing, China, October 22–24, 2009 Proceedings (pp. 147–158). Springer Berlin Heidelberg (2009)

  9. Hilbert, M., López, P.: The world’s technological capacity to store, communicate, and compute information. Science 332(6025), 60–65 (2011)

    Article  CAS  PubMed  Google Scholar 

  10. Bishop B., Mccorkle N., Zhirnov.: Technology working group meeting on future DNA synthesis technologies. Summary Report. Arlington, VA (2017)

  11. Kim, S. J., et al.: The bottom of the memory hierarchy: semiconductor and DNA data storage. MRS Bulletin, 48(5), 547–559 (2023)

    Article  Google Scholar 

  12. Xu, C., Zhao, C., Ma, B., Liu, H.: Uncertainties in synthetic DNA-based data storage. Nucleic Acids Res. 49(10), 5451–5469 (2021)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Raza, M.H., Desai, S., Aravamudhan, S., Zadegan, R.: An outlook on the current challenges and opportunities in DNA data storage. Biotechnol. Adv. 66, 108155 (2023)

    Article  CAS  PubMed  Google Scholar 

  14. Ezekannagha, C., Becker, A., Heider, D., Hattab, G.: Design considerations for advancing data storage with synthetic DNA for long-term archiving. Mater. Today Bio 15, 100306 (2022)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Goldman, N., et al.: Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature 494(7435), 77–80 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Zhirnov, V., Zadegan, R.M., Sandhu, G.S., Church, G.M., Hughes, W.L.: Nucleic acid memory. Nat. Mater. 15(4), 366–370 (2016)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Panda, D., et al.: DNA as a digital information storage device: hope or hype? 3 Biotech 8, 1–9 (2018)

    Article  Google Scholar 

  18. International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome. Nature 431(7011), 931–945 (2004)

    Article  Google Scholar 

  19. Song, X., Shah, S., Reif, J.: Multidimensional data organization and random access in large-scale DNA storage systems. Theoret. Comput. Sci. 894, 190–202 (2021)

    Article  MathSciNet  Google Scholar 

  20. Andrews, B.I., et al.: Sustainability challenges and opportunities in oligonucleotide manufacturing. J. Org. Chem. 86(1), 49–61 (2020)

    Article  PubMed  PubMed Central  Google Scholar 

  21. Agilent Technologies. Agilent’s SurePrint G3 CGH+SNP Microarray Platform. https://www.agilent.com/Library/brochures/5990-6422en_lo.pdf. Accessed 15 Nov 2023

  22. Dong, Y., Sun, F., Ping, Z., Ouyang, Q., Qian, L.: DNA storage: research landscape and future prospects. Natl. Sci. Rev. 7(6), 1092–1107 (2020)

    Article  PubMed  PubMed Central  Google Scholar 

  23. Illumina. NovaSeq X Specifications: Capacity for high-intensity genomics. NovaSeq X Specifications | Capacity for high-intensity genomics. https://sapac.illumina.com/systems/sequencing-platforms/novaseq-x-plus/specifications.html. Accessed 10 Nov 2023

  24. Beaucage, S.L., Caruthers, M.H.: Deoxynucleoside phosphoramidites—a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Lett. 22(20), 1859–1862 (1981)

    Article  CAS  Google Scholar 

  25. Schott, H., Schrade, H.: Single-step elongation of oligodeoxynucleotides using terminal deoxynucleotidyl transferase. Eur. J. Biochem. 143(3), 613–620 (1984)

    Article  CAS  PubMed  Google Scholar 

  26. Hoose, A., Vellacott, R., Storch, M., Freemont, P.S., Ryadnov, M.G.: DNA synthesis technologies to close the gene writing gap. Nat. Rev. Chem. 7(3), 144–161 (2023)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Eisenstein, M.: Enzymatic DNA synthesis enters new phase. Nat. Biotechnol. 38(10), 1113–1116 (2020)

    Article  CAS  PubMed  Google Scholar 

  28. Verardo, D., et al.: Multiplex enzymatic synthesis of DNA with single-base resolution. Sci. Adv. 9(27), eadi0263 (2023)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Septak, M.: Kinetic studies on depurination and detritylation of CPG-bound intermediates during oligonucleotide synthesis. Nucleic Acids Res. 24(15), 3053–3058 (1996)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Beaucage, S. L.: Oligodeoxyribonucleotides synthesis: phosphoramidite approach. Protocols for Oligonucleotides and Analogs: synthesis and properties, pp. 33–61, Springer (1993)

  31. Kretschy, N., Holik, A.K., Somoza, V., Stengele, K.P., Somoza, M.M.: Next-generation o-nitrobenzyl photolabile groups for light-directed chemistry and microarray synthesis. Angew. Chem. Int. Ed. 54(29), 8555–8559 (2015)

    Article  CAS  Google Scholar 

  32. Lee, H.H., Kalhor, R., Goela, N., Bolot, J., Church, G.M.: Terminator-free template-independent enzymatic DNA synthesis for digital information storage. Nat. Commun. 10(1), 2383 (2019)

    Article  PubMed  PubMed Central  Google Scholar 

  33. Palluk, S., et al.: De novo DNA synthesis using polymerase-nucleotide conjugates. Nat. Biotechnol. 36(7), 645–650 (2018)

    Article  CAS  PubMed  Google Scholar 

  34. Lausted, C., et al.: POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer. Genome Biol. 5(8), 1–17 (2004)

    Article  Google Scholar 

  35. Nguyen, B.H., et al.: Scaling DNA data storage with nanoscale electrode wells. Sci.Adv. 7(48), eabi6714 (2021)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Singh-Gasson, S., et al.: Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat. Biotechnol. 17(10), 974–978 (1999)

    Article  CAS  PubMed  Google Scholar 

  37. Lee, H., et al.: Photon-directed multiplexed enzymatic DNA synthesis for molecular digital data storage. Nat. Commun. 11(1), 5246 (2020)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Smith, J.A., et al.: Spatially selective electrochemical cleavage of a polymerase-nucleotide conjugate. ACS Synth. Biol. 12(6), 1716–1726 (2023)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Wang, P., Mu, Z., Sun, L., Si, S., Wang, B.: Hidden addressing encoding for DNA storage. Front. Bioeng. Biotechnol. 10, 916615 (2022)

    Article  PubMed  PubMed Central  Google Scholar 

  40. Hao, Y., Li, Q., Fan, C., Wang, F.: Data storage based on DNA. Small Struct. 2(2), 2000046 (2021)

    Article  CAS  Google Scholar 

  41. Lu, Y., & Lu, Y.: Highly robust DNA data storage based on controllable GC content and homopolymer of 64-element coded tables. bioRxiv 2023–09 (2023)

  42. Ceze, L., Nivala, J., Strauss, K.: Molecular digital data storage using DNA. Nat. Rev. Genet. 20(8), 456–466 (2019)

    Article  CAS  PubMed  Google Scholar 

  43. Doricchi, A., et al.: Emerging approaches to DNA data storage: challenges and prospects. ACS Nano 16(11), 17552–17571 (2022)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Anchordoquy, T.J., Molina, M.C.: Preservation of DNA. Cell Preserv. Technol. 5(4), 180–188 (2007)

    Article  CAS  Google Scholar 

  45. Grass, R.N., Heckel, R., Puddu, M., Paunescu, D., Stark, W.J.: Robust chemical preservation of digital information on DNA in silica with error-correcting codes. Angew. Chem. Int. Ed. 54(8), 2552–2555 (2015)

    Article  CAS  Google Scholar 

  46. Chen, W.D., et al.: Combining data longevity with high storage capacity—layer-by-layer DNA encapsulated in magnetic nanoparticles. Adv. Func. Mater. 29(28), 1901672 (2019)

    Article  Google Scholar 

  47. Matange, K., Tuck, J.M., Keung, A.J.: DNA stability: a central design consideration for DNA data storage systems. Nat. Commun. 12(1), 1358 (2021)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Organick, L., et al.: Random access in large-scale DNA data storage. Nat. Biotechnol. 36(3), 242–248 (2018)

    Article  CAS  PubMed  Google Scholar 

  49. Tabatabaei Yazdi, S.H., Yuan, Y., Ma, J., Zhao, H., Milenkovic, O.: A rewritable, random-access DNA-based storage system. Sci. Rep. 5(1), 14138 (2015)

    Article  CAS  PubMed Central  Google Scholar 

  50. Organick, L., et al.: Probing the physical limits of reliable DNA data retrieval. Nat. Commun. 11(1), 616 (2020)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Kim, J., Jung, C.: SF-qPCR: strand displacement-based fast quantitative polymerase chain reaction. BioChip J. 16(1), 41–48 (2022)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Hu, T., Chitnis, N., Monos, D., Dinh, A.: Next-generation sequencing technologies: an overview. Hum. Immunol. 82(11), 801–811 (2021)

    Article  CAS  PubMed  Google Scholar 

  53. Luo, C., Tsementzi, D., Kyrpides, N., Read, T., Konstantinidis, K.T.: Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 7(2), e30087 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Stoler, N., Nekrutenko, A.: Sequencing error profiles of Illumina sequencing instruments. NAR Genom. Bioinform. 3(1), lqab019 (2021)

    Article  PubMed  PubMed Central  Google Scholar 

  55. Goodwin, S., McPherson, J.D., McCombie, W.R.: Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet. 17(6), 333–351 (2016)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Anavy, L., Vaknin, I., Atar, O., Amit, R., & Yakhini, Z.: Improved DNA based storage capacity and fidelity using composite DNA letters. bioRxiv 433524 (2018)

  57. Choi, Y., et al.: High information capacity DNA-based data storage with augmented encoding characters using degenerate bases. Sci. Rep. 9(1), 6582 (2019)

    Article  MathSciNet  PubMed  PubMed Central  Google Scholar 

  58. Blawat, M., et al.: Forward error correction for DNA data storage. Procedia Comput. Sci. 80, 1011–1022 (2016)

    Article  Google Scholar 

  59. Binkowski, B.F., Richmond, K.E., Kaysen, J., Sussman, M.R., Belshaw, P.J.: Correcting errors in synthetic DNA through consensus shuffling. Nucleic Acids Res. 33(6), e55–e55 (2005)

    Article  PubMed  PubMed Central  Google Scholar 

  60. Xiong, A.S., et al.: Chemical gene synthesis: strategies, softwares, error corrections, and applications. FEMS Microbiol. Rev. 32(3), 522–540 (2008)

    Article  CAS  PubMed  Google Scholar 

  61. Erlich, Y., Zielinski, D.: DNA fountain enables a robust and efficient storage architecture. Science 355(6328), 950–954 (2017)

    Article  CAS  PubMed  Google Scholar 

  62. Michelson, A.M., Todd, A.R.: Nucleotides part XXXII. Synthesis of a dithymidine dinucleotide containing a 3′: 5′-internucleotidic linkage. J. Chem. Soc. (Resumed) (1955). https://doi.org/10.1039/JR9550002632

    Article  Google Scholar 

  63. Schaller, H., Weimann, G., Lerch, B., Khorana, H.G.: Studies on polynucleotides. XXIV. 1 The stepwise synthesis of specific deoxyribopolynucleotides (4). 2 Protected derivatives of deoxyribonucleosides and new syntheses of deoxyribonucleoside-3″ phosphates 3. J. Am. Chem. Soc. 85(23), 3821–3827 (1963)

    Article  CAS  Google Scholar 

  64. Merrifield, R.B.: Solid phase peptide synthesis. I. The synthesis of a tetrapeptide. J. Am. Chem. Soc. 85(14), 2149–2154 (1963)

    Article  CAS  Google Scholar 

  65. Letsinger, R.L., Mahadevan, V.: Oligonucleotide synthesis on a polymer support1, 2. J. Am. Chem. Soc. 87(15), 3526–3527 (1965)

    Article  CAS  PubMed  Google Scholar 

  66. Letsinger, R.L., Caruthers, M.H., Jerina, D.M.: Reactions of nucleosides on polymer supports. Synthesis of thymidylylthymidylylthymidine. Biochemistry 6(5), 1379–1388 (1967)

    Article  CAS  PubMed  Google Scholar 

  67. Letsinger, R.L., Lunsford, W.B.: Synthesis of thymidine oligonucleotides by phosphite triester intermediates. J. Am. Chem. Soc. 98(12), 3655–3661 (1976)

    Article  CAS  PubMed  Google Scholar 

  68. Matteucci, M.D., Caruthers, M.H.: Synthesis of deoxyoligonucleotides on a polymer support. J. Am. Chem. Soc. 103(11), 3185–3191 (1981)

    Article  CAS  Google Scholar 

  69. Letsinger, R.L., Ogilvie, K.K.: Nucleotide chemistry. XIII. Synthesis of oligothymidylates via phosphotriester intermediates. J. Am. Chem. Soc. 91(12), 3350–3355 (1969)

    Article  CAS  Google Scholar 

  70. Russell, M.A., Laws, A.P., Atherton, J.H., Page, M.I.: The mechanism of the phosphoramidite synthesis of polynucleotides. Org. Biomol. Chem. 6(18), 3270–3275 (2008)

    Article  CAS  PubMed  Google Scholar 

  71. Kong, D.S., Carr, P.A., Chen, L., Zhang, S., Jacobson, J.M.: Parallel gene synthesis in a microfluidic device. Nucleic Acids Res. 35(8), e61 (2007)

    Article  PubMed  PubMed Central  Google Scholar 

  72. LeProust, E., Zhang, H., Yu, P., Zhou, X., Gao, X.: Characterization of oligodeoxyribonucleotide synthesis on glass plates. Nucleic Acids Res. 29(10), 2171–2180 (2001)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Antkowiak, P.L., et al.: Low cost DNA data storage using photolithographic synthesis and advanced information reconstruction and error correction. Nat. Commun. 11(1), 5345 (2020)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Li, H., et al.: An oligonucleotide synthesizer based on a microreactor chip and an inkjet printer. Sci. Rep. 9(1), 5058 (2019)

    Article  PubMed  PubMed Central  Google Scholar 

  75. LeProust, E.M., et al.: Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res. 38(8), 2522–2540 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Hughes, T.R., et al.: Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19(4), 342–347 (2001)

    Article  CAS  PubMed  Google Scholar 

  77. Volkel, K., Tomek, K.J., Keung, A.J., Tuck, J.M.: DINOS: Data INspired Oligo synthesis for DNA data storage. ACM J. Emerg. Technol. Comput. Syst. (JETC) 18(3), 1–35 (2022)

    Article  Google Scholar 

  78. Ghindilis, A.L., et al.: CombiMatrix oligonucleotide arrays: genotyping and gene expression assays employing electrochemical detection. Biosens. Bioelectron. 22(9–10), 1853–1860 (2007)

    Article  CAS  PubMed  Google Scholar 

  79. Ghadami, O., et al.: Helix: an electrochemical CMOS DNA synthesizer. In 2022 IEEE Symposium on VLSI Technology and Circuits (VLSI Technology and Circuits), (pp. 66–67). IEEE (2022)

  80. Maurer, K., Cooper Jr, J. J., Fujii, H. S., Leonetti, J.: US Patent Application No. 9,394,167 (2020)

  81. Chun, H., Chung, T.D.: Iontronics. Annu. Rev. Anal. Chem. 8, 441–462 (2015)

    Article  CAS  Google Scholar 

  82. CustomArray. MSC Technology. https://www.customarrayinc.com/msc-technology. Accessed 24 Oct 2023

  83. Agbavwe, C., et al.: Efficiency, error and yield in light-directed maskless synthesis of DNA microarrays. J. Nanobiotechnol. 9, 1–17 (2011)

    Article  Google Scholar 

  84. Tian, J., et al.: Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432(7020), 1050–1054 (2004)

    Article  CAS  PubMed  Google Scholar 

  85. Fenart, S., et al.: Intra-platform comparison of 25-mer and 60-mer oligonucleotide Nimblegen DNA microarrays. BMC. Res. Notes 6, 1–11 (2013)

    Article  Google Scholar 

  86. Kunkel, T.A., Bebenek, K.: DNA replication fidelity. Annu. Rev. Biochem. 69(1), 497–529 (2000)

    Article  CAS  PubMed  Google Scholar 

  87. Bell, S.P., Dutta, A.: DNA replication in eukaryotic cells. Annu. Rev. Biochem. 71(1), 333–374 (2002)

    Article  CAS  PubMed  Google Scholar 

  88. Soni, G.V., Meller, A.: Progress toward ultrafast DNA sequencing using solid-state nanopores. Clin. Chem. 53(11), 1996–2001 (2007)

    Article  CAS  PubMed  Google Scholar 

  89. McNally, B., et al.: Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. Nano Lett. 10(6), 2237–2244 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Milton, J., Nayyar, S., Riedl, J., Ogaki, R.: US Patent Application No. 17/260,615 (2022)

  91. Hoff, K., Halpain, M., Garbagnati, G., Edwards, J.S., Zhou, W.: Enzymatic synthesis of designer DNA using cyclic reversible termination and a universal template. ACS Synth. Biol. 9(2), 283–293 (2020)

    Article  CAS  PubMed  Google Scholar 

  92. Heppel, L.A., Ortiz, P.J., Ochoa, S.: Studies on polynucleotides synthesized by polynucleotide phosphorylase: I. structure of polynucleotides with one type of nucleotide unit. J. Biol. Chemi. 229(2), 679–694 (1957)

    Article  CAS  Google Scholar 

  93. Mackey, J.K., Gilham, P.T.: New approach to the synthesis of polyribonucleotides of defined sequence. Nature 233(5321), 551–553 (1971)

    Article  CAS  PubMed  Google Scholar 

  94. Kaufmann, G., Fridkin, M., Zutra, A., Littauer, U.Z.: Monofunctional substrates of polynucleotide phosphorylase: The monoaddition of 2′(3′)-O-isovaleryl-nucleoside diphosphate to an initiator oligonucleotide. Eur. J. Biochem. 24(1), 4–11 (1971)

    Article  CAS  PubMed  Google Scholar 

  95. Gillam, S., Waterman, K., Doel, M., Smith, M.: Enzymatic synthesis of deoxyribo-oiigonucleotides of defined asequence. Deoxyribo-oligonucleotide synthesis. Nucleic Acids Res. 1(12), 1649–1664 (1974)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Gilham, S., Smith, M.: Enzymatic synthesis of deoxyribo-oligonucleotides of defined sequence. Nat. New Biol. 238(86), 233–234 (1972)

    Article  CAS  PubMed  Google Scholar 

  97. Cardenas, P.P., et al.: Polynucleotide phosphorylase exonuclease and polymerase activities on single-stranded DNA ends are modulated by RecN, SsbA and RecA proteins. Nucleic Acids Res. 39(21), 9250–9261 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Kimhi, Y., Littauer, U.Z.: Purification and properties of polynucleotide phosphorylase from Escherichia coli. J. Biol. Chem. 243(2), 231–240 (1968)

    Article  CAS  PubMed  Google Scholar 

  99. Silber, R., Malathi, V.G., Hurwitz, J.: Purification and properties of bacteriophage T4-induced RNA ligase. Proc. Natl. Acad. Sci. 69(10), 3009–3013 (1972)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Hinton, D.M., Baez, J.A., Gumport, R.I.: T4 RNA Ligase joins 2’-deoxyribonucleoside 3’, 5’-bisphosphates to oligodeoxyribonucleotides. Biochemistry 17(24), 5091–5097 (1978)

    Article  CAS  PubMed  Google Scholar 

  101. Mclaughlin, L.W., Romaniuk, E., Romaniuk, P.J., Neilson, T.: The effect of acceptor oligoribonucleotide sequence on the T4 RNA ligase reaction. Eur. J. Biochem. 125(3), 639–643 (1982)

    Article  PubMed  Google Scholar 

  102. Schmitz, C., Reetz, M.T.: Solid-phase enzymatic synthesis of oligonucleotides. Org. Lett. 1(11), 1729–1731 (1999)

    Article  CAS  PubMed  Google Scholar 

  103. Lenzer, J.: Arthur Kornberg. BMJ 7364, 50–50 (2008)

    Article  Google Scholar 

  104. Wu, W.J., Yang, W., Tsai, M.D.: How DNA polymerases catalyse replication and repair with contrasting fidelity. Nat. Rev. Chem. 1(9), 0068 (2017)

    Article  CAS  Google Scholar 

  105. Fowler, J.D., Suo, Z.: Biochemical, structural, and physiological characterization of terminal deoxynucleotidyl transferase. Chem. Rev. 106(6), 2092–2110 (2006)

    Article  CAS  PubMed  Google Scholar 

  106. McElhinny, S.A.N., et al.: A gradient of template dependence defines distinct biological roles for family X polymerases in nonhomologous end joining. Mol. Cell 19(3), 357–366 (2005)

    Article  Google Scholar 

  107. Jensen, M.A., Davis, R.W.: Template-independent enzymatic oligonucleotide synthesis (TiEOS): its history, prospects, and challenges. Biochemistry 57(12), 1821–1832 (2018)

    Article  CAS  PubMed  Google Scholar 

  108. Thai, T.H., Purugganan, M.M., Roth, D.B., Kearney, J.F.: Distinct and opposite diversifying activities of terminal transferase splice variants. Nat. Immunol. 3(5), 457–462 (2002)

    Article  CAS  PubMed  Google Scholar 

  109. Bentolila, L.A., et al.: The two isoforms of mouse terminal deoxynucleotidyl transferase differ in both the ability to add N regions and subcellular localization. EMBO J. 14(17), 4221–4229 (1995)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Ramadan, K., Shevelev, I.V., Maga, G., Hübscher, U.D.: novo DNA synthesis by human DNA polymerase λ, DNA polymerase μ and terminal deoxyribonucleotidyl transferase. J. Mol. Biol. 339(2), 395–404 (2004)

    Article  CAS  PubMed  Google Scholar 

  111. Chang, L.M., Bollum, F.J., Gallo, R.C.: Molecular biology of terminal transferas. Crit. Rev. Biochem. 21(1), 27–52 (1986)

    Article  CAS  Google Scholar 

  112. Boyer, P.D., Krebs, E.G.: The Enzymes. Academic Press, Cambridge (1986)

    Google Scholar 

  113. Bhan, N., et al.: Recording temporal signals with minutes resolution using enzymatic DNA synthesis. J. Am. Chem. Soc. 143(40), 16630–16640 (2021)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Delarue, M., et al.: Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase. EMBO J. 21(3), 427–439 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Motea, E.A., Berdis, A.J.: Terminal deoxynucleotidyl transferase: the story of a misguided DNA polymerase. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1804(5), 1151–1166 (2010)

    Article  CAS  PubMed  Google Scholar 

  116. Yoo, E., Choe, D., Shin, J., Cho, S., Cho, B.K.: Mini review: enzyme-based DNA synthesis and selective retrieval for data storage. Comput. Struct. Biotechnol. J. 19, 2468–2476 (2021)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Loc’hh, J., Delarue, M.: Terminal deoxynucleotidyltransferase: the story of an untemplated DNA polymerase capable of DNA bridging and templated synthesis across strands. Curr. Opin. Struct. Biol. 53, 22–31 (2018)

    Article  Google Scholar 

  118. Hutchison, C.A., III., et al.: Design and synthesis of a minimal bacterial genome. Science 351(6280), aad6253 (2016)

    Article  PubMed  Google Scholar 

  119. Roquet, N., et al.: US Patent Application No. 16/414,752 (2019)

  120. Roquet, N., et al.: DNA-based data storage via combinatorial assembly. bioRxiv 2021-04 (2021)

  121. Ju, J., et al.: Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc. Natl. Acad. Sci. 103(52), 19635–19640 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Wu, J., et al.: 3′-O-modified nucleotides as reversible terminators for pyrosequencing. Proc. Natl. Acad. Sci. 104(42), 16462–16467 (2007)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Chen, C.Y.: DNA polymerases drive DNA sequencing-by-synthesis technologies: both past and present. Front. Microbiol. 5, 305 (2014)

    Article  PubMed  PubMed Central  Google Scholar 

  124. Ruparel, H., et al.: Design and synthesis of a 3′-O-allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis. Proc. Natl. Acad. Sci. 102(17), 5932–5937 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Mathews, A.S., Yang, H., Montemagno, C.: Photo-cleavable nucleotides for primer free enzyme mediated DNA synthesis. Org. Biomol. Chem. 14(35), 8278–8288 (2016)

    Article  CAS  PubMed  Google Scholar 

  126. Wu, W., et al.: Termination of DNA synthesis by N 6-alkylated, not 3′-O-alkylated, photocleavable 2′-deoxyadenosine triphosphates. Nucleic Acids Res. 35(19), 6339–6349 (2007)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Bentley, D.R., et al.: Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456(7218), 53–59 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Mathews, A.S., Yang, H., Montemagno, C.: 3′-O-Caged 2′-deoxynucleoside triphosphates for light-mediated, enzyme-catalyzed, template-independent DNA synthesis. Curr. Protoc. Nucleic Acid Chem. 71(1), 13–17 (2017)

    Article  Google Scholar 

  129. Arlow, D., Palluk, S.: US Patent Application No. 17/571,529 (2022)

  130. Camena Bioscience. gSynth™. https://www.camenabio.com/assets/media/2019-10-24-pplication-note.pdf. Accessed 1 Dec 2023

  131. Stemple, D. L., Fraser, A. G., Mankowska, S., Bell, N.: US Patent No. 11,667,941 (2023)

  132. Stemple, D. L., Mankowska, S. A., Harvey, S. A.: International Publication No. WO2018152323A1 (2018)

  133. Efcavitch, J. W., Siddiqi, S.: US Patent Application No. 10,041,110 (2018)

  134. Efcavitch, J. W., Tubbs, J. L.: US Patent Application No. 15/926,642 (2018)

  135. Soskine, M., Champion, E.: US Patent Application No. 17/919,649 (2023)

  136. Eimerman, P., et al.: Development of a simple and versatile enzymatic DNA synthesis system that enables accurate, fast, and long oligos on demand. J. Biomol. Tech.: JBT 31(Suppl), S10 (2020)

    PubMed Central  Google Scholar 

  137. Perkel, J.M.: The race for enzymatic DNA synthesis heats up. Nature 566(7745), 565 (2019)

    Article  CAS  PubMed  Google Scholar 

  138. Jung, H.S., et al.: CMOS electrochemical pH localizer-imager. Sci. Adv. 8(30), eabm6815 (2022)

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Research Foundation of Korea (NRF) (NRF-2020R1A2C3010322 and NRF-2018M3A9D7079485).

Funding

This article is funded by National Research Foundation of Korea, NRF-2020R1A2C3010322, Honggu Chun, Naional Research Foundation of Korea, NRF-2018M3A9D7079485, Honggu Chun.

Author information

Author notes

  1. David Baek and Sung-Yune Joe contributed equally to this work.

Authors and Affiliations

  1. Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841, Korea

    David Baek, Sung-Yune Joe, Haewon Shin, Chaewon Park, Seokwoo Jo & Honggu Chun

  2. Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841, Korea

    David Baek, Sung-Yune Joe, Haewon Shin, Chaewon Park, Seokwoo Jo & Honggu Chun

Authors
  1. David Baek
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sung-Yune Joe
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Haewon Shin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Chaewon Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Seokwoo Jo
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Honggu Chun
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Honggu Chun.

Ethics declarations

Conflict of Interest

The authors declare no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Baek, D., Joe, SY., Shin, H. et al. Recent Progress in High-Throughput Enzymatic DNA Synthesis for Data Storage. BioChip J (2024). https://doi.org/10.1007/s13206-024-00146-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s13206-024-00146-2

Keywords

Search

Navigation