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Template-dependent DNA ligation for the synthesis of modified oligonucleotides

Author

Listed:
  • Nazarii Sabat

    (rue du Docteur Roux)

  • Andreas Stämpfli

    (Grenzacherstrasse 124)

  • Steven Hanlon

    (Grenzacherstrasse 124)

  • Serena Bisagni

    (Grenzacherstrasse 124)

  • Filippo Sladojevich

    (Grenzacherstrasse 124)

  • Kurt Püntener

    (Grenzacherstrasse 124)

  • Marcel Hollenstein

    (rue du Docteur Roux)

Abstract

Chemical modification of DNA is a common strategy to improve the properties of oligonucleotides, particularly for therapeutics and nanotechnology. Existing synthetic methods essentially rely on phosphoramidite chemistry or the polymerization of nucleoside triphosphates but are limited in terms of size, scalability, and sustainability. Herein, we report a robust alternative method for the de novo synthesis of modified oligonucleotides using template-dependent DNA ligation of shortmer fragments. Our approach is based on the fast and scaled accessibility of chemically modified shortmer monophosphates as substrates for the T3 DNA ligase. This method has shown high tolerance to chemical modifications, flexibility, and overall efficiency, thereby granting access to a broad range of modified oligonucleotides of different lengths (20 → 120 nucleotides). We have applied this method to the synthesis of clinically relevant antisense drugs and ultramers containing diverse modifications. Furthermore, the designed chemoenzymatic approach has great potential for diverse applications in therapeutics and biotechnology.

Suggested Citation

  • Nazarii Sabat & Andreas Stämpfli & Steven Hanlon & Serena Bisagni & Filippo Sladojevich & Kurt Püntener & Marcel Hollenstein, 2024. "Template-dependent DNA ligation for the synthesis of modified oligonucleotides," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-52141-8
    DOI: 10.1038/s41467-024-52141-8
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    References listed on IDEAS

    as
    1. Alexander F. Sandahl & Thuy J. D. Nguyen & Rikke A. Hansen & Martin B. Johansen & Troels Skrydstrup & Kurt V. Gothelf, 2021. "On-demand synthesis of phosphoramidites," Nature Communications, Nature, vol. 12(1), pages 1-7, December.
    2. Hui Lv & Nuli Xie & Mingqiang Li & Mingkai Dong & Chenyun Sun & Qian Zhang & Lei Zhao & Jiang Li & Xiaolei Zuo & Haibo Chen & Fei Wang & Chunhai Fan, 2023. "DNA-based programmable gate arrays for general-purpose DNA computing," Nature, Nature, vol. 622(7982), pages 292-300, October.
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