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Expedient production of site specifically nucleobase-labelled or hypermodified RNA with engineered thermophilic DNA polymerases

Author

Listed:
  • Mária Brunderová

    (Czech Academy of Sciences
    Charles University
    Cambridge Biomedical Campus)

  • Vojtěch Havlíček

    (Czech Academy of Sciences
    Charles University)

  • Ján Matyašovský

    (Czech Academy of Sciences)

  • Radek Pohl

    (Czech Academy of Sciences)

  • Lenka Poštová Slavětínská

    (Czech Academy of Sciences)

  • Matouš Krömer

    (Czech Academy of Sciences
    Harwell Campus)

  • Michal Hocek

    (Czech Academy of Sciences
    Charles University)

Abstract

Innovative approaches to controlled nucleobase-modified RNA synthesis are urgently needed to support RNA biology exploration and to synthesize potential RNA therapeutics. Here we present a strategy for enzymatic construction of nucleobase-modified RNA based on primer-dependent engineered thermophilic DNA polymerases – SFM4-3 and TGK. We demonstrate introduction of one or several different base-modified nucleotides in one strand including hypermodified RNA containing all four modified nucleotides bearing four different substituents, as well as strategy for primer segment removal. We also show facile site-specific or segmented introduction of fluorophores or other functional groups at defined positions in variety of RNA molecules, including structured or long mRNA. Intriguing translation efficacy of single-site modified mRNAs underscores the necessity to study isolated modifications placed at designer positions to disentangle their biological effects and enable development of improved mRNA therapeutics. Our toolbox paves the way for more precise dissecting RNA structures and functions, as well as for construction of diverse types of base-functionalized RNA for therapeutic applications and diagnostics.

Suggested Citation

  • Mária Brunderová & Vojtěch Havlíček & Ján Matyašovský & Radek Pohl & Lenka Poštová Slavětínská & Matouš Krömer & Michal Hocek, 2024. "Expedient production of site specifically nucleobase-labelled or hypermodified RNA with engineered thermophilic DNA polymerases," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47444-9
    DOI: 10.1038/s41467-024-47444-9
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    References listed on IDEAS

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    1. Florian Praetorius & Benjamin Kick & Karl L. Behler & Maximilian N. Honemann & Dirk Weuster-Botz & Hendrik Dietz, 2017. "Biotechnological mass production of DNA origami," Nature, Nature, vol. 552(7683), pages 84-87, December.
    2. Thomas Philipp Hoernes & Klaus Faserl & Michael Andreas Juen & Johannes Kremser & Catherina Gasser & Elisabeth Fuchs & Xinying Shi & Aaron Siewert & Herbert Lindner & Christoph Kreutz & Ronald Micura , 2018. "Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    3. Yu Liu & Erik Holmstrom & Jinwei Zhang & Ping Yu & Jinbu Wang & Marzena A. Dyba & De Chen & Jinfa Ying & Stephen Lockett & David J. Nesbitt & Adrian R. Ferré-D’Amaré & Rui Sousa & Jason R. Stagno & Yu, 2015. "Synthesis and applications of RNAs with position-selective labelling and mosaic composition," Nature, Nature, vol. 522(7556), pages 368-372, June.
    4. Annette B. Vogel & Isis Kanevsky & Ye Che & Kena A. Swanson & Alexander Muik & Mathias Vormehr & Lena M. Kranz & Kerstin C. Walzer & Stephanie Hein & Alptekin Güler & Jakob Loschko & Mohan S. Maddur &, 2021. "BNT162b vaccines protect rhesus macaques from SARS-CoV-2," Nature, Nature, vol. 592(7853), pages 283-289, April.
    5. Ronald R. Breaker, 2004. "Natural and engineered nucleic acids as tools to explore biology," Nature, Nature, vol. 432(7019), pages 838-845, December.
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