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Circular single-stranded DNA as a programmable vector for gene regulation in cell-free protein expression systems

Author

Listed:
  • Zhijin Tian

    (University of Science & Technology of China
    Chinese Academy of Sciences)

  • Dandan Shao

    (Shanghai Jiao Tong University)

  • Linlin Tang

    (Chinese Academy of Sciences
    Shanghai Jiao Tong University)

  • Zhen Li

    (Shanghai Jiao Tong University)

  • Qian Chen

    (Northeast Forestry University)

  • Yongxiu Song

    (Chinese Academy of Sciences
    Ningbo institute of Dalian University of Technology)

  • Tao Li

    (University of Science & Technology of China)

  • Friedrich C. Simmel

    (Technische Universität München)

  • Jie Song

    (Chinese Academy of Sciences
    Shanghai Jiao Tong University)

Abstract

Cell-free protein expression (CFE) systems have emerged as a critical platform for synthetic biology research. The vectors for protein expression in CFE systems mainly rely on double-stranded DNA and single-stranded RNA for transcription and translation processing. Here, we introduce a programmable vector - circular single-stranded DNA (CssDNA), which is shown to be processed by DNA and RNA polymerases for gene expression in a yeast-based CFE system. CssDNA is already widely employed in DNA nanotechnology due to its addressability and programmability. To apply above methods in the context of synthetic biology, CssDNA can not only be engineered for gene regulation via the different pathways of sense CssDNA and antisense CssDNA, but also be constructed into several gene regulatory logic gates in CFE systems. Our findings advance the understanding of how CssDNA can be utilized in gene expression and gene regulation, and thus enrich the synthetic biology toolbox.

Suggested Citation

  • Zhijin Tian & Dandan Shao & Linlin Tang & Zhen Li & Qian Chen & Yongxiu Song & Tao Li & Friedrich C. Simmel & Jie Song, 2024. "Circular single-stranded DNA as a programmable vector for gene regulation in cell-free protein expression systems," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49021-6
    DOI: 10.1038/s41467-024-49021-6
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    References listed on IDEAS

    as
    1. Linlin Tang & Zhijin Tian & Jin Cheng & Yijing Zhang & Yongxiu Song & Yan Liu & Jinghao Wang & Pengfei Zhang & Yonggang Ke & Friedrich C. Simmel & Jie Song, 2023. "Circular single-stranded DNA as switchable vector for gene expression in mammalian cells," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Jessica A. Kretzmann & Anna Liedl & Alba Monferrer & Volodymyr Mykhailiuk & Samuel Beerkens & Hendrik Dietz, 2023. "Gene-encoding DNA origami for mammalian cell expression," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    3. Kathrin Leppek & Gun Woo Byeon & Wipapat Kladwang & Hannah K. Wayment-Steele & Craig H. Kerr & Adele F. Xu & Do Soon Kim & Ved V. Topkar & Christian Choe & Daphna Rothschild & Gerald C. Tiu & Roger We, 2022. "Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    4. Kilian Vogele & Thomas Frank & Lukas Gasser & Marisa A. Goetzfried & Mathias W. Hackl & Stephan A. Sieber & Friedrich C. Simmel & Tobias Pirzer, 2018. "Towards synthetic cells using peptide-based reaction compartments," Nature Communications, Nature, vol. 9(1), pages 1-7, December.
    5. Rey W. Martin & Benjamin J. Des Soye & Yong-Chan Kwon & Jennifer Kay & Roderick G. Davis & Paul M. Thomas & Natalia I. Majewska & Cindy X. Chen & Ryan D. Marcum & Mary Grace Weiss & Ashleigh E. Stodda, 2018. "Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
    6. Melissa K. Takahashi & Xiao Tan & Aaron J. Dy & Dana Braff & Reid T. Akana & Yoshikazu Furuta & Nina Donghia & Ashwin Ananthakrishnan & James J. Collins, 2018. "A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
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