IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-49021-6.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-49021-6
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-49021-6?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    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. 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.
    3. 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.
    4. 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.
    5. 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.
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Sebastian Castillo-Hair & Stephen Fedak & Ban Wang & Johannes Linder & Kyle Havens & Michael Certo & Georg Seelig, 2024. "Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Yasmine S. Zubi & Kosuke Seki & Ying Li & Andrew C. Hunt & Bingqing Liu & Benoît Roux & Michael C. Jewett & Jared C. Lewis, 2022. "Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    3. Tin-Lok Wong & Jia-Jian Loh & Shixun Lu & Helen H. N. Yan & Hoi Cheong Siu & Ren Xi & Dessy Chan & Max J. F. Kam & Lei Zhou & Man Tong & John A. Copland & Leilei Chen & Jing-Ping Yun & Suet Yi Leung &, 2023. "ADAR1-mediated RNA editing of SCD1 drives drug resistance and self-renewal in gastric cancer," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    4. 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.
    5. Andrew C. Hunt & Bastian Vögeli & Ahmed O. Hassan & Laura Guerrero & Weston Kightlinger & Danielle J. Yoesep & Antje Krüger & Madison DeWinter & Michael S. Diamond & Ashty S. Karim & Michael C. Jewett, 2023. "A rapid cell-free expression and screening platform for antibody discovery," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    6. Joongoo Lee & Jaime N. Coronado & Namjin Cho & Jongdoo Lim & Brandon M. Hosford & Sangwon Seo & Do Soon Kim & Camila Kofman & Jeffrey S. Moore & Andrew D. Ellington & Eric V. Anslyn & Michael C. Jewet, 2022. "Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    7. Tony Z. Jia & Yutetsu Kuruma, 2019. "Recent Advances in Origins of Life Research by Biophysicists in Japan," Challenges, MDPI, vol. 10(1), pages 1-21, April.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49021-6. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.