IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-46001-8.html
   My bibliography  Save this article

Topological barrier to Cas12a activation by circular DNA nanostructures facilitates autocatalysis and transforms DNA/RNA sensing

Author

Listed:
  • Fei Deng

    (University of New South Wales
    University of New South Wales)

  • Yi Li

    (University of New South Wales
    University of New South Wales)

  • Biyao Yang

    (University of New South Wales
    University of New South Wales)

  • Rui Sang

    (University of New South Wales
    University of New South Wales)

  • Wei Deng

    (University of Technology Sydney)

  • Maya Kansara

    (Garvan Institute of Medical Research, Darlinghurst
    University of New South Wales
    University of New South Wales)

  • Frank Lin

    (Garvan Institute of Medical Research, Darlinghurst
    University of Sydney)

  • Subotheni Thavaneswaran

    (Garvan Institute of Medical Research, Darlinghurst
    University of New South Wales
    University of Sydney)

  • David M. Thomas

    (Garvan Institute of Medical Research, Darlinghurst
    University of New South Wales
    University of New South Wales)

  • Ewa M. Goldys

    (University of New South Wales
    University of New South Wales)

Abstract

Control of CRISPR/Cas12a trans-cleavage is crucial for biosensor development. Here, we show that small circular DNA nanostructures which partially match guide RNA sequences only minimally activate Cas12a ribonucleoproteins. However, linearizing these structures restores activation. Building on this finding, an Autocatalytic Cas12a Circular DNA Amplification Reaction (AutoCAR) system is established which allows a single nucleic acid target to activate multiple ribonucleoproteins, and greatly increases the achievable reporter cleavage rates per target. A rate-equation-based model explains the observed near-exponential rate trends. Autocatalysis is also sustained with DNA nanostructures modified with fluorophore-quencher pairs achieving 1 aM level (

Suggested Citation

  • Fei Deng & Yi Li & Biyao Yang & Rui Sang & Wei Deng & Maya Kansara & Frank Lin & Subotheni Thavaneswaran & David M. Thomas & Ewa M. Goldys, 2024. "Topological barrier to Cas12a activation by circular DNA nanostructures facilitates autocatalysis and transforms DNA/RNA sensing," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46001-8
    DOI: 10.1038/s41467-024-46001-8
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-46001-8
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-46001-8?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. Yongmoon Jeon & You Hee Choi & Yunsu Jang & Jihyeon Yu & Jiyoung Goo & Gyejun Lee & You Kyeong Jeong & Seung Hwan Lee & In-San Kim & Jin-Soo Kim & Cherlhyun Jeong & Sanghwa Lee & Sangsu Bae, 2018. "Direct observation of DNA target searching and cleavage by CRISPR-Cas12a," Nature Communications, Nature, vol. 9(1), pages 1-11, 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. Margot Karlikow & Evan Amalfitano & Xiaolong Yang & Jennifer Doucet & Abigail Chapman & Peivand Sadat Mousavi & Paige Homme & Polina Sutyrina & Winston Chan & Sofia Lemak & Alexander F. Yakunin & Adam, 2023. "CRISPR-induced DNA reorganization for multiplexed nucleic acid detection," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    2. Santosh R. Rananaware & Emma K. Vesco & Grace M. Shoemaker & Swapnil S. Anekar & Luke Samuel W. Sandoval & Katelyn S. Meister & Nicolas C. Macaluso & Long T. Nguyen & Piyush K. Jain, 2023. "Programmable RNA detection with CRISPR-Cas12a," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Aakash Saha & Mohd Ahsan & Pablo R. Arantes & Michael Schmitz & Christelle Chanez & Martin Jinek & Giulia Palermo, 2024. "An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

    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_s41467-024-46001-8. 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.