IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-46767-x.html
   My bibliography  Save this article

CRISPR-powered quantitative keyword search engine in DNA data storage

Author

Listed:
  • Jiongyu Zhang

    (University of Connecticut Health Center
    University of Connecticut)

  • Chengyu Hou

    (University of Connecticut Health Center
    University of Connecticut)

  • Changchun Liu

    (University of Connecticut Health Center)

Abstract

Despite the growing interest of archiving information in synthetic DNA to confront data explosion, quantitatively querying the data stored in DNA is still a challenge. Herein, we present Search Enabled by Enzymatic Keyword Recognition (SEEKER), which utilizes CRISPR-Cas12a to rapidly generate visible fluorescence when a DNA target corresponding to the keyword of interest is present. SEEKER achieves quantitative text searching since the growth rate of fluorescence intensity is proportional to keyword frequency. Compatible with SEEKER, we develop non-collision grouping coding, which reduces the size of dictionary and enables lossless compression without disrupting the original order of texts. Using four queries, we correctly identify keywords in 40 files with a background of ~8000 irrelevant terms. Parallel searching with SEEKER can be performed on a 3D-printed microfluidic chip. Overall, SEEKER provides a quantitative approach to conducting parallel searching over the complete content stored in DNA with simple implementation and rapid result generation.

Suggested Citation

  • Jiongyu Zhang & Chengyu Hou & Changchun Liu, 2024. "CRISPR-powered quantitative keyword search engine in DNA data storage," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46767-x
    DOI: 10.1038/s41467-024-46767-x
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-46767-x
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-46767-x?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. Lee Organick & Yuan-Jyue Chen & Siena Dumas Ang & Randolph Lopez & Xiaomeng Liu & Karin Strauss & Luis Ceze, 2020. "Probing the physical limits of reliable DNA data retrieval," Nature Communications, Nature, vol. 11(1), pages 1-7, December.
    2. Callista Bee & Yuan-Jyue Chen & Melissa Queen & David Ward & Xiaomeng Liu & Lee Organick & Georg Seelig & Karin Strauss & Luis Ceze, 2021. "Molecular-level similarity search brings computing to DNA data storage," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
    3. Mazhar Adli, 2018. "The CRISPR tool kit for genome editing and beyond," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    4. Lee Organick & Yuan-Jyue Chen & Siena Dumas Ang & Randolph Lopez & Xiaomeng Liu & Karin Strauss & Luis Ceze, 2020. "Author Correction: Probing the physical limits of reliable DNA data retrieval," Nature Communications, Nature, vol. 11(1), pages 1-1, December.
    5. Xiong Ding & Kun Yin & Ziyue Li & Rajesh V. Lalla & Enrique Ballesteros & Maroun M. Sfeir & Changchun Liu, 2020. "Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    6. Tom van der Valk & Patrícia Pečnerová & David Díez-del-Molino & Anders Bergström & Jonas Oppenheimer & Stefanie Hartmann & Georgios Xenikoudakis & Jessica A. Thomas & Marianne Dehasque & Ekin Sağlıcan, 2021. "Million-year-old DNA sheds light on the genomic history of mammoths," Nature, Nature, vol. 591(7849), pages 265-269, March.
    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. Christopher N. Takahashi & David P. Ward & Carlo Cazzaniga & Christopher Frost & Paolo Rech & Kumkum Ganguly & Sean Blanchard & Steve Wender & Bichlien H. Nguyen & Jake A. Smith, 2024. "Evaluating the risk of data loss due to particle radiation damage in a DNA data storage system," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    2. Cheng Kai Lim & Jing Wui Yeoh & Aurelius Andrew Kunartama & Wen Shan Yew & Chueh Loo Poh, 2023. "A biological camera that captures and stores images directly into DNA," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    3. Afsaneh Sadremomtaz & Robert F. Glass & Jorge Eduardo Guerrero & Dennis R. LaJeunesse & Eric A. Josephs & Reza Zadegan, 2023. "Digital data storage on DNA tape using CRISPR base editors," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    4. Jeong Moon & Changchun Liu, 2023. "Asymmetric CRISPR enabling cascade signal amplification for nucleic acid detection by competitive crRNA," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    5. Shimei Shen & Wen Wang & Yuanyan Ma & Shilei Wang & Shaocheng Zhang & Xuefei Cai & Liang Chen & Jin Zhang & Yalan Li & Xiaoli Wu & Jie Wei & Yanan Zhao & Ailong Huang & Siqiang Niu & Deqiang Wang, 2024. "Affinity molecular assay for detecting Candida albicans using chitin affinity and RPA-CRISPR/Cas12a," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    6. 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.
    7. Sehrish Khan & Muhammad Shahid Mahmood & Sajjad ur Rahman & Farzana Rizvi & Aftab Ahmad, 2020. "Evaluation of the CRISPR/Cas9 system for the development of resistance against Cotton leaf curl virus in model plants," Plant Protection Science, Czech Academy of Agricultural Sciences, vol. 56(3), pages 154-162.
    8. Yuqian Guo & Yaofeng Zhou & Hong Duan & Derong Xu & Min Wei & Yuhao Wu & Ying Xiong & Xirui Chen & Siyuan Wang & Daofeng Liu & Xiaolin Huang & Hongbo Xin & Yonghua Xiong & Ben Zhong Tang, 2024. "CRISPR/Cas-mediated “one to more” lighting-up nucleic acid detection using aggregation-induced emission luminogens," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    9. Aaron A. Smargon & Assael A. Madrigal & Brian A. Yee & Kevin D. Dong & Jasmine R. Mueller & Gene W. Yeo, 2022. "Crosstalk between CRISPR-Cas9 and the human transcriptome," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    10. Zhichen Xu & Dongjuan Chen & Tao Li & Jiayu Yan & Jiang Zhu & Ting He & Rui Hu & Ying Li & Yunhuang Yang & Maili Liu, 2022. "Microfluidic space coding for multiplexed nucleic acid detection via CRISPR-Cas12a and recombinase polymerase amplification," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    11. Lifu Song & Feng Geng & Zi-Yi Gong & Xin Chen & Jijun Tang & Chunye Gong & Libang Zhou & Rui Xia & Ming-Zhe Han & Jing-Yi Xu & Bing-Zhi Li & Ying-Jin Yuan, 2022. "Robust data storage in DNA by de Bruijn graph-based de novo strand assembly," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    12. Dalton T. Ham & Tyler S. Browne & Pooja N. Banglorewala & Tyler L. Wilson & Richard K. Michael & Gregory B. Gloor & David R. Edgell, 2023. "A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    13. Yekaterina S Pavlova & David Paez-Espino & Andrew Yu Morozov & Ilya S Belalov, 2021. "Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling," PLOS Computational Biology, Public Library of Science, vol. 17(3), pages 1-21, March.
    14. Yunxiang Wang & Hong Chen & Kai Lin & Yongjun Han & Zhixia Gu & Hongjuan Wei & Kai Mu & Dongfeng Wang & Liyan Liu & Ronghua Jin & Rui Song & Zhen Rong & Shengqi Wang, 2024. "Ultrasensitive single-step CRISPR detection of monkeypox virus in minutes with a vest-pocket diagnostic device," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    15. Chang Yeol Lee & Hyunho Kim & Ismail Degani & Hanna Lee & Angel Sandoval & Yoonho Nam & Madeleine Pascavis & Hyun Gyu Park & Thomas Randall & Amy Ly & Cesar M. Castro & Hakho Lee, 2024. "Empowering the on-site detection of nucleic acids by integrating CRISPR and digital signal processing," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    16. Nic Robertson & Vadim Shchepachev & David Wright & Tomasz W. Turowski & Christos Spanos & Aleksandra Helwak & Rose Zamoyska & David Tollervey, 2022. "A disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    17. Daniel C. Volke & Román A. Martino & Ekaterina Kozaeva & Andrea M. Smania & Pablo I. Nikel, 2022. "Modular (de)construction of complex bacterial phenotypes by CRISPR/nCas9-assisted, multiplex cytidine base-editing," Nature Communications, Nature, vol. 13(1), pages 1-14, 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_s41467-024-46767-x. 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.