IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-36297-3.html
   My bibliography  Save this article

DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage

Author

Listed:
  • Marius Welzel

    (University of Marburg
    University of Marburg)

  • Peter Michael Schwarz

    (University of Marburg
    University of Marburg)

  • Hannah F. Löchel

    (University of Marburg
    University of Marburg)

  • Tolganay Kabdullayeva

    (University of Marburg)

  • Sandra Clemens

    (University of Marburg
    University of Marburg)

  • Anke Becker

    (University of Marburg)

  • Bernd Freisleben

    (University of Marburg
    University of Marburg)

  • Dominik Heider

    (University of Marburg
    University of Marburg)

Abstract

The extensive information capacity of DNA, coupled with decreasing costs for DNA synthesis and sequencing, makes DNA an attractive alternative to traditional data storage. The processes of writing, storing, and reading DNA exhibit specific error profiles and constraints DNA sequences have to adhere to. We present DNA-Aeon, a concatenated coding scheme for DNA data storage. It supports the generation of variable-sized encoded sequences with a user-defined Guanine-Cytosine (GC) content, homopolymer length limitation, and the avoidance of undesired motifs. It further enables users to provide custom codebooks adhering to further constraints. DNA-Aeon can correct substitution errors, insertions, deletions, and the loss of whole DNA strands. Comparisons with other codes show better error-correction capabilities of DNA-Aeon at similar redundancy levels with decreased DNA synthesis costs. In-vitro tests indicate high reliability of DNA-Aeon even in the case of skewed sequencing read distributions and high read-dropout.

Suggested Citation

  • Marius Welzel & Peter Michael Schwarz & Hannah F. Löchel & Tolganay Kabdullayeva & Sandra Clemens & Anke Becker & Bernd Freisleben & Dominik Heider, 2023. "DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36297-3
    DOI: 10.1038/s41467-023-36297-3
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-36297-3
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-36297-3?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. Chao Pan & S. Kasra Tabatabaei & S. M. Hossein Tabatabaei Yazdi & Alvaro G. Hernandez & Charles M. Schroeder & Olgica Milenkovic, 2022. "Rewritable two-dimensional DNA-based data storage with machine learning reconstruction," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Randolph Lopez & Yuan-Jyue Chen & Siena Dumas Ang & Sergey Yekhanin & Konstantin Makarychev & Miklos Z Racz & Georg Seelig & Karin Strauss & Luis Ceze, 2019. "DNA assembly for nanopore data storage readout," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
    3. Karishma Matange & James M. Tuck & Albert J. Keung, 2021. "DNA stability: a central design consideration for DNA data storage systems," Nature Communications, Nature, vol. 12(1), pages 1-9, 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. 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. Ruohong Shi & Kuan-Lin Chen & Joshua Fern & Siming Deng & Yixin Liu & Dominic Scalise & Qi Huang & Noah J. Cowan & David H. Gracias & Rebecca Schulman, 2024. "Programming gel automata shapes using DNA instructions," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. 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.
    4. Adam Kuzdraliński & Marek Miśkiewicz & Hubert Szczerba & Wojciech Mazurczyk & Jeff Nivala & Bogdan Księżopolski, 2023. "Unlocking the potential of DNA-based tagging: current market solutions and expanding horizons," Nature Communications, Nature, vol. 14(1), pages 1-7, December.
    5. Andreas L. Gimpel & Wendelin J. Stark & Reinhard Heckel & Robert N. Grass, 2023. "A digital twin for DNA data storage based on comprehensive quantification of errors and biases," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    6. 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.

    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:14:y:2023:i:1:d:10.1038_s41467-023-36297-3. 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.