IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-30588-x.html
   My bibliography  Save this article

A framework to efficiently describe and share reproducible DNA materials and construction protocols

Author

Listed:
  • Hideto Mori

    (The University of Tokyo
    Keio University
    Keio University)

  • Nozomu Yachie

    (The University of Tokyo
    The University of British Columbia)

Abstract

DNA constructs and their annotated sequence maps have been rapidly accumulating with the advancement of DNA cloning, synthesis, and assembly methods. Such resources have also been utilized in designing and building new DNA materials. However, as commonly seen in the life sciences, no framework exists to describe reproducible DNA construction processes. Furthermore, the use of previously developed DNA materials and building protocols is usually not appropriately credited. Here, we report a framework QUEEN (framework to generate quinable and efficiently editable nucleotide sequence resources) to resolve these issues and accelerate the building of DNA. QUEEN enables the flexible design of new DNA by using existing DNA material resource files and recording its construction process in an output file (GenBank file format). A GenBank file generated by QUEEN can regenerate the process code such that it perfectly clones itself and bequeaths the same process code to its successive GenBank files, recycling its partial DNA resources. QUEEN-generated GenBank files are compatible with existing DNA repository services and software. We propose QUEEN as a solution to start significantly advancing the material and protocol sharing of DNA resources.

Suggested Citation

  • Hideto Mori & Nozomu Yachie, 2022. "A framework to efficiently describe and share reproducible DNA materials and construction protocols," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30588-x
    DOI: 10.1038/s41467-022-30588-x
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-30588-x
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-30588-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. Jonathan Tellechea-Luzardo & Leanne Hobbs & Elena Velázquez & Lenka Pelechova & Simon Woods & Víctor Lorenzo & Natalio Krasnogor, 2022. "Versioning biological cells for trustworthy cell engineering," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Jessica S. Dymond & Sarah M. Richardson & Candice E. Coombes & Timothy Babatz & Héloïse Muller & Narayana Annaluru & William J. Blake & Joy W. Schwerzmann & Junbiao Dai & Derek L. Lindstrom & Annabel , 2011. "Synthetic chromosome arms function in yeast and generate phenotypic diversity by design," Nature, Nature, vol. 477(7365), pages 471-476, September.
    3. Wenjun Jiang & Xuejin Zhao & Tslil Gabrieli & Chunbo Lou & Yuval Ebenstein & Ting F. Zhu, 2015. "Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters," Nature Communications, Nature, vol. 6(1), pages 1-8, November.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Jeanet Mante & Chris J. Myers, 2023. "Advancing reuse of genetic parts: progress and remaining challenges," Nature Communications, Nature, vol. 14(1), pages 1-3, December.

    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. Alessandro L. V. Coradini & Christopher Ne Ville & Zachary A. Krieger & Joshua Roemer & Cara Hull & Shawn Yang & Daniel T. Lusk & Ian M. Ehrenreich, 2023. "Building synthetic chromosomes from natural DNA," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    2. Huiming Zhang & Xian Fu & Xuemei Gong & Yun Wang & Haolin Zhang & Yu Zhao & Yue Shen, 2022. "Systematic dissection of key factors governing recombination outcomes by GCE-SCRaMbLE," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    3. Lei Pei & Michele Garfinkel & Markus Schmidt, 2022. "Bottlenecks and opportunities for synthetic biology biosafety standards," Nature Communications, Nature, vol. 13(1), pages 1-4, December.
    4. Tiantian Chang & Weichao Ding & Shirui Yan & Yun Wang & Haoling Zhang & Yu Zhang & Zhi Ping & Huiming Zhang & Yijian Huang & Jiahui Zhang & Dan Wang & Wenwei Zhang & Xun Xu & Yue Shen & Xian Fu, 2023. "A robust yeast biocontainment system with two-layered regulation switch dependent on unnatural amino acid," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    5. Taotao Li & Duo Du & Dandan Zhang & Yicheng Lin & Jiakang Ma & Mengyu Zhou & Weida Meng & Zelin Jin & Ziqiang Chen & Haozhe Yuan & Jue Wang & Shulong Dong & Shaoyang Sun & Wenjing Ye & Bosen Li & Houb, 2023. "CRISPR-based targeted haplotype-resolved assembly of a megabase region," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    6. Dariusz R. Kutyna & Cristobal A. Onetto & Thomas C. Williams & Hugh D. Goold & Ian T. Paulsen & Isak S. Pretorius & Daniel L. Johnson & Anthony R. Borneman, 2022. "Construction of a synthetic Saccharomyces cerevisiae pan-genome neo-chromosome," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    7. Yuting Chen & Eriona Hysolli & Anlu Chen & Stephen Casper & Songlei Liu & Kevin Yang & Chenli Liu & George Church, 2022. "Multiplex base editing to convert TAG into TAA codons in the human genome," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    8. Shuangying Jiang & Zhouqing Luo & Jie Wu & Kang Yu & Shijun Zhao & Zelin Cai & Wenfei Yu & Hui Wang & Li Cheng & Zhenzhen Liang & Hui Gao & Marco Monti & Daniel Schindler & Linsen Huang & Cheng Zeng &, 2023. "Building a eukaryotic chromosome arm by de novo design and synthesis," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    9. Charlotte Cautereels & Jolien Smets & Peter Bircham & Dries De Ruysscher & Anna Zimmermann & Peter De Rijk & Jan Steensels & Anton Gorkovskiy & Joleen Masschelein & Kevin J. Verstrepen, 2024. "Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    10. Yuqian Tang & Debin Qin & Zhexian Tian & Wenxi Chen & Yuanxi Ma & Jilong Wang & Jianguo Yang & Dalai Yan & Ray Dixon & Yi-Ping Wang, 2023. "Diurnal switches in diazotrophic lifestyle increase nitrogen contribution to cereals," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    11. Li Cheng & Shijun Zhao & Tianyi Li & Sha Hou & Zhouqing Luo & Jinsheng Xu & Wenfei Yu & Shuangying Jiang & Marco Monti & Daniel Schindler & Weimin Zhang & Chunhui Hou & Yingxin Ma & Yizhi Cai & Jef D., 2024. "Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae," Nature Communications, Nature, vol. 15(1), pages 1-15, 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:13:y:2022:i:1:d:10.1038_s41467-022-30588-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.