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

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  • 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
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    References listed on IDEAS

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    1. 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.
    2. 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.
    3. 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.
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    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.

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