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Sequencing a DNA analog composed of artificial bases

Author

Listed:
  • Christopher A. Thomas

    (University of Washington)

  • Henry Brinkerhoff

    (University of Washington)

  • Jonathan M. Craig

    (University of Washington)

  • Shuichi Hoshika

    (Foundation for Applied Molecular Evolution)

  • Desislava Mihaylova

    (University of Washington)

  • Akira M. Pfeffer

    (University of Washington)

  • Michaela C. Franzi

    (University of Washington)

  • Sarah J. Abell

    (University of Washington)

  • Jessica D. Carrasco

    (University of Washington)

  • Jens H. Gundlach

    (University of Washington)

  • Steven A. Benner

    (Foundation for Applied Molecular Evolution)

  • Andrew H. Laszlo

    (University of Washington)

Abstract

“ALternative Isoinformational ENgineered” (ALIEN) DNA is a biomimetic polymer composed of four entirely anthropogenic nucleotides. These alternative nucleosides form base pairs orthogonal to canonical bases and fold into the familiar B-form DNA double-helix, endowing ALIEN DNA with valuable biotechnological applications. The ability to sequence ALIEN DNA is essential for its continued development. However traditional sequencing approaches rely on chemical recognition of ACGT-DNA and cannot be easily adapted to ALIEN DNA. Here we demonstrate de novo nanopore sequencing of DNA comprised entirely of the four anthropogenic DNA bases. We show direct, label-free, single-molecule sequencing of such nucleic acids without the requirements of fluorescent labels, transliteration, amplification, or enzymatic synthesis. This paves the way for routine, accessible, and high-accuracy sequencing of DNA beyond A, C, G, and T.

Suggested Citation

  • Christopher A. Thomas & Henry Brinkerhoff & Jonathan M. Craig & Shuichi Hoshika & Desislava Mihaylova & Akira M. Pfeffer & Michaela C. Franzi & Sarah J. Abell & Jessica D. Carrasco & Jens H. Gundlach , 2025. "Sequencing a DNA analog composed of artificial bases," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61991-9
    DOI: 10.1038/s41467-025-61991-9
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    References listed on IDEAS

    as
    1. Nick Goldman & Paul Bertone & Siyuan Chen & Christophe Dessimoz & Emily M. LeProust & Botond Sipos & Ewan Birney, 2013. "Towards practical, high-capacity, low-maintenance information storage in synthesized DNA," Nature, Nature, vol. 494(7435), pages 77-80, February.
    2. Brian C Ross, 2014. "Mutual Information between Discrete and Continuous Data Sets," PLOS ONE, Public Library of Science, vol. 9(2), pages 1-5, February.
    3. Hinako Kawabe & Christopher A. Thomas & Shuichi Hoshika & Myong-Jung Kim & Myong-Sang Kim & Logan Miessner & Nicholas Kaplan & Jonathan M. Craig & Jens H. Gundlach & Andrew H. Laszlo & Steven A. Benne, 2023. "Enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
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