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Oligonucleotide subsets selection by single nucleotide resolution barcode identification

Author

Listed:
  • Woojin Kim

    (Gwangju Institute of Science and Technology (GIST))

  • Mingweon Chon

    (Seoul National University)

  • Yoonhae Koh

    (Gwangju Institute of Science and Technology (GIST))

  • Hansol Choi

    (Seoul National University
    Seoul National University
    Harvard Medical School)

  • Eunjin Choi

    (Gwangju Institute of Science and Technology (GIST))

  • Hyewon Park

    (ATG Lifetech Inc.)

  • Yushin Jung

    (ATG Lifetech Inc.)

  • Taehoon Ryu

    (ATG Lifetech Inc.)

  • Sunghoon Kwon

    (Seoul National University
    Seoul National University)

  • Yeongjae Choi

    (Gwangju Institute of Science and Technology (GIST))

Abstract

Effective subset selection from complex oligonucleotide libraries is crucial for genomics, synthetic biology, and DNA data storage. The polymerase chain reaction, foundational for amplifying target subsets is limited by primer design and length for specificity, which constrains the scalability of oligo libraries and increases the synthesis burden for primers. We introduce an oligo subset selection methodology that utilizes sequence-specific cyclic nucleotide synthesis and blocking of the template oligos. This approach eliminates the need for primers for selective hybridization and enables the encoding and selection of hundreds of subsets with barcode lengths of fewer than five nucleotides. Moreover, cyclic selection enables a hierarchical data structure in the oligo library, enhancing the programmability. This advancement offers a scalable and cost-effective solution for handling complex oligo libraries.

Suggested Citation

  • Woojin Kim & Mingweon Chon & Yoonhae Koh & Hansol Choi & Eunjin Choi & Hyewon Park & Yushin Jung & Taehoon Ryu & Sunghoon Kwon & Yeongjae Choi, 2025. "Oligonucleotide subsets selection by single nucleotide resolution barcode identification," Nature Communications, Nature, vol. 16(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56856-0
    DOI: 10.1038/s41467-025-56856-0
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    References listed on IDEAS

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