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Rapid and robust assembly and decoding of molecular tags with DNA-based nanopore signatures

Author

Listed:
  • Kathryn Doroschak

    (University of Washington)

  • Karen Zhang

    (University of Washington)

  • Melissa Queen

    (University of Washington)

  • Aishwarya Mandyam

    (University of Washington)

  • Karin Strauss

    (Microsoft Research)

  • Luis Ceze

    (University of Washington)

  • Jeff Nivala

    (University of Washington)

Abstract

Molecular tagging is an approach to labeling physical objects using DNA or other molecules that can be used when methods such as RFID tags and QR codes are unsuitable. No molecular tagging method exists that is inexpensive, fast and reliable to decode, and usable in minimal resource environments to create or read tags. To address this, we present Porcupine, an end-user molecular tagging system featuring DNA-based tags readable within seconds using a portable nanopore device. Porcupine’s digital bits are represented by the presence or absence of distinct DNA strands, called molecular bits (molbits). We classify molbits directly from raw nanopore signal, avoiding basecalling. To extend shelf life, decrease readout time, and make tags robust to environmental contamination, molbits are prepared for readout during tag assembly and can be stabilized by dehydration. The result is an extensible, real-time, high accuracy tagging system that includes an approach to developing highly separable barcodes.

Suggested Citation

  • Kathryn Doroschak & Karen Zhang & Melissa Queen & Aishwarya Mandyam & Karin Strauss & Luis Ceze & Jeff Nivala, 2020. "Rapid and robust assembly and decoding of molecular tags with DNA-based nanopore signatures," Nature Communications, Nature, vol. 11(1), pages 1-8, December.
  • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19151-8
    DOI: 10.1038/s41467-020-19151-8
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    Cited by:

    1. Jan Kretschmer & Tomáš David & Martin Dračínský & Ondřej Socha & Daniel Jirak & Martin Vít & Radek Jurok & Martin Kuchař & Ivana Císařová & Miloslav Polasek, 2022. "Paramagnetic encoding of molecules," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. 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.
    3. Xuyang Zhao & Junyao Li & Qingyuan Fan & Jing Dai & Yanping Long & Ronghui Liu & Jixian Zhai & Qing Pan & Yi Li, 2024. "Composite Hedges Nanopores codec system for rapid and portable DNA data readout with high INDEL-Correction," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    4. Tomáš David & Miroslava Šedinová & Aneta Myšková & Jaroslav Kuneš & Lenka Maletínská & Radek Pohl & Martin Dračínský & Helena Mertlíková-Kaiserová & Karel Čížek & Blanka Klepetářová & Miroslava Liteck, 2024. "Ultra-inert lanthanide chelates as mass tags for multiplexed bioanalysis," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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