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Porcupine: Rapid and robust tagging of physical objects using nanopore-orthogonal DNA strands

View ORCID ProfileKathryn Doroschak, View ORCID ProfileKaren Zhang, Melissa Queen, Aishwarya Mandyam, View ORCID ProfileKarin Strauss, View ORCID ProfileLuis Ceze, View ORCID ProfileJeff Nivala
doi: https://doi.org/10.1101/2020.03.06.981514
Kathryn Doroschak
1Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA
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  • ORCID record for Kathryn Doroschak
Karen Zhang
1Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA
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Melissa Queen
1Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA
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Aishwarya Mandyam
1Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA
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Karin Strauss
2Microsoft, Redmond, WA
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Luis Ceze
1Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA
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Jeff Nivala
1Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA
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  • For correspondence: jmdn@cs.washington.edu
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Abstract

Molecular tagging is an approach to labeling physical objects using DNA or other molecules that can be used in cases where methods like RFID tags and QR codes are not suitable. No molecular tagging method exists that is inexpensive, fast and reliable to decode, and usable outside a lab setting to create or read tags. To address this, we present Porcupine, an end-user molecular tagging system that features DNA-based tags readable within seconds using a portable nanopore device. Porcupine’s digital bits are represented by the presence or absence of distinct, nanopore-orthogonal DNA strands, which we call molecular bits (molbits). We classify molbits directly from the raw nanopore signal, avoiding basecalling. To extend the tag’s 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 a novel approach to developing nanopore-orthogonal barcodes.

One sentence summary Porcupine lets end-users label physical objects with custom DNA tags, without requiring a lab to create or read tags, and offers rapid readout using nanopore sequencing.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted March 08, 2020.
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Porcupine: Rapid and robust tagging of physical objects using nanopore-orthogonal DNA strands
Kathryn Doroschak, Karen Zhang, Melissa Queen, Aishwarya Mandyam, Karin Strauss, Luis Ceze, Jeff Nivala
bioRxiv 2020.03.06.981514; doi: https://doi.org/10.1101/2020.03.06.981514
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Porcupine: Rapid and robust tagging of physical objects using nanopore-orthogonal DNA strands
Kathryn Doroschak, Karen Zhang, Melissa Queen, Aishwarya Mandyam, Karin Strauss, Luis Ceze, Jeff Nivala
bioRxiv 2020.03.06.981514; doi: https://doi.org/10.1101/2020.03.06.981514

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