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

Kathryn Doroschak, Karen Zhang, Melissa Queen, Aishwarya Mandyam, Karin Strauss, Luis Ceze and Jeff Nivala ()
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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

Nature Communications, 2020, vol. 11, issue 1, 1-8

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-19151-8

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