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.
Highlights
Molecular tagging is an approach to labeling physical objects using DNA or other molecules that can be used when methods such as radio-frequency identification (RFID) tags and QR codes are unsuitable
Tagging physical objects has proven useful for a range of formats and scenarios like UPC barcodes in packaging, QR codes for easy association of digital information with printed material, and radio-frequency identification (RFID) tags for inventory tracking
The development of portable, real-time nanopore sequencing[9], together with new methods that simplify the modular assembly of predefined DNA sequences[10], creates additional opportunities for rapid writing and on-demand readout in low resource environments
Summary
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. Molbits are prepared for readout (sequencing) prior to tag application and can be stabilized by dehydration, an approach that extends tag shelf life, decreases decoding time, and reduces contamination from environmental DNA. The result is a highly accurate real-time tagging system that includes an approach to developing highly separable barcodes These barcodes, and the methods we use to develop them, are extensible; they can be used both within Porcupine to tag physical objects and beyond this system for other molecule-level tagging needs like sample multiplexing for nanopore sequencing
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