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

Doroschak, Kathryn; Zhang, Karen; Queen, Melissa; Strauß, Karin; Ceze, Luís; Nivala, Jeff

doi:10.1038/s41467-020-19151-8

Cited by 40 publications

(33 citation statements)

References 17 publications

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“…[ 31 ] We have demonstrated that nanopore sensing might be an alternative readout method for DNA tags in comparison to nanopore sequencing. [ 32 ] We created multiple copies of a specific data file written in a DNA structural annotation that can expand the potential of DNA nanostructures and nanopores as a feasible way to archive and access data.…”

Section: Discussionmentioning

confidence: 99%

DNA Structural Barcode Copying and Random Access

et al. 2021

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Digitally encoded deoxyribonucleic acid (DNA) nanostructures built via DNA self‐assembly have established applications in multiplexed biosensing and storing digital information. However, a key challenge is that DNA structures are not easily copied which is of vital importance for their large‐scale production and access to desired molecules by target‐specific amplification. Herein, DNA structural barcodes are built and the copying and random access of the barcodes from a library of molecules is demonstrated using a modified polymerase chain reaction (PCR). The structural barcodes are assembled by annealing a single‐stranded DNA scaffold with complementary short oligonucleotides containing protrusions as digital bits at defined locations. DNA nicks in these structures are ligated to facilitate barcode copying using PCR. To randomly access a target from a library of barcodes, a non‐complementary end in the DNA construct that serves as a barcode‐specific primer‐template is used. Readout of the DNA structural barcodes is performed with nanopore measurements. The study provides a roadmap for the convenient production of large quantities of self‐assembled DNA nanostructures. In addition, this strategy offers access to specific targets, a crucial capability for multiplexed single‐molecule sensing, and DNA data storage.

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Section: Discussionmentioning

confidence: 99%

DNA Structural Barcode Copying and Random Access

et al. 2021

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“…It is important to note the distinction between uses of the term DNA barcoding, as DNA barcoding is used for classifying species (different gene regions function as barcodes to identify organisms) 39,40 , to study molecular systems (for example in the form of unique molecular identifiers to eliminate PCR bias) 41 , or to tag products [42][43][44] . A molecular product tag is a pre-defined amount of DNA that is added to the building blocks of a certain substance.…”

Section: Logic Gates and Circuitsmentioning

confidence: 99%

Synthetic DNA applications in information technology

et al. 2022

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Synthetic DNA is a growing alternative to electronic-based technologies in fields such as data storage, product tagging, or signal processing. Its value lies in its characteristic attributes, namely Watson-Crick base pairing, array synthesis, sequencing, toehold displacement and polymerase chain reaction (PCR) capabilities. In this review, we provide an overview of the most prevalent applications of synthetic DNA that could shape the future of information technology. We emphasize the reasons why the biomolecule can be a valuable alternative for conventional electronic-based media, and give insights on where the DNA-analog technology stands with respect to its electronic counterparts.

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“…[ 8–10 ] Data decoding of DNA nanostructure‐based storage is often based on gel electrophoresis, which severely restricted the reading speed and data capacity. As an emerging technique, nanopore sequencing has been utilized to decode data saved in DNA sequences with advantages in terms of cost and readout speed, [ 11–14 ] but it is almost helpless for DNA nanostructure‐based storage. Even if the sequence is decoded, it is still difficult to reproduce the whole structure accurately, which indicates the higher security of this storage method from this perspective.…”

Section: Introductionmentioning

confidence: 99%

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Image Encoding Using Multi‐Level DNA Barcodes with Nanopore Readout

Zhu

Ermann

Chen

et al. 2021

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and readout speed, [11][12][13][14] but it is almost helpless for DNA nanostructure-based storage. Even if the sequence is decoded, it is still difficult to reproduce the whole structure accurately, which indicates the higher security of this storage method from this perspective. Additionally, hardware encryption with physical keys can further improve the security of the information saved by this strategy. [10,15] Solid-state nanopore provides us with a versatile tool to investigate the biomole cules, such as DNA, ribonucleic acid (RNA), and proteins, at the singlemolecule level. [16,17] We recently introduced a solid-state nanopore sensing platform to read bits encoded by 56 DNA hairpins on a 7.2 kb DNA carrier. [18] Readout of the structures required glass nanopores with diameters of around 5 nm. Such a small diameter complicates the fabrication process and reduces the success rates compared to easily manufactured >10 nm glass nanopores. The smaller diameter also leads to more non-specific interaction and pore clogging. [19] In further work, we used a streptavidin-labelled DNA scaffold to build a secure data storage method with binary codes. [15] While protein labels can be used with larger diameter pores, they complicate the molecular assembly and set an upper bound on the data density through their defined size. Additionally, the number of usable protein labels is limited due to the high monovalent salt concentrations required for the readout. The presence of proteins also reduces the lifetime of solid-state nanopores and hence has a detrimental effect on the viability of the readout.In this work, we replace protein barcodes with multi-way DNA junctions to address the shortcoming and limitations of our prior approaches. Inspired by the work of Wang and Seaman [20] we designed a multi-level storage architecture. Building on our established DNA carrier-based rewritable storage system with 14 nm diameter nanopores, [19] we use three DNA junction structures of different sizes (4-way junction, 6-way junction, and 12-way junction) to generate a quaternary encoding system (0-3) on the long linear DNA carrier, which increases the data density compared to classic binary encoding. Through toehold-mediated strand displacement reaction (SDR), [21][22][23] the presence of nanostructures on the carrier can be precisely controlled, allowing data reading and writing. Based on this storage system, we successfully save a grayscale image into the DNA nanostructures on 16 different carriers and read out the information in the mixture. Furthermore, using SDR the image information can be easily encrypted and decrypted.Deoxyribonucleic acid (DNA) nanostructure-based data encoding is an emerging information storage mode, offering rewritable, editable, and secure data storage. Herein, a DNA nanostructure-based storage method established on a solid-state nanopore sensing platform to save and encrypt a 2D grayscale image is proposed. DNA multi-way junctions of different sizes are attached to a double strand of DNA carriers, resulting i...

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

Cited by 40 publications

References 17 publications

DNA Structural Barcode Copying and Random Access

DNA Structural Barcode Copying and Random Access

Synthetic DNA applications in information technology

Image Encoding Using Multi‐Level DNA Barcodes with Nanopore Readout

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