DNA Structural Barcode Copying and Random Access
Open accessPublished version of a preprint
Abstract
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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In nanopore reads of labeled DNA, each label is read in [10-1; 101] ms.
“Conversely, in regards to nanopore reads of labeled DNA, each label is read in [10–1; 101] ms.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [101]
Each of those structures had a noncomplementary end that acted as a barcode-specific primer template for the random access of data.
“Each of these structures had a noncomplementary end, which acted as a barcode-specific primer template for the random access of data.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [101]
Bošković et al. performed random access of DNA barcodes by exploiting a modified PCR method to increase the number of target DNA nanostructures.
“In their work, random access of DNA barcodes was performed by exploiting a modified PCR method to increase the number of the target DNA nanostructures.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [101]
Random access of DNA barcodes was demonstrated in 2021 by Bošković et al.
“Another important feature is random access, as demonstrated in 2021 by Bošković et al.101”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [101]
In those structures, DNA nicks were ligated to favor the copy of the barcode by PCR.
“In these structures, DNA nicks were ligated to favor the copy of the barcode by PCR.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [101]
In Bošković et al.'s structures, DNA structural barcodes were annealed as short oligonucleotides containing protrusions on single-stranded DNA scaffolds to form digital bits at precise locations.
“Indeed, DNA structural barcodes were annealed as short oligonucleotides containing protrusions on single-stranded DNA (ssDNA) scaffolds to form digital bits at precise locations.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [101]
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- Authors
- Bošković, F., Ohmann, A., Keyser, U. F., & Chen, K.
- Affiliations
- University of Cambridge (GB)
- Corresponding author
- Keyser, Ulrich F.
- Chen, Kaikai
- Venue
- Small Structures
- Publisher
- Wiley
- Published
- 2021-02-22
- Volume
- 2
- Issue
- 5
- ISSN
- 2688-4062 (ISSN-L)
- OpenAlex
- W3133305921
- Cited by
- 24
- References
- 38
- Citations by year
- 2025: 5 · 2024: 5 · 2023: 3 · 2022: 7 · 2021: 4
- FWCI
- 1.49
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Small Structures (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo
- Funders
- European Research Council (647144)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Physical Sciences › Engineering › Biomedical Engineering › Nanopore and Nanochannel Transport Studies
- Keywords
- DNA self-assembly, DNA nanostructures, random access, DNA nicks, ligation, DNA data storage, digital information storage
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