Driving the Scalability of DNA-Based Information Storage Systems
Open accessPublished version of a preprint
Abstract
The extreme density of DNA presents a compelling advantage over current storage media; however, to reach practical capacities, new systems for organizing and accessing information are needed. Here, we use chemical handles to selectively extract unique files from a complex database of DNA mimicking 5 TB of data and design and implement a nested file address system that increases the theoretical maximum capacity of DNA storage systems by five orders of magnitude. These advancements enable the development and future scaling of DNA-based data storage systems with modern capacities and file access capabilities.
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A different method of random access using bead extraction utilized 10^18 unique sequences.
“In more recent work, a different method of random access using bead extraction of desired strands prior to PCR random access utilized 1018 unique sequences11.”
From Probing the physical limits of reliable DNA data retrieval. (2020) · cites this paper as [11]
Incorporation of random-access priming regions into each oligo decreases the available space for data-encoding bases, thereby decreasing storage density, currently by about 15% per address region.
“First, the incorporation of random-access priming regions into each oligo decreases the available space for data-encoding bases, thereby also decreasing the storage density (currently by about 15% per address region).71,75”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [71]
Currently, the highest demonstrated data capacity for random access is on the order of terabytes of data.
“Currently, the highest demonstrated data capacity for random access is on the order of terabytes of data.6,12,71”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [71]
Biotin-labeled primers can be used to address and extract specific files via streptavidin magnetic beads based on file-specific random access regions in encoding oligos.
“As mentioned above, biotin-labeled primers can be used to address and extract specific files via streptavidin magnetic beads on the basis of file-specific random access regions in encoding oligos, similarly to PCR-based addressing.71,78”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [71]
Nested addressing barcodes have been used to uniquely identify a greater number of files, and biochemical affinity tags have been used to selectively pull down oligos for targeted amplification.
“Nested addressing barcodes14–16 have also been used to uniquely identify a greater number of files, as well as biochemical affinity tags to selectively pull down oligos for targeted amplification17.”
From Random access DNA memory using Boolean search in an archival file storage system (2021) · cites this paper as [17]
For an exabyte-scale data pool, each file requires at least three barcodes, or up to sixty nucleotides in total barcode sequence length, thereby reducing the number of nucleotides that can be used for data encoding.
“For example, for an exabyte-scale data pool, each file requires at least three barcodes17, or up to sixty nucleotides in total barcode sequence length, thereby reducing the number of nucleotides that can be used for data encoding.”
From Random access DNA memory using Boolean search in an archival file storage system (2021) · cites this paper as [17]
Because encapsulation of the DNA file sequence relies only on electrostatic interactions between positively-charged silica and the phosphate backbone of DNA, the approach can equally encapsulate any molecular weight of DNA molecule applicable to MB and larger file sizes, and is compatible with alternative DNA file compositions such as 100-200-mer oligonucleotides or multiple layers of encapsulated
“Because encapsulation of the DNA file sequence relies only on electrostatic interactions between positively-charged silica and the phosphate backbone of DNA, our approach can equally encapsulate any molecular weight of DNA molecule applicable to MB and larger file sizes, as demonstrated previously23, and is compatible with alternative DNA file compositions such as 100–200-mer oligonucleotides that”
From Random access DNA memory using Boolean search in an archival file storage system (2021) · cites this paper as [17]
Unlike PCR that requires 20-30 rounds of heating and cooling to selectively amplify the selected sequence, the authors' approach selects files directly without need for thermal cycling and amplification.
“While comparable in sensitivity to a nested PCR barcoding data indexing approach17, unlike PCR that requires 20–30 of rounds of heating and cooling to selectively amplify the selected sequence, our approach selects files directly without need for thermal cycling and amplification.”
From Random access DNA memory using Boolean search in an archival file storage system (2021) · cites this paper as [17]
The file system overcomes several challenges associated with pre-existing PCR-based file systems, including obviating the need for numerous heating and cooling cycles and enzymatic synthesis, and eliminating non-specific crosstalk between file sequences and barcodes, while enabling arbitrary Boolean logical search queries.
“Our file system overcomes several challenges associated with pre-existing PCR-based file systems, including obviating the need for numerous heating and cooling cycles and enzymatic synthesis, and eliminating non-specific crosstalk between file sequences and barcodes17,19,21, while enabling arbitrary Boolean logical search queries.”
From Random access DNA memory using Boolean search in an archival file storage system (2021) · cites this paper as [17]
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- Authors
- Tomek, K. J., Volkel, K., Simpson, A., Hass, A. G., Indermaur, E. W., Tuck, J. M., & Keung, A. J.
- Affiliations
- North Carolina State University (US)
- Corresponding author
- Tuck, James M.
- Keung, Albert J.
- Venue
- ACS Synthetic Biology
- Publisher
- American Chemical Society (ACS)
- Published
- 2019-05-22
- Volume
- 8
- Issue
- 6
- Pages
- 1241-1248
- ISSN
- 2161-5063 (ISSN-L)
- OpenAlex
- W2951989222
- Cited by
- 100
- References
- 20
- Citations by year
- 2026: 16 · 2025: 18 · 2024: 16 · 2023: 14 · 2022: 11 · 2021: 16 · 2020: 7 · 2019: 2
- FWCI
- 2.98
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- ACS Synthetic Biology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- North Carolina State University (2018-2509)
- North Carolina Biotechnology Center
- National Science Foundation (CNS-1650148)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Physical Sciences › Computer Science › Computer Networks and Communications › Advanced Data Storage Technologies
- Keywords
- DNA data storage, scalability, file retrieval, storage capacity, synthetic DNA, information storage systems
- MeSH terms
- DNA, Information Storage and Retrieval, Sequence Analysis, DNA, Databases, Nucleic Acid, Synthetic Biology, High-Throughput Nucleotide Sequencing
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