DNA‐Based Concatenated Encoding System for High‐Reliability and High‐Density Data Storage
Abstract
Information storage based on DNA molecules provides a promising solution with advantages of low‐energy consumption, high storage efficiency, and long lifespan. However, there are only four natural nucleotides and DNA storage is thus limited by 2 bits per nucleotide. Here, artificial nucleotides into DNA data storage to achieve higher coding efficiency than 2 bits per nucleotide is introduced. To accommodate the characteristics of DNA synthesis and sequencing, two high‐reliability encoding systems suitable for four, six, and eight nucleotides, i.e., the RaptorQ‐Arithmetic‐LZW‐RS (RALR) and RaptorQ‐Arithmetic‐Base64‐RS (RABR) systems, are developed. The two concatenated encoding systems realize the advantages of correcting DNA sequence losses, correcting errors within DNA sequences, reducing homopolymers, and controlling specific nucleotide contents. The average coding efficiencies with error correction and without arithmetic compression by the RALR system using four, six, and eight nucleotides reach 1.27, 1.61, and 1.85 bits per nucleotide, respectively. While the average coding efficiencies by the RABR system are up to 1.50, 2.00, and 2.35 bits per nucleotide, respectively. The coding efficiency, versatility, and tunability of the developed artificial DNA systems might provide significant guidance for high‐reliability and high‐density data storage.
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Physical and logical redundancy lower the storage density of DNA.
“While physical and logical redundancy lower the storage density of DNA, recent works have proposed to raise it by expanding the DNA alphabet using composite natural letters7,51,52 or chemically modified nucleotides.53”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [52]
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Self-citation
- Authors
- Ren, Y., Zhang, Y., Liu, Y., Wu, Q., Su, J., Wang, F., Chen, D., Fan, C., Liu, K., & Zhang, H.
- Affiliations
- Tsinghua University (CN)
- Chinese Academy of Sciences (CN)
- State Key Laboratory Fluid Power and Mechatronic Systems (CN)
- University of Chinese Academy of Sciences (CN)
- Shanghai Jiao Tong University (CN)
- Corresponding author
- Su, Juanjuan
- Wang, Fan
- Chen, Dong
- Liu, Kai
- ORCID
- Venue
- Small Methods
- Publisher
- Wiley
- Published
- 2022-02-10
- Volume
- 6
- Issue
- 4
- Pages
- e2101335-e2101335
- ISSN
- 2366-9608 (ISSN-L)
- OpenAlex
- W4211073903
- Cited by
- 55
- References
- 40
- Citations by year
- 2026: 6 · 2025: 19 · 2024: 13 · 2023: 11 · 2022: 6
- FWCI
- 4.00
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Small Methods (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (21 877 104, 21 834 007, 21 907 088, 21 878 258, 22 020 102 003, 22 125 701)
- Natural Science Foundation of Zhejiang Province (Y20B060027)
- Youth Innovation Promotion Association of the Chinese Academy of Sciences (2020228)
- Key Technologies Research and Development Program (2020YFA0712102)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Physical Sciences › Computer Science › Computer Networks and Communications › Error Correcting Code Techniques
- Keywords
- DNA data storage, LZW compression, Reed-Solomon error correction, coding efficiency
- MeSH terms
- DNA, Nucleotides, Reproducibility of Results, Information Storage and Retrieval, Sequence Analysis, DNA
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