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Cited by 136DNA and Biological ComputingAdvanced biosensing and bioanalysis techniquesDNA and Nucleic Acid Chemistry

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An artificial chromosome for data storage

Open access
Chen, Weigang, Han, Mingzhe, Zhou, Jianting, Ge, Qi, Wang, Panpan, Zhang, Xinchen, Zhu, Siyu, Song, Lifu, Yuan, Yingjin·2021·National Science Review
DOI 10.1093/nsr/nwab028PMC PMC8288405
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Abstract

Abstract DNA digital storage provides an alternative for information storage with high density and long-term stability. Here, we report the de novo design and synthesis of an artificial chromosome that encodes two pictures and a video clip. The encoding paradigm utilizing the superposition of sparsified error correction codewords and pseudo-random sequences tolerates base insertions/deletions and is well suited to error-prone nanopore sequencing for data retrieval. The entire 254 kb sequence was 95.27% occupied by encoded data. The Transformation-Associated Recombination method was used in the construction of this chromosome from DNA fragments and necessary autonomous replication sequences. The stability was demonstrated by transmitting the data-carrying chromosome to the 100th generation. This study demonstrates a data storage method using encoded artificial chromosomes via in vivo assembly for write-once and stable replication for multiple retrievals, similar to a compact disc, with potential in economically massive data distribution.

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Figure 1. Design and assembly of a data-carrying artificial chromosome. (A) Schematic diagram of the data-carrying chromosome. Four additional ARSs were inserted at specific positions as labeled, and BB is short for building block. (B) The encoding scheme. Superposition coding with LDPC codes (R = 5/6) and pseudo-random sequences converted information sub-chunks (54 000 bits) into the DNA sequence (40 500 bp). The design is detailed in Note S1. (C) The NotI digestion of the artificial chromosome released two bands. Payload bands, 244 kb; backbone band, 10 kb. (D) The workflow of this digital data storage mode.
Figure 1. Design and assembly of a data-carrying artificial chromosome. (A) Schematic diagram of the data-carrying chromosome. Four additional ARSs were inserted at specific positions as labeled, and BB is short for building block. (B) The encoding scheme. Superposition coding with LDPC codes (R = 5/6) and pseudo-random sequences converted information sub-chunks (54 000 bits) into the DNA sequence (40 500 bp). The design is detailed in Note S1. (C) The NotI digestion of the artificial chromosome released two bands. Payload bands, 244 kb; backbone band, 10 kb. (D) The workflow of this digital data storage mode.CC BY · PubMed Central
Figure 2. Encoding scheme for chromosome-based DNA storage. (A) Error correction coding. Digital files were divided into bit blocks, denoted as m, which was multiplied by generator matrix G for LDPC and NB LDPC codewords. (B) Sparsification of codewords. The codewords were randomly interleaved. The interleaved codewords were then sparsified by converting every 4 to 5 bits according to the sparsification table. (C) The sparsified codewords were superposed with a predetermined pseudo-random sequence (called watermark) by exclusive or XOR operation. (D) The DNA sequence was obtained by transcoding every 2 bits to 1 base according to the transcoding table.
Figure 2. Encoding scheme for chromosome-based DNA storage. (A) Error correction coding. Digital files were divided into bit blocks, denoted as m, which was multiplied by generator matrix G for LDPC and NB LDPC codewords. (B) Sparsification of codewords. The codewords were randomly interleaved. The interleaved codewords were then sparsified by converting every 4 to 5 bits according to the sparsification table. (C) The sparsified codewords were superposed with a predetermined pseudo-random sequence (called watermark) by exclusive or XOR operation. (D) The DNA sequence was obtained by transcoding every 2 bits to 1 base according to the transcoding table.CC BY · PubMed Central
Figure 3. Rationale for ARSs added to the artificial chromosome. (A) Comparison of the GC contents in different assemblies. The DNA sequence as labeled was fragmented into 300 bp, and the GC content of each fragment was calculated. The number of fragments corresponding to different GC contents was normalized by the total fragment number and plotted. (B) Comparison of the maps of different assemblies showing the distribution of various GC contents. (C) Comparison of ACS counts in different assemblies.
Figure 3. Rationale for ARSs added to the artificial chromosome. (A) Comparison of the GC contents in different assemblies. The DNA sequence as labeled was fragmented into 300 bp, and the GC content of each fragment was calculated. The number of fragments corresponding to different GC contents was normalized by the total fragment number and plotted. (B) Comparison of the maps of different assemblies showing the distribution of various GC contents. (C) Comparison of ACS counts in different assemblies.CC BY · PubMed Central
Figure 4. Analyses of the growth effect and stability of the data-carrying chromosome. (A) The effect of the artificial chromosome on the growth of the host. Yeast strains yMH007 and yMH104 (control) were serially diluted and spotted on the agar plate for growth. Cells were passed for different generations as indicated in liquid media before the assay. (B) Stability of the data-carrying chromosome. Same number of cells passed for different generations as indicated were sprayed on the SC-Ura and 5'-FOA plates. The colonies on both plates were calculated and their ratios were presented. The results were representative of three independent biological experiments with the corresponding standard deviations.
Figure 4. Analyses of the growth effect and stability of the data-carrying chromosome. (A) The effect of the artificial chromosome on the growth of the host. Yeast strains yMH007 and yMH104 (control) were serially diluted and spotted on the agar plate for growth. Cells were passed for different generations as indicated in liquid media before the assay. (B) Stability of the data-carrying chromosome. Same number of cells passed for different generations as indicated were sprayed on the SC-Ura and 5'-FOA plates. The colonies on both plates were calculated and their ratios were presented. The results were representative of three independent biological experiments with the corresponding standard deviations.CC BY · PubMed Central
Figure 5. Error processing and data recovery. (A) Schematic flow of data recovery from nanopore sequencing reads. (B) Error rate distribution of reads from the artificial chromosome. Inset: error rate distribution by error typing. (C) Error rate distributions among six information sub-chunks after RACON polishing. Types of errors are labeled in different colors as indicated. (D) The distributions of substitution error rates among six information sub-chunks after indel identification and correction. (E) Recovery tests with various reads.
Figure 5. Error processing and data recovery. (A) Schematic flow of data recovery from nanopore sequencing reads. (B) Error rate distribution of reads from the artificial chromosome. Inset: error rate distribution by error typing. (C) Error rate distributions among six information sub-chunks after RACON polishing. Types of errors are labeled in different colors as indicated. (D) The distributions of substitution error rates among six information sub-chunks after indel identification and correction. (E) Recovery tests with various reads.CC BY · PubMed Central

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Metadata

Authors
Chen, W., Han, M., Zhou, J., Ge, Q., Wang, P., Zhang, X., Zhu, S., Song, L., & Yuan, Y.
Affiliations
  • Tianjin University (CN)
  • Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
ORCID
Venue
National Science Review
Publisher
Oxford University Press (OUP)
Published
2021-02-12
Volume
8
Issue
5
Pages
nwab028-nwab028
ISSN
  • 2053-714X (ISSN-L)
  • 2095-5138
DOI
10.1093/nsr/nwab028
PMC
PMC8288405
OpenAlex
W3130820694
Cited by
136
References
43
Citations by year
2026: 22 · 2025: 36 · 2024: 24 · 2023: 23 · 2022: 23 · 2021: 7
FWCI
6.04
Type
journal article
Language
en
Open access
Licence
Locations
  • National Science Review (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
National Natural Science Foundation of China (21621004)
Topics
  • Physical Sciences › Mathematics › Theoretical Computer Science › DNA and Biological Computing
  • 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 Nucleic Acid Chemistry
Keywords
DNA data storage, artificial chromosomes, error correction coding, nanopore sequencing, transformation-associated recombination, in vivo assembly, autonomous replication sequence, data retrieval

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