首页 > 过刊浏览>2024年第13卷第3期 >25-38. DOI:10.12146/j.issn.2095-3135.20231031002
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DNA 数据存储中信息处理技术的研究进展与挑战
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TB34

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国家重点研发计划项目(2018YFA0902600, 2021YFF1200300)


Research Progress and Challenges of Data Processing Technology for DNA-Based Information Storage
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This work is supported by National Key Research and Development Program of China (2018YFA0902600, 2021YFF1200300)

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    摘要:

    作为新一代信息存储介质，DNA 具有高信息密度和长期保存能力，有望解决全球数据存储介质耗竭的问题。但目前 DNA 信息存储技术的发展主要围绕信息“冷存储”开展，这使得存储过程中出现修改、更新、删除、销毁等需求时束手无策。该文从“冷存储”技术的现状出发，通过归纳总结 DNA 信息存储介质难以实现“热存储”应用的原因，解析用于信息处理功能的一系列“热存储”技术，包括加密销毁、重写再生、擦除恢复、运算记录等，详细论证 DNA 介质用作信息处理载体的可行性与有效性，分析各技术之间的关联性和挑战性，以期为 DNA 存储技术低能耗、高精准、高效率、高安全性的应用奠定基础，并推动新一代智能型信息存储介质和信息处理系统的发展。

    Abstract:

    DNA molecules exhibit highly promising properties of high storage density and extended lifespan as a medium for next generation digital data storage. Thus, it is expected to act as an alternative to address the global issue of insufficient data storage materials. However, the current advances of DNA-based information storage are mainly focused on “the cold storage of information”, so that it is difficult to realize quick data processing in DNA, such as rewriting, updating, deleting, and erasure. Based on the current situation of “cold storage” technology, the reasons why DNA information storage media is difficult to achieve “hot storage” applications has been summarized. In that context, the data processing including destruction, encryption, rewriting, regeneration, decay, recovery, and arithmetic recording can be realized. The feasibility of using DNA media as an information processing carrier has been comprehensively demonstrated, and corresponding advantages and disadvantages were emphasized. This review aims to highlight the importance of DNA storage technology with the potential low energy consumption, high accuracy, high efficiency, and high security. Additionally, it will show the perspective regarding the integration of DNA characteristics for the next generation of intelligent information storage and processing systems.

    参考文献
    [1] Wang S, Mao X, Wang F, et al. Data Storage Using Dna[J]. Advanced Materials, 2023: e2307499.
    [2] Organick L, Ang SD, Chen YJ, et al. Random access in large-scale DNA data storage[J]. Nature Biotechnology, 2018, 36(3): 242-248.
    [3] Bornholt J, Lopez R, Carmean DM, et al. A DNA-based archival storage system[Z]. Proceedings of the Twenty-First International Conference on Architectural Support for Programming Languages and Operating Systems. Atlanta, GA, USA. 2016: 637-649.10.1145/2872362.2872397
    [4] Erlich Y, Zielinski D. DNA Fountain enables a robust and efficient storagearchitecture[J]. Science, 2017, 355: 950-954.
    [5] Lee H, Wiegand DJ, Griswold K, et al. Photon-directed multiplexed enzymatic DNA synthesis for molecular digital data storage[J]. Nature Communications, 2020, 11(1): 5246.
    [6] Lee HH, Kalhor R, Goela N, et al. Terminator-free template-independent enzymatic DNA synthesis for digital information storage[J]. Nature Communications, 2019, 10(1): 2383.
    [7] Xu C, Zhao C, Ma B, et al. Uncertainties in synthetic DNA-based data storage[J]. Nucleic Acids Research, 2021, 49(10): 5451-5469.
    [8] Hsi-Yang Fritz M, Leinonen R, Cochrane G, et al. Efficient storage of high throughput DNA sequencing data using Reference-based compression[J]. Genome Research, 2011, 21(5): 734-740.
    [9] Meiser LC, Antkowiak PL, Koch J, et al. Reading and writing digital data in DNA[J]. Nature Protocols, 2020, 15(1): 86-101.
    [10] Shipman SL, Nivala J, Macklis JD, et al. CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria[J]. Nature, 2017, 547(7663): 345-349.
    [11] Bennet D, Vo‐Dinh T, Zenhausern F. Current and emerging opportunities in biological medium‐based computing and digital data storage[J]. Nano Select, 2021: 1-20.
    [12] Banal JL, Shepherd TR, Berleant J, et al. Random access DNA memory using Boolean search in an archival file storage system[J]. Nature Materials, 2021, 20: 1272–1280.
    [13] Tomek KJ, Volkel K, Simpson A, et al. Driving the Scalability of DNA-Based Information Storage Systems[J]. ACS Synthetic Biology, 2019, 8(6): 1241-1248.
    [14] Meiser LC, Nguyen BH, Chen YJ, et al. Synthetic DNA applications in information technology[J]. Nature Communications, 2022, 13(1): 352.
    [15] van der Valk T, Pecnerova P, Diez-Del-Molino D, et al. Million-year-old DNA sheds light on the genomic history of mammoths[J]. Nature, 2021, 591(7849): 265-269.
    [16] Antkowiak PL, Koch J, Nguyen BH, et al. Integrating DNA Encapsulates and Digital Microfluidics for Automated Data Storage in DNA[J]. Small, 2022, 18(15): e2107381.
    [17] Matange K, Tuck JM, Keung AJ. DNA stability: a central design consideration for DNA data storage systems[J]. Nature Communications, 2021, 12(1): 1358.
    [18] Fei Z, Gupta N, Li M, et al. Toward highly effective loading of DNA in hydrogels for high-density and long-term information storage[J]. Science Advances, 2023, 9(19): eadg9933.
    [19] Cao B, Zhang X, Cui S, et al. Adaptive coding for DNA storage with high storage density and low coverage[J]. NPJ Syst Biol Appl, 2022, 8(1): 23.
    [20] Gimpel AL, Stark WJ, Heckel R, et al. A digital twin for DNA data storage based on comprehensive quantification of errors and biases[J]. Nature Communications, 2023, 14(1): 6026.
    [21] Organick L, Nguyen BH, McAmis R, et al. An Empirical Comparison of Preservation Methods for Synthetic DNA Data Storage[J]. Small Methods, 2021, 5(5): e2001094.
    [22] Bonnet J, Colotte M, Coudy D, et al. Chain and conformation stability of solid-state DNA: implications for room temperature storage[J]. Nucleic Acids Research, 2010, 38(5): 1531-1546.
    [23] Mayer C, McInroy GR, Murat P, et al. An epigenetics-inspired DNA-based data storage system[J]. Angewandte Chemie International Edition, 2016, 55(37): 11144-11148.
    [24] Chen WD, Kohll AX, Nguyen BH, et al. Combining Data Longevity with High Storage Capacity—Layer‐by‐Layer DNA Encapsulated in Magnetic Nanoparticles[J]. Advanced Functional Materials, 2019, 29(28): 1901672.
    [25] Ma J-Y, Wang K-X, Ma M, et al. Magnetic Microsphere/Silica Nanoparticle Composite Structures for Switchable DNA Storage[J]. ACS Applied Nano Materials, 2022, 5(10): 15619-15628.
    [26] Yu M, Lim D, Kim J, et al. Processing DNA Storage through Programmable Assembly in a Droplet-Based Fluidics System[J]. Adv Sci (Weinh), 2023: e2303197.
    [27] Geng C, Liu S, Jiang X. A nanoparticle-coated microfluidic chip for automated, non-destructive extraction of encapsulated DNA in data storage[J]. Chemical Science, 2023, 14(15): 3973-3981.
    [28] Nguyen BH, Takahashi CN, Gupta G, et al. Scaling DNA data storage with nanoscale electrode wells[J]. Science Advances, 2021, 7: eabi6714.
    [29] Newman S, Stephenson AP, Willsey M, et al. High density DNA data storage library via dehydration with digital microfluidic retrieval[J]. Nature Communications, 2019, 10(1): 1706.
    [30] Grass RN, Heckel R, Puddu M. Robust chemical preservation of digital information on DNA in silica with error‐correcting codes[J]. Angewandte Chemie International Edition, 2015, 54(8): 2552-2555.
    [31] Zhang Y, Wang F, Chao J, et al. DNA origami cryptography for secure communication[J]. Nature Communications, 2019, 10(1): 5469.
    [32] Seeman NC, Sleiman HF. DNA nanotechnology[J]. Nature Reviews Materials, 2017, 3(1): 1-23.
    [33] Tomek KJ, Volkel K, Indermaur EW, et al. Promiscuous molecules for smarter file operations in DNA-based data storage[J]. Nature Communications, 2021, 12(1): 3518.
    [34] Xu C, Ma B, Gao Z, et al. Electrochemical DNA synthesis and sequencing on a single electrode with scalability for integrated data storage[J]. Science Advances, 2021, 7: eabk0100.
    [35] Lopez R, Chen YJ, Dumas Ang S, et al. DNA assembly for nanopore data storage readout[J]. Nature Communications, 2019, 10(1): 2933.
    [36] Bogels BWA, Nguyen BH, Ward D, et al. DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access[J]. Nature Nanotechnology, 2023, 18(8): 912-921.
    [37] Lau B, Chandak S, Roy S, et al. Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing[J]. Scientific Reports, 2023, 13(1): 8514.
    [38] Koch J, Gantenbein S, Masania K, et al. A DNA-of-things storage architecture to create materials with embedded memory[J]. Nature Biotechnology, 2020, 38(1): 39-43.
    [39] Antkowiak PL, Lietard J, Darestani MZ, et al. Low cost DNA data storage using photolithographic synthesis and advanced information reconstruction and error correction[J]. Nature Communications, 2020, 11(1): 5345.
    [40] Anavy L, Vaknin I, Atar O, et al. Data storage in DNA with fewer synthesis cycles using composite DNA letters[J]. Nature Biotechnology, 2019, 37(10): 1229-1236.
    [41] Choi Y, Ryu T, Lee AC, et al. High information capacity DNA-based data storage with augmented encoding characters using degenerate bases[J]. Scientific Reports, 2019, 9(1): 6582.
    [42] Goldman N, Bertone P, Chen S, et al. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA[J]. Nature, 2013, 494(7435): 77-80.
    [43] Song L, Geng F, Gong ZY, et al. Robust data storage in DNA by de Bruijn graph-based de novo strand assembly[J]. Nature Communications, 2022, 13(1): 5361.
    [44] Zhang Y, Kong L, Wang F, et al. Information stored in nanoscale: Encoding data in a single DNA strand with Base64[J]. Nano Today, 2020, 33: 100871.
    [45] Ren Y, Zhang Y, Liu Y, et al. DNA-Based Concatenated Encoding System for High-Reliability and High-Density Data Storage[J]. Small Methods, 2022: e2101335.
    [46] Yim SS, McBee RM, Song AM, et al. Robust direct digital-to-biological data storage in living cells[J]. Nature Chemical Biology, 2021, 17: 246–253
    [47] Zhang Y, Ren Y, Liu Y, et al. Preservation and Encryption in DNA Digital Data Storage[J]. ChemPlusChem, 2022, 87: e202200183.
    [48] Hao M, Qiao H, Gao Y, et al. A mixed culture of bacterial cells enables an economic DNA storage on a large scale[J]. Communications Biology, 2020, 3(1): 416.
    [49] Chen W, Han M, Zhou J, et al. An artificial chromosome for data storage[J]. National Science Review, 2021, 8(5): nwab028.
    [50] Sun F, Dong Y, Ni M, et al. Mobile and Self-Sustained Data Storage in an Extremophile Genomic DNA[J]. Advanced Science, 2023, 10(10): e2206201.
    [51] Grass RN, Heckel R, Dessimoz C, et al. Genomic Encryption of Digital Data Stored in Synthetic DNA[J]. Angewandte Chemie International Edition in English, 2020, 59(22): 8476-8480.
    [52] Zheng LL, Li JZ, Wen M, et al. Enthalpy and entropy synergistic regulation–based programmable DNA motifs for biosensing and information encryption[J]. Science Advances, 2023, 9: eadf5868.
    [53] Fan C, Deng Q, Zhu TF. Bioorthogonal information storage in L-DNA with a high-fidelity mirror-image Pfu DNA polymerase[J]. Nature Biotechnology, 2021, 39(12): 1548-1555.
    [54] Li SY, Liu JK, Zhao GP, et al. CADS: CRISPR/Cas12a-Assisted DNA Steganography for Securing the Storage and Transfer of DNA-Encoded Information[J]. ACS Synthetic Biology, 2018, 7(4): 1174-1178.
    [55] Kim J, Bae JH, Baym M, et al. Metastable hybridization-based DNA information storage to allow rapid and permanent erasure[J]. Nature Communications, 2020, 11(1): 5008.
    [56] Yazdi SM, Yuan Y, Ma J, et al. A rewritable, random-access DNA-based storage system[J]. Scientific Reports, 2015, 5: 14138.
    [57] Chandrasekaran AR, Levchenko O, Patel DS, et al. Addressable configurations of DNA nanostructures for rewritable memory[J]. Nucleic Acids Research, 2017, 45(19): 11459-11465.
    [58] Liu Y, Ren Y, Li J, et al. In vivo processing of digital information molecularly with targeted specificity and robust reliability[J]. Science Advances, 2022, 8(31): eabo7415.
    [59] Sadremomtaz A, Glass RF, Guerrero JE, et al. Digital data storage on DNA tape using CRISPR base editors[J]. Nature Communications, 2023, 14(1): 6472.
    [60] Liu F, Li J, Zhang T, et al. Engineered Spore-Forming Bacillus as a Microbial Vessel for Long-Term DNA Data Storage[J]. ACS Synthetic Biology, 2022, 11(11): 3583–3591.
    [61] Xu C, Ma B, Dong X, et al. Assembly of Reusable DNA Blocks for Data Storage Using the Principle of Movable Type Printing[J]. ACS Applied Materials Interfaces, 2023, 15(20): 24097-24108.
    [62] Yan Y, Pinnamaneni N, Chalapati S, et al. Scaling logical density of DNA storage with enzymatically-ligated composite motifs[J]. Scientific Reports, 2023, 13(1): 15978.
    [63] Welzel M, Schwarz PM, Lochel HF, et al. DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage[J]. Nature Communications, 2023, 14(1): 628.
    [64] Park SJ, Kim S, Jeong J, et al. Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads[J]. Bioinformatics, 2023, 39(9): btad548.
    [65] Pan C, Tabatabaei SK, Tabatabaei Yazdi SMH, et al. Rewritable two-dimensional DNA-based data storage with machine learning reconstruction[J]. Nature Communications, 2022, 13(1): 2984.
    [66] Meiser LC, Gimpel AL, Deshpande T, et al. Information decay and enzymatic information recovery for DNA data storage[J]. Communications Biology, 2022, 5(1): 1117.
    [67] Wang F, Lv H, Li Q, et al. Implementing digital computing with DNA-based switching circuits[J]. Nature Communications, 2020, 11(1): 121.
    [68] Bee C, Chen YJ, Queen M, et al. Molecular-level similarity search brings computing to DNA data storage[J]. Nature Communications, 2021, 12(1): 4764.
    [69] Bhattarai-Kline S, Lear SK, Fishman CB, et al. Recording gene expression order in DNA by CRISPR addition of retron barcodes[J]. Nature, 2022, 608: 217–225.
    [70] Sheth RU, Sung Sun Yim, Wu FL, et al. multiplex recording of cellular events over time on CRISPR biological tape[J]. Science, 2017, 358: 1457–1461.
    [71] Bonnet J, Subsoontorn P, Endy D. Rewritable digital data storage in live cells via engineered control of recombination directionality[J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(23): 8884-8889.
    [72] Rutten MGTA, Vaandrager FW, Elemans JAAW, et al. Encoding information into polymers[J]. Nature Reviews Chemistry, 2018, 2(11): 365-381.
    [73] Liu Y, Zhao K, Ren Y, et al. Highly Plasticized Lanthanide Luminescence for Information Storage and Encryption Applications[J]. Advanced Science, 2022, 9(7): e2105108.
    [74] Ren Y, Zhang Y, Liu Y, et al. Highly reliable and efficient encoding systems for hexadecimal polypeptide-based data storage[J]. Fundamental Research, 2021: 1-7.
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引文格式
刘杨奕,张 轶,刘 凯. DNA 数据存储中信息处理技术的研究进展与挑战 [J].集成技术,2024,13(3):25-38

Citing format
LIU Yangyi, ZHANG Yi, LIU Kai. Research Progress and Challenges of Data Processing Technology for DNA-Based Information Storage[J]. Journal of Integration Technology,2024,13(3):25-38

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  • 收稿日期:2023-10-31
  • 最后修改日期:2023-10-31
  • 录用日期:2024-01-23
  • 在线发布日期: 2024-01-23
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