Advanced Search
Volume 42 Issue 6
Jun.  2020
Turn off MathJax
Article Contents
Xiuhai MAO, Fan LI, Xiaolei ZUO. DNA Data Storage[J]. Journal of Electronics & Information Technology, 2020, 42(6): 1303-1312. doi: 10.11999/JEIT190852
Citation: Xiuhai MAO, Fan LI, Xiaolei ZUO. DNA Data Storage[J]. Journal of Electronics & Information Technology, 2020, 42(6): 1303-1312. doi: 10.11999/JEIT190852

DNA Data Storage

doi: 10.11999/JEIT190852
Funds:  The Ministry of Science and Technology of China (2018YFA0902600), The National Natural Science Foundation of China (21804019, 21804088), Shanghai Pujiang Program (19PJ1407300)
  • Received Date: 2019-11-01
  • Rev Recd Date: 2020-05-18
  • Available Online: 2020-05-21
  • Publish Date: 2020-06-22
  • Molecular data storage has great potential as durable and high-density data-storage media, which will deal with the growing gap between produced information and the data storage ability. With storing data in molecular form, DNA can provide alternative substrates for storage to overcome the physical limits for existing medias. This review provides an overview of the history, process and the current status of the DNA data storage, and presents the problems of current data storage technology.
  • loading
  • GANTZ J and REINSEL D. The digital universe in 2020: Big data, bigger digital shadows, and biggest growth in the far East[R]. IDC iView, 2012: 1–16.
    EXTANCE A. How DNA could store all the world’s data[J]. Nature, 2016, 537(7618): 22–24. doi: 10.1038/537022a
    ZHIRNOV V, ZADEGAN R M, SANDHU G S, et al. Nucleic acid memory[J]. Nature Materials, 2016, 15(4): 366–370. doi: 10.1038/nmat4594
    COLQUHOUN H and LUTZ J F. Information-containing macromolecules[J]. Nature Chemistry, 2014, 6(6): 455–456. doi: 10.1038/nchem.1958
    王君珂, 印珏, 牛人杰, 等. DNA计算与DNA纳米技术[J]. 电子与信息学报, 2020, 42(6): 1313–1325. doi: 10.11999/JEIT190826.

    WANG Junke, YIN Jue, NIU Renjie, et al. DNA computing and DNA nanotechnology[J]. Journal of Electronics & Information Technology, 2020, 42(6): 1313–1325. doi: 10.11999/JEIT190826.
    许进, 强小利, 张凯, 等. 基于探针图的并行型图顶点着色DNA计算模型(英文)[J]. 工程, 2018, 4(1): 61–77. doi: 10.1016/j.eng.2018.02.011

    XU Jin, QIANG Xiaoli, ZHANG Kai, et al. A DNA computing model for the graph vertex coloring problem based on a probe graph[J]. Engineering, 2018, 4(1): 61–77. doi: 10.1016/j.eng.2018.02.011
    蓝雯飞, 邢志宝, 黄俊, 等. DNA自组装计算模型求解二部图完美匹配问题[J]. 计算机研究与发展, 2016, 53(11): 2583–2593. doi: 10.7544/issn1000-1239.2016.20150312

    LAN Wenfei, XING Zhibao, HUANG Jun, et al. The DNA self-assembly computing model for solving perfect matching problem of bipartite graph[J]. Journal of Computer Research and Development, 2016, 53(11): 2583–2593. doi: 10.7544/issn1000-1239.2016.20150312
    朱维军, 周清雷, 张钦宪. 基于DNA计算的线性时序逻辑模型检测方法[J]. 计算机学报, 2016, 39(12): 2578–2597. doi: 10.11897/SP.J.1016.2016.02578

    ZHU Weijun, ZHOU Qinglei, and ZHANG Qinxian. A LTL model checking approach based on DNA computing[J]. Chinese Journal of Computers, 2016, 39(12): 2578–2597. doi: 10.11897/SP.J.1016.2016.02578
    夏宏, 张实君. 基于分子计算的逻辑模型构建[J]. 科技通报, 2016, 32(5): 11–15. doi: 10.3969/j.issn.1001-7119.2016.05.003

    XIA Hong and ZHANG Shijun. Constructing the logical model based on molecular computing[J]. Bulletin of Science and Technology, 2016, 32(5): 11–15. doi: 10.3969/j.issn.1001-7119.2016.05.003
    周旭, 周炎涛, 欧阳艾嘉, 等. 一种最大团问题的tile自组装高效模型[J]. 计算机研究与发展, 2014, 51(6): 1253–1262. doi: 10.7544/issn1000-1239.2014.20120904

    ZHOU Xu, ZHOU Yantao, OUYANG Aijia, et al. An efficient tile assembly model for maximum clique problem[J]. Journal of Computer Research and Development, 2014, 51(6): 1253–1262. doi: 10.7544/issn1000-1239.2014.20120904
    周旭, 周炎涛, 李肯立, 等. 基于tile自组装模型的最大匹配问题算法研究[J]. 电子学报, 2015, 43(2): 262–268. doi: 10.3969/j.issn.0372-2112.2015.02.009

    ZHOU Xu, ZHOU Yantao, LI Kenli, et al. Efficient maximum matching problem algorithms in the tile assembly model[J]. Acta Electronica Sinica, 2015, 43(2): 262–268. doi: 10.3969/j.issn.0372-2112.2015.02.009
    ORGANICK L, ANG S D, CHEN Y J, et al. Random access in large-scale DNA data storage[J]. Nature Biotechnology, 2018, 36(3): 242–248. doi: 10.1038/nbt.4079
    RUTTEN M G T A, VAANDRAGER F W, ELEMANS J A A W, et al. Encoding information into polymers[J]. Nature Reviews Chemistry, 2018, 2(11): 365–381. doi: 10.1038/s41570-018-0051-5
    DNA to the rescue for data storage[J]. Chemical & Engineering News, 2015, 93(35): 40-41.
    陈为刚, 黄刚, 李炳志, 等. 音视频文件的DNA信息存储[J]. 中国科学: 生命科学, 2020, 50(1): 81–85. doi: 10.1360/SSV-2019-0211

    CHEN Weigang, HUANG Gang, LI Bingzhi, et al. DNA information storage for audio and video files[J]. Scientia Sinica Vitae, 2020, 50(1): 81–85. doi: 10.1360/SSV-2019-0211
    GREENGARD S. Cracking the code on DNA storage[J]. Communications of the ACM, 2017, 60(7): 16–18. doi: 10.1145/3088493
    GRASS R N, HECKEL R, PUDDU M, et al. Robust chemical preservation of digital information on DNA in silica with error-correcting codes[J]. Angewandte Chemie International Edition, 2015, 54(8): 2552–2555. doi: 10.1002/anie.201411378
    LUNT B M. How long is long-term data storage?[C]. Archiving Conference, Society for Imaging Science and Technology, 2011: 29–33.
    SHRIVASTAVA S and BADLANI R. Data storage in DNA[J]. International Journal of Electrical Energy, 2014, 2(2): 119–124.
    GREENBERG A, HAMILTON J, MALTZ D A, et al. The cost of a cloud: Research problems in data center networks[J]. ACM SIGCOMM Computer Communication Review, 2008, 39(1): 68–73. doi: 10.1145/1496091.1496103
    SHETH R U and WANG H H. DNA-based memory devices for recording cellular events[J]. Nature Reviews Genetics, 2018, 19(11): 718–732. doi: 10.1038/s41576-018-0052-8
    WIENER N. Interview: Machines smarter than men[J]. US News World Report, 1964, 56: 84–86.
    NEIMAN M S. On the molecular memory systems and the directed mutations[J]. Radiotekhnika, 1965, 6: 1–8.
    DAVIS J. Microvenus[J]. Art Journal, 1996, 55(1): 70–74. doi: 10.1080/00043249.1996.10791743
    CLELLAND C T, RISCA V, and BANCROFT C. Hiding messages in DNA microdots[J]. Nature, 1999, 399(6736): 533–534. doi: 10.1038/21092
    BANCROFT C, BOWLER T, BLOOM B, et al. Long-term storage of information in DNA[J]. Science, 2001, 293(5536): 1763–1765.
    AILENBERG M and ROTSTEIN O D. An improved huffman coding method for archiving text, images, and music characters in DNA[J]. BioTechniques, 2009, 47(3): 747–754. doi: 10.2144/000113218
    WONG P C, WONG K K, and FOOTE H. Organic data memory using the DNA approach[J]. Communications of the ACM, 2003, 46(1): 95–98. doi: 10.1145/602421.602426
    ARITA M and OHASHI Y. Secret signatures inside genomic DNA[J]. Biotechnology Progress, 2004, 20(5): 1605–1607. doi: 10.1021/bp049917i
    YACHIE N, SEKIYAMA K, SUGAHARA J, et al. Alignment-based approach for durable data storage into living organisms[J]. Biotechnology Progress, 2007, 23(2): 501–505. doi: 10.1021/bp060261y
    CHURCH G M, GAO Yuan, and KOSURI S. Next-generation digital information storage in DNA[J]. Science, 2012, 337(6102): 1628. doi: 10.1126/science.1226355
    GOLDMAN N, BERTONE P, CHEN Siyuan, et al. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA[J]. Nature, 2013, 494(7435): 77–80. doi: 10.1038/nature11875
    GIBSON D G, GLASS J I, LARTIGUE C, et al. Creation of a bacterial cell controlled by a chemically synthesized genome[J]. Science, 2010, 329(5987): 52–56. doi: 10.1126/science.1190719
    HECKEL R, SHOMORONY I, RAMCHANDRAN K, et al. Fundamental limits of DNA storage systems[C]. 2017 IEEE International Symposium on Information Theory, Aachen, Germany, 2017: 3130–3134.
    KOSURI S and CHURCH G M. Large-scale de novo DNA synthesis: Technologies and applications[J]. Nature Methods, 2014, 11(5): 499–507. doi: 10.1038/nmeth.2918
    BORNHOLT J, LOPEZ R, CARMEAN D M, et al. A DNA-based archival storage system[J]. ACM SIGPLAN Notices, 2016, 50(4): 637–649.
    YAZDI S M H T, YUAN Yongbo, MA Jian, et al. A rewritable, random-access DNA-based storage system[J]. Scientific Reports, 2015, 5: 14138. doi: 10.1038/srep14138
    ERLICH Y and ZIELINSKI D. DNA fountain enables a robust and efficient storage architecture[J]. Science, 2017, 355(6328): 950–954. doi: 10.1126/science.aaj2038
    谭丽, 孙季丰, 郭礼华. 基于memetic算法的DNA序列数据压缩方法[J]. 电子与信息学报, 2014, 36(1): 121–127.

    TAN Li, SUN Jifeng, and GUO Lihua. DNA sequence data compression method based on memetic algorithm[J]. Journal of Electronics &Information Technology, 2014, 36(1): 121–127.
    SHANNON C E. A mathematical theory of communication[J]. The Bell System Technical Journal, 1948, 27(3): 379–423. doi: 10.1002/j.1538-7305.1948.tb01338.x
    HECKEL R, MIKUTIS G, and GRASS R N. A characterization of the DNA data storage channel[J]. Scientific Reports, 2019, 9(1): 9663. doi: 10.1038/s41598-019-45832-6
    REED I S and SOLOMON G. Polynomial codes over certain finite fields[J]. Journal of the Society for Industrial and Applied Mathematics, 1960, 8(2): 300–304. doi: 10.1137/0108018
    ANAVY L, VAKNIN I, ATAR O, et al. Improved DNA based storage capacity and fidelity using composite DNA letters[J]. bioRxiv, 2018. doi: 10.1101/433524
    CHOI Y, RYU T, LEE A C, et al. Addition of degenerate bases to DNA-based data storage for increased information capacity[J]. bioRxiv, 2018. doi: 10.1101/367052
    YAZDI S M H T, GABRYS R, and MILENKOVIC O. Portable and error-free DNA-based data storage[J]. Scientific Reports, 2017, 7: 5011. doi: 10.1038/s41598-017-05188-1
    BLAWAT M, GAEDKE K, HÜTTER I, et al. Forward error correction for DNA data storage[J]. Procedia Computer Science, 2016, 80: 1011–1022. doi: 10.1016/j.procs.2016.05.398
    LEE H H, KALHOR R, GOELA N, et al. Enzymatic DNA synthesis for digital information storage[J]. bioRxiv, 2018. doi: 10.1101/348987
    BAUM E. Building an associative memory vastly larger than the brain[J]. Science, 1995, 268(5210): 583–585. doi: 10.1126/science.7725109
    CARUTHERS M H. The chemical synthesis of DNA/RNA: Our gift to science[J]. Journal of Biological Chemistry, 2013, 288(2): 1420–1427. doi: 10.1074/jbc.X112.442855
    GOODWIN S, MCPHERSON J D, and MCCOMBIE W R. Coming of age: Ten years of next-generation sequencing technologies[J]. Nature Reviews Genetics, 2016, 17(6): 333–351. doi: 10.1038/nrg.2016.49
    SHENDURE J, BALASUBRAMANIAN S, CHURCH G M, et al. DNA sequencing at 40: Past, present and future[J]. Nature, 2017, 550(7676): 345–353. doi: 10.1038/nature24286
    DEAMER D, AKESON M, and BRANTON D. Three decades of nanopore sequencing[J]. Nature Biotechnology, 2016, 34(5): 518–524. doi: 10.1038/nbt.3423
    FONTANA JR R E and DECAD G M. Moore’s law realities for recording systems and memory storage components: HDD, tape, NAND, and optical[J]. AIP Advances, 2018, 8(5): 056506. doi: 10.1063/1.5007621
    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. doi: 10.1093/nar/gkp1060
    PRAKADAN S M, SHALEK A K, and WEITZ D A. Scaling by shrinking: Empowering single-cell 'omics' with microfluidic devices[J]. Nature Reviews Genetics, 2017, 18(6): 345–361. doi: 10.1038/nrg.2017.15
    NEWMAN S, STEPHENSON A P, WILLSEY M, et al. High density DNA data storage library via dehydration with digital microfluidic retrieval[J]. Nature Communications, 2019, 10(1): 1706. doi: 10.1038/s41467-019-09517-y
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(1)  / Tables(1)

    Article Metrics

    Article views (4236) PDF downloads(240) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return