高级搜索

留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

DNA存储及其研究进展

许鹏 方刚 石晓龙 刘文斌

许鹏, 方刚, 石晓龙, 刘文斌. DNA存储及其研究进展[J]. 电子与信息学报, 2020, 42(6): 1326-1331. doi: 10.11999/JEIT190863
引用本文: 许鹏, 方刚, 石晓龙, 刘文斌. DNA存储及其研究进展[J]. 电子与信息学报, 2020, 42(6): 1326-1331. doi: 10.11999/JEIT190863
Peng XU, Gang FANG, Xiaolong SHI, Wenbin LIU. DNA Storage and Its Research Progress[J]. Journal of Electronics & Information Technology, 2020, 42(6): 1326-1331. doi: 10.11999/JEIT190863
Citation: Peng XU, Gang FANG, Xiaolong SHI, Wenbin LIU. DNA Storage and Its Research Progress[J]. Journal of Electronics & Information Technology, 2020, 42(6): 1326-1331. doi: 10.11999/JEIT190863

DNA存储及其研究进展

doi: 10.11999/JEIT190863
基金项目: 国家重点研发计划(2019YFA0706402),国家自然科学基金(61572367, 61573017, 61972107, 61972109)
详细信息
    作者简介:

    许鹏:男,1986年生,博士后,研究方向为生物信息学

    方刚:男,1969年生,教授,研究方向为生物信息学

    石晓龙:男,1975年生,教授,研究方向为生物信息学

    刘文斌:男,1969年生,教授,研究方向为生物信息学

    通讯作者:

    刘文斌 wbliu6910@126.com

  • 中图分类号: TP301

DNA Storage and Its Research Progress

Funds: The National Key R&D Program of China (2019YFA0706402), The National Natural Science Foundation of China (61572367, 61573017, 61972107, 61972109)
  • 摘要: DNA存储是一种以生物大分子DNA作为信息载体的一种新的存储技术。与传统的电子信息存储相比,DNA存储具有容量大、密度高、低能耗等优点。随着DNA合成、测序技术的发展以及大数据时代对数据存储需求的指数增长,近年来DNA存储在存储容量、密度以及可靠性等方面都取得了巨大的进展。该文主要介绍了DNA存储的发展历史、DNA存储的基本流程、DNA存储在数据库、文档存储以及体内存储的研究进展。最后,总结了DNA存储未来面临的挑战以及发展方向。
  • 图  1  DNA存储的主要流程

    图  2  检索链和信息存贮链示意图

    图  3  基于磁珠的DNA数据库示意图

    图  4  2种数据链冗余设计策略

  • FEYNMAN R P. There’s plenty of room at the bottom[J]. Resonance, 2011, 16(9): 890. doi: 10.1007/s12045-011-0109-x
    ADLEMAN L M. Molecular computation of solutions to combinatorial problems[J]. Science, 1994, 266(5187): 1021–1024. doi: 10.1126/science.7973651
    BAUM E B. Building an associative memory vastly larger than the brain[J]. Science, 1995, 268(5210): 583–585. doi: 10.1126/science.7725109
    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
    LEIER A, RICHTER C, BANZHAF W, et al. Cryptography with DNA binary strands[J]. Biosystems, 2000, 57(1): 13–22. doi: 10.1016/S0303-2647(00)00083-6
    REIF J H, LABEAN T H, PIRRUNG M, et al. Experimental construction of very large scale DNA databases with associative search capability[C]. The 7th International Workshop on DNA-Based Computers, Tampa, USA, 2002: 231–247. doi: 10.1007/3-540-48017-X_22.
    CHURCH G M, GAO Yuan, and KOSURI S. Next-generation digital information storage in DNA[J]. Science, 2012, 337(6102): 1628–1628. doi: 10.1126/science.1226355
    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. doi: 10.1109/ISIT.2017.8007106.
    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
    HOSHIKA S, LEAL N A, KIM M J, et al. Hachimoji DNA and RNA: A genetic system with eight building blocks[J]. Science, 2019, 363(6429): 884–887. doi: 10.1126/science.aat0971
    BANCROFT C, BOWLER T, BLOOM B, et al. Long-term storage of information in DNA[J]. Science, 2001, 293(5536): 1763–1765. doi: 10.1126/science.293.5536.1763c
    GARZON M H and DEATON R J. Codeword design and information encoding in DNA ensembles[J]. Natural Computing, 2004, 3(3): 253–292. doi: 10.1023/B:NACO.0000036818.27537.c9
    王向红, 刘文斌, 朱翔鸥, 等. DNA计算中的单模板编码方法改进研究[J]. 电子学报, 2009, 37(12): 2720–2724. doi: 10.3321/–j.issn:0372-2112.2009.12.021

    WANG Xianghong, LIU Wenbin, ZHU Xiangou, et al. Improving the single template method in DNA computing[J]. Acta Electronica Sinica, 2009, 37(12): 2720–2724. doi: 10.3321/–j.issn:0372-2112.2009.12.021
    刘文斌, 朱翔鸥, 王向红, 等. 一种优化DNA计算模板性能的新方法[J]. 电子与信息学报, 2008, 30(5): 1131–1135. doi: 10.3724/SP.J.1146.2006.01640

    LIU Wenbin, ZHU Xiangou, WANG Xianghong, et al. A new method to optimize the template set in DNA computing[J]. Journal of Electronics &Information Technology, 2008, 30(5): 1131–1135. doi: 10.3724/SP.J.1146.2006.01640
    刘文斌, 陈丽春, 白宝钢, 等. DNA计算中的模板框优化方法研究[J]. 电子学报, 2007, 35(8): 1490–1494. doi: 10.3321/j.issn:0372-2112.2007.08.014

    LIU Wenbin, CHEN Lichun, BAI Baogang, et al. Research on optimizing the template frame in DNA computing[J]. Acta Electronica Sinica, 2007, 35(8): 1490–1494. doi: 10.3321/j.issn:0372-2112.2007.08.014
    KASHIWAMURA S, YAMAMOTO M, KAMEDA A, et al. Potential for enlarging DNA memory: The validity of experimental operations of scaled-up nested primer molecular memory[J]. Biosystems, 2005, 80(1): 99–112. doi: 10.1016/j.biosystems.2004.10.007
    KASHIWAMURA S, YAMAMOTO M, KAMEDA A, et al. Experimental challenge of scaled-up hierarchical DNA memory expressing a 10, 000-address space[C]. Preliminary Proceeding of 11th International Meeting on DNA based Computers, London, UK, 2005.
    YAMAMOTO M, KASHIWAMURA S, OHUCHI A, et al. Large-scale DNA memory based on the nested PCR[J]. Natural Computing, 2008, 7(3): 335–346. doi: 10.1007/s11047-008-9076-x
    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
    STEWART K, CHEN Y J, WARD D, et al. A content-addressable DNA database with learned sequence encodings[C]. The 24th International Conference on DNA Computing and Molecular Programming, Jinan, China, 2018: 55–70. doi: 10.1007/978-3-030-00030-1_4.
    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
    BORNHOLT J, LOPEZ R, CARMEAN D M, et al. A DNA-based archival storage system[J]. ACM SIGARCH Computer Architecture News, 2016, 44(2): 637–649. doi: 10.1145/2980024.2872397
    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
    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
    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
    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
    MEISER L C, ANTKOWIAK P L, KOCH J, et al. Reading and writing digital data in DNA[J]. Nature Protocols, 2020, 15(1): 86–101. doi: 10.1038/s41596-019-0244-5
    Anavy, L., Vaknin, I., Atar, O. et al. Data storage in DNA with fewer synthesis cycles using composite DNA letters[J]. Nat Biotechnol 2019, 37, 1229–1236. doi: https://doi.org/10.1038/s41587-019-0240-x.
    LENZ A, SIEGEL P H, WACHTER-ZEH A, et al. Coding over Sets for DNA storage[C]. 2018 IEEE International Symposium on Information Theory, Vail, USA, 2018: 2411–2415. doi: 10.1109/ISIT.2018.8437544.
    YACHIE N, OHASHI Y, and TOMITA M. Stabilizing synthetic data in the DNA of living organisms[J]. Systems and Synthetic Biology, 2008, 2(1/2): 19–25. doi: 10.1007/s11693-008-9020-5
    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
    SHIPMAN S L, NIVALA J, MACKLIS J D, 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. doi: 10.1038/nature23017
    FARZADFARD F, GHARAEI N, HIGASHIKUNI Y, et al. Single-nucleotide-resolution computing and memory in living cells[J]. Molecular Cell, 2019, 75(4): 769–780.E4. doi: 10.1016/j.molcel.2019.07.011
  • 加载中
图(4)
计量
  • 文章访问数:  3627
  • HTML全文浏览量:  2032
  • PDF下载量:  362
  • 被引次数: 0
出版历程
  • 收稿日期:  2019-11-01
  • 修回日期:  2020-04-23
  • 网络出版日期:  2020-05-13
  • 刊出日期:  2020-06-22

目录

    /

    返回文章
    返回