DNA信息存储：生命系统与信息系统的桥梁

doi:10.12211/2096-8280.2021-001

摘要/Abstract

摘要：

DNA信息存储通过编解码、合成、编辑和测序等过程，实现数字信息写入、存储与读出。其在密度、寿命、能耗和抗电磁干扰等方面较磁、光、电等常规的信息存储介质有较大优势。随着全球数据总量的快速增长，DNA信息存储的优势特性和发展潜力受到了研究者的广泛关注。本文阐述了DNA信息存储的基本原理和技术流程，分析了DNA信息存储与生命系统和信息系统的关联，并依据读写技术特点归纳近年来涌现的“DNA硬盘”“DNA光盘”“DNA磁带”等几种主要模式、发展现状及技术路线。在此基础上，探讨DNA信息存储商业化、大规模应用面临的主要挑战，讨论更低成本的数据写入和更快速的数据读出，并指出可行的发展路线。最后，展望了DNA作为新型存储介质在现代存储系统中的发展演化趋势。

关键词: 合成生物学, 数字信息存储, DNA合成, DNA测序, 信息编码

Abstract:

The external preservation of information enables reliable inheritance of human thoughts, playing important roles in the progress of human civilization. Starting from tying knots in ropes to storing data in magnetic and optical media, these technologies have documented and will continue to record the splendid civilization. However, driven by the global digitalization, the global data volume is growing rapidly and challenging the storage capability of existing storage technologies. DNA, as the natural carrier of genetic information, is believed to be a potential candidate to deal with the data storage challenge due to the revealed high density, long-term duration and low maintaining cost features. In this review, we first describe the fundamental principles and technical processes of DNA information storage. The pivotal position of DNA information storage bridging the biological and digital world is also pointed out. Then, according to the different characteristics of data writing and reading, we categorize these technologies into three storage modes, termed as "DNA hard drive", "DNA compact disc" and "DNA tape", by analogy with the popular storage media correspondingly. "DNA hard drive" mode shows the potential in the volume enlargement of the existing information storage system using oligonucleotide pools. "DNA compact disc" mode provides direct in vivo processing on DNA data storage enabling massive data distribution at low cost. "DNA tape" mode provides intracellular information recoding solutions, which may promote the future developments of cellular computing and communication. The up-to-date progress of these three modes is also summarized. We then discuss the main obstacles and potential technical routes towards practical applications of DNA information storage. We envision a cheaper, faster DNA information storage technology, and its appropriate integration with information storage systems in the future. Finally, we conclude that DNA information storage is a cutting-edge interdisciplinary technology and hope this review can bring more focus and research efforts from various fields to DNA information storage.

Key words: synthetic biology, digital information storage, DNA synthesis, DNA sequencing, information encoding

中图分类号:

Q819

韩明哲, 陈为刚, 宋理富, 李炳志, 元英进. DNA信息存储：生命系统与信息系统的桥梁[J]. 合成生物学, 2021, 2(3): 309-322.

Mingzhe HAN, Weigang CHEN, Lifu SONG, Bingzhi LI, Yingjin YUAN. DNA information storage： bridging biological and digital world[J]. Synthetic Biology Journal, 2021, 2(3): 309-322.

参考文献 94

1	Semiconductor Industry Association. Decadal plan for semiconductors [EB/OL]. [2020-12-02]. .
2	FONTANA R E, DECAD G M, HETZLER S R. Volumetric density trends (TB/in.3) for storage components: TAPE, hard disk drives, NAND, and Blu-ray[J]. Journal of Applied Physics, 2015, 117(17): 17E301.
3	ZHIRNOV V, ZADEGAN R M, SANDHU G S, et al. Nucleic acid memory[J]. Nature Materials, 2016, 15(4): 366-370.
4	KOSURI S, CHURCH G M. Large-scale de novo DNA synthesis: technologies and applications[J]. Nature Methods, 2014, 11(5): 499-507.
5	WU Y, LI B Z, ZHAO M, et al. Bug mapping and fitness testing of chemically synthesized chromosome X[J]. Science, 2017, 355(6329): eaaf4706.
6	XIE Z X, LI B Z, MITCHELL L A, et al. "Perfect" designer chromosome V and behavior of a ring derivative[J]. Science, 2017, 355(6329): eaaf4704.
7	陈欣懋, 欧阳颀. 生物逆向工程设计在合成生物学中的应用[J]. 合成生物学, 2020, 1(1): 29-43.
	CHEN X M, OUYANG Q. The application of biological reverse engineering in synthetic biology[J]. Synthetic Biology Journal, 2020, 1(1): 29-43.
8	彭凯, 逯晓云, 程健, 等. DNA合成、组装与纠错技术研究进展[J]. 合成生物学, 2020, 1(6): 697-708.
	PENG K, LU X Y, CHENG J, et al. Advances in technologies for de novo DNA synthesis, assembly and error correction[J]. Synthetic Biology Journal, 2020, 1(6): 697-708.
9	曹中正, 张心怡, 徐艺源, 等. 基因组编辑技术及其在合成生物学中的应用[J]. 合成生物学, 2020, 1(4): 413-426.
	CAO Z Z, ZHANG X Y, XU Y Y, et al. Genome editing technology and its applications in synthetic biology[J]. Synthetic Biology Journal, 2020, 1(4): 413-426.
10	王会, 戴俊彪, 罗周卿. 基因组的"读-改-写"技术[J]. 合成生物学, 2020, 1(5): 503-515.
	WANG H, DAI J B, LUO Z Q. Reading, editing, and writing techniques for genome research[J]. Synthetic Biology Journal, 2020, 1(5): 503-515.
11	丁明珠, 李炳志, 王颖, 等. 合成生物学重要研究方向进展[J]. 合成生物学, 2020, 1(1): 7-28.
	DING M Z, LI B Z, WANG Y, et al. Significant research progress in synthetic biology[J]. Synthetic Biology Journal, 2020, 1(1): 7-28.
12	Wire Business. Twist Bioscience, Illumina and Western Digital form alliance with Microsoft to advance data storage in DNA [EB/OL]. [2020-11-12]. .
13	CEZE L, NIVALA J, STRAUSS K. Molecular digital data storage using DNA[J]. Nature Reviews Genetics, 2019, 20(8): 456-66.
14	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.
15	DONG Y, SUN F, PING Z, et al. DNA storage: research landscape and future prospects[J]. National Science Review, 2020, 7(6): 1092-1107.
16	PING Z, MA D, HUANG X, et al. Carbon-based archiving: current progress and future prospects of DNA-based data storage[J]. GigaScience, 2019, 8(6): giz075.
17	LIM C K, NIRANTAR S, YEW W S, et al. Novel modalities in DNA data storage[J]. Trends in Biotechnology, 2021. DOI: https://doi.org/10.1016/j.tibtech.2020.12.008. DOI
18	周廷尧, 罗源, 蒋兴宇. DNA数据存储:保存策略与数据加密[J]. 合成生物学, 2021, 2(3): 371-383.
	ZHOU T Y, LUO Y, JIANG X Y. DNA data storage: preservation approach and data encryption[J]. Synthetic Biology Journal, 2021, 2(3): 371-383.
19	CHURCH G M, GAO Y, KOSURI S. Next-generation digital information storage in DNA[J]. Science, 2012, 337(6102): 1628.
20	KEIGER D. DNA hard drive [EB/OL]. [2012-11-30]. .
21	毕昆, 顾万君, 陆祖宏. DNA 存储中的编码技术[J]. 生物信息学, 2020, 18(2): 76-85.
	BI K, GU W J, LU Z H. Coding algorithms in DNA storage[J]. Chinese Journal of Bioinformatics, 2020, 18(2): 76-85.
22	Bioscience Twist. Product sheet of Twist oligo pools [EB/OL]. [2019-08-29].
23	GenScript. Precise synthetic oligo pools [EB/OL]. [2021-02-01]. .
24	LIU L, LI Y, LI S, et al. Comparison of next-generation sequencing systems [J]. Journal of Biomedicine and Biotechnology, 2012, 2012: 251364.
25	GOLDMAN N, BERTONE P, CHEN S Y, et al. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA [J]. Nature, 2013, 494(7435): 77-80.
26	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.
27	ERLICH Y, ZIELINSKI D. DNA Fountain enables a robust and efficient storage architecture[J]. Science, 2017, 355(6328): 950-953.
28	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.
29	CHOI Y, RYU T, LEE A C, et al. High information capacity DNA-based data storage with augmented encoding characters using degenerate bases[J]. Scientific Reports, 2019, 9(1): 6582.
30	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.
31	HECKEL R, SHOMORONY I, RAMCHANDRAN K, et al. Fundamental limits of DNA storage systems[C]//2017 IEEE International Symposium on Information Theory (ISIT). Aachen, Germany: IEEE, 2017: 3130-3134.
32	PRESS W H, HAWKINS J A, JONES S K, et al. HEDGES error-correcting code for DNA storage corrects indels and allows sequence constraints[J]. Proceedings of the National Academy of Sciences of the United States of America, 2020, 117(31): 18489-18496.
33	SABARY O, YUCOVICH A, SHAPIRA G, et al. Reconstruction Algorithms for DNA-Storage Systems[EB/OL]. [2021-05-25]. .
34	SONG L, GENG F, GONG Z, et al. Super-robust data storage in DNA by de Bruijn graph-based decoding[EB/OL]. [2021-05-25]. .
35	LEE H H, KALHOR R, GOELA N, et al. Terminator-free template-independent enzymatic DNA synthesis for digital information storage[J]. Nature Communications, 2019, 10(1): 2383.
36	LEE H, WIEGAND D J, GRISWOLD K, et al. Photon-directed multiplexed enzymatic DNA synthesis for molecular digital data storage[J]. Nature Communications, 2020, 11(1): 5246.
37	LIN K N, VOLKEL K, TUCK J M, et al. Dynamic and scalable DNA-based information storage[J]. Nature Communications, 2020, 11(1), 2981.
38	CHOI Y, BAE H J, LEE A C, et al. DNA micro‐disks for the management of DNA‐based data storage with Index and Write‐Once-Read‐Many (WORM) memory features[J]. Advanced Materials, 2020, 32(37): 2001249.
39	GAO Y, CHEN X, QIAO H, et al. Low-bias manipulation of DNA oligo pool for robust data storage[J]. ACS Synthetic Biology, 2020, 9(12): 3344-3352.
40	ORGANICK L, ANG S D, CHEN Y J, et al. Random access in large-scale DNA data storage[J]. Nature Biotechnology, 2018, 36(7): 242-248.
41	TAKAHASHI C N, NGUYEN B H, STRAUSS K, et al. Demonstration of end-to-end automation of DNA data storage[J]. Scientific Reports, 2019, 9(1): 4998.
42	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.
43	SHANKLAND S. Startup packs all 16GB of Wikipedia onto DNA strands to demonstrate new storage tech [EB/OL]. [2019-07-02]. .
44	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, 2019, 50(1): 81-85.
	CHEN W G, HUANG G, LI B Z, et al. DNA information storage for audio and video files[J]. SCIENTIA SINICA Vitae, 2019, 50(1): 81-85.
45	PING Z, CHEN S, ZHOU G, et al. Towards practical and robust DNA-based data archiving by codec system named 'Yin-Yang'[EB/OL]. [2021-05-25]. .
46	BORNHOLT J, LOPEZ R, CARMEAN D M, et al. Toward a DNA-based archival storage system[J]. IEEE Micro, 2017, 37(3): 98-104.
47	YAZDI S M H T, YUAN Y, MA J, et al. A rewritable, random-access DNA-based storage system[J]. Scientific Reports, 2015, 5(1): 14138.
48	CHEN W G, HAN M Z, ZHOU J T, et al. An artificial chromosome for data storage[J]. National Science Review, 2021, 8(5): nwab028.
49	ZHU Y O, SIEGAl M L, HALL D W, et al. Precise estimates of mutation rate and spectrum in yeast[J]. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111(22): E2310-E2318.
50	LEE H, POPODI E, TANG H, et al. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing[J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(41): E2774-E2783.
51	SONG L F, ZENG A P. Orthogonal information encoding in living cells with high error- tolerance, safety, and fidelity [J]. ACS Synthetic Biology, 2018, 7(3): 866-874.
52	DEAMER D, AKESON M, BRANTON D. Three decades of nanopore sequencing[J]. Nature Biotechnology, 2016, 34(5): 518-524.
53	DAVIS J. Microvenus[J]. Art Journal, 1996, 55(1): 70-74.
54	BANCROFT C, BOWLER T, BLOOM B, et al. Long-term storage of information in DNA[J]. Science, 2001, 293(5536): 1763-1765.
55	WONG P C, WONG K K, FOOTE H. Organic data memory using the DNA approach[J]. Communications of the ACM, 2003, 46(1): 95-98.
56	GUSTAFSSON C. For anyone who ever said there's no such thing as a poetic gene[J]. Nature, 2009, 458(7239): 703.
57	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.
58	AILENBERG M, ROTSTEIN O D. An improved Huffman coding method for archiving text, images, and music characters in DNA[J]. Biotechniques, 2009, 47(3): 747-751.
59	NGUYEN H H, PARK J, PARK S J, et al. Long-term stability and integrity of plasmid-based DNA data storage[J]. Polymers, 2018, 10(1): 28.
60	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.
61	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.
62	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.
63	AUSLÄNDER S, FUSSENEGGER M. Dynamic genome engineering in living cells[J]. Science, 2014, 346(6211): 813-814.
64	FARZADFARD F, LU T K. Emerging applications for DNA writers and molecular recorders[J]. Science, 2018, 361(6405): 870-875.
65	FARZADFARD F, LU T K. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations[J]. Science, 2014, 346(6211): .
66	SHETH R U, YIM S S, WU F L, et al. Multiplex recording of cellular events over time on CRISPR biological tape[J]. Science, 2017, 358(6369): 1457-1461.
67	TANG W, LIU D R. Rewritable multi-event analog recording in bacterial and mammalian cells[J]. Science, 2018, 360(6385): eaap8992.
68	PERLI S D, CUI C H, LU T K. Continuous genetic recording with self-targeting CRISPR-Cas in human cells[J]. Science, 2016, 353(6304): aag0511.
69	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.
70	YIM S S, MCBEE R M, SONG A M, et al. Robust direct digital-to-biological data storage in living cells[J]. Nature Chemical Biology, 2021, 17(3):246-253.
71	TABATABAEI S K, WANG B, ATHREYA N B M, et al. DNA punch cards for storing data on native DNA sequences via enzymatic nicking[J]. Nature communications, 2020, 11(1): 1742.
72	CHEN K, KONG J, ZHU J, et al. Digital data storage using DNA nanostructures and solid-state nanopores[J]. Nano Letters, 2018, 19(2): 1210-1215.
73	CHEN K, ZHU J, BOSKOVIC F, et al. Nanopore-based DNA hard drives for rewritable and secure data storage[J]. Nano Letters, 2020, 20(5): 3754-3760.
74	LOPEZ R, CHEN Y J, ANG S D, et al. DNA assembly for nanopore data storage readout[J]. Nature Communications, 2019, 10(1): 2933.
75	ZHANG Y, WANG F, CHAO J, et al. DNA origami cryptography for secure communication[J]. Nature Communications, 2019, 10(1): 5469.
76	Semiconductor Research Corporation. 2018 semiconductor synthetic biology roadmap [R]. Durham, NC, USA: SRC, 2018.
77	MCCALLUM J C. Disk drive prices1955+ [EB/OL]. [2021-05-25]. .
78	IARPA. IARPA BAA on molecular information storage [EB/OL]. [2021-05-25]. .
79	MARKOWITZ D. SRC/IARPA Workshop on DNA-based massive information storage [EB/OL]. [2021-05-25]. .
80	ANTKOWIAK P L, LIETARD J, DARESTANI M Z, et al. Low cost DNA data storage using photolithographic synthesis and advanced information reconstruction and error correction[J]. Nature Communications, 2020, 11(1): 5345.
81	Illumina. Illumina sequencing platforms [EB/OL]. [2021-05-25].
82	Illumina. Run time estimates for each sequencing step on the Illumina sequencing platforms. [EB/OL]. [2021-05-25]. .
83	KONO N, ARAKAWA K. Nanopore sequencing: review of potential applications in functional genomics[J]. Development, Growth & Differentiation, 2019, 61(5): 316-326.
84	YUAN Z, LIU Y, DAI M, et al. Controlling DNA translocation through solid-state nanopores[J]. Nanoscale Research Letters, 2020, 15: 80.
85	STANLEY P M, STRITTMATTER L M, VICKERS A M, et al. Decoding DNA data storage for investment[J]. Biotechnology Advances, 2020, 45: 107639.
86	HECKEL R, MIKUTIS G, GRASS R N. A characterization of the DNA data storage channel[J]. Scientific Reports, 2019, 9(1): 9663.
87	MAO W, DIGGAVI S N, KANNAN S. Models and information-theoretic bounds for nanopore sequencing[J]. IEEE Transactions on Information Theory, 2018, 64(4): 3216-3236.
88	MERCIER H, BHARGAVA V K, TAROKH V. A survey of error-correcting codes for channels with symbol synchronization errors[J]. IEEE Communications Surveys & Tutorials, 2010, 12(1): 87-96.
89	平质, 张颢龄, 陈世宏, 等. Chamaeleo: DNA存储碱基编解码算法的可拓展集成与系统评估平台[J]. 合成生物学, 2021, 2(3): 412-427.
	PING Z, ZHANG H L, CHEN S H, et al. Chamaeleo: an integrated evaluation platform for DNA storage[J]. Synthetic Biology Journal, 2021, 2(3): 412-427.
90	Semiconductor Research Corporation. Decadal plan for semiconductors full report [R]. Durham: SRC, 2021.
91	PUZIS R, FARBIASH D, BRODT O, et al. Increased cyber-biosecurity for DNA synthesis [J]. Nature Biotechnology, 2020, 38(12): 1379-1381.
92	NEY P, KOSCHER K, ORGANICK L, et al. Computer security, privacy, and DNA sequencing: compromising computers with synthesized DNA, privacy leaks, and more[C]//26th USENIX Security Symposium (USENIX Security 17). Vancouver, BC, Canada: USENIX Association, 2017: 765-779.
93	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.
94	Gartner. Gartner unveils top predictions for IT organizations and users in 2021 and beyond [EB/OL]. Gartner [2020-10-21]. .

[1]	刁志钿, 王喜先, 孙晴, 徐健, 马波. 单细胞拉曼光谱测试分选装备研制及应用进展[J]. 合成生物学, 2023, 4(5): 1020-1035.
[2]	卢挥, 张芳丽, 黄磊. 合成生物学自动化装置iBioFoundry的构建与应用[J]. 合成生物学, 2023, 4(5): 877-891.
[3]	白仲虎, 任和, 聂简琪, 孙杨. 高通量平行发酵技术的发展与应用[J]. 合成生物学, 2023, 4(5): 904-915.
[4]	吴玉洁, 刘欣欣, 刘健慧, 杨开广, 随志刚, 张丽华, 张玉奎. 基于高通量液相色谱质谱技术的菌株筛选与关键分子定量分析研究进展[J]. 合成生物学, 2023, 4(5): 1000-1019.
[5]	胡哲辉, 徐娟, 卞光凯. 自动化高通量技术在天然产物生物合成中的应用[J]. 合成生物学, 2023, 4(5): 932-946.
[6]	刘欢, 崔球. 原位电离质谱技术在微生物菌株筛选中的应用进展[J]. 合成生物学, 2023, 4(5): 980-999.
[7]	王雁南, 孙宇辉. 碱基编辑技术及其在微生物合成生物学中的应用[J]. 合成生物学, 2023, 4(4): 720-737.
[8]	刘晚秋, 季向阳, 许慧玲, 卢屹聪, 李健. 限制性内切酶的无细胞快速制备研究[J]. 合成生物学, 2023, 4(4): 840-851.
[9]	孙美莉, 王凯峰, 陆然, 纪晓俊. 解脂耶氏酵母底盘细胞的工程改造及应用[J]. 合成生物学, 2023, 4(4): 779-807.
[10]	孙智, 杨宁, 娄春波, 汤超, 杨晓静. 功能拓扑的理性设计及其在合成生物学中的应用[J]. 合成生物学, 2023, 4(3): 444-463.
[11]	赖奇龙, 姚帅, 查毓国, 白虹, 宁康. 微生物组生物合成基因簇发掘方法及应用前景[J]. 合成生物学, 2023, 4(3): 611-627.
[12]	孟巧珍, 郭菲. “可折叠性”在酶智能设计改造中的应用研究——以AlphaFold2为例[J]. 合成生物学, 2023, 4(3): 571-589.
[13]	王晟, 王泽琛, 陈威华, 陈珂, 彭向达, 欧发芬, 郑良振, 孙瑨原, 沈涛, 赵国屏. 基于人工智能和计算生物学的合成生物学元件设计[J]. 合成生物学, 2023, 4(3): 422-443.
[14]	吕海龙, 王建, 吕浩, 王金, 徐勇, 顾大勇. 合成生物学在下一代基因诊断技术中的应用进展[J]. 合成生物学, 2023, 4(2): 318-332.
[15]	申赵铃, 吴艳玲, 应天雷. 合成生物学与病毒疫苗研发[J]. 合成生物学, 2023, 4(2): 333-346.