DNA数据存储：保存策略与数据加密

doi:10.12211/2096-8280.2020-084

摘要/Abstract

摘要：

随着信息技术和互联网应用的不断升级，人类社会进入数据爆炸式增长的时代。为缓解海量数据与存储技术不足之间的矛盾，人们开始寻求新一代的存储方式。DNA作为一种新兴的数据存储媒介，具有巨大的发展潜力，其优势包括超高的数据存储密度（理论可达现有技术10⁶倍）、能耗低以及寿命长（理论可达数十万年）。这些特点可有效克服传统存储介质如硬盘、光盘和固体闪存等的不足。本文以DNA数据存储为主线，阐述了DNA数据存储的基本理论和工作流程，重点介绍了DNA保存的方法与策略研究进展，简要总结了信息安全与数据加密的最新研究成果，最后讨论DNA数据存储现阶段面临的主要挑战及发展趋势，特别是，DNA数据存储效率提升、存储读取高度集成自动化以及数据加密新策略等方面将是DNA数据存储的重要研究方向。相信随着合成生物学的不断发展，DNA数据存储将成为未来最具应用潜力的新型存储方式。

关键词: 数据存储, DNA, 生物矿化, 细胞内保存, 数据加密

Abstract:

With the rapid development of information technology and the Internet, human society has entered a new big data era. According to the global DataSphere by international data corporation (IDC), more than 5.9×10²² bytes of data will be created and consumed within 2020, and a 26% data growth rate will be sustained through 2024. These data have outpaced the existing storage formats' capability, including magnetic, optical and electronic media. To alleviate the growing gap between explosive data production and current storage capability, it is highly desirable to explore novel solutions for data storage. As an emerging data storage medium, DNA offers substantial advantages over conventional media, including ultra-high data storage density (theoretically 10⁶ times higher than existing technology), low energy consumption, and long lifetime (up to several hundred thousand years in theory), and has great potential applications in the future. In this review, we present the basic theory and the workflow of DNA data storage, including encode, write, store and encrypt, random access, read, and decode. We also discuss the research progress on data retention strategies, highlighting in vitro and in vivo DNA storage. In comparison with in vivo strategy, in vitro storage may have the greatest potential for applications in consideration of cost, durability, and scalability. We briefly summarize the latest research about information security and data encryption using DNA. Finally, we discuss the current challenges and emerging trends in DNA data storage. The cost of DNA synthesis and sequencing largely restricts the rapid development of DNA data storage. Further unresolved questions include efficient preservation and feasible random access. To solve the challenges, improving the efficiency of DNA data storage, storage, and reading automation and new strategies for data encryption will be important research directions for DNA data storage. It is believed that with the continuous development of synthetic biology, DNA data storage will become the most promising form for information storage in the future.

Key words: data storage, DNA, biomineralization, in vivo storage, data encryption

中图分类号:

R 318

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.

Tingyao ZHOU, Yuan LUO, Xingyu JIANG. DNA data storage： preservation approach and data encryption[J]. Synthetic Biology Journal, 2021, 2(3): 371-383.

图/表 7

图1 DNA数据存储的基本工作流程［主要包括编码（i）、写入（ii）、保存和加密（iii）、随机访问（iv）、读出（v）与解码（vi）］

Fig. 1 Major steps of DNA data storage[including encode (i), write (ii), store and encrypt (iii), random access (iv), read (v) and decode (vi)]

图2 基于数字微流控的高密度干粉DNA数据存储［（a）干粉DNA保存在玻璃板上；（b）将玻璃板置于数字微流控装备上便于检索数据，插图为一个斑点成像图，比例尺为275 μm；（c）夹在玻璃板与电极间的水滴被激活，并移动到斑点DNA下进行补水［39］］

Fig. 2 High density dehydrated DNA data storage with digital microfluidic retrieval[(a) Dehydrated DNA stored on glass cartridges; (b) Cartridge was loaded onto digital microfluidic device to retrieve data, and inset showed photograph of an actual magnified spot, scale bar: 275 μm; (c) A water droplet sandwiched between cartridge and electrodes was actuated to move under spotted DNA for rehydration[39]]

表1 不同DNA保存介质的比较

Tab. 1 Comparison of different DNA storage media

Storage media	DNA loading	Year of invention	Half life	Reference
Earth alkaline salts	>30%	2020	about 109 years	[41]
DNA in silica	0.7%	2013	about 527 years	[24, 42]
DNA in magnetic NPs	3.4%	2019	about 527 years	[43]

图3 DNA框架结构诱导合成磷酸钙［51］

Fig. 3 Schematic Illustration for preparation of CaP templated by DNA-framework[51]

图4 基于DNA折纸的分子加密系统工作流程［90］

Fig. 4 Workflow of DNA origami cryptography for secure information communication [90]

图5 基于亚稳定杂交的DNA数据存储系统的原理［（a）图片文件被编码为DNA序列，可以在室温下稳定地长时间保存，但是在暴露于95 ℃时会被永久快速擦除；（b）基于DNA杂交的真实信息编码［98］］

Fig. 5 Metastable hybridization-based DNA data storage[(a) Image file was encoded as DNA sequences, which could be stored steadily at room temperature for long periods of time, but was permanently and quickly erased when exposed to 95 ℃. (b) Truthful information encoding based on DNA hybridization[98]]

图6 DNA数据存储的主要工作流程及其应用

Fig. 6 Process overview and applications of DNA Data Storage

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