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.

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

图/表 7

图1 DNA存储的原理模型、技术流程和应用模式(The basic principle is the conversion of digital information between binary code stream, quaternary base sequence and actual DNA fragment. The technical work flow includes Information encoding, data writing, media storage and reliable reading. Storage modes include "DNA hard drive", "DNA CD", "DNA tape" and others)

Fig. 1 The basic principle, technical work flow and storage modes of DNA information storage

图2 基于de Bruijn图论的DNA序列重建算法［34］(There are four major steps in this algorithm: Step 1—Construct the de Bruijn graph using the sequencing results; Step 2—Eliminate the noisy k-mers by removing the low coverage k-mers; Step 3—Greedy path search with the simplified de Bruijn graph to reveal all possible paths associated with specific indexes; Step 4—Select the correct paths, i.e. the correct strands, based on the embedded EC codes)

Fig. 2 Algorithm of de Bruijn graph-based reconstruction of DNA strands[34]

图3 “DNA硬盘”模式示意图［44］[(a) Encoding data into DNA. The original files were converted into 89 standard data blocks and then divided into sub-blocks after error correction coding. Each 192-nt sub-block was transcoded into a 96-nt DNA sequence, and then the sub-block index, block index, and primers are added to form an oligonucleotide structure. (b) Data retrieval from sequencing reads. After PCR and 2nd-generation sequencing of synthesized oligo pool, data blocks with substitutions and erasures were obtained from sequencing reads according to indexes. With the help of error correction coding, original files were finally recovered]

Fig. 3 Schematic diagram of "DNA hard drive"[44]

图4 “DNA光盘”模式示意图［48］[(a) Construction of the data-carrying chromosome. The DNA sequences encoded from original files were synthesized and in vivo assembled into a 254 886 bp chromosome. (b) Encoding scheme. The encoding process included LDPC coding, random interleaver, sparsification, superposition with watermark sequences, and transcoding into DNA sequences. (c) Data retrieval from nanopore readout. The data retrieval process included de novo assembly, polishing, locating, indel correction with watermark sequences, and substitution error correction with the LDPC code]

Fig. 4 Schematic diagram of "DNA CD"[48]

图5 DNA信息存储成本比较与预测(Blue spots, HDD; green spots, floppy disk; purple spots, RAM; orange spots, DNA information storage)

Fig. 5 Comparison and forecast of cost by DNA information storage

图6 DNA信息存储读取速度对比

Fig. 6 Comparison of reading rate for DNA information storage

图7 DNA信息存储与现代存储系统的融合(Synthetic DNA enriches the modern data storage media including SSD, HDD, CD, tape. The introduced new property by DNA requires not only suited low-level techniques including synthesis, amplification and sequencing, but also reliability guarantee schemes such as error correction codes, erasure correction, redundancy eliminating schemes, etc. New application paradigms also should be explored to dig out this new medium. The new medium changes all the elements in the 7 levels of OSI reference model and reforms the classic storage hierarchical architecture)

Fig. 7 Fusion of DNA information storage and information storage system

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