DNA数字信息存储的研究进展

doi:10.12211/2096-8280.2020-086

摘要/Abstract

摘要：

随着计算机技术的发展，数字化信息存储改变了我们的生活。信息正在以越来越快的速度产生着，但与此伴生的，是如何有效存储数据的问题。诸如磁盘、硬盘、闪存等磁学或光学等传统存储介质已经逐渐不能满足全世界范围内数据存储的需要。DNA分子凭借其稳定性、高存储密度和低维护成本，有望成为实用的新型信息存储介质。本文首先介绍了利用DNA分子进行数据存储的工作流程，继而介绍了DNA数据存储领域的研究历史和研究进展，包括存储方式、读取方式、编码方式等。为实现DNA信息存储，通过信息编码将二进制信息转换成DNA序列信息；DNA合成实现信息写入；最后通过基因测序获取序列信息，进而进行信息解码得到原始信息。而现代分子生物学技术的发展，尤其是DNA合成和测序技术的飞跃，使DNA分子大规模存储人工数据逐渐成为现实。之后，对比了DNA分子相对于传统数据存储介质的优劣，介绍了基于DNA分子的数据存储的风险与挑战，如数据安全性、信息读写的速度和成本等。最后，对DNA数据存储领域未来研究的方向进行了展望，介绍了一些与该领域具备交叉潜力的新兴生物技术领域，如“DNA条形码”“DNA折纸”。

关键词: DNA分子, 信息存储, DNA合成, DNA测序, 存储密度

Abstract:

With the development of information technology, the approach of digital information storage has gone through unprecedented changes. Traditional storage media such as magnetic and optical devices have gradually fallen short to satisfy the global need for data storage, which calls for storage media with more effective data storage. The extraordinary stability, storage capacity, and storage density of DNA molecules promise it to become a novel information storage medium. In this review, we first introduce the basic principles and processes of using DNA molecules to store artificial information, and highlight the latest research results of DNA storage during the past few years. Next, we compare DNA molecules with current mainstream data storage media in terms of performance and cost. DNA molecules excel in data storage density, storage life, maintenance cost and its potential involvement with living cells. Finally, we provide a detailed review of factors that curb the development of DNA information storage, such as data security, writing and reading speeds and storage cost. Meanwhile, we briefly give comments on emerging biotechnological areas that potentially bring breakthroughs to the field of DNA storage, such as DNA barcoding and DNA origami. Perceivably, information storage with DNA molecules provide a novel solution to cold data storage. However, we would not refrain from the optimistic conjecture that multidisciplinary principles and techniques will continuously expand the application scenarios for DNA information storage.

Key words: DNA molecule, information storage, DNA synthesis, DNA sequencing, coding density

中图分类号:

Q819

董一名, 孙法家, 武瑞君, 钱珑. DNA数字信息存储的研究进展[J]. 合成生物学, 2021, 2(3): 323-334.

Yiming DONG, Fajia SUN, Ruijun WU, Long QIAN. Research progress on DNA molecules for digital information storage[J]. Synthetic Biology Journal, 2021, 2(3): 323-334.

图/表 3

图1 DNA信息存储流程［11］

Fig. 1 The process of DNA-based information storage[11]

图2 DNA存储研究中使用的信息编码方法（前向纠错体系）［（a）直接转换，不包含纠错方案。在这种方案中，数据被读取为数字流，然后转换为DNA序列。例如，Church等［28］和Goldman等［29］分别将二进制数字流和三进制数字流中的每一位转换为一个DNA碱基。（b）线性分组码，即通过线性运算，从原始信息（信息码元）产生用于纠错的冗余（称为“校验码元”或“监督码元”）。在解码时，与生成矩阵相对应的校验矩阵可以用于校验接收到的信息中是否包含错误，并进行纠正。（c）喷泉码，即将原始信息转换为大量较短的信息，这些较短的信息并非原始信息的一部分，而是将原始信息中的符号通过特定的分布进行异或运算得到的。在解码时，只要获得了足够数量的短信息，就可以恢复原始信息。（d）卷积码，即“有记忆”的编码方案。在编码用于传输的符号时，不仅需要处理当前的信息符号，还要对当前位置之前的数个信息符号进行运算］

Fig. 2 Information encoding method (forward error correction system) used in DNA storage research[(a) Direct conversion without error correction scheme. In this method, the data is read as a digital stream and then converted into DNA sequences. For example, Church et al.[28] and Goldman et al.[29] converted each bit in a binary number stream and a ternary number stream into a DNA base, respectively.(b) Linear block code, namely, generating redundancy for error correction (called "check symbols" or "supervision symbols") from the original information (information symbols) through linear operations. In the decoding process, the check matrix corresponding to the generator matrix can be used to check whether the received information contains errors and then correct them. (c) Fountain code, which converts the original information into a large number of shorter sequences. These shorter sequences are not part of the original information, but obtained by performing XOR operations on the symbols in the original information according to a specific distribution. In the decoding process, as long as a sufficient number of shorter sequences are obtained, the original information can be restored. (d) Convolutional codes, that is, coding schemes "with memory". Both the current information symbol and several information symbols before the current position are used to generate the encoding symbols]

图3 DNA信息存储的载体

Fig. 3 The carrier of DNA-based information storage

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