DNA synthesis technology: foundation of DNA data storage

HUANG Xiaoluo; DAI Junbiao

doi:10.12211/2096-8280.2020-088

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DNA synthesis technology: foundation of DNA data storage

Invited Review | 更新时间：2025-03-20

- DNA synthesis technology: foundation of DNA data storage
- Synthetic Biology Journal Vol. 2, Issue 3, Pages: 335-353(2021)
- 作者机构：
  
  中国科学院深圳先进技术研究院，深圳合成生物学创新研究院，广东省合成基因组学重点实验室，深圳市合成基因组学重点实验室，广东深圳　518055
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2020-088
  CLC： Q-1;Q819
- Received：14 December 2020，
  
  Revised：2021-04-07，
  
  Published：30 June 2021
- 稿件说明：
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黄小罗，戴俊彪. 人工DNA合成技术：DNA数据存储的基石［J］. 合成生物学， 2021， 2（3）： 335-353

HUANG Xiaoluo， DAI Junbiao. DNA synthesis technology： foundation of DNA data storage［J］. Synthetic Biology Journal， 2021， 2（3）： 335-353
黄小罗，戴俊彪. 人工DNA合成技术：DNA数据存储的基石［J］. 合成生物学， 2021， 2（3）： 335-353 DOI： 10.12211/2096-8280.2020-088.

HUANG Xiaoluo， DAI Junbiao. DNA synthesis technology： foundation of DNA data storage［J］. Synthetic Biology Journal， 2021， 2（3）： 335-353 DOI： 10.12211/2096-8280.2020-088.

摘要

DNA数据存储由于在存储应用上的诸多优点而日渐受到广泛关注。DNA数据存储流程包括将0/1二进制信息转换为A/T/C/G碱基序列，利用人工DNA合成技术将碱基序列合成为DNA多聚物分子，以及通过测序技术进行数据读出等环节。然而，目前的人工DNA合成成本依然高昂，严重制约了以DNA为介质的数据存储技术的快速发展及其产业化应用。人工DNA合成作为DNA数据存储的基础技术和成本关键，是决定DNA数据存储从理论走向应用的主要因素。本文以DNA合成的发展历程出发，系统地总结了其关键技术的研究进展，包括柱式化学寡核苷酸合成、芯片化学寡核苷酸合成、寡核苷酸纯化、寡核苷酸拼装、基因合成纠错与克隆筛选、大片段基因合成组装及基因组合成，以及新一代酶法合成等。同时，进一步总结和分析了DNA合成技术关键参数长度、成本及速度对DNA数据存储商业化发展的影响，以期为DNA数据存储的全流程技术开发和应用研究提供一定的参考和思路。降低DNA合成成本，开发更加高效的基因组合成策略，进一步发展新一代酶法DNA合成技术，以及建立面向DNA数据存储的长片段、低成本、快写入等功能应用的DNA合成技术等是未来DNA合成技术的重要发展趋势。

Abstract

DNA-based data storage technology has many considerable advantages

and been suggested as one of the most promising technologies to cope up with future crisis in information storage. It involves the conversion of real information into A/T/C/G sequences

synthesis of preservable DNA polymers by DNA synthesis technology

and data deciphering by DNA sequencing technology. Nevertheless

the current cost of DNA synthesis is still high

which greatly limits the rapid development and industrial application of DNA data storage. As the key technology of DNA data storage

DNA synthesis lays the foundation for the practical application of DNA data storage. Since the first oligonucleotides were made in the 1950 s

DNA synthesis technology has been rapidly developed and commercialized

spawning the emergence of DNA synthesizers with different throughput

which achieved oligonucleotides synthesis with dozens of nucleotides to MB-level microbial genomes. In this review

we systematically summarized the key research progress of DNA synthesis technology in terms of its historical development

which includes column-based chemical oligonucleotide synthesis

chip-based chemical oligonucleotide synthesis

oligonucleotide purification

oligonucleotide assembly

error correction and gene cloning

large fragment gene synthesis

genome synthesis and next generation enzymatic DNA synthesis. Currently

the widely used DNA synthesis technology starts from chemical synthesis of oligonucleotide. Although a number of chemical technologies have been proposed

the one typically used is the "phosphoramide" method

which includes the steps of "deprotection"

"coupling"

"capping" and "oxidation". The chemical synthesis generally produces single-stranded oligonucleotide with less than 200 nt. For double-stranded DNA synthesis

the single-stranded oligonucleotides need to be assembled

. The oligonucleotide assembly technologies including ligase chain assembly (LCA) and polymerase chain assembly (PCA) were thus developed

and have been well applied in the commercialized gene synthesis. Following the development of chemical oligonucleotide synthesis technology and gene synthesis technology

several bacterial genomes and yeast chromosomes have been successfully synthesized

by employing the strategies of "one time

de novo

synthesis" or "gradual replacement synthesis". Meanwhile

new enzymatic DNA synthesis technology has also made considerable progress in the recent years

opening up a new path for synthetic biologists. In addition to these key research developments

we further summarized and analyzed the impact of key parameters of DNA synthesis technology

such as length

cost and speed

on DNA data storage

in order to provide some references and ideas for the development and the practical application of the entire DNA data storage process. Finally

we envisioned the future trend of DNA synthesis technology

including cost reduction

further development of genome synthesis technology and enzymatic DNA synthesis technology

as well as the establishment of a faster DNA synthesis technology with a longer fragment and lower-cost for DNA data storage.

关键词

Keywords

references

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