A practical DNA data storage using an expanded alphabet introducing 5-methylcytosine.

IF 1.2 GigaByte (Hong Kong, China) Pub Date : 2025-01-24 eCollection Date: 2025-01-01 DOI:10.46471/gigabyte.147

Deruilin Liu, Demin Xu, Liuxin Shi, Jiayuan Zhang, Kewei Bi, Bei Luo, Chen Liu, Yuxiang Li, Guangyi Fan, Wen Wang, Zhi Ping

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Abstract

The DNA molecule is a promising next-generation data storage medium. Recently, it has been theoretically proposed that non-natural or modified bases can serve as extra molecular letters to increase the information density. However, this strategy is challenging due to the difficulty in synthesizing non-natural DNA sequences and their complex structure. Here, we described a practical DNA data storage transcoding scheme named R+ based on an expanded molecular alphabet that introduces 5-methylcytosine (5mC). We demonstrated its experimental validation by encoding one representative file into several 1.3∼1.6 kbps in vitro DNA fragments for nanopore sequencing. Our results show an average data recovery rate of 98.97% and 86.91% with and without reference, respectively. Our work validates the practicability of 5mC in DNA storage systems, with a potentially wide range of applications.

Availability and implementation: R+ is implemented in Python and the code is available under a MIT license at https://github.com/Incpink-Liu/DNA-storage-R_plus.

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一个实用的DNA数据存储使用扩展字母表引入5-甲基胞嘧啶。

DNA分子是一种很有前途的下一代数据存储介质。近年来，从理论上提出非天然或修饰碱基可以作为额外的分子字母来增加信息密度。然而，由于合成非天然DNA序列的困难及其复杂的结构，这种策略具有挑战性。在这里，我们描述了一种实用的DNA数据存储转编码方案，名为R+，该方案基于扩展的分子字母表，引入了5-甲基胞嘧啶（5mC）。我们通过将一个代表性文件编码为几个1.3 ~ 1.6 kbps的体外DNA片段进行纳米孔测序来验证其实验有效性。结果表明，在有参考文献和无参考文献的情况下，平均数据恢复率分别为98.97%和86.91%。我们的工作验证了5mC在DNA存储系统中的实用性，具有潜在的广泛应用。可用性和实现：R+是用Python实现的，其代码在MIT许可下可在https://github.com/Incpink-Liu/DNA-storage-R_plus上获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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