Towards practical and robust DNA-based data archiving using the yin–yang codec system
Zhi Ping, Shihong Chen, Guangyu Zhou, Xiaoluo Huang, Sha Zhu, Haoling Zhang, Henry H. Lee, Zhaojun Lan, Jie Cui, Tai Chen, Wenwei Zhang, Huanming Yang, Xun Xu, George M. Church, Yue Shen
Abstract
Abstract DNA is a promising data storage medium due to its remarkable durability and space-efficient storage. Early bit-to-base transcoding schemes have primarily pursued information density, at the expense of introducing biocompatibility challenges or decoding failure. Here we propose a robust transcoding algorithm named the yin–yang codec, using two rules to encode two binary bits into one nucleotide, to generate DNA sequences that are highly compatible with synthesis and sequencing technologies. We encoded two representative file formats and stored them in vitro as 200 nt oligo pools and in vivo as a ~54 kbps DNA fragment in yeast cells. Sequencing results show that the yin–yang codec exhibits high robustness and reliability for a wide variety of data types, with an average recovery rate of 99.9% above 10 4 molecule copies and an achieved recovery rate of 87.53% at ≤10 2 copies. Additionally, the in vivo storage demonstration achieved an experimentally measured physical density close to the theoretical maximum.