R&D: Robust Storage in DNA by de Bruijn Graph-Based de Novo Strand Assembly

Nature Communications has published an article written by Lifu Song, Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China, Feng Geng, College of Pharmacy, Binzhou Medical University, Yantai, 264003, Shandong Province, China, Zi-Yi Gong, Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China, Xin Chen, Centor for Applied Mathematics, Tianjin University, Tianjin, 300072, China, Jijun Tang, School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China, Chunye Gong, National SuperComputer Center in Tianjin, Tianjin, 300457, China, Libang Zhou, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China, Rui Xia, National SuperComputer Center in Tianjin, Tianjin, 300457, China, Ming-Zhe Han, Jing-Yi Xu, Bing-Zhi Li, and Ying-Jin Yuan, Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.

Abstract: “DNA data storage is a rapidly developing technology with great potential due to its high density, long-term durability, and low maintenance cost. The major technical challenges include various errors, such as strand breaks, rearrangements, and indels that frequently arise during DNA synthesis, amplification, sequencing, and preservation. In this study, a de novo strand assembly algorithm (DBGPS) is developed using de Bruijn graph and greedy path search to meet these challenges. DBGPS shows substantial advantages in handling DNA breaks, rearrangements, and indels. The robustness of DBGPS is demonstrated by accelerated aging, multiple independent data retrievals, deep error-prone PCR, and large-scale simulations. Remarkably, 6.8MB of data is accurately recovered from a severely corrupted sample that has been treated at 70 °C for 70 days. With DBGPS, we are able to achieve a logical density of 1.30 bits/cycle and a physical density of 295 PB/g.“

Resource:
Article on the Tianjin University website: Chinese scientists find new way for robust DNA data storage