R&D: DNA StairLoop, Enabling High-fidelity Data Recovery and Robust Error Correction in DNA-based Data Storage

Nature Communications has published an article written by Zihui Yan, Center for Applied Mathematics, Tianjin University, Tianjin, China, State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, China, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China, and School of Synthetic Biology and Biomanufacturing, Tianjin University, Tianjin, China, Guanjin Qu, Center for Applied Mathematics, Tianjin University, Tianjin, China, Xin Chen, Center for Applied Mathematics, Tianjin University, Tianjin, China, and State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, China, Gang Zheng, National Supercomputer Center in Tianjin, Tianjin, China, and Huaming Wu, Center for Applied Mathematics, Tianjin University, Tianjin, China, and State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, China.

Abstract: “High-throughput electrochemical synthesis is an emerging DNA synthesis technology that has attracted considerable attention due to its scalability and cost-effectiveness. However, its high error rates and poor synthesis uniformity pose significant challenges for applications in DNA data storage, where high fidelity is essential. In this study, we present StairLoop, a coding scheme designed to address these error characteristics, providing robust error-correcting capabilities. Validated through in-vitro experiments, StairLoop successfully recovers original data under harsh conditions, including nucleotide error rates exceeding 6% or dropout rates over 30% within a block, with sequencing depths of less than 3x . Moreover, the simulation results show that StairLoop can achieve an error correction capability of 10% at the mean coverage rate of 15x. These results highlight StairLoop’s potential to enhance the reliability and practicality of electrochemical DNA synthesis for data storage applications.“