DNA StairLoop: enabling high-fidelity data recovery and robust error correction in DNA-based data storage

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.