High-Data-Density, High-Decoding-Speed, and High-Decoding-Accuracy DNA Data Ink for Digital Preservation.

Abstract

DNA-based storage offers exceptional information density, durability, and energy efficiency compared to conventional digital media, yet practical implementation faces challenges including high synthesis costs, sequencing errors, and slow access speeds. Here, we present an integrated DNA storage system with optimized encoding and processing strategies to address practical implementation issues. Our approach achieves 9.78 bits/nt net information density with a flexible index allocation system handling data volume from 0.37 KB to 2.79 × 10²² YB. The decoding process delivers 360× faster throughput than traditional methods, processing 4.57 million reads (1.63 GB) in 34.5 s and demonstrating perfect data retrieval from down-sampled (×5.33) sequencing in 2.47 s. Our error correction system combines inner Reed-Solomon with outer XOR code, ensuring reliable recovery with large reading sequences (92,626) and low copy number data (×0.52). The streamlined NGS preparation workflow reduces processing time from ∼4.5 to ∼2 h while decreasing per-sample costs from ∼$60 to ∼$0.50. The system demonstrates versatility through high-fidelity DNA data storage ink and implementations ranging from physical stamps to VR platforms. This technology establishes a foundation for practical DNA data storage solutions applicable to cultural heritage preservation, autonomous vehicle data management, and matrix-based machine learning applications.