R&D: Massively Parallel Homogeneous Amplification of Chip-scale DNA for DNA Information Storage (MPHAC-DIS)

Nature Communications has published an article written by Zhi Weng, Jiangxue Li, Yi Wu, Xuehao Xiu, School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China, Fei Wang, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China, Xiaolei Zuo, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China, Ping Song, School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China, and Chunhai Fan, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.

Abstract: “Chip scale DNA synthesis offers a high-throughput and cost-effective method for large-scale DNA-based information storage. Nevertheless, unbiased information retrieval from low-copy-number sequences remains a barricade that largely arises from the indispensable DNA amplification. Here, we devise a simulation-guided quantitative primer-template hybridization strategy to realize massively parallel homogeneous amplification of chip-scale DNA for DNA information storage (MPHAC-DIS). Using a fixed-energy primer design, we demonstrate the unbiasedness of MPHAC for amplifying 100,000-plex sequences. Simulations reveal that MPHAC achieves a fold-80 value of 1.0 compared to 3.2 with conventional fixed-length primers, lowering costs by up to four orders of magnitude through reduced over-sequencing. The MPHAC-DIS system using 35,406 encoded oligonucleotide allows simultaneous access of multimedia files including text, images, and videos with high decoding accuracy at very low sequencing depths. Specifically, even a ~ 1 ×  sequencing depth, with the combination of machine learning, results in an acceptable decoding accuracy of ~80%. The programmable and predictable MPHAC-DIS method thus opens new door for DNA-based large-scale data storage with potential industrial applications.“