R&D: Rewritable 2D DNA-Based Storage With ML Reconstruction

Nature Communications has published an article written by Chao Pan, Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA, S. Kasra Tabatabaei, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA, S. M. Hossein Tabatabaei Yazdi, Dorna Robotics, Upland, CA, 91786, USA, Alvaro G. Hernandez, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA , Charles M. Schroeder, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA, and Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA, and Olgica Milenkovic, Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.

Abstract: “DNA-based data storage platforms traditionally encode information only in the nucleotide sequence of the molecule. Here we report on a two-dimensional molecular data storage system that records information in both the sequence and the backbone structure of DNA and performs nontrivial joint data encoding, decoding and processing. Our 2DDNA method efficiently stores images in synthetic DNA and embeds pertinent metadata as nicks in the DNA backbone. To avoid costly worst-case redundancy for correcting sequencing/rewriting errors and to mitigate issues associated with mismatched decoding parameters, we develop machine learning techniques for automatic discoloration detection and image inpainting. The 2DDNA platform is experimentally tested by reconstructing a library of images with undetectable or small visual degradation after readout processing, and by erasing and rewriting copyright metadata encoded in nicks. Our results demonstrate that DNA can serve both as a write-once and rewritable memory for heterogenous data and that data can be erased in a permanent, privacy-preserving manner. Moreover, the storage system can be made robust to degrading channel qualities while avoiding global error-correction redundancy.“