BO-DNA: Biologically optimized encoding model for a highly-reliable DNA data storage

• Published in: Computers in biology and medicine Vol. 165; p. 107404
• Main Authors: Rasool, Abdur, Hong, Jingwei, Jiang, Qingshan, Chen, Hui, Qu, Qiang
• Format: Journal Article
• Language: English
• Published: Oxford Elsevier Ltd 01.10.2023; Elsevier Limited
• Subjects: Algorithms; Binary data; Bio-constrained codes; Biocomputing; Constraints; Data storage; Density; Deoxyribonucleic acid; Design; DNA; DNA data storage; Efficiency; Error correction & detection; Errors; Gene sequencing; Heuristic; Hybridization; Information storage; Lower bounds; Medical imaging; Medical research; Methods; Nucleotide sequence; Nucleotides; Optimization; Optimization algorithms; Optimized encoding; Reliability; Reliable storage; Simulation; Reliable storage; Biocomputing; Optimized encoding; Bio-constrained codes; DNA data storage
• ISSN: 0010-4825; 1879-0534
• DOI: 10.1016/j.compbiomed.2023.107404

DNA data storage is a promising technology that utilizes computer simulation, and synthetic biology, offering high-density and reliable digital information storage. It is challenging to store massive data in a small amount of DNA without losing the original data since nonspecific hybridization errors occur frequently and severely affect the reliability of stored data. This study proposes a novel biologically optimized encoding model for DNA data storage (BO-DNA) to overcome the reliability problem. BO-DNA model is developed by a new rule-based mapping method to avoid data drop during the transcoding of binary data to premier nucleotides. A customized optimization algorithm based on a tent chaotic map is applied to maximize the lower bounds that help to minimize the nonspecific hybridization errors. The robustness of BO-DNA is computed by four bio-constraints to confirm the reliability of newly generated DNA sequences. Experimentally, different medical images are encoded and decoded successfully with 12%–59% improved lower bounds and optimally constrained-based DNA sequences reported with 1.77bit/nt average density. BO-DNA's results demonstrate substantial advantages in constructing reliable DNA data storage. •Tackling data reliability lost due to nonspecific hybridization errors in DNA data storage.•Introducing novel rule-based mapping to avoid data drop during the transcoding.•Constructing customized optimization algorithms to improve lower bounds on optimized DNA codes.•Developing bio-constrained threshold to confirm the DNA sequence's reliability.•Reporting 12%–59% improved lower bounds with 1.77 average density ensuring DNA storage reliability.