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

Abdur Rasool; Jingwei Hong; Qingshan Jiang; Hui Chen; Qiang Qu

doi:10.1016/j.compbiomed.2023.107404

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

Comput Biol Med. 2023 Oct:165:107404. doi: 10.1016/j.compbiomed.2023.107404. Epub 2023 Aug 28.

Authors

Abdur Rasool¹, Jingwei Hong², Qingshan Jiang³, Hui Chen⁴, Qiang Qu⁵

Affiliations

¹ Shenzhen Key Laboratory for High Performance Data Mining, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Beijing, 100049, China. Electronic address: rasool@siat.ac.cn.
² Shenzhen Key Laboratory for High Performance Data Mining, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; College of Mathematics and Information Science, Hebei University, Baoding, 071002, China.
³ Shenzhen Key Laboratory for High Performance Data Mining, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China. Electronic address: qs.jiang@siat.ac.cn.
⁴ Shenzhen Polytechnic University, Shenzhen, 518055, Guangdong, China.
⁵ Shenzhen Key Laboratory for High Performance Data Mining, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China. Electronic address: qiang@siat.ac.cn.

PMID: 37666064
DOI: 10.1016/j.compbiomed.2023.107404

Abstract

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.

Keywords: Bio-constrained codes; Biocomputing; DNA data storage; Optimized encoding; Reliable storage.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Computer Simulation
DNA* / genetics
Reproducibility of Results

Substances

DNA