Li Shangzhe, Shi Yue, Yang Jing, Liu Haizhou, Jia Lijia, Liu Di
Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
University of Chinese Academy of Sciences, Beijing 101408, China.
Biosaf Health. 2025 Mar 27;7(2):132-139. doi: 10.1016/j.bsheal.2025.03.006. eCollection 2025 Apr.
Deoxyribonucleic acid (DNA) information storage has emerged as a promising solution to address the challenges of traditional silicon-based data storage systems. However, the biosafety implications of artificially synthesized DNA sequences in this technology remain understudied. This research evaluates the biosafety risks associated with five representative DNA storage encoding methods [Church, Goldman, DNA Fountain, Grass, and movable-type (MT) encoding] by analyzing their sequence similarities to natural biological DNA. Through Kraken2 taxonomic classification and Basic Local Alignment Search Tool for nucleotides (BLASTn) alignment analysis, we found that while most artificially designed DNA sequences showed significant differences from known biological sequences, specific encoding methods produced sequences similar to natural genomes. The MT encoding method showed the highest annotation rate (4.59 %) in Kraken2 analysis, while Goldman and Fountain methods demonstrated significant local sequence alignments in BLASTn analysis. Sequence length positively correlated with annotation rates, suggesting longer sequences pose potentially higher biosafety risks. Furthermore, aligned sequences often exhibited characteristics of tandem repeats, particularly in non-coding regions. These findings highlight the importance of incorporating biosafety considerations in DNA storage encoding method development and suggest that randomization strategies may help mitigate potential risks. Our study provides valuable insights into the safe advancement of DNA storage technology and emphasizes the need for comprehensive biosafety evaluation in synthetic biology applications.
脱氧核糖核酸（DNA）信息存储已成为一种有前景的解决方案，以应对传统硅基数据存储系统的挑战。然而，该技术中人工合成DNA序列的生物安全影响仍未得到充分研究。本研究通过分析五种代表性DNA存储编码方法（丘奇法、戈德曼法、DNA喷泉法、格拉斯法和活字编码法）与天然生物DNA的序列相似性，评估了与之相关的生物安全风险。通过Kraken2分类学分类和核苷酸基本局部比对搜索工具（BLASTn）比对分析，我们发现虽然大多数人工设计的DNA序列与已知生物序列存在显著差异，但特定的编码方法产生的序列与天然基因组相似。活字编码法在Kraken2分析中显示出最高的注释率（4.59%），而戈德曼法和喷泉法在BLASTn分析中显示出显著的局部序列比对。序列长度与注释率呈正相关，表明较长的序列可能带来更高的生物安全风险。此外，比对的序列通常表现出串联重复的特征，尤其是在非编码区域。这些发现凸显了在DNA存储编码方法开发中纳入生物安全考量的重要性，并表明随机化策略可能有助于降低潜在风险。我们的研究为DNA存储技术的安全发展提供了有价值的见解，并强调了在合成生物学应用中进行全面生物安全评估的必要性。
