Zhang Rui, Wu Huaming
Chern Institute of Mathematics, Nankai University, Tianjin, 300071, China.
Center for Applied Mathematics, Tianjin University, Tianjin, 300072, China.
Comput Struct Biotechnol J. 2023 Nov 29;23:140-147. doi: 10.1016/j.csbj.2023.11.035. eCollection 2024 Dec.
A secondary structure in single-stranded DNA refers to its propensity to undergo self-folding, leading to functional inactivity and irreparable failures within DNA storage systems. Consequently, the property of secondary structure avoidance (SSA) becomes a crucial criterion in the design of single-stranded DNA sequences for DNA storage, as it prohibits the inclusion of reverse-complement subsequences that contribute to such structures. This work is specifically focused on addressing the avoidance of secondary structures in single-stranded DNA sequences. We propose a novel sequence replacement approach, which successfully resolves the SSA problem under conditions where the stem exceeds a length of , and the loop is of length . These parameters have been carefully chosen to closely resemble the real-world scenarios encountered in biochemical processes, enhancing the practical relevance of our study.
单链DNA中的二级结构是指其发生自我折叠的倾向，这会导致DNA存储系统内功能失活和不可修复的故障。因此，避免二级结构（SSA）的特性成为设计用于DNA存储的单链DNA序列的关键标准，因为它禁止包含有助于形成此类结构的反向互补子序列。这项工作专门致力于解决单链DNA序列中二级结构的避免问题。我们提出了一种新颖的序列替换方法，该方法在茎超过 长度且环长度为 的条件下成功解决了SSA问题。这些参数经过精心选择，以紧密模拟生化过程中遇到的实际情况，增强了我们研究的实际相关性。
