R&D: Secondary Structure in DNA Storage

Computational and Structural Biotechnology Journal has published an article written by Rui Zhang, Chern Institute of Mathematics, Nankai University, Tianjin, 300071, China, and Huaming Wu, Center for Applied Mathematics, Tianjin University, Tianjin, 300072, China.

Abstract: “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.“