Investigating enhanced stability in CTAB(C)-compacted DNA under aging conditions for data storage

Abstract

The pursuit of long-term data storage has increasingly turned toward DNA as a viable medium owing to its exceptional information density and longevity. Despite its potential, maintaining DNA integrity over extended periods is challenging. Here, we investigated the effectiveness of surfactant-mediated DNA compaction and cyclodextrin-driven decompaction for long-term storage of both natural and synthetic DNA. Cetyltrimethylammonium bromide (CTAB) and cetyltrimethylammonium chloride (CTAC) were used to compact salmon-derived DNA (sDNA) and custom-designed synthetic DNA (synDNA), which were then subjected to accelerated aging at various temperatures (4 °C to 70 °C) and 50% relative humidity for 4, 8, and 12 d. The compacted DNA was decompacted using 2-hydroxypropyl-β-cyclodextrin (2HP-β-CD), and the recovered DNA was analyzed using absorbance measurements, quantitative PCR, and Sanger sequencing. The results demonstrated the efficacy of the compaction and decompaction process, with successful recovery of both sDNA and synDNA after accelerated aging. Notably, compacted synDNA exhibited superior stability to pristine synDNA under thermal stress, particularly at 60 °C. Sanger sequencing of recovered synDNA revealed high sequence identities, confirming the preservation of encoded information. The half-lives of decompacted aged-synDNA at 50 °C and 60 °C were comparable to those of DNA extrapolated and preserved in silica matrices, while offering advantages in simplicity and recovery rates. The successful recovery and sequencing of synDNA encoding visual information after accelerated aging highlight the potential of this method for practical DNA-based data storage applications. This study presents a promising approach for long-term DNA storage, combining efficiency, stability, and simplicity, paving the way for future advancements in DNA-based data storage technologies.

Keywords: DNA; accelerated aging; cationic surfactants; compaction and decompaction; data storage.