Magnetic Bead Spherical Nucleic Acid Microstructure for Reliable DNA Preservation and Repeated DNA Reading

Abstract

DNA is an attractive medium for long-term data storage because of its density, ease of copying, sustainability, and longevity. Recent advances have focused on the development of new encoding algorithms, automation, and sequencing technologies. Despite progress in these subareas, the most challenging hurdle in the deployment of DNA storage remains the reliability of preservation and the repeatability of reading. Herein, we report the construction of a magnetic bead spherical nucleic acid (MB-SNA) composite microstructure and its use as a cost-effective platform for reliable DNA preservation and repeated reading. MB-SNA has an inner core of silica@γ-Fe2O3@silica microbeads and an outer spherical shell of double-stranded DNA (dsDNA) with a density as high as 34 pmol/cm2. For MB-SNA, each strand of dsDNA stored a piece of data, and the high-density packing of dsDNA achieved high-capacity storage. MB-SNA was advantageous in terms of reliable preservation over free DNA. By accelerated aging tests, the data of MB-SNA is demonstrated to be readable after 0.23 million years of preservation at −18 °C and 50% relative humidity. Moreover, MB-SNA facilitated repeated reading by facile PCR-magnetic separation. After 10 cycles of PCR access, the retention rate of dsDNA for MB-SNA is demonstrated to be as high as 93%, and the accuracy of sequencing is more than 98%. In addition, MB-SNA makes cost-effective DNA storage feasible. By serial dilution, the physical limit for MB-SNA to achieve accurate reading is probed to be as low as two microstructures.

Construction and bioanalytical applications of poly-adenine-mediated gold nanoparticle-based spherical nucleic acids

“…Spherical nucleic acids (SNAs) are polyvalent nucleic acid–nanoparticle conjugates, which consist of an inorganic nanoparticle as a core and a dense oligonucleotide shell. Since the pioneering work of Mirkin in 1996, 1 there has been great interest in constructing SNAs with various metal-based nanoparticles, such as gold nanoparticles (AuNPs), 2,3 quantum dots, 4 iron oxide, 5,6 silver, 7,8 or metal-free nanoparticles, such as hollow silica, 9 liposomes, 10 micelles, 11 cross-linked oligodeoxyribonucleotides, 12 and proteins. 13 The wide range of SNAs that have been generated indicates that their properties are not reliant on the core but instead determined by the distinct structure of the nucleic acid shell.…”