journal article·2025-10-28

DNA encapsulation in mesoporous silica–sodium alginate hybrid gel platforms: Proof-of-concept for data storage applications

Derya Kapusuz Yavuz

Journal of Materials Research· Volume 40· Issue 20
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Abstract

Given the parallels between therapeutic gene delivery and DNA encapsulation for data storage, mesoporous silica emerges as a promising platform. Here, for the first time in literature, the loading, preservation, and release of DNA in mesoporous silica–sodium alginate (MPS–NaAlg) hybrids are explored. Double-stranded DNA was encapsulated during sol–gel synthesis of hybrids containing 0.15–0.60 g NaAlg. Encapsulation, stability, and accessibility were assessed by microscopy, FTIR, XPS, PL spectroscopy, and BET; functional stability/accessibility were further probed via ethidium bromide intercalation, bovine serum albumin adsorption, and release in phosphate-buffered saline. Spectroscopic and BET analyses validated DNA preservation, highlighting MPS–NaAlg—especially with optimized NaAlg content—as a viable substrate for stable, accessible DNA encapsulation in bio-based data storage. Notably, the 0.15 g NaAlg hybrid showed superior structural integrity, low nonspecific binding, and sustained DNA accessibility. These hybrids also offer ample scope for modification/functionalization to enhance next-generation performance.Graphical abstract
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References (46)

Show source-provided references
1. T.B. Huq, P. Anil Kumar Jeeja, S.K. Dam, S.S. Das, J.L. Vivero-Escoto, Recent applications of mesoporous silica nanoparticles in gene therapy. Adv. Healthcare Mater. (2025). https://doi.org/10.1002/adhm.20240478110.1002/adhm.202404781 ↗
2. Y. Song, B. Zhou, X. Du, Y. Wang, J. Zhang, Y. Ai et al., Folic acid (FA)-conjugated mesoporous silica nanoparticles combined with MRP-1 siRNA improves the suppressive effects of myricetin on non-small cell lung cancer (NSCLC). Biomed. Pharmacother. 125, 109561 (2020). https://doi.org/10.1016/j.biopha.2019.10956110.1016/j.biopha.2019.109561 ↗
3. J. Shen, H. Liu, C. Mu, J. Wolfram, W. Zhang, H.-C. Kim et al., Multi-step encapsulation of chemotherapy and gene silencing agents in functionalized mesoporous silica nanoparticles. Nanoscale 9, 5329–5341 (2017). https://doi.org/10.1039/C7NR00377C10.1039/C7NR00377C ↗
4. Y. Cai, Z. Liu, H. Wang, H. Meng, Y. Cao, Mesoporous silica nanoparticles mediate siRNA delivery for long-term multi-gene silencing in intact plants. Adv. Sci. 11, 2301358 (2024). https://doi.org/10.1002/advs.20230135810.1002/advs.202301358 ↗
5. A. Ramos-Valle, L. Marín-Caba, L.G. Hevia, M.A. Correa-Duarte, M.L. Fanarraga, One-pot synthesis of compact DNA silica particles for gene delivery and extraordinary DNA preservation. Mater. Today Adv. 18, 100357 (2023). https://doi.org/10.1016/j.mtadv.2023.10035710.1016/j.mtadv.2023.100357 ↗
6. H. Na, M. Kim, K. Park, S. Ryoo, K.E. Lee, H. Jeon et al., Efficient functional delivery of siRNA using mesoporous silica nanoparticles with ultralarge pores. Small 8, 1752–1761 (2012). https://doi.org/10.1002/smll.20120002810.1002/smll.201200028 ↗
7. R.N. Grass, R. Heckel, M. Puddu, D. Paunescu, W.J. Stark, Robust chemical preservation of digital information on DNA in silica with error-correcting codes. Angew. Chem. Int. Ed. 54, 2552–2555 (2015). https://doi.org/10.1002/anie.20141137810.1002/anie.201411378 ↗
8. J.G. Croissant, K.S. Butler, J.I. Zink, C.J. Brinker, Synthetic amorphous silica nanoparticles: toxicity, biomedical and environmental implications. Nat. Rev. Mater. 5, 886–909 (2020). https://doi.org/10.1038/s41578-020-0230-010.1038/s41578-020-0230-0 ↗
9. 3rd International Conference on Innovative Mechanisms for Industry Applications (ICIMIA-2023): 21–23, December 2023, Bengaluru, India: proceedings. Piscataway, NJ: IEEE; 2023. https://doi.org/10.1109/ICIMIA60377.2023.10.1109/ICIMIA60377.2023 ↗
10. T. Buko, N. Tuczko, T. Ishikawa, DNA data storage. Biotech 12, 44 (2023). https://doi.org/10.3390/biotech1202004410.3390/biotech12020044 ↗
11. M. Yu, X. Tang, Z. Li, W. Wang, S. Wang, M. Li et al., High-throughput DNA synthesis for data storage. Chem. Soc. Rev. 53, 4463–4489 (2024). https://doi.org/10.1039/D3CS00469D10.1039/D3CS00469D ↗
12. M.H. Raza, S. Desai, S. Aravamudhan, R. Zadegan, An outlook on the current challenges and opportunities in DNA data storage. Biotechnol. Adv. 66, 108155 (2023). https://doi.org/10.1016/j.biotechadv.2023.10815510.1016/j.biotechadv.2023.108155 ↗
13. C. Ezekannagha, A. Becker, D. Heider, G. Hattab, Design considerations for advancing data storage with synthetic DNA for long-term archiving. Mater. Today Bio. 15, 100306 (2022). https://doi.org/10.1016/j.mtbio.2022.10030610.1016/j.mtbio.2022.100306 ↗
14. T. Lindahl, Recovery of antediluvian DNA. Nature 365, 700–700 (1993). https://doi.org/10.1038/365700a010.1038/365700a0 ↗
15. S. Pääbo, J.A. Gifford, A.C. Wilson, Mitochondrial DNA sequences from a 7000-year old brain. Nucl. Acids Res. 16, 9775–9787 (1988). https://doi.org/10.1093/nar/16.20.977510.1093/nar/16.20.9775 ↗
16. D. Coudy, M. Colotte, A. Luis, S. Tuffet, J. Bonnet, Long term conservation of DNA at ambient temperature. Implications for DNA data storage. PLoS ONE 16, e0259868 (2021). https://doi.org/10.1371/journal.pone.025986810.1371/journal.pone.0259868 ↗
17. D. Kapusuz, Exploring the structure of sol-gel-derived hybrids for immobilization of RNA: influence of RNA content. Colloid Polym. Sci. 299, 63–72 (2021). https://doi.org/10.1007/s00396-020-04768-410.1007/s00396-020-04768-4 ↗
18. D. Kapusuz, Sol–gel derived silica/polyethylene glycol hybrids as potential oligonucleotide vectors. J. Mater. Res. 34, 3787–3797 (2019). https://doi.org/10.1557/jmr.2019.34110.1557/jmr.2019.341 ↗
19. D. Kapusuz, C. Durucan, Exploring encapsulation mechanism of DNA and mononucleotides in sol-gel derived silica. J. Biomater. Appl. 32, 114–125 (2017). https://doi.org/10.1177/088532821771310410.1177/0885328217713104 ↗
20. D. Kapusuz, C. Durucan, Synthesis of DNA-encapsulated silica elaborated by sol–gel routes. J. Mater. Res. 28, 175–184 (2013). https://doi.org/10.1557/jmr.2012.30910.1557/jmr.2012.309 ↗
21. X. Li, Y. Chen, M. Wang, Y. Ma, W. Xia, H. Gu, A mesoporous silica nanoparticle – PEI – fusogenic peptide system for siRNA delivery in cancer therapy. Biomaterials 34, 1391–1401 (2013). https://doi.org/10.1016/j.biomaterials.2012.10.07210.1016/j.biomaterials.2012.10.072 ↗
22. D. Zheng, K. Wang, B. Bai, A critical review of sodium alginate-based composites in water treatment. Carbohydr. Polym. 331, 121850 (2024). https://doi.org/10.1016/j.carbpol.2024.12185010.1016/j.carbpol.2024.121850 ↗
23. R. Abka-khajouei, L. Tounsi, N. Shahabi, A.K. Patel, S. Abdelkafi, P. Michaud, Structures, properties and applications of alginates. Mar. Drugs 20, 364 (2022). https://doi.org/10.3390/md2006036410.3390/md20060364 ↗
24. D. Kołodyńska, M. Gęca, E. Skwarek, O. Goncharuk, Titania-coated silica alone and modified by sodium alginate as sorbents for heavy metal ions. Nanoscale Res. Lett. 13, 96 (2018). https://doi.org/10.1186/s11671-018-2512-710.1186/s11671-018-2512-7 ↗
25. N. Yuan, S. Li, G. Li, Sodium alginate coated mesoporous silica for dual bio-responsive controlled drug delivery. J. Drug Deliv. Sci. Technol. 46, 348–353 (2018). https://doi.org/10.1016/j.jddst.2018.05.02610.1016/j.jddst.2018.05.026 ↗
26. M. Popova, A. Szegedi, K. Yoncheva, S. Konstantinov, G.P. Petrova, H.A. Aleksandrov et al., New method for preparation of delivery systems of poorly soluble drugs on the basis of functionalized mesoporous MCM-41 nanoparticles. Microporous Mesoporous Mater. 198, 247–255 (2014). https://doi.org/10.1016/j.micromeso.2014.07.04410.1016/j.micromeso.2014.07.044 ↗
27. T. Coradin, J. Livage, Mesoporous alginate/silica biocomposites for enzyme immobilisation. C. R. Chim. 6, 147–152 (2003). https://doi.org/10.1016/S1631-0748(03)00006-710.1016/S1631-0748(03)00006-7 ↗
28. X. Han, J. Liang, S. Fukuda, L. Zhu, S. Wang, Sodium alginate–silica composite aerogels from rice husk ash for efficient absorption of organic pollutants. Biomass Bioenerg. 159, 106424 (2022). https://doi.org/10.1016/j.biombioe.2022.10642410.1016/j.biombioe.2022.106424 ↗
29. H.H.C. De Lima, V.L. Kupfer, M.P. Moisés, M.R. Guilherme, J. De C. Rinaldi, S.L. Felisbino et al., Bionanocomposites based on mesoporous silica and alginate for enhanced drug delivery. Carbohydr. Polym. 196, 126–134 (2018). https://doi.org/10.1016/j.carbpol.2018.04.10710.1016/j.carbpol.2018.04.107 ↗
30. M. Thommes, K. Kaneko, A.V. Neimark, J.P. Olivier, F. Rodriguez-Reinoso, J. Rouquerol et al., Physisorption of gases, with special reference to the evaluation of surface area and pore size distribution (IUPAC technical report). Pure Appl. Chem. 87, 1051–1069 (2015). https://doi.org/10.1515/pac-2014-111710.1515/pac-2014-1117 ↗
31. Sotomayor FJ, Cychosz KA, Thommes M. Characterization of micro/mesoporous materials by physisorption: concepts and case studies. Acc. Mater. Surf. Res. 3, 34–50 (n.d.)
32. D.A. Stephenson, N.J. Binkowski, X-ray photoelectron spectroscopy of silica in theory and experiment. J. Non-Cryst. Solids 22, 399–421 (1976). https://doi.org/10.1016/0022-3093(76)90069-710.1016/0022-3093(76)90069-7 ↗
33. M.E. Simonsen, C. Sønderby, Z. Li, E.G. Søgaard, XPS and FT-IR investigation of silicate polymers. J. Mater. Sci. 44, 2079–2088 (2009). https://doi.org/10.1007/s10853-009-3270-910.1007/s10853-009-3270-9 ↗
34. F. Miyaji, M. Iwai, T. Kokubo, T. Nakamura, Chemical surface treatment of silicone for inducing its bioactivity. J. Mater. Sci. Mater. Med. 9, 61–65 (1998). https://doi.org/10.1023/A:100888672905010.1023/A:1008886729050 ↗
35. D. Labou, S. Neophytides, Combined XPS, electrochemical and Kelvin probe measurements of NaY zeolite. Solid State Ionics 177, 971–977 (2006). https://doi.org/10.1016/j.ssi.2006.03.01410.1016/j.ssi.2006.03.014 ↗
36. K. Kishi, H. Kirimura, Y. Fujimoto, XPS studies for NaCl deposited on the Ni(111) surface. Surf. Sci. 181, 586–595 (1987). https://doi.org/10.1016/0039-6028(87)90207-X10.1016/0039-6028(87)90207-X ↗
37. M.T. Kim, Deposition behavior of hexamethydisiloxane films based on the FTIR analysis of Si–O–Si and Si–CH3 bonds. Thin Solid Films 311, 157–163 (1997). https://doi.org/10.1016/S0040-6090(97)00683-410.1016/S0040-6090(97)00683-4 ↗
38. A. Fidalgo, L.M. Ilharco, The defect structure of sol–gel-derived silica/polytetrahydrofuran hybrid films by FTIR. J. Non-Cryst. Solids 283, 144–154 (2001). https://doi.org/10.1016/S0022-3093(01)00418-510.1016/S0022-3093(01)00418-5 ↗
39. J.C. Steinbach, M. Schneider, O. Hauler, G. Lorenz, K. Rebner, A. Kandelbauer, A process analytical concept for in-line FTIR monitoring of polysiloxane formation. Polymers 12, 2473 (2020). https://doi.org/10.3390/polym1211247310.3390/polym12112473 ↗
40. M. Feig, B.M. Pettitt, A molecular simulation picture of DNA hydration around A- and B-DNA. Biopolymers 48, 199 (1998)10.1002/(SICI)1097-0282(1998)48:4<199::AID-BIP2>3.0.CO;2-5 ↗
41. K.A. Melzak, C.S. Sherwood, R.F.B. Turner, C.A. Haynes, Driving forces for DNA adsorption to silica in perchlorate solutions. J. Colloid Interface Sci. 181, 635–644 (1996). https://doi.org/10.1006/jcis.1996.042110.1006/jcis.1996.0421 ↗
42. S. Jafari, H. Derakhshankhah, L. Alaei, A. Fattahi, B.S. Varnamkhasti, A.A. Saboury, Mesoporous silica nanoparticles for therapeutic/diagnostic applications. Biomed. Pharmacother. 109, 1100–1111 (2019). https://doi.org/10.1016/j.biopha.2018.10.16710.1016/j.biopha.2018.10.167 ↗
43. H.-S. Shin, Y.-K. Hwang, S. Huh, Facile preparation of ultra-large pore mesoporous silica nanoparticles and their application to the encapsulation of large guest molecules. ACS Appl. Mater. Interfaces 6, 1740–1746 (2014). https://doi.org/10.1021/am404709w10.1021/am404709w ↗
44. S.V. Paston, A.M. Polyanichko, O.V. Shulenina, D.N. Osinnikova, A study of the DNA structure in films using FTIR spectroscopy. Biophysics 65, 900–906 (2020). https://doi.org/10.1134/S000635092006015910.1134/S0006350920060159 ↗
45. G.I. Dovbeshko, Gold and colloidal gold surface influence on DNA conformational change. Semicond. Phys. Quantum Electron. Optoelectron. 7(3), 318–325 (2004). https://doi.org/10.15407/spqeo7.03.31810.15407/spqeo7.03.318 ↗
46. B. Pan, D. Cui, P. Xu, Q. Li, T. Huang, R. He et al., Study on interaction between gold nanorod and bovine serum albumin. Colloids Surf A Physicochem Eng Asp 295, 217–222 (2007). https://doi.org/10.1016/j.colsurfa.2006.09.00210.1016/j.colsurfa.2006.09.002 ↗