Exploring encapsulation mechanism of DNA and mononucleotides in sol-gel derived silica

Abstract

The encapsulation mechanism of DNA in sol-gel derived silica has been explored in order to elucidate the effect of DNA conformation on encapsulation and to identify the nature of chemical/physical interaction of DNA with silica during and after sol-gel transition. In this respect, double stranded DNA and dAMP (2'-deoxyadenosine 5'-monophosphate) were encapsulated in silica using an alkoxide-based sol-gel route. Biomolecule-encapsulating gels have been characterized using UV-Vis, Si NMR, FTIR spectroscopy and gas adsorption (BET) to investigate chemical interactions of biomolecules with the porous silica network and to examine the extent of sol-gel reactions upon encapsulation. Ethidium bromide intercalation and leach out tests showed that helix conformation of DNA was preserved after encapsulation. For both biomolecules, high water-to-alkoxide ratio promoted water-producing condensation and prevented alcoholic denaturation. NMR and FTIR analyses confirmed high hydraulic reactivity (water adsorption) for more silanol groups-containing DNA and dAMP encapsulated gels than plain silica gel. No chemical binding/interaction occurred between biomolecules and silica network. DNA and dAMP encapsulated silica gelled faster than plain silica due to basic nature of DNA or dAMP containing buffer solutions. DNA was not released from silica gels to aqueous environment up to 9 days. The chemical association between DNA/dAMP and silica host was through phosphate groups and molecular water attached to silanols, acting as a barrier around biomolecules. The helix morphology was found not to be essential for such interaction. BET analyses showed that interconnected, inkbottle-shaped mesoporous silica network was condensed around DNA and dAMP molecules.

Sol-Gel Coatings with Azofoska Fertilizer Deposited onto Pea Seeds

“…In some plant species, silica creates intracellular or extracellular silica bodies (phytolites) which are necessary for growth, mechanical strength, stiffness, and protection against fungi [ 28 ]. Silica prepared under mild conditions using the sol-gel method seem to be ideal for encapsulating fertilizer ingredients, since it is possible to enclose inside them sensitive biological materials such as enzymes [ 29 ], live cells [ 30 ], bacteria [ 31 ], algae [ 32 ], and others [ 33 ]. Encapsulated materials are not damaged.…”

Long term conservation of DNA at ambient temperature. Implications for DNA data storage

“…Many systems, often based on dehydration, have been used for room temperature storage of purified DNA: freeze-drying [ 11 ], inclusion in soluble matrices including liposomes, polymers such as silk [ 12 ] or pullulan [ 13 ] or adsorption on solid supports such as natural or treated cellulose [ 14 – 16 ]. Other procedures use encapsulation in sol-gel-based silica [ 17 , 18 ] or in silica nanoparticles [ 19 , 20 ], inclusion in salts [ 21 ] or layered double hybrids [ 22 ], dissolution in deep eutectic solvents [ 23 ] or ionic liquids [ 24 ]. As none of these procedures can totally protect DNA from atmosphere or moisture, other ways have been proposed: protection under a gold film [ 25 ] or encapsulation under an inert atmosphere in hermetic stainless-steel capsules, the DNAshells™ (Imagene SA, France) [ 6 , 26 , 27 ].…”

Long term conservation of DNA at ambient temperature. Implications for DNA data storage

“…Many systems, often based on dehydration, have been used for room temperature storage of purified DNA: freeze-drying [11], inclusion in soluble matrices including liposomes, polymers such as silk [12] or pullulan [13] or adsorption on solid supports such as natural or treated cellulose [14,15,16]. Other procedures use encapsulation in sol-gel-based silica [17,18] or in silica nanoparticles [19,20], inclusion in salts [21] or layered double hybrids [22], dissolution in deep eutectic solvents [23] or ionic liquids [24]. As none of these procedures can totally protect DNA from atmosphere or moisture, other ways have been proposed: protection under a gold film [25] or encapsulation under an inert atmosphere in hermetic stainless-steel capsules, the DNAshells™ (Imagene SA, France) [6,26,27].…”