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

Durucan, Caner
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-29 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.


Investigation of structural properties of methylated human promoter regions in terms of DNA helical rise
Yaldız, Burcu; Aydın Son, Yeşim; Department of Bioinformatics (2014)
The infamous double helix structure of DNA was assumed to be a rigid, uniformly observed structure throughout the genomic DNA. However, the differences in physical structure of DNA in terms of local helical parameters such as twist, tilt, roll, rise and angles between adjacent base pairs in B-DNA molecule have been shown in many studies. This observed flexibility satisfies the known physical and chemical properties of DNA while providing a better model to explain how DNA fulfills its biological functions. W...
Design and construction of double promoter systems and their use in pharmaceutical protein production in P. Pastoris
Demir, İrem; Çalık, Pınar; Department of Chemical Engineering (2019)
Intracellular phenomena such as promoter strength, mRNA secondary structure, translation efficiency and codon preference, 5′-untranslated region processing, and protein turnover, have impacts directly on the expression of heterologous genes. Design of multi-promoter expression systems with constituent strong promoters and engineered promoter variants is a novel metabolic engineering strategy for increasing the promoter strength further, and tuning the expression for recombinant protein (r-protein) productio...
A mechanistic insight into selective de novo DNA methylation regulated by base-specific hydrogen bonding profile
Barlas , Ayşe Berçin; Karaca , Ezgi (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10)
The mammalian DNA methylation regulates diverse biological processes at the epigenetic level, such as ageing, embryonic development, reprogramming, chromatin modification, and X chromosome inactivation. Abnormalities in the DNA methylation disrupts integral molecular signaling mechanisms, leading to the severe diseases, especially cancer. DNA methylation occurs mainly at CpG islands through the transfer of a methyl group from S-adenosyl-L-methionine (SAM) to the 5' carbon of the target cytosine. De novo met...
The Effect of physical properties of the ELP-collagen based patterned surfaces on cell attachment and deformation
Antmen, Ezgi; Hasırcı, Vasıf Nejat; Demirci, Utkan; Department of Biology (2013)
Cell and substrate interactions are important in tissue engineering products especially on the behavior of the cells such as adhesion, migration, proliferation, and differentiation. These have been widely studied using substrates with different physical, chemical, and mechanical properties and form. In this study, elastin-like recombinamers (ELRs) were used blended with collagen or only collagen as the surface material. The ELR used in this study has Valine-Proline-Glycine-X-Glycine aminoacid sequences in i...
Analysis of genetic relationships among perennial and annual Cicer species growing in Turkey using RAPD markers
Sudupak, MA; Akkaya, Mahinur; Kence, A (2002-12-01)
Random amplified polymorphic DNA (RAPD) fragments were used to assess genetic relationships among Cicer spp. growing in Turkey. Seven 10-mer primers selected from a 50 random oligonucleotide primer set, depending on their ability to amplify genomic DNA in all species, were used to detect RAPD variation in 43 wild and cultivated accessions representing ten species. These primers yielded 95 reproducible amplification products, 92 of which were polymorphic. Pairwise,genetic distances of accessions estimated ac...
Citation Formats
D. KAPUSUZ and C. Durucan, “Exploring encapsulation mechanism of DNA and mononucleotides in sol-gel derived silica,” JOURNAL OF BIOMATERIALS APPLICATIONS, pp. 114–125, 2017, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/35834.