Chemical Engineering / Kimya Mühendisliği
Permanent URI for this collectionhttps://hdl.handle.net/11147/14
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Article Citation - WoS: 2Citation - Scopus: 2Morphology of Sodium Salt of Calf Thymus Dna on Mica, Alumina, and Silica Surfaces: Effect of Solvent and Drying Method(Taylor and Francis Ltd., 2017) Yetgin, Senem; Balköse, DevrimInvestigation of morphology of deoxyribonucleotide triphosphate (DNA) dried on different surfaces by atomic force microscopy (AFM) is important in DNA research that is focused on subjects of condensation for gene therapy, sizing, DNA mapping, and cancer examination. The solvent, the surface type, and the method of drying effect the morphology of DNA on solid surfaces. Ethanol and water were used as solvents, flat mica, silica, and alumina surfaces were used as the substrates in the present study. Different methods such as ambient air-drying, N2-forced flow regime drying, and freeze-drying have been applied to droplets of DNA solutions in water or ethanol on the substrates. Forced flow drying regime causes nonlinear DNA attachment on the surface and self-assembly. DNA vertical distance on mica surface was found to be 6 and 1.4 nm for DNA dried in ambient air from ethanol and water solutions, respectively. It was 1.6 nm for N2 flow drying of aqueous DNA solution on mica surface. It was 4.6, 4.6, and 1.99 nm for ambient, N2 flow, and freeze-dried aqueous DNA on alumina surfaces, respectively. Aqueous solution of DNA dried under N2 flow on silica surface had 0.8 nm vertical distance. The smallest standard deviation of 0.05 nm was observed for DNA dried under N2 flow on alumina surface.Article Citation - WoS: 65Citation - Scopus: 72Effect of Peg Grafting Density and Hydrodynamic Volume on Gold Nanoparticle-Cell Interactions: an Investigation on Cell Cycle, Apoptosis, and Dna Damage(American Chemical Society, 2016) Uz, Metin; Bulmuş, Volga; Alsoy Altınkaya, SacideIn this study, interactions of polyethylene glycol (PEG)-coated gold nanoparticles (AuNPs) with cells were investigated with particular focus on the relationship between the PEG layer properties (conformation, grafting density, and hydrodynamic volume) and cell cycle arrest, apoptosis, and DNA damage. Steric hindrance and PEG hydrodynamic volume controlled the protein adsorption, whereas the AuNP core size and PEG hydrodynamic volume were primary factors for cell uptake and viability. At all PEG grafting densities, the particles caused significant cell cycle arrest and DNA damage against CaCo2 and PC3 cells without apoptosis. However, at a particular PEG grafting density (∼0.65 chains/nm2), none of these severe damages were observed on 3T3 cells indicating discriminating behavior of the healthy (3T3) and cancer (PC3 and CaCo2) cells. It was concluded that the PEG grafting density and hydrodynamic volume, tuned with the PEG concentration and AuNP size, played an important role in particle-cell interactions.Article Citation - WoS: 11Citation - Scopus: 12Calf Thymus Dna Characterization and Its Adsorption on Different Silica Surfaces(Royal Society of Chemistry, 2015) Yetgin, Senem; Balköse, DevrimDNA adsorption is the initial stage of gene therapy for drug delivery systems and solid phase extraction methods of DNA purification. High pore volume and high adsorption capacity are simple requirements not only for producing 'smart' drug delivery systems but also the development of purification kits. Silica is the most used material for this purpose. The present study aimed at elucidating the calf thymus DNA biosorption process by the characterization of calf thymus DNA and silica to increase the efficiency of the currently used silica material. Mesoporous silica has long been used for DNA adsorption and silica aerogel is the new adsorbent investigated in the present study. When DNA solution was freeze dried on a silica wafer, self-assembled super helices formed as shown by atomic microscopy (AFM). Thus DNA existed not as single molecules but as large sized agglomerates in water. Thus it could be adsorbed in the macropores and on the external surface of adsorbents. Adsorption of calf thymus DNA to a silica aerogel, a mesoporous silica gel and a silica wafer was investigated in the present study. Silica aerogel was synthesized from TEOS by a supercritical ethanol drying process. The DNA adsorption capacity of the silica aerogel was nearly two times that of the mesoporous silica gel due to its macroporous structure and its higher silanol content. Silica aerogel was found to be a very promising material for DNA adsorption. Therefore silica aerogel can be considered as a good candidate for the delivery of DNA.Article Citation - WoS: 20Citation - Scopus: 22A New Proton Sponge Polymer Synthesized by Raft Polymerization for Intracellular Delivery of Biotherapeutics(Royal Society of Chemistry, 2014) Kurtuluş, Işıl; Yılmaz, Gökhan; Üçüncü, Muhammed; Emrullahoğlu, Mustafa; Becer, C. Remzi; Bulmuş, VolgaA spermine-like polymer was synthesized via reversible addition- fragmentation chain transfer polymerization as a potential endosomal escaping agent. A new methacrylate monomer, 2-((tert-butoxycarbonyl)(2-((tert- butoxycarbonyl)amino)ethyl)amino)ethylmethacrylate (BocAEAEMA), was prepared and then polymerized via RAFT polymerization at constant monomer or initiator concentration at varying [M]/[R]/[I] ratios. In all polymerizations, ln[M] 0/[M] increased linearly with time. The linear increase in M n with monomer conversion was also observed. P(BocAEAEMA)s with controlled molecular weights and narrow molecular weight distributions were obtained. The in vitro cytotoxicity and proton sponge capacity of deprotected polymers P(AEAEMA) were investigated in comparison with a widely used endosomal-disruptive polymer, PEI. P(AEAEMA)s were found to possess proton sponge capacity comparable with PEI. More importantly, P(AEAEMA)s were not toxic on NIH 3T3 cells at concentrations where PEI (25 kDa) was highly toxic (0.4 μM and above). P(AEAEMA) was able to fully condense a DNA fragment at nitrogen/phosphate (N/P) ratios of 10 and above, as evidenced by gel electrophoresis. P(BocAEAEMA) was then chain-extended with a model sugar monomer, mannose-acrylate (ManAc), to yield P(AEAEMA)-b-P(ManAc) block copolymers, to potentially provide cell-recognition ability to the polyplex particles. Although the presence of the P(ManAc) block partially inhibited the interaction of P(AEAEMA) with DNA, P(AEAEMA)13-b-P(ManAc)7 was able to form polyplexes with DNA at N/P ratios ranging between 20/1 and 2/1. Dynamic light scattering measurements showed that while P(AEAEMA) (M n = 5.5 kDa) and DNA formed polyplex particles having a hydrodynamic diameter (Dh) of 125 ± 51 nm, P(AEAEMA)13-b- P(ManAc)7 and DNA formed particles with a smaller Dh of 38 ± 10 nm.