Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 1Citation - Scopus: 1Shape and Surface Modification Dependent Cellular Interactions of Gold Nanoparticles in a 3D Blood-Brain Supported Neurospheroid Model(Churchill Livingstone, 2025) Tomak, Aysel; Saglam-Metiner, Pelin; Coban, Reyhan; Oksel-Karakus, Ceyda; Yesil-Celiktas, OzlemRecent investigations have begun to explore the cellular interactions of nanoparticles (NPs) in three-dimensional (3D) neuro-spheroid models of the blood-brain barrier (BBB), offering novel insights into NP transport across the barrier and their potential neurotoxic effects. Building on these findings, we investigated the effects of particle shape and surface modification on the transport dynamics and cellular interactions of gold NPs (AuNPs) using a multicellular 3D spheroid model of the BBB. AuNPs with two different morphologies, spherical and rod-like, were synthesized, modified with polyethylene glycol (PEG) and characterized in detail using Ultraviolet-Visible (UV-Vis) Spectroscopy, Scanning Electron Microscopy (SEM), Dynamic Light Scattering (DLS) and Inductively Coupled Plasma Mass Spectrometry (ICP-MS) techniques. A 3D neuro-spheroid model consisting of mouse brain endothelial cells (bEnd.3), motor neuron-like hybrid cells (NSC-34) and glial cells (C6) was employed to evaluate the BBB transport characteristics and cytotoxicity of bare and PEG-coated spherical and rod-shaped AuNPs. Our results indicated that 3D neurospheroid models can serve as orchestral platforms for studying cellular behaviour of NPs. PEGylation of NPs substantially reduced cytotoxic effects compared to bare particles. While spherical AuNPs showed limited translocation through the endothelial barrier, those that entered the spheroid were found to be distributed deeper within the interior. In contrast, rod-shaped particles exhibited a greater capacity to cross the BBB but tended to accumulate near the periphery without deeper penetration. These findings underscore the critical role of shape and surface chemistry in nanoparticle-mediated BBB transport and support the utility of 3D neuro-spheroid models in predicting nanoparticle behavior in brain tissue.Article Citation - WoS: 69Citation - Scopus: 73Nanoparticle-Protein Corona Complex: Understanding Multiple Interactions Between Environmental Factors, Corona Formation, and Biological Activity(Taylor & Francis, 2021) Öksel Karakuş, Ceyda; Tomak, Aysel; Çeşmeli, Selin; Hanoğlu, Berçem Dilan; Winkler, DavidThe surfaces of pristine nanoparticles become rapidly coated by proteins in biological fluids, forming the so-called protein corona. The corona modifies key physicochemical characteristics of nanoparticle surfaces that modulate its biological and pharmacokinetic activity, biodistribution, and safety. In the two decades since the protein corona was identified, the importance of nano particles surface properties in regulating biological responses have been recognized. However, there is still a lack of clarity about the relationships between physiological conditions and cor ona composition over time, and how this controls biological activities/interactions. Here we review recent progress in characterizing the structure and composition of protein corona as a function of biological fluid and time. We summarize the influence of nanoparticle characteristics on protein corona composition and discuss the relevance of protein corona to the biological activity and fate of nanoparticles. The aim is to provide a critical summary of the key factors that affect protein corona formation (e.g. characteristics of nanoparticles and biological environ ment) and how the corona modulates biological activity, cellular uptake, biodistribution, and drug delivery. In addition to a discussion on the importance of the characterization of protein corona adsorbed on nanoparticle surfaces under conditions that mimic relevant physiological environment, we discuss the unresolved technical issues related to the characterization of nano particle-protein corona complexes during their journey in the body. Lastly, the paper offers a perspective on how the existing nanomaterial toxicity data obtained from in vitro studies should be reconsidered in the light of the presence of a protein corona, and how recent advances in fields, such as proteomics and machine learning can be integrated into the quantitative analysis of protein corona components.Article Citation - WoS: 16Citation - Scopus: 18Bacterial Detection Using Bacteriophages and Gold Nanorods by Following Time-Dependent Changes in Raman Spectral Signals(Informa Healthcare, 2018) Moghtader, Farzaneh; Tomak, Aysel; Zareie, Hadi M.; Pişkin, ErhanThis study attemps to develop bacterial detection strategies using bacteriophages and gold nanorods (GNRs) by Raman spectral analysis. Escherichia coli was selected as the target and its specific phage was used as the bioprobe. Target bacteria and phages were propagated/purified by traditional techniques. GNRs were synthesized by using hexadecyltrimethyl ammonium bromide (CTAB) as stabilizer. A two-step detection strategy was applied: Firstly, the target bacteria were interacted with GNRs in suspensions, and then they were dropped onto silica substrates for detection. It was possible to obtain clear surface-enchanced Raman spectroscopy (SERS) peaks of the target bacteria, even without using phages. In the second step, the phage nanoemulsions were droped onto the bacterial-GNRs complexes on those surfaces and time-dependent changes in the Raman spectra were monitored at different time intervals upto 40 min. These results demonstrated that how one can apply phages with plasmonic nanoparticles for detection of pathogenic bacteria very effectively in a quite simple test.Article Citation - WoS: 6Citation - Scopus: 6Few-Layer Mos2 as Nitrogen Protective Barrier(IOP Publishing Ltd., 2017) Akbalı, Barış; Yanılmaz, Alper; Tomak, Aysel; Tongay, Sefaattin; Çelebi, Cem; Şahin, HasanWe report experimental and theoretical investigations of the observed barrier behavior of few-layer MoS2 against nitrogenation. Owing to its low-strength shearing, low friction coefficient, and high lubricity, MoS2 exhibits the demeanor of a natural N-resistant coating material. Raman spectroscopy is done to determine the coating capability of MoS2 on graphene. Surface morphology of our MoS2/graphene heterostructure is characterized by using optical microscopy, scanning electron microscopy, and atomic force microscopy. In addition, density functional theory-based calculations are performed to understand the energy barrier performance of MoS2 against nitrogenation. The penetration of nitrogen atoms through a defect-free MoS2 layer is prevented by a very high vertical diffusion barrier, indicating that MoS2 can serve as a protective layer for the nitrogenation of graphene. Our experimental and theoretical results show that MoS2 material can be used both as an efficient nanocoating material and as a nanoscale mask for selective nitrogenation of graphene layer.Article Citation - WoS: 36Citation - Scopus: 38Effect of Molecular Architecture on Cell Interactions and Stealth Properties of Peg(American Chemical Society, 2017) Özer, İmran; Tomak, Aysel; Zareie, Hadi M.; Baran, Yusuf; Bulmuş, VolgaPEGylation, covalent attachment of PEG to therapeutic biomolecules, in which suboptimal pharmacokinetic profiles limiting their therapeutic utility are of concern, is a widely applied technology. However, this technology has been challenged by reduced bioactivity of biomolecules upon PEGylation and immunogenicity of PEG triggering immune response and abrogating clinical efficacy, which collectively necessitate development of stealth polymer alternatives. Here we demonstrate that comb-shape poly[oligo(ethylene glycol) methyl ether methacrylate] (POEGMA), a stealth polymer alternative, has a more compact structure than PEG and self-organize into nanoparticles in a molecular weight dependent manner. Most notably, we show that comb-shape POEGMA promotes significantly higher cellular uptake and exhibits less steric hindrance imposed on the conjugated biomolecule than PEG. Collectively, comb-shape POEGMA offers a versatile alternative to PEG for stealth polymer-biomolecule conjugation applications.Article Citation - WoS: 2Citation - Scopus: 2Structural Changes in a Schiff Base Molecular Assembly Initiated by Scanning Tunneling Microscopy Tip(IOP Publishing Ltd., 2016) Tomak, Aysel; Bacaksız, Cihan; Mendirek, Gizem; Şahin, Hasan; Hür, Deniz; Görgün, Kamuran; Senger, Ramazan Tuğrul; Birer, Özgür; Peeters, François M.; Zareie, Hadi M.We report the controlled self-organization and switching of newly designed Schiff base (E)-4-((4-(phenylethynyl) benzylidene) amino) benzenethiol (EPBB) molecules on a Au (111) surface at room temperature. Scanning tunneling microscopy and spectroscopy (STM/STS) were used to image and analyze the conformational changes of the EPBB molecules. The conformational change of the molecules was induced by using the STM tip while increasing the tunneling current. The switching of a domain or island of molecules was shown to be induced by the STM tip during scanning. Unambiguous fingerprints of the switching mechanism were observed via STM/STS measurements. Surface-enhanced Raman scattering was employed, to control and identify quantitatively the switching mechanism of molecules in a monolayer. Density functional theory calculations were also performed in order to understand the microscopic details of the switching mechanism. These calculations revealed that the molecular switching behavior stemmed from the strong interaction of the EPBB molecules with the STM tip. Our approach to controlling intermolecular mechanics provides a path towards the bottom-up assembly of more sophisticated molecular machines.Article Citation - WoS: 26Citation - Scopus: 26Controlled Growth Mechanism of Poly (3-Hexylthiophene) Nanowires(IOP Publishing Ltd., 2016) Kıymaz, D.; Yağmurcukardeş, Mehmet; Tomak, Aysel; Şahin, Hasan; Senger, Ramazan Tugrul; Peeters, François M.; Zareie, Hadi M.; Zafer, CeylanSynthesis of 1D-polymer nanowires by a self-assembly method using marginal solvents is an attractive technique. While the formation mechanism is poorly understood, this method is essential in order to control the growth of nanowires. Here we visualized the time-dependent assembly of poly (3-hexyl-thiophene-2,5-diyl) (P3HT) nanowires by atomic force microscopy and scanning tunneling microscopy. The assembly of P3HT nanowires was carried out at room temperature by mixing cyclohexanone (CHN), as a poor solvent, with polymer solution in 1,2-dichlorobenzene (DCB). Both π-π stacking and planarization, obtained at the mix volume ratio of P3HT (in DCB):CHN (10:7), were considered during the investigation. We find that the length of nanowires was determined by the ordering of polymers in the polymer repetition direction. Additionally, our density functional theory calculations revealed that the presence of DCB and CHN molecules that stabilize the structural distortions due to tail group of polymers was essential for the core-wire formation.Article Citation - WoS: 15Citation - Scopus: 15Bodipy-Conjugated Chitosan Nanoparticles as a Fluorescent Probe(Taylor and Francis Ltd., 2017) Bor, Gizem; Üçüncü, Muhammed; Emrullahoğlu, Mustafa; Tomak, Aysel; Şanlı Mohamed, GülşahRecently, development of fluorescent nanoparticle-based probes for various bioimaging applications has attracted great attention. This work aims to develop a new type fluorescent nanoparticle conjugate and evaluate its cytotoxic effects on A549 and BEAS 2B cell lines. Throughout the study, ionically crosslinked chitosan nanoparticles (CNs) were conjugated with carboxylated 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY-COOH). The results of conjugates (BODIPY-CNs) were investigated with regard to their physic-chemical, optical, cytotoxic properties and cellular internalization. The morphology of BODIPY-CNs was found to be spherical in shape and quite uniform having average diameter of 70.25 ± 11.99 nm. Cytotoxicty studies indicated that although BODIPY-COOH itself was quite toxic on both A549- and BEAS 2B-treated cells, CNs increased the cell viability of both cell lines via conjugation to BODIPY-COOH fluorescent molecule up to 67% for A549 and 74% for BEAS 2B cells. These results may suggest a possible utilization of the new fluorescent nanoparticle-based probe for bioimaging in biology and medicine.