WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Review Citation - WoS: 69Nanoparticle-Protein Corona Complex: Understanding Multiple Interactions Between Environmental Factors, Corona Formation, and Biological Activity(TAYLOR & FRANCIS LTD, 2021) Tomak, Aysel; Tomak, Aysel; Çesmeli, Selin; Öksel Karakuş, Ceyda; Hanoglu, Bercem D.; Winkler, David; Oksel Karakus, CeydaThe 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 nanoparticles surface properties in regulating biological responses have been recognized. However, there is still a lack of clarity about the relationships between physiological conditions and corona 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 environment) 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 nanoparticle-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.Conference Object Investigation of the Cytotoxicity of Bioceramic Nanoparticles on Saos-2 Cells by an Alternative Method(Elsevier Ireland Ltd, 2022) Tomak, Aysel; Önder, A. C.; Öksel Karakuş, CeydaArticle Citation - WoS: 17Citation - Scopus: 22Protein Corona Formation on Silver Nanoparticles Under Different Conditions(Elsevier, 2022) Tomak, Aysel; Yılancıoğlu, Buket; Winkler, David; Öksel Karakuş, CeydaThe surfaces of nanoparticles become covered by biomolecules in biological fluids. This protein ‘corona’ modifies materials’ characteristics and biological activity. The composition of the protein corona is dynamic, abundant biomolecules that bind first are subsequently replaced by less abundant but more tightly bound ones. Here, we explore the formation of the silver nanoparticle protein corona on exposure to cell culture media containing 10 % fetal bovine serum supplemented Dulbecco's Modified Eagle's medium. Sodium dodecyl-sulfate polyacrylamide gel electrophoresis and liquid chromatography-mass spectrometry/mass spectrometry analysis were used to monitor how different parameters such as incubation time, heating duration, cell culture medium, incubation temperature, and the number of washes affect the nanoparticle–protein corona complex. silver nanoparticles with and without bound proteins were characterized by electron microscopy, dynamic light scattering, and ultraviolet-visible-near-IR spectroscopy. The tetrazolium-based MTT assay was used to determine viability of A549 human lung adenocarcinoma cells treated with silver nanoparticles. Characterization of the nanoparticles before and after protein binding provided insights into their changing morphology on corona formation. Our results confirmed that the physiological environment directly affects protein corona formation on nanoparticle surfaces. In particular, incubation condition-dependent differences in the amount of bound proteins were observed. This work highlights the importance of environmental drivers of protein adsorption, which should be considered when predicting and/or controlling protein targets of silver nanoparticles.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: 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: 54Citation - Scopus: 53Nitrogen Doping for Facile and Effective Modification of Graphene Surfaces(Royal Society of Chemistry, 2017) Yanılmaz, Alper; Tomak, Aysel; Akbalı, Barış; Bacaksız, Cihan; Özçeri, Elif; Arı, Ozan; Senger, Ramazan Tuğrul; Selamet, Yusuf; Zareie, Hadi M.We report experimental and theoretical investigations of nitrogen doped graphene. A low-pressure Chemical Vapor Deposition (CVD) system was used to grow large-area graphene on copper foil, using ethylene as the carbon source. Nitrogen-doped graphene (N-graphene) was prepared by exposing the graphene transferred to different substrates to atomic nitrogen plasma. The effect of varying nitrogen flow rates on doping of graphene was investigated while keeping the power and time constant during the process. The N-graphene was characterized via Raman Spectroscopy, X-ray Photoelectron Spectroscopy (XPS), Scanning Tunneling Microscopy and Spectroscopy (STM and STS), and Fourier Transform Infrared spectroscopy (FTIR). Raman mapping of N-graphene was also performed to show homogeneity of nitrogen on the graphitic lattice. XPS results have revealed the presence of different nitrogen configurations in the graphitic lattice with similar doping concentrations. Density functional theory (DFT) based calculations showed that the periodic adsorption of N atoms predominantly occurs on top of the C atoms rather than through substitution of C in our N-graphene samples. Our results indicate a feasible procedure for producing N-graphene with homogenous and effective doping which would be valuable in electronic and optical 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: 3Citation - Scopus: 3Gold Nanorod Encapsulated Bubbles(Royal Society of Chemistry, 2015) Tomak, Aysel; Zareie, Hadi M.A simple method has been described for synthesizing gold nanorods (GNRs) encapsulated bubbles in a controlled manner. The method involves the use of nitrogen gas in the seed-mediated synthesis method routinely used for synthesis of GNRs. Control over the morphology of the nanostructures was achieved by nitrogen gas flow. The synthesized structures were examined by UV-Vis Spectroscopy, Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). New structures of this type could conceivably serve as plasmonic biosensors, nanodevices and photothermal theranostics with dual modality imaging functionality. © The Royal Society of Chemistry 2015.