Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
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Article Citation - WoS: 39Citation - Scopus: 37Flow-Through Colorimetric Assay for Detection of Nucleic Acids in Plasma(Elsevier, 2019) Ammanath, Gopal; Yeasmi, Sanjida; Srinivasulu, Yuvasri; Vats, Mukti; Cheema, Jamal Ahmed; Nabilah, Fairuz; Liedberg, Bo; Yıldız, Ümit HakanA flow-through colorimetric assay for detection of nucleic acids in plasma is reported. The proposed assay features an array of four polyvinylidene fluoride (PVDF) membranes impregnated with cationic poly (3-alkoxy-4-methylthiophene) (PT) as an optical reporter. The sensing strategy is based on monitoring the changes in optical properties of PT, upon complexation with target nucleic acids in the presence and in the absence of their corresponding complementary peptide nucleic acids (PNAs). As a proof of concept, the proposed methodology is validated using two biomarkers; lung cancer associated microRNA (mir21) and hepatitis B virus DNA (HBV-DNA). The flow-through colorimetric assay enabled detection of mir21 and HBV-DNA in plasma without requiring tedious sample pre-treatment and clean up protocols. Colorimetric responses for mir21 and HBV-DNA were obtained at nanomolar concentrations over five orders of magnitudes (from 1 nM to 10 mu M), with a limit of detection of -0.6 nM and -2 nM in DI water and plasma, respectively. A logic gate system was developed to utilize the colorimetric assay responses as inputs for discrimination of mir21 and HBV-DNA and subsequently to obtain a profile of nucleic acids in samples that exceed respective clinical threshold limits, thereby enabling rapid and point of care (POC) disease diagnosis. Furthermore, the proposed methodology can be utilized for detection of a large number of nucleic acids in plasma by extending the array of PT impregnated membranes incorporated with their corresponding complementary PNAs. (C) 2019 Elsevier B.V. All rights reserved.Article Citation - WoS: 13Citation - Scopus: 13Single Chain Cationic Polymer Dot as a Fluorescent Probe for Cell Imaging and Selective Determination of Hepatocellular Carcinoma Cells(American Chemical Society, 2019) Özenler, Sezer; Yücel, Müge; Tüncel, Özge; Kaya, Hakan; Özçelik, Serdar; Yıldız, Ümit HakanThis letter describes formation of single chain cationic polymer dots (Pdots) made of poly[1,4-dimethy1-1-(34(2,4,5-trimethylthiophen-3-yl)oxy)propyl)piperazin-1-ium bromide] conjugated polyelectrolyte (CPE). The single chain Pdot formation relies on a simple process which is a rapid nanophase separation between CPE solution of ethylene glycol and water. Pdots show narrow monodisperse size distribution with a 3.6 nm in diameter exhibiting high brightness and excellent colloidal and optical stability. It has been demonstrated that photoluminescent Pdots provide selective nuclear translocation to hepatocellular carcinoma cells as compared to healthy liver cells. The Pdot labeling effectively discriminates cancer cells in the coculture media. Pdots hold great promise as a luminescent probe to diagnose cancer cells in histology and may guide surgeons during operations to precisely separate out cancerous tissue due to augmented fluorescence brightness.Article Citation - WoS: 169Citation - Scopus: 177Thin Film Microextraction: Towards Faster and More Sensitive Microextraction(Elsevier Ltd., 2019) Ölçer, Yekta Arya; Tascon, Marcos; Eroğlu, Ahmet Emin; Boyacı, EzelThin film microextraction (TFME) is an analytical tool that has been proven to be suitable for integrated sampling and sample preparation of a wide variety of routine and on-site applications. Compared to the traditional microextraction techniques, the most important advantage of TFME is its enhanced sensitivity due to the relatively larger extractive phase spread over a larger surface area. The technique, in this way, facilitates fast extraction kinetics and high extractive capacity. Moreover, TFME offers high versatility for device development over classical SPME technologies due to the plethora of available extractive phases, coating methods and geometry options. The goal of this review is to provide a comprehensive summary of the contemporary advances in this exciting field covering novel extractive phases, technological and methodological developments, and relevant cutting-edge applications. Finally, a critical discussion of the future trends on TFME is also presented. (C) 2019 Elsevier B.V. All rights reserved.Article Citation - WoS: 21Citation - Scopus: 22Redox-Responsive Release of Active Payloads From Depolymerized Nanoparticles(Royal Society of Chemistry, 2017) Lv, Li-Ping; Jiang, Shuai; İnan, Alper; Landfester, Katharina; Crespy, DanielThe difference in the reactivity of two monomers, aniline (ANI) and 2,5-dimercapto-1,3,4-thiadiazole (DMcT), was employed to design nanoparticles with completely different nanostructures. The monomers were simultaneously polymerized by tandem oxidative polymerization occurring in the miniemulsion droplets. DMcT is also a corrosion inhibitor and its polymer can be depolymerized by reduction, which avoids the unwanted release of the payload DMcT when the capsules are not activated. The redox-responsive release profile of DMcT from the composite particles is controlled by the morphology of the particles and it was investigated for monolithic, multi-hollow, and yolk-shell structures. These PANI/PDMcT composite particles may find potential application in Li-S batteries or in the self-healing systems for corrosion protection.Article Citation - WoS: 6Citation - Scopus: 6Esterification of 1-Octanol on Clinoptilolite-Supported Tio2 Catalysts(Springer Verlag, 2019) Özyağcı, Bensu; Şahin, Volkan; Karabakan, AbdulkerimIn this study, a natural type of zeolite, Clinoptilolite (CLI), is used as a support for TiO2. First, TiO2-supported heterogeneous catalysts originated from the high temperature calcination of TiCl4 groups, which were thermally immobilized on clinoptilolite, were obtained. Powder-XRD and EDX analyzes showed that the oxide form of Ti-immobilized on dealuminated clinoptilolite were formed in the anatase phase, and the zeolite structure was preserved. As seen in TGA/DTA analyzes, this catalyst could be efficient and have high stability for many reactions. Second, the esterification reaction of 1-octanol with acetic acid is used as a reference reaction for this catalyst.Article Citation - WoS: 90Citation - Scopus: 101A Rapid Atr-Ftir Spectroscopic Method for Classification of Gelatin Gummy Candies in Relation To the Gelatin Source(Elsevier, 2019) Çebi, Nur; Doğan, Canan Ekinci; Ekin Meşe, Ayten; Özdemir, Durmuş; Arıcı, Muhammet; Sağdıç, OsmanGelatin is widely used in gummy candies because of its unique functional properties. Generally, porcine and bovine gelatins are used in the food industry. FTIR-ATR combined with chemometrics analysis such as hierarchical cluster analysis (HCA) (OPUS Version 7.2 software), principal component analysis (PCA) (OPUS Version 7.2 software) and partial least squares-discriminant analysis (PLS-DA) (Matlab R2017b) were used for classification and discrimination of gelatin gummy candies related to their gelatin source. The spectral region between 1734 and 1528 cm(-1) was selected for chemometric analysis. The potential of FTIR spectroscopy for determination of bovine and porcine source in gummy candies was examined and validated by a real-time polymerase chain reaction (PCR) method. Twenty commercial samples were tested by developed ATR-FTIR methodology and RT-PCR technique, mutually confirming and supporting results were obtained. Gummy candies were classified and discriminated in relation to the bovine or porcine source of gelatin with 100% success without any sample preparation using FTIR-ATR technique.Article Citation - WoS: 34Citation - Scopus: 36Biomimetic Hybrid Scaffold Consisting of Co-Electrospun Collagen and Pllcl for 3d Cell Culture(Elsevier Ltd., 2019) Türker, Esra; Yıldız, Ümit Hakan; Arslan Yıldız, AhuElectrospun collagen is commonly used as a scaffold in tissue engineering applications since it mimics the content and morphology of native extracellular matrix (ECM) well. This report describes "toxic solvent free" fabrication of electrospun hybrid scaffold consisting of Collagen (Col) and Poly(L-lactide-co-epsilon-caprolactone) (PLLCL) for three-dimensional (3D) cell culture. Biomimetic hybrid scaffold was fabricated via co-spinning approach where simultaneous electrospinning of PLLCL and Collagen was mediated by polymer sacrificing agent Polyvinylpyrrolidone (PVP). Acidified aqueous solution of PVP was used to solubilize collagen without using toxic solvents for electrospinning, and then PVP was readily removed by rinsing in water. Mechanical characterizations, protein adsorption, as well as biodegradation analysis have been conducted to investigate feasibility of biomimetic hybrid scaffold for 3D cell culture applications. Electrospun biomimetic hybrid scaffold, which has 3D-network structure with 300-450 nm fiber diameters, was found to be maximizing cell adhesion through assisting NIH 3T3 mouse fibroblast cells. 3D cell culture studies confirmed that presence of collagen in biomimetic hybrid scaffold have created a major impact on cell proliferation compared to conventional 2D systems on long-term, also cell viability increased with the increasing amount of collagen. (c) 2019 Elsevier B.V. All rights reserved.Article Citation - WoS: 16Citation - Scopus: 17Antiproliferative Activity of (r)-4 '-methylklavuzon on Hepatocellular Carcinoma Cells and Epcam(+)/Cd133(+) Cancer Stem Cells Via Sirt1 and Exportin-1 (crm1) Inhibition(Elsevier Ltd., 2019) Delman, Murat; Avcı, Sanem Tercan; Akçok, İsmail; Kanbur, Tuğçe; Erdal, Esra; Çağır, AliCytotoxic effects of (R)-4'-methylklavuzon were investigated on hepatocellular carcinoma cells (HuH-7 and HepG2) and HuH-7 EpCAM(+)/CD133(+) cancer stem cells. IC50 of (R)-4'-methylklavuzon was found as 1.25 mu M for HuH-7 parental cells while it was found as 2.50 mu M for HuH-7 EpCAM(+)/CD133(+) cancer stem cells. (R)-4'-methylklavuzon tended to show more efficient in vitro cytotoxicity with its lower IC50 values on hepatocellular carcinoma cell lines compared to its lead molecule, goniothalamin and FDA-approved drugs, sorafenib and regorafenib. Cell-based Sirtuin/HDAC enzyme activity measurements revealed that endogenous Sirtuin/HDAC enzymes were reduced by 40% compared to control. SIRT1 protein levels were upregulated indicating triggered DNA repair mechanism. p53 was overexpressed in HepG2 cells. (R)-4'methylklavuzon inhibited CRM1 protein providing increased retention of p53 and RIOK2 protein in the nucleus. HuH-7 parental and EpCAM(+)/CD133(+) cancer stem cell spheroids lost intact morphology. 3D HepG2 spheroid viabilities were decreased in a correlation with upregulation in p53 protein levels. (C) 2019 Elsevier Masson SAS. All rights reserved.Article Citation - WoS: 45Citation - Scopus: 46Electrospun Polystyrene Fibers Knitted Around Imprinted Acrylate Microspheres as Sorbent for Paraben Derivatives(Elsevier, 2018) Demirkurt, Merve; Ölçer, Yekta Arya; Demir, Mustafa Muammer; Eroğlu, Ahmet EroğluParabens are used as antimicrobial preservatives in food, cosmetic products and pharmaceuticals regardless of their endocrine disrupting effect. In this study, highly selective molecular imprinted polymers (MIPs) were synthesized in submicron-sizes and converted to an SPME fiber coating through electrospinning process in order to determine parabens in water samples. Conversion of MIP to a fiber is achieved via creation of spacial knitting around MIP by polystyrene. The selectivity and extraction ability of the fibers were compared with the commercial fibers and the corresponding non-imprinted polymer (NIP) coated fiber. The coated fiber showed better extraction ability among them. Also, the results revealed that the fiber has better selectivity for benzyl paraben and the other structurally-related compounds, such as methyl and propyl paraben. Extraction efficiency of prepared fibers for three parabens has been tested by spiking bottled, tap and sea water samples. The recoveries changed between 92.2 ± 0.8 and 99.8 ± 0.1 for three different water types. This method could be used for selective and sensitive determination of parabens in aqueous samples.Article Citation - WoS: 12Citation - Scopus: 13History of Spectroscopy and Modern Micromachined Disposable Si Atr-Ir Spectroscopy(Taylor and Francis Ltd., 2018) Koç, Mert; Karabudak, EnginIn this article, the historical development of spectroscopy is examined and the spectroscopy devices used today are described. Then, we focus on infrared (IR) spectroscopy, which cannot give valuable signal in aqueous solution. Attenuated total reflection (ATR)-IR technique solves the problem. In addition, we specifically mention newly developed disposable ATR-IR crystals and micromachined silicon (Si) ATR-IR. Disposable crystal systems and microfluidics systems can be integrated with existing miniature ATR analyzers. If the integration is successful, the technique might be used in biomedical measuring instruments, reactions' analyses, and ultra-high-pressure analyses.