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    A Sensitive Epinephrine Sensor Based on Photochemically Synthesized Gold Nanoparticles
    (2025) Metin, Eyüp; Batibay, Gonul S. ; Aydın, Meral; Arsu, Nergis
    In this study, gold nanoparticles (AuNPs) and AuNPs-graphene oxide (AuNPs@GO) nanostructures were synthesized in aqueous media using an in-situ photochemical method with bis-acyl phosphine oxide (BAPO) photoinitiator as a photoreducing agent in the presence of HAuCl4. The parameters for synthesis were arranged to obtain stable and reproducible dispersions with desirable chemical and optical properties. Both AuNPs and AuNPs@GO were employed as sensing platforms for the detection of epinephrine in two concentration ranges: micromolar (µM) and nanomolar (nM). Field emission scanning electron microscopy (FE-SEM), Dynamic Light Scattering (DLS), UV-Vis absorption, fluorescence emission, and Fourier Transform Infrared (FT-IR) spectroscopy techniques were used to investigate the morphological, optical, and chemical properties of the nanostructures as well as their sensing ability towards epinephrine. Fluorescence spectroscopy played a crucial role in demonstrating the high sensitivity and effectiveness of these systems, especially in the low concentration (nM) range, confirming their strong potential as fluorescence-based sensors. By constructing calibration curves on best linear subranges, limit of detection (LOD) and limit of quantification (LOQ) were calculated with two different approaches, SEintercept and Sy/x. Among all the investigated nanostructures, AuNPs@GO exhibited the highest sensitivity towards epinephrine. The efficiency and reproducibility of the in-situ photochemical AuNPs synthesis approach highlight its applicability in small-molecule detection and particularly in analytical and bio-sensing applications.
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    DNA groove binder and significant cytotoxic activity on human colon cancer cells: Potential of a dimeric zinc (II) phthalocyanine derivative
    (2023) Batibay, Gonul S.; Karaoğlan, Gülnur Keser; Köse, Gülşah Gümrükçü; Kazancıoğlu, Elif Özçelik; Metin, Eyüp; Kalındemirtaş, Ferdane Danışman; Kuruca, Serap Erdem; Arsu, Nergis
    The interaction of a multi-component system consisting of benzene-1,4-diyldimethanimine-bridged dimeric zinc-phthalocyanine groups (4OMPCZ) with calf thymus DNA (ct-DNA) was investigated using UV-Vis absorption, fluorescence emission spectroscopy methods, and viscosity measurements. The binding constant, Kb, which is an important parameter to gain information about the binding mode, was found as 9.7 x 107 M-1 from the UV-Vis absorption studies. Another important spectrophotometric tool is competitive displacement assays with Ethidium bromide and Hoechst 33342. Through this experiment, a higher KSV value was obtained with Hoechst for the phthalocyanine derivative, 4OMPCZ, and the ct-DNA complex than with ethidium bromide. Additionally, mo-lecular docking studies were conducted to calculate the theoretical binding constant and visualize the in-teractions of 4OMPCZ with a model DNA. According to docking results, although the interactions are mainly located in the major groove of the DNA helix, due to the wrapping, these interactions can also be extended to the minor groove of the DNA. Spectrophotometric, molecular docking, and viscosity studies revealed that the interaction of 4OMPCZ with DNA is likely to be via the major and minor grooves. The in vitro cytotoxic activity of 4OMPCZ was evaluated by MTT assay on human colon cancer cells (HT29) after 72 h of treatment. 4OMPCZ indicated significant cytotoxic activity when stimulated with UV light compared to the standard chemotherapy drugs, fluorouracil (5-FU), and cisplatin on HT29 colon cancer cells. The IC50 value of 4OMPCZ displayed considerably lower concentrations compared to the standard drugs, 5-FU, and cisplatin.
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    In–situ formation of self-assembled Ag nanoclusters on ct-DNA in the presence of 2-mercaptothioxanthone by using UV–vis light irradiation
    (Elsevier, 2018) Metin, Eyüp; Batibay, Gonul S.; Arsu, Nergis
    Self-assembled silver nanoparticles (Ag NPs) on calf thymus DNA (ct-DNA) chains were synthesized in the presence of 2-mercaptothioxanthone (TX-SH) by use of UV irradiation technique. Thioxanthone itself and its derivatives show interesting photochemical and biological properties. The formation of Ag NPs on the ct-DNA was achieved with and without TX-SH as a thioxanthone derivative photoinitiator which played a photoreducing role for the formation of Ag NPs. The photoreducing reaction of Ag ions to Ag NPs was followed by UV-vis absorption spectroscopy. A new band was observed at 428 nm which was a good sign of the surface plasmon resonance (SPR) of Ag NPs. Fluorescence quenching was effectively observed depending on the irradiation time of the solution, possibly as a result of Ag NPs size. Particle size analysis and Scanning Electron Microscopy (SEM) imaging confirmed the size of the formed Ag NPs and silver nanoclusters (Ag NCs) effectively. In this study, we report for the first time the formation of self-assembled Ag NPs on ct-DNA in the presence of 2-mercaptothioxanthone by photoirradiation technique. TX-SH played two important roles; photoreducing and photostabilizing agent for the formation of Ag NCs on ct-DNA. Fluorophore character of synthesized Ag NPs on DNA may help to develop new techniques for biological and medical aspects. (C) 2017 Elsevier B.V. All rights reserved.
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    SARS-CoV-2 main protease targeting potent fluorescent inhibitors : repurposing thioxanthones
    (TÜBİTAK Academic Journals, 2023) Batibay, Gonul S.; Metin, Eyüp
    The coronavirus disease, COVID-19, is the major focus of the whole world due to insufficient treatment options. It has spread all around the world and is responsible for the death of numerous human beings. The future consequences for the disease survivors are still unknown. Hence, all contributions to understand the disease and effectively inhibit the effects of the disease have great importance. In this study, different thioxanthone based molecules, which are known to be fluorescent compounds, were selectively chosen to study if they can inhibit the main protease of SARS-CoV-2 using various computational tools. All candidate ligands were optimized, molecular docking and adsorption, distribution, metabolism, excretion, and toxicity (ADMET) studies were conducted and subsequently, some were subjected to 100 ns molecular dynamics simulations in conjunction with the known antiviral drugs, favipiravir, and hydroxychlo-roquine. It was found that different functional groups containing thioxanthone based molecules are capable of different intermolecular interactions. Even though most of the studied ligands showed stable interactions with the main protease, para- oxygen-di-acetic acid functional group containing thioxanthone was found to be a more effective inhibitor due to the higher number of intermolecular interactions and higher stability during the simulations.