Browsing by Author "Seferoglu, Zeynel"

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Citation - WoS: 8
Citation - Scopus: 8
Fluorene/Fluorenone Carboxamide Derivatives as Selective Light-Up Fluorophores for C-Myc G-Quadruplex
(Pergamon-Elsevier Science Ltd, 2021-03) Duyar, Halil; Portakal, Hüseyin Saygın; Yalcin, Ergin; Kanat, Beyza; Doluca, Osman; Seferoglu, Zeynel
The development of fluorescent dyes capable of selective recognition of G-quadruplexes is essential for studying its localization and biological functions. However, considering the G-quadruplex topologies may vary significantly, the synthesis of compounds showing both selectivity and strong fluorescence properties still remains a great challenge. Recently we have developed fluorene/fluorenone derivatives with structure-specific binding towards dsRNA, indicating its potential for structure-selective ligands. Herein, we report the synthesis of novel fluorene/fluorenone derivatives and their selectivity towards various DNA structures, particularly G-quadruplexes, two of which showed strong affinity to the proto-oncogene c-myc promoter G-quadruplex.
Citation - WoS: 51
Citation - Scopus: 54
A Novel and Synthetically Facile Coumarin-Thiophene Schiff Base for Selective Fluorescent Detection of Cyanide Anions in Aqueous Solution: Synthesis, Anion Interactions, Theoretical Study and Dna-Binding Properties
(Pergamon-Elsevier Science Ltd, 2018-11) Chemchem, Meryem; Yahaya, Issah; Aydiner, Burcu; Seferoglu, Nurgul; Doluca, Osman; Merabet, Naima; Seferoglu, Zeynel
A colorimetric and fluorescent chemosensor (chemosensor 2) for the detection of cyanide anions in aqueous solution has been designed and synthesized in high yield. The sensing mechanism of the chemosensor was verified via UV-vis, fluorimetric, and NMR titrations, and was theoretically explained using DFT and TD-DFT calculations. The chemosensor could optically discriminate the presence of fluoride ions over other anions by a color change from yellow to red with an enhancement of pink fluorescence in DMSO. However, it showed strong green fluorescence when CN- was added to a mixture of DMSO/water (6:4 v/v). Thus, the chemosensor can be employed in selective detecting of CN- besides other interference anions (F-, AcO(- )and H2PO4-) in aqueous solution. Moreover, 2 can be used to detect CN(- )at a concentration as low as 0.32 mu M, which is lower than the WHO guideline (2.7 mu M) for cyanide. A low quantity of CN- (1.08 mu M) can be detected and quantified using the prepared chemosensor. Moreover, the UV-vis and fluorescence spectroscopy studies of the interactions between 2 and dublex DNA revealed intercalative binding of calf thymus DNA to the chemosensor. (C) 2018 Elsevier Ltd. All rights reserved.
Citation - WoS: 23
Citation - Scopus: 24
Substituent Dependent Selectivity of Fluorescent Chemosensors Derived From Coumarin for Biologically Relevant Dna Structures and Anions
(Elsevier Science Sa, 2020-02) Chemchem, Meryem; Yahaya, Issah; Aydiner, Burcu; Doluca, Osman; Seferoglu, Nurgul; Seferoglu, Zeynel
In this study, we describe facile synthesis of a series of coumarin appended Schiff base chemosensors for the detection of spesific anions such as F-, CN-, AcO-, and H2PO4-. The sensors have been also employed for signaling singlestranded, doublestranded, as well as parallel, anti-parallel and hybrid G-quadruplex DNA structures and increased specificity was detected towards CN- and parallel G-quadruplex structure. The substituents and their positions (ortho, meta, or para) in relation to the OH impacted significantly on the sensing of the anions as well as the acidity of the OH group, in the recognition of the anions. The deprotonation and addition sensing mechanisms of the probes were investigated through UV-vis, fluorimetric, and NMR titration methods. The two signalling mechanisms also have been confirmed using DFT calculations. The bias studies of all the compounds indicated an immediate visible fluorescence change when CN was added to a partial aqueous mixture of DMSO/tap water (6:4, v/v). Furthermore, the chemosensor were studied in neutral and basic mixtures of DMSO/buffer (6:4, v/v) for absorption and emission spectra in the presence and absence of CN-. In the case of DNA structures, up to 5.5-fold fluorescence enhancement was observed in the presence of parallel G-quadruplex as compared with only 1.3-fold in the presence of duplex DNA. Molecular docking studies revealed that, the selectivity is as a result of increased number of H-bonds between DNA and 2b due to modified substituent. In a nutshell, all the fluorophores can be employed in sensing CN- in partial aqueous solution, while 2a, 2b, 2e and 2f showed strong selectivity towards parallel G-quadruplexes over other DNA topologies. Thermal studies of the compounds have shown that the compounds have enough thermal stability properties for application as optic dye.
Citation - WoS: 41
Citation - Scopus: 45
Synthesis, Biological Properties, and Acid Dissociation Constant of Novel Naphthoquinone-Triazole Hybrids
(Academic Press Inc Elsevier Science, 2020-12) Nural, Yahya; Ozdemir, Sadin; Doluca, Osman; Demir, Bunyamin; Yalcin, Mustafa Serkan; Atabey, Hasan; Kanat, Beyza; Seferoglu, Zeynel
A series of novel 1,4-naphthoquinone-triazole hybrids, N-(3-amino-1,4-dioxo-1,4-dihydronaphthalen-2-yl)-2-(4-R-1H-1,2,3-triazol-1-yl)acetamide, was synthesized by click chemistry in the presence of sodium ascorbate and copper(II) sulfate pentahydrate in 81-94% yield. Various biological properties of the synthesized compounds including DNA binding/cleavage, antioxidant, antibacterial and antifungal properties were evaluated. The DNA binding study was performed using dsDNA and G-quadruplex DNA. All of the compounds showed fluorescence increase in the presence of DNA, regardless of the structure. Up to 2.9 and 2.5 times fluorescence increase upon incubation with double stranded or G-quadruplex DNA was detected for 5f and 5g, respectively. The docking studies performed on dsDNA and G-quadruplex structures suggested compounds' mode of interactions were populated around the grooves. All of the compounds showed excellent DNA cleavage activity and 5e was almost degraded the plasmid DNA. The highest radical scavenging activity was obtained as 89.9% at 200 mg/L with 5d. However, the highest ferrous chelating activity was obtained as 68.1% at 200 mg/L with 5g. The compounds exhibited antimicrobial activity against Bacillus cereus, Legionella pneumophila subsp. pneumophila, Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli and Enterococcus hirae as bacteria strains and Candida albicans and Candida tropicalis as microfungus strains. The compounds exhibited antibacterial and antifungal activity in the range of 4-128 mu g/mL and 16-128 mu g/mL, respectively. The best antimicrobial activity was obtained with 5d and 5e with a MIC value of 4 mu g/mL against Enterococcus hirae. The acid dissociation constants (pK(a)) were determined potentiometrically in 20% (v/v) dimethyl sulfoxide-water hydro-organic solvent at an ionic background of 0.1 mol/L of NaCl, at 25 +/- 0.1 degrees C. Five pK(a) values were obtained for each ligand.