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A Fluorescent Aptasensor for Sensitive and Selective Determination of Epigenetic Cancer Biomarker N1-Methyladenosine in Urine Samples
(Wiley-V C H Verlag Gmbh, 2025) Bagda, Esra; Bagda, Efkan; Liu, Juewen
N1-methyladenosine (m1A) level in urine increases in the presence of cancer and is associated with the tumor size and stage. In the present study, we aimed to develop a method for rapid, sensitive and accurate determination of m1A in urine samples. The capture systematic evolution of ligands by exponential enrichment (SELEX) method was used to isolate aptamers that could selectively bind to m1A. We successfully isolated two sequences that have high selectivity toward m1A. The affinities against m1A were determined by isothermal titration calorimetry (ITC) and thioflavin T (ThT) assays. The N1MA1a aptamer has a Kd of 1.9 +/- 0.1 mu m determined by the ThT assay and 0.75 +/- 0.04 mu m determined by ITC. A strand-displacement biosensor was designed by labeling the aptamer with a carboxy fluorescein (FAM) and hybridizing it with a quencher-labeled complementary DNA strand. Using this biosensing system, m1A was detected with a detection limit of 1.9 mu m. The system shows high selectivity to m1A and high tolerance to adenosine, cytidine, guanosine, thymidine, uridine and N6-methyladenosine (m6A) as well as urine constituents at their real levels in urine. The sensor has been applied to five different human urine samples showing quantitative recovery values, which indicates practical potential of this aptamer-based biosensor.
Analytical approaches for clarification of DNA-double decker phthalocyanine binding mechanism: As an alternative anticancer chemotherapeutic
(PERGAMON-ELSEVIER SCIENCE LTD, 2017) Bagda, Esra; Yabas, Ebru; Bagda, Efican
In the present study a novel water soluble double-decker phthalocyanine was synthesized and calf thymus DNA interaction of the synthesized double-decker phthalocyanine was investigated. 5-(3-pyridyl)-1,3,4-oxadiazole substituted phthalonitrile 1 was prepared by a nucleophilic displacement reaction of 4-nitrophthalonitrile with 5-(3-pyridyl)-1,3,4-oxadiazole-2-thiol. Lutetium(III) double-decker phthalocyanine 2 was prepared by cyclotetramerization of compound 1. Water soluble lutetium(III) double-decker phthalocyanine 3 was prepared with quaternarization of compound 2. The synthesized double-decker phthalocyanine and calf thymus DNA interaction was investigated with UV-vis titrimetric methods, gel electrophoresis, and viscosity measurements. The fluorometric ethidium bromide replacement assay was conducted to clarify the binding mode of water soluble double-decker phthalocyanine. The thermodynamic parameters for interaction, K, Delta G(0), Delta H-0 and Delta S-0 were calculated between the temperature ranges of 25 degrees C-75 degrees C. To the best of our knowledge, this is the first study about a double-decker phthalocyanine and DNA interaction. (C) 2016 Published by Elsevier B.V.
BSA/DNA binding behavior and the photophysicochemical properties of novel water soluble zinc(II)phthalocyanines directly substituted with piperazine groups
(Springer, 2021) Khezami, Khaoula; Harmandar, Kevser; Bagda, Esra; Bagda, Efkan; Sahin, Gamze; Karakodak, Nursen; Durmus, Mahmut
In the current research, two novel zinc(II) phthalocyanines (ZnPcs) (1 and 2) directly connecting with 4-(4-methylpiperazin-1-yl)phenyl groups have been synthesized through the Suzuki-Miyaura coupling reaction. These ZnPcs 1 and 2 were converted to their water-soluble derivatives (1Q and 2Q) by quaternization. The photochemical and photophysical properties were determined in DMSO for the non-ionic zinc(II) phthalocyanines (1 and 2) and in both DMSO and aqueous solutions for the quaternized cationic derivatives (1Q and 2Q) to establish their photosensitizer capabilities in photodynamic therapy (PDT). The spectrofluorometric and spectrophotometric techniques were employed for the determination of interaction between water-soluble ZnPcs (1Q and 2Q) and BSA or ct-DNA. The binding constants of these compounds to BSA were found in the order of 10(8) M-1. The binding constant of the ct-DNA interaction with 2Q (1.09 x 10(5) M-1) was found higher than 1Q (6.87 x 10(4) M-1). The thermodynamic constants were determined for both 1Q and 2Q. The endothermic and spontaneous nature of interaction was observed with ct-DNA. Besides, the thermal denaturation and viscosity studies proved the non-intercalative mode of binding for both compounds to ct-DNA. [GRAPHICS] .
Circular dichroism spectroscopic investigation of double-decker phthalocyanine with G-Quadruplex as promising telomerase inhibitor
(ELSEVIER SCIENCE BV, 2017) Bagda, Efkan; Bagda, Esra; Yabas, Ebru
In the present study, interaction of a double-decker phthalocyanine with two G-quadruplex DNA, Tel 21 and cMYC, was investigated. To the best of our knowledge, this is the first study about G-quadruplex-double decker phthalocyanine interaction. The spectrophotometric titration method was used for binding constant calculations. From the binding constants, it can be said that double-decker phthalocyanine more likely to bind Tel 21 rather than cMYC. The conformational changes upon binding were monitored via circular dichroism spectroscopy. The ethidium bromide replacement assay was investigated spectrofluorometrically. (C) 2016 Published by Elsevier B.V.
Crosslinked Egg White as Eco-Friendly, Reusable, and Cost-Effective Biosorbent for Rapid Removal of Indigo Carmine
(WILEY, 2018) Oymak, Tulay; Bagda, Esra
In the present study, crosslinked egg white is used as a low-cost biosorbent for removal of a toxic dye, indigo carmine. The biosorbent preparation is easy and only N, N'-methylenebisi(acrylamide) is added for crosslinking. The characterization of the prepared material is done with scanning electron microscopy and IR spectroscopy. The surface charge is determined with point of zero charge method. The prepared biosorbent is used for removal of indigo carmine. The experimental parameters i(e. g., pH of solution, initial dye concentration, time) are optimized to achieve quantitative removal. The biosorption data of indigo carmine on crosslinked egg white is fitted with the Langmuir model with a Qmax value of 67.56mg g(-1). The kinetic data are treated with pseudo-first-and second-order models. The second-order model best explains the kinetic behavior of the process. The quantitative extraction of indigo carmine is achieved for 25 mgg(-1) of IC within 30 min at pH 2. The crosslinked egg white can be used several times after regeneration.
Determination of uranium in water samples with chromogenic reagent 4-(2-thiazolylazo) resorcinol after ionic liquid based dispersive liquid liquid microextraction
(SPRINGER, 2016) Bagda, Esra; Tuzen, Mustafa
A simple extraction and spectrophotometric determination of trace amount of uranium was described. The method is based on complex formation between uranium and 4-(2-thiazolylazo)resorcinol (TAR), a well known ligand, C9H7N3O2S, and preconcentration of formed complex into a room temperature ionic liquid (RTIL), 1-methyl-3-octylimidazolium hexafluorophosphate. Under optimum conditions, the method is linear in the range of 7.14-1429 A mu g L-1, and 3S (b)/m value was calculated as 0.26 A mu g L-1. The method was applied to uranium spiked water samples. To the best of knowledge, the use of TAR as chromogenic agent with 1-methyl-3-octylimidazolium hexafluorophosphate as extractive medium is the first for the versatile determination of uranium. The accuracy of the method was confirmed with certified reference material (TM 28.3 fortified water).
Determination of vanadium in groundwater samples with an improved kinetic spectrophotometric method
(TAYLOR & FRANCIS LTD, 2014) Bagda, Esra
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Determination of zirconium in water, dental materials and artificial saliva after surfactant assisted dispersive ionic liquid based microextraction
(ROYAL SOC CHEMISTRY, 2015) Bagda, Esra; Tuzen, Mustafa
In this study, an extractive spectrophotometric method is proposed for the determination of trace amounts of zirconium. The method is based on the complex formation between zirconium and 2-(5-bromo-2-pyridylazo)-5-(diethylamino) phenol. Then, the formed complex is concentrated in an ionic liquid (1-hexyl-3-methylimidazolium hexafluorophosphate) phase. The parameters were optimized and analytical figures of merit were obtained. The tolerance limits for diverse ions were calculated. The enhancement factor (EF) and limit of detection (LOD) were found to be 156 and 0.012 mu g L-1, respectively. The relative standard deviation (RSD) was found to be lower than 6%. The proposed method has been successfully applied to water and environmental materials.
Development of deep eutectic solvent extraction method for extraction of Zn2+ from powdered milk and baby formula samples and its determination by ICP-OES
(Springer, 2020) Kurt, Aylin; Bagda, Esra; Altundag, Huseyin
In the present study, the deep eutectic solvent-based extraction method has been developed for separation of Zn prior to ICP-OES analysis. Five different choline chloride-based deep eutectic solvents were prepared. The Zn extraction ability of DESs from milk powder and baby formulation samples which contain a high amount of milk protein was investigated. The parameters affecting the extraction efficiency such as the amount and type of solvent, extraction time and ambient temperature were optimized. Oxalic acid-based DES gave the highest yield and reproducible results and appropriate preparation criteria. It is concluded from the results that DES-oxalic can quantitatively extract Zn from milky samples. The analytical parameters such as linear calibration range, limit of detection (4.2 mu g L-1) and quantification (14.1 mu g L-1) were also calculated. The added-found method is successfully applied to ERM BD 150 standard reference material, and the recovery values and standard deviation values were found between the ranges of 79.4-97.21 mu g L-1 and 4.1-6.31 mu g L-1, respectively. The method was also applied to real samples, and the recovery values were found between 73 and 106% in the spiked samples.
Effective uranium biosorption by macrofungus (Russula sanguinea) from aqueous solution: equilibrium, thermodynamic and kinetic studies
(SPRINGER, 2018) Bagda, Esra; Sari, Ahmet; Tuzen, Mustafa
Russula sanguinea (R. sanguninea) macrofungus was employed as a novel cost-effective biosorbent for efficient removal of U(VI) ions from aqueous solution. FT-IR spectroscopy and SEM/EDS technique were used for morphological and chemical characterizations. The maximum adsorption capacity of the macrofungus was found as 174.3 mg/g at pH 5 and 20 A degrees C. The kinetic data best fit with the pseudo-second-order kinetic model (r (2) > 0.99 for the studied temperatures). The exothermic and spontaneous nature of the biosorption process was confirmed by the thermodynamic findings. The reusability test demonstrated that the macrofungus had a good sorption/desorption performance.
Equilibrium, thermodynamic and kinetic investigations for biosorption of uranium with green algae (Cladophora hutchinsiae)
(ELSEVIER SCI LTD, 2017) Bagda, Esra; Tuzen, Mustafa; Sari, Ahmet
Removal of toxic chemicals from environmental samples with low-cost methods and materials are very useful approach for especially large-scale applications. Green algae are highly abundant biomaterials which are employed as useful biosorbents in many studies. In the present study, an interesting type of green algae, Cladophora hutchinsiae (C. hutchinsiae) was used for removal of highly toxic chemical such as uranium. The pH, biosorbent concentration, contact time and temperature were optimized as 5.0, 12 g/L, 60 min and 20 degrees C, respectively. For the equilibrium calculations, three well known isotherm models (Langmuir, Freundlich and Dubinin-Radushkevich) were employed. The maximum biosorption capacity of the biosorbent was calculated as about 152 mg/g under the optimum batch conditions. The mean energy of biosorption was calculated as 8.39 kJ/mol from the D-R biosorption isotherm. The thermodynamic and kinetic characteristics of biosorption were also investigated to explain the nature of the process. The kinetic data best fits the pseudo-second-order kinetic model with a regression coefficient of > 0.99 for all studied temperatures. The calculated Delta H degrees and Delta G degrees values showed that the biosorption process is exothermic and spontaneous for temperatures between 293 and 333 K. Furthermore, after seven cycling process, the sorption and desorption efficiencies of the biosorbent were found to be 70, and 58%, respectively meaning that the biosorbent had sufficiently high reusability performance as a cleanup tool. (C) 2017 Elsevier Ltd. All rights reserved.
EXTRACTION AND DETERMINATION OF Cd, Co, Se, V AND Ag LEVELS IN COW?S MUSCLE, LIVER, KIDNEY, LUNG, SPLEEN AND BRAIN SAMPLES
(Editura Acad Romane, 2022) Bagda, Esra; Altundag, Hueseyin; Keskin, Can Serkan
A deep eutectic solvent (DES) consisting of oxalic acid and choline chloride was prepared and used to extract Cd, Co, Se, V, and Ag from meats. The metal levels were determined in muscle, liver, kidney, lung, spleen, and brain samples using ICP-OES. The total youden blank method was employed to eliminate the matrix effect. The order of Cd concentration in the cow's organs was spleen> brain>lung>liver>kidney>muscle. The higher and lowest concentration of Co was determined in the lung and muscle samples. Se was found in all kinds of examined cow's parts and the higher concentration was determined in the liver samples. V was not determined in the muscle and spleen samples and the abundance order in the cow's part was lung>liver>brain>kidney. Ag was determined in only one of the kidney samples.
Feasibility of tetracycline, a common antibiotic, as chelating agent for spectrophotometric determination of UO22+ after cloud point extraction
(SPRINGER, 2014) Bagda, Esra; Yabas, Ebru; Karakus, Nihat
A cloud point extraction (CPE) procedure was presented for the preconcentration of UO22+ ion in different water samples. Tetracycline (TC) is the second most widely used antibiotics in the world and is used as chelating agent. To the best of our knowledge, this is the first work that an antibiotic is used as a chelating agent for CPE of UO22+. Besides, the use of TC as complexing agent provides excellent chelating features. TC molecule has large numbers of functional groups (adjacent hydroxyl oxygen atoms and cyclohexanone oxygen atoms, amide groups) which can form stable complex with UO22+. After complexation with TC, UO22+ ions were quantitatively recovered in Triton X-100 after cooling in the ice bath. 3.0 mL of acetate buffer was added to the surfactant-rich phase prior to its analysis by UV-Vis spectrophotometer. The influence of analytical parameters including pH, buffer volume, TC, Triton X-100 concentrations, bath temperature, incubation time were optimized. The effect of the matrix ions on the recovery of UO22+ ions was investigated. The limit of detection was 0.0746 mu g mL(-1) along with enrichment factor of 14.3 with a R. S. D. of 3.6 %. The proposed procedure was applied to the analysis of various environmental water samples. On the other hand, the electronic distribution of TC molecule is investigated with their frontier molecular orbital density distributions.
The feasibility of using Rosa canina galls as an effective new biosorbent for removal of methylene blue and crystal violet
(DESALINATION PUBL, 2012) Bagda, Esra
In this study, removal of two cationic dyes, basic blue 9 (BB9) and basic violet 3 (BV3) with Rosa canina galls (RCG), was investigated. The parameters that affect the biosorption process such as pH of the solution, amount of biosorbent and initial dye concentration were studied. The kinetic and thermodynamic parameters of biosorption were calculated with batch systems. The optimum pH for the adsorption system was 5.0 and 7.0 for BB9 and BV3, respectively. The adsorption process followed the Freundlich model and pseudo-second-order kinetics. The maximum adsorption capacities were 107.53 mg g(-1) and 312.50 mg g(-1) for BB9 and BV3, respectively. The thermodynamic study indicated that the adsorptions of these cationic dyes were spontaneous and endothermic. The results show that RCG has a potential as an effective low-cost biosorbent for removal of cationic dyes.
G-quadruplex and calf thymus DNA interaction of quaternized tetra and octa pyridyloxy substituted indium (III) phthalocyanines
(ELSEVIER SCIENCE SA, 2017) Bagda, Efkan; Bagda, Esra; Durmus, Mahmut
The interactions of small molecules with G-quadruplex and double stranded DNA are important due to their potential biological and medical usages. In the present paper, the interactions of indium (III) phthalocyanines (quaternized 2,3,9,10,16,17,23,24-octakis-[(3-pyridyloxy) phthalocyaninato] chloroindium(III): OInPc and quaternized 2(3),9(10),16(17),23(24)-tetrakis-[(3-pyridyloxy) phthalocyaninato] chloroindium(III): TInPc) with hybrid G-quadruplex (Tel 21) and parallel G-quadruplexes (nucleolin, KRAS, c-MYC, vegf) were studied. The interactions of these phthalocyanines with ctDNA were also investigated. These interactions were measured by different spectroscopic techniques such as UV-Vis, fluorescence and circular dichroism. The UV-Vis spectroscopic data treated with Benesi-Hildebrand equation and Benesi-Hildebrand constants (K-BH) were calculated. These constants were found higher for octa peripheral pyridyloxy substituted phthalocyanine, OInPc. Besides, UV-Vis analysis showed that the interaction of G-quadruplexes with tetra peripheral pyridyloxy substituted phthalocyanine derivative (TInPc) resulted in removal of central indium (III) atom from the cavity of phthalocyanine macrocycle. The UV-Vis melting studies as well as fluorescence replacement techniques were also employed for clarification of mechanism. The binding mode of molecules with ct DNA was also supported with viscosity measurements. From the results, the stabilization and destabilization of G-quadruplex depending on the concentration of the OInPc and TInPc showed that these two indium (III) phthalocyanines have the potential of both the elucidation role of G-quadruplexes in gene expression and the usage in cancer therapy.
Highly Simple Deep Eutectic Solvent Extraction of Manganese in Vegetable Samples Prior to Its ICP-OES Analysis
(HUMANA PRESS INC, 2017) Bagda, Esra; Altundag, Huseyin; Soylak, Mustafa
In the present work, simple and sensitive extraction methods for selective determination of manganese have been successfully developed. The methods were based on solubilization of manganese in deep eutectic solvent medium. Three deep eutectic solvents with choline chloride (vitamin B4) and tartaric/oxalic/citric acids have been prepared. Extraction parameters were optimized with using standard reference material (1573a tomato leaves). The quantitative recovery values were obtained with 1.25 g/L sample to deep eutectic solvent (DES) volume, at 95 A degrees C for 2 h. The limit of detection was found as 0.50, 0.34, and 1.23 mu g/L for DES/tartaric, DES/oxalic, and DES/citric acid, respectively. At optimum conditions, the analytical signal was linear for the range of 10-3000 mu g/L for all studied DESs with the correlation coefficient > 0.99. The extraction methods were applied to different real samples such as basil herb, spinach, dill, and cucumber barks. The known amount of manganese was spiked to samples, and good recovery results were obtained.
Hydrophilic vs. amphiphilic anionic Zn(II) phthalocyanines for photodynamic therapy
(Elsevier, 2025) Al-Hamdan, Nouf S.; Makhseed, Ethar S.; Husain, Ali; Bagda, Efkan; Bagda, Esra; Duman, Didem; Ayhan, Ebubekir
Two sets of water-soluble zinc (II) phthalocyanines (Zn[II]Pcs) were synthesized and examined for use as photosensitizers in photodynamic therapy. These Zn(II)Pcs contained numerous negatively charged electronwithdrawing carboxylic acid substituents in a rigid arrangement at peripheral positions, subsequently converted into sodium salts. Additionally, the impact of the number and distribution of charged groups on the planar hydrophobic core was examined to assess their influence on the photophysical properties and self-aggregation behavior of the Pcs in an aqueous media. The photophysical findings indicate that the amphiphilic macrocycles (2A, 3A, and 4A) produce more singlet oxygen than the hydrophilic ones (2H, 3H, and 4H) in DMF. The photodynamic activity of sodium salts of Zn(II)Pcs bearing anionic substituents (compounds 4A and 4H) was evaluated in vitro against oral squamous cell carcinoma (SCC-9) and mouse fibroblast (L-929) cell lines to help elucidate the cell death mechanism. The results confirmed that 4A exhibits high selectivity and efficiency in causing phototoxicity, with an IC50 value of around 3.8 mu M. This work provides new insights into the advanced development of dual-directional ZnPc-based photodynamic therapy agents for treating oral squamous cell cancer.
Interaction of water soluble phthalocyanine compounds with parallel and hybrid G-quadruplex DNA molecules
(Pergamon-Elsevier Science Ltd, 2023) Aydin, Fadime; Bagda, Esra; Bagda, Efkan; Durmus, Mahmut
G-quadruplex DNAs are secondary DNA structures formed in guanine-rich genome sequences, such as telomeres. Due to the increased metabolic activities of cancer cells, the formation probability of G-quadruplex structures increases. Since the formation of G-quadruplex structures and their stabilization with various ligands prevents DNA's turning into straight strands, which are necessary for some processes such as transcription and translation, it may cause disruptions in cell proliferation. Therefore, these DNA constructs are important for anticancer drug targets. In the present study, the interactions of water-soluble MnPc and ZnPc compounds with G-quadruplex DNAs with parallel and hybrid conformation were investigated. KD constants were calculated with spectroscopic titration data. Stoichiometric ratios of DNA-phthalocyanine interactions were determined by Job's method and found between 1:1 to 1:2 for MnPc and 1:1 for ZnPc. The effect of phthalocyanine on the G-quadruplex conformation was investigated by circular dichroism (CD) spectroscopy. Capillary gel electrophoresis studies supported the existence of interactions. DNA polymerase stop assay further supported stabilizing AS1411 and Tel21 G-quadruplex structures with Pc compounds. This work is on a molecular level study. The in vitro and in vivo images can be different because MPcs are localized in the cytoplasmic organelles but rare in the nucleus.
Investigation of kinetic and thermodynamic characteristics of removal of tetracycline with sponge like, tannin based cryogels
(ELSEVIER SCIENCE BV, 2013) Ersan, Mehtap; Bagda, Esra; Bagda, Efkan
The removal of tetracycline (TC) from aqueous environment by new type of sorbents, tannin based cryogels (TAB CRGs) and control cryogels (CRGs) was studied in a batch system. The experimental parameters that affect the sorption of TC were optimized to achieve maximum removal yield. Prepared cryogels were characterized by SEM imaging, IR spectroscopy (ATR). Produced TAB cryogels have thin polymeric walls and interconnected large pores. The TAB cryogels are elastic and sponge like; its water content can easily be removed by only compressed with hand. The TAB cryogels restore their original shape and size within seconds after soaked in water. On the other, elasticity of blank CRG is lower. The Freundlich and Langmuir adsorption isotherms were conducted to deduce the mechanism of the process. The kinetics of TC adsorption was moderately fast and almost reached equilibrium in 150 min and the results followed pseudo-second-order kinetic model. (c) 2012 Elsevier B.V. All rights reserved.
Ionic liquid dispersive microextraction and spectrophotometric determination of trace uranyl ion in water samples
(SPRINGER, 2015) Bagda, Esra; Tuzen, Mustafa
In the present study, spectrophotometric determination of uranyl with 2-(5-Bromo-2-pyridylazo)-5-(diethylamino) phenol after ionic liquid based microextraction has been developed. Effect of experimental parameters were optimized to achieve high sensitivity and stability of the complex. The analytical parameters such as linear range (1.33-670 mu g L-1), limit of detection (0.97 mu g L-1) and enrichment factor (150) were calculated for the method. The relative standard deviation of ten replicate measurement of uranyl was 6.53 and 2.59 % for 66 and 133 mu g L-1 uranium, respectively. The proposed method was used to determine the uranyl ions in spiked water samples.

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