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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.
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.
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.
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.
Insights into the G-quadruplex DNA interaction landscape: Comparative analysis of anionic Zn(II) and Co(II) phthalocyanine-tetrasulfonate complexes
(Wiley, 2024) Bagda, Efkan
G-quadruplexes play a pivotal role in regulating various cellular processes, including gene expression and replication, making them essential structures in understanding, and manipulating cellular functions. The development of G-quadruplex ligands holds significant promise in therapeutic and research applications, offering targeted tools to modulate G-quadruplex structures and potentially influence critical biological pathways. An exciting frontier in G-quadruplex research lies in the exploration of anionic ligands, and their profound impact on stabilizing and modulating G-quadruplex DNA. In this study, the interaction of two anionic phthalocyanine compounds (Zinc (II) phthalocyanine 3,4 ',4 '',4'-tetrasulfonic acid, tetrasodium salt, ZnAPC; cobalt (II) phthalocyanine 3,4 ',4 '',4'-tetrasulfonic acid, tetrasodium salt, CoAPC) and three separate G-quadruplex-forming DNA sequences was investigated. Interactions were carried out by DNA polymerase stop studies along with spectroscopic studies. According to the results of experimental data, it was determined that ZnAPC actively interacts with the G-quadruplex DNA structures. On the other hand, it was thought that the interaction with CoAPC was less and even occurred in simple electrostatic interactions. KD constants and Bmax constants for the interaction with ZnAPC were calculated. The KD constants for ZnAPC were found to be (1.16 +/- 0.07) x 10-5, (9.75 +/- .24) x 10-6 and (1.00 +/- 0.36) x 10-4 M for AS1411, Vegf, and Tel21, respectively. Accordingly, it was concluded that ZnAPC interacts with G-quadruplex DNA ligands effectively.
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.
Lower genetic structuring in mitochondrial DNA than nuclear DNA among the nesting colonies of green turtles (Chelonia mydas) in the Mediterranean
(PERGAMON-ELSEVIER SCIENCE LTD, 2012) Bagda, Efkan; Bardakci, Fevzi; Turkozan, Oguz
Genetic structure of Chelonia mydas in the nesting beaches of Turkey and Northern Cyprus was analyzed using mitochondrial DNA control region and nuclear DNA. Tissue samples were collected from 256 different nests located on six nesting beaches. Sequencing of 859 bp fragment of control region revealed six distinct mtDNA haplotypes of which three were described for the first time in this study. Haplotype CM-A13 was the major one uncounted for 97.3% and others were differed by one substitution. Low level of mtDNA variation in green turtle across the study area makes it impractical for determination of genetic structuring of nesting aggregates and female philopatry. Findings from this study showed higher genetic variation and structuring in nDNA than mtDNA among the Mediterranean nesting aggregates. Analysis of microsatellite data of the Mediterranean green turtle revealed sufficient amount of genetic variation suggesting each nesting colony as a management unit. (C) 2012 Elsevier Ltd. All rights reserved.
Photodynamic activity of cationic ball-type zinc phthalocyanine in cell culture experiments with MCF-7 and MG63 cancer cells
(World Scientific Publ Co Pte Ltd, 2024) Soylu, Sinan; Bagda, Efkan; Altun, Ahmet; Bagda, Esra; Kurt, Atilla; Erden, Fuat; Yabas, Ebru
Effective binding of cationic ball-type zinc phthalocyanine (BT-Pc) to G-quadruplex (G4) DNA molecules has already been demonstrated previously. This motivated us to investigate the PDT performance of BT-Pc in cell culture studies. Accordingly, the present work involves the application of BT-Pc to breast (MCF-7) and osteosarcoma (MG63) cancer cells, and also to healthy fibroblast cells (L929). Cell lines (CL) were irradiated at 640 nm wavelength, and the photodynamic activity was evaluated. The results show that cytotoxicity was significantly stronger in MCF-7 cells than in both L929 and MG63 cells (p < 0.05) in the absence of IPL irradiation. Also, we report that the application of l IPL provided significant photodynamic activity in MCF-7 and MG63 cells (p < 0.05). These results further suggest that BT-Pc might become a promising photosensitizer for future clinical trials.
REMOVAL OF BASIC BLUE AND CRYSTAL VIOLET WITH A NOVEL BIOSORBENT: OAK GALLS
(SCIBULCOM LTD, 2012) Bagda, Esra; Bagda, Efkan
In this study, the use of an extraordinary plant tissue, gall, has been studied for the removal of 2 differrent dyes. The adsorptions of basic blue (BB) and crystal violet (CV) were studied on raw Quercus macranthera galls (QMG). The effect of initial pH, contact time, initial dye concentration, and temperature was studied to explain batch adsorption process of the dyes on galls. Experimental data were assayed on pseudo-second order kinetic equations. The equilibrium process were well fitted with the Freundlich isotherm model for basic blue with the regression coefficients of 0.995, and the Langmuir isotherm for crystal violet with a regression coefficient of 0.993. The maximum adsorption capacities were 45.45 and 90.90 mg g(-1) for basic blue and crystal violet, respectively. The results show that QMG has a great potential as an effective low-cost sorbent for removal of dyes from aquatic media.
Removal of basic blue and crystal violet with a novel biosorbent: Oak galls
(2012) Bagda, Esra; Bagda, Efkan
In this study, the use of an extraordinary plant tissue, gall, has been studied for the removal of 2 differrent dyes. The adsorptions of basic blue (BB) and crystal violet (CV) were studied on raw Quercus macranthera galls (QMG). The effect of initial pH, contact time, initial dye concentration, and temperature was studied to explain batch adsorption process of the dyes on galls. Experimental data were assayed on pseudo-second order kinetic equations. The equilibrium process were well fitted with the Freundlich isotherm model for basic blue with the regression coefficients of 0.995, and the Langmuir isotherm for crystal violet with a regression coefficient of 0.993. The maximum adsorption capacities were 45.45 and 90.90 mg g-1 for basic blue and crystal violet, respectively. The results show that QMG has a great potential as an effective low-cost sorbent for removal of dyes from aquatic media.
The new water soluble zinc(II) phthalocyanines substituted with morpholine groups- synthesis and optical properties
(Elsevier Science Sa, 2020) Khezami, Khaoula; Harmandar, Kevser; Bagda, Esra; Bagda, Efkan; Sahin, Gamze; Karakodak, Nursen; Jamoussi, Bassem
Two new tetra- or octa-substituted zinc(II) phthalocyanines (1 and 2) bearing 3-(morpholinomethyl)phenyl groups were synthesized via Suzuki-Miyaura coupling method. These phthalocyanines (1 and 2) were converted to their water-soluble derivatives (1Q and 2Q) by quaternization of nitrogen atoms on the morpholine groups. The photochemical and photophysical properties of the non-ionic zinc(II) phthalocyanines (1 and 2) were explored in DMSO. On the other hand, these properties of the quaternized cationic derivatives (1Q and 2Q) were studied in both DMSO and aqueous solutions for determination of their photosensitizing capabilities in photodynamic therapy. The ct-DNA interaction of synthesized 1Q and 2Q were investigated and binding constants were found as 6.3 x 10(4) and 1.5 x 10(5) M, respectively. The binding constant values were found at similar levels of ethidium bromide (EB), which is a well-known intercalator. The spontaneous and exothermic nature of binding mechanisms were proved according to the calculated thermodynamic constants. Strong interactions of 1Q and 2Q with ct-DNA were also found with EB displacement assay and gel electrophoresis. Additionally, the bovine serum albumin (BSA) binding behavior of the new compounds (1Q and 2Q) were determined in water solution to verify the transporting capability of these phthalocyanines in the circulatory system and these values were found as 7.0 x 10(5) and 1.6 x 10(7) M-1 for 1Q and 2Q, respectively.
The targeted photodynamic therapy of breast cancer with novel AS1411-indium(III) phthalocyanine conjugates
(Elsevier, 2024) Akkus, Nurefsan; Eksin, Ece; Sahin, Gamze; Yildiz, Esma; Bagda, Efkan; Altun, Ahmet; Bagda, Esra
In the study, the novel indium(III) phthalocyanines containing 4-mercaptopyridine groups as substituents on the peripheral (Pc3) or non-peripheral (Pc8) tetra-and peripheral octa (Pc13) positions were synthesized. After then, the synthesized phthalocyanines were converted to their water-soluble derivatives that are Pc5, Pc10, and Pc15 by the quaternization of the nitrogen atoms on the substituents. These new phthalocyanines have been characterized by various spectroscopic methods such as FT-IR, 1H-NMR, elemental analysis, UV-vis, MALDI-TOF mass spectra. Photochemical properties were also investigated for the synthesized phthalocyanines. In this study; quaternized derivatives were studied in DMSO and aqueous solutions, while non-quaternized derivatives were studied only in DMSO. The interaction between AS1411 and three phthalocyanines (Pc5, Pc10, and Pc15) was investigated using spectroscopic methods and electrochemical impedance spectroscopy technique combined with pencil graphite electrodes (PGEs). The cytotoxic activity of AS1411 and each phthalocyanine was investigated in the MCF-7 and doxorubicin (Dox) resistant MCF-7/DOX-R cell lines in the presence and absence of Dox. The photodynamic therapy (PDT) activity of Pc5, Pc10, and Pc15 and their AS1411 conjugates was investigated on MCF-7, MCF-7/DOX-R and MCF-10A cells. The IC50 values for MCF-7 cells were found as 1.1, 0.46, and 0.46 mM for Pc5 and 0.58, 0.34, and 0.32 mM for Pc5-AS1411 conjugate in the absence of irradiation and radiation with 7 J and 20 J. The values for MCF-7/DOX-R cells were found 0.81, 0.30, and 0.11 mM for Pc5 and 0.39, 0.12, and 0.15 mM for Pc5-AS1411 conjugate without irradiation and radiation with 7 J and 20 J, respectively. Apoptosis and cell imaging studies showed that conjugation of the phthalocyanines with AS1411 induced apoptosis in both cell lines and increases the intracellular entry of phthalocyanine Pc5.
Thermodynamic and structural investigation of the interaction of quaternized 2,3-octakis-[(2-mercaptopyridine)phthalocyaninato] copper (II) sulfate (CuPc) with parallel and hybrid type G-quadruplex
(Wiley, 2024) Sahin, Gamze; Bagda, Esra; Temiz, Ozge Goktug; Bagda, Efkan; Ayhan, Ebubekir; Durmus, Mahmut
G-quadruplexes are important drug targets and get attention due to their existence in telomere, ribosomal DNA, promoter regions of some oncogenes, and the untranslated regions of mRNA. Due to the biological roles of G-quadruplexes, investigating of the G-quadruplex-small molecule interaction is essential. The primary motivation for these studies is the possibility of inhibiting cell functions associated with G-quadruplex sequences by binding with small molecules. Targeting the small molecules to desired tissue with the G-quadruplex vehicles is the second important goal of the G-quadruplex-small molecule interaction studies. In the present study, the new peripherally 2-mercaptopyridine octasubstituted copper(II) phthalocyanine and its quaternized derivative (CuPc) were synthesized and characterized by elemental analysis FT-IR, UV-Vis, and mass spectra. The excellent solubility of CuPc in water is essential for its transport in the organism. Because of this feature, its affinity toward G-quadruplex forming aptamers, AS1411, Tel21, and Tel45, was investigated. The UV-Vis spectrophotometric titration data confirmed the prevention of aggregation upon interaction with G-quadruplex, which is very important for biomedical applications. The CD spectroscopic analyses and binding stoichiometry confirmed the end stacking model for interaction of AS1411 with CuPc. The interaction of CuPc caused the equilibrium shift from hybrid conformation to antiparallel conformation for Tel21 and Tel45. The isothermal titration calorimeter (ITC) was used for the determination of thermodynamic parameters. The thermodynamic data of the interaction was fitted well with the one-site model. The negative values of Gibbs free energy change confirmed the spontaneous nature of the reactions. Besides, the negative values of enthalpy change and entropy change proved that the nature of processes was enthalpy driven. The interaction stoichiometry was 2 for AS1411 and Tel21 and 1.5 for Tel45. The binding constants were 1.3(+/- 0.3) x 10(5), 3.2(+/- 0.4) x 10(5), and 1.1(+/- 0.3) x 10(5) M-1, which were at the level of ethidium bromide intercalation binding constant given in the literature. The DNA polymerase stop assay further supported the interaction of CuPc with G-quadruplex DNA. The experimental results confirm that the CuPc has a potential photosensitizer behaviour for photodynamic therapy.
The water soluble ball-type phthalocyanine as new potential anticancer drugs
(ELSEVIER SCI LTD, 2015) Yabas, Ebru; Bagda, Efkan; Bagda, Esra
Compound 1 has been prepared by the reaction of 4-nitrophthalonitrile with triethanolamine. Compound 3 has been synthesized with quaternarization of compound 2 which prepared by cyclotetramerization of compound 1. The synthesized compounds have been characterized by elemental analysis, H-1 NMR, UV Vis, IR and MALDI-TOF MS spectral data. The interaction of compound 3 with calf thymus DNA was investigated spectrophotometrically. The phthalocyanine-DNA binding mechanism as well as the thermodynamic properties of binding was studied. The thermal denaturation profile, gel electrophoresis studies and the viscosity experiments were also conducted to clarify the mechanism. The replacement of ethidium bromide with phthalocyanine was monitored flourometrically to verify the binding mode. The Stern Volmer plot has nonlinear characteristic that implies both collisions of molecules and formation of ground state complexes which causes the fluorescence quenching. The experimental results indicate that the synthesized ball type water soluble phthalocyanine binds to calf thymus DNA via mainly intercalation. (C) 2015 Elsevier Ltd. All rights reserved.

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