Browsing by Author "Kanat, Beyza"

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Development of G-Quadruplex Assisted Hybridization Chain Reaction System
(İzmir Ekonomi Üniversitesi, 2021) Kanat, Beyza; Doluca, Osman
Hibridizasyon zincir reaksiyonu (HCR) nükleik asitlerin teşhisi için kullanılan ve enzim gerektirmeyen bir tekniktir. Bu teknikte hedef molekül olan DNA veya RNA ile hibridizasyon kaskadı başlatılır ve ortamda bulunan hairpin sekansları arasında "toehold mediated strand displacement" aracılığı ile gerçekleştirilir. Sonuçta amaç sinyal amplifikasyonunu gerçekleştirmektir. HCR metodu PCR (polimerizasyon zincir reaksiyonu) metoduna alternatif olarak düşünülse de halen daha ölçüm hassasiyetinin düşük olması yeni tasarımlar yapılmasına yönlendirmiştir. Bu tezde de yeni bir HCR tasarımı ile ilgili çalışma gerçekleştirilmiştir. G-quadrupleks denilen alternatif DNA yapılarının yardımı ile floresan etiketleme tekniklerinin de kullanılması sonucunda yeni bir HCR mekanizması geliştirilmiştir. Bu tasarımda teşhis limitinin düşük olması ve ölçüm hassasiyetinin yüksek olması amaçlanmıştır. Bu tezde açıklanan HCR sistemi 20 pM kadar düşük konsantrasyon seviyesinde nükleik asit teşhisi için G-quadrupleks ve floresan etiketlemeyi birlikte kullanmıştır. Bu çalışmada kullanılan Amplex Red (™)'in floresan artışını sağladığı ve teşhis limitini 10 kat düşürdüğü sonucuna ulaşılmakta ve bu tezde açıklanmaktadır.
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) 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: 3
Citation - Scopus: 3
A Novel Method for Conserved Sequence Extraction With Prospective Mutation Prediction for Sars-Cov Pcr Primer Design
(Elsevier, 2021) Portakal, Saygin Huseyin; Kanat, Beyza; Sayan, Murat; Berber, Burak; Doluca, Osman
While the whole genomic sequence of SARS-CoV-2 had been revealed, it was also demonstrated that the genome of SARS-CoV-2 exhibits identity with the genome of SARS-CoV and MERS-CoV with ratios of 80 % and 50 % respectively. In the light of SARS-CoV-2 infection and mortality data, diagnosis and treatment of COVID-19 came into prominence around the world. As such many RT-PCR kits have been developed by biotechnology scientists. However viruses are fast mutating organisms and in order to increase accuracy, feasibility in long term and avoid the off target results of RT-PCR assays, regions of viral genome with low mutation rate and designing of primers targeting these regions are quite important. In this scope, we are presenting a novel algorithm that could be used for finding low mutation rate regions of SARS-CoV-2 and primers that were designed according to findings from our algorithm in this study.
Citation - WoS: 11
Citation - Scopus: 11
dna Binding Effects of 2,2'-bipyridine and 1,10-Phenanthroline Ligands Synthesized With Benzimidazole Copper (ii) Complexes: Crystal Structure, Molecular Docking, Dna Binding and Anti-Cancer Studies
(Pergamon-Elsevier Science Ltd, 2022) Unver, Hakan; Berber, Burak; Kanat, Beyza; Arafat, Mahmoud; Koparal, Ayse Tansu; Doluca, Osman
Two new copper(II) complexes, [Cu(benzim)2(bipy)(MeOH)](ClO4)(2) (Complex 1) and Cu(benzim)2(phen) (MeOH)](ClO4)(2) (Complex 2)] (bipy = 2,2'-bipyridine, phen = 1,10-phenanthroline and benzim = 1-benzyl-1Hbenzimidazole) have been synthesized and successfully characterized with single crystal x-ray diffraction analysis. Crystal structures of complexes revealed that both possess distorted square pyramidal geometries coordinated with a solvent molecule (CH3OH) at apical positions. The in vitro cytotoxicity of these Cu(II) complexes was carried out in HCC1428 and HUVEC cell lines. Molecular docking was also used to evaluate and understand the interaction modes of the complexes with the molecular target DNA and HSA (Human Serum Albumin). DNA binding capacities of complexes were analyzed by fluorescent titration method. Structural changes in the nucleus as a result of the effects of the complexes were discussed by viewing them with DAPI staining. Furthermore, biological activities of complexes and ligands were analyzed in silico. The cell lines IC50 results were obtained at similar rates (~8-fold) to the constant inhibition values obtained by docking studies. In addition, the fluorescence titration and circular dichrosim studies of the compounds with dsDNA-TO complexes showed results in agreement with docking studies. In our study, it was determined that phen ligand has a much more effective biological activity than bipy ligand in copper(II) complex synthesized with benzimidazole.
Citation - WoS: 41
Citation - Scopus: 45
Synthesis, Biological Properties, and Acid Dissociation Constant of Novel Naphthoquinone-Triazole Hybrids
(Academic Press Inc Elsevier Science, 2020) Nural, Yahya; Ozdemir, Sadin; Doluca, Osman; Demir, Bunyamin; Yalcin, Mustafa Serkan; Atabey, Hasan; Kanat, Beyza
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.