Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
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Article Free-Standing Three-Dimensional Graphene Scaffolds for Protease Functional Assay(Elsevier Science Sa, 2024) Ng, Zhi Kai; Yan, Evelias; Goyal, Garima; Gudlur, Sushanth; Kanagavel, Deepankumar; Yildiz, Umit Hakan; Teo, Edwin Hang TongThree-dimensional graphene scaffolds (3d-GS) of high porosity possessing good fluorescence quenching properties are potential candidates for the development of optical biosensors. Herein, we demonstrate the feasibility of utilising intact and free-standing 3d-GS for sensitive detection of proteases, a class of disease diagnosis bio-markers of significant interest. Recombinant OmpT was employed as a model protease for validating the pro-posed methodology. A short (15-residue) peptide sequence encoding a specific recognition site for OmpT was end-labelled with a fluorescent dye (5-FAM) whose fluorescence is quenched when the peptide is anchored to 3d-GS. However, in the presence of OmpT, the peptide is cleaved and released from 3d-GS, resulting in a sig-nificant recovery in fluorescence. The functional assay described herein involves a single step fabrication process of anchoring the peptide to 3d-GS. The integrity of the 3d-GS is hypothesised to overcome the concern of dynamic requenching associated with the typical homogeneous assays based on graphene, yielding a limit of detection (LOD) of similar to 140 nM, which is over an order higher than homogeneous assays performed using the same composition of graphene in powdered form. To the best of our knowledge, this is the first report on utilising free-standing 3d-GS for facile assaying of proteases.Article Citation - WoS: 6Citation - Scopus: 6A Novel 2-Aminophenalenone Fluorescent Probe Designed for Monitoring H2o2 for in Vitro and in Vivo Bioimaging(Elsevier, 2024) Saygılı, Ecem; Ersöz Gülseven, Esra; Kıbrıs, Erman; Çakan Akdoğan, Gülçin; Üçüncü, MuhammedA significant compound in living organisms, hydrogen peroxide (H2O2) plays a dual role as a signalling molecule in cellular communication and as a pivotal biomarker in assessing disease and oxidative stress. Thus, the detection of abnormal changes in H2O2 levels is essential to understanding its function and involvement in biological systems. The growing demand to meet the specific needs for applications, particularly in biological systems, has sharpened focus on highly sensitive, highly selective molecular sensors and, in turn, heightened interest in these diagnostic tools with innovative designs. In our study, 2-aminophenalenone (2-AP) was used for the first time as a fluorophore in a fluorescent probe. The 2-APB molecule obtained from the reaction of 2-AP with 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl) benzyl chloroformate exhibited a highly selective and sensitive (i.e. 62 nM) detection profile for H2O2 compared with the other reactive oxygen species, anions, and metal cations. Moreover, offering naked-eye detection in aqueous solutions, 2-APB demonstrated excellent sensing performance, detection and real-time monitoring in relation to exogenous H2O2 in cells and endogenous H2O2 in zebrafish embryos. © 2024 Elsevier B.V.Article Citation - WoS: 2Citation - Scopus: 3A Phenomenological Kinetic Flotation Model: Distinct Time-Variant Floatability Distributions for the Pulp and Froth Materials(Elsevier, 2023) Polat, Mehmet; Polat, HürriyetA simple and easy-to-use phenomenological kinetic flotation model, strongly connected with the physics of the process, is proposed in this paper. The model explicitly contains the cell volume, aeration rate, volumetric holdup, mean bubble size, and particle density as input variables. It can be employed to characterize the floatability distributions of the particles in the pulp and the froth separately any time during the flotation process. Two new time-dependent kinetic parameters, the bubble loading factor & phi;(t) and the maximum cell mass transfer capacity Mmax(t) also appear in the model expression. & phi;(t) is a measure of the degree of crowding of the bubble surfaces and accounts for the deviations from the first-order rate equation. Mmax(t) describes the maximum amount of mass that can be transported to the froth phase by the bubble population in the cell. Screen fractionation of each froth product collected at different time intervals during a single kinetic flotation test is sufficient to generate the data required by the model for analysis. Application of the model to this data yields directly time-dependent functions for the floatability of the particles reporting to froth Kf(t) or remaining in the cell Kp(t) for each size fraction separately, without the need for any empirical parameters. The test of the model was carried out using published kinetic flotation data from the literature.Article Citation - WoS: 5Citation - Scopus: 4Polarity Induced Vapochromism and Vapoluminescence of Polythiophene Derivatives for Volatile Organic Compounds Classification(Elsevier, 2023) Karabacak, Soner; Qun, David Lee Chao; Ammanath, Gopal; Yeasmin, Sanjida; Yağmurcukardeş, Mehmet; Palaniappan, Alagappan; Liedberg, Bo; Yıldız, Ümit HakanPolarity induced vapochromic and vapoluminescent properties of cationic poly-3-alkoxythiophene derivatives (PT) casted on polyvinylidene fluoride (PVDF) membranes are reported. PT with six different pendant groups are designed to differentially interact with volatile organic compounds (VOC) of varying polarities, thereby enabling their classification. PT exhibit a rapid vapochromic response with a concurrent modulation of vapoluminescence due to the non-covalent cation-? interactions between the pendant groups and the PT backbone. Adsorption of VOC on pendant groups alters the conformation of PT backbone, thus resulting in an increase in intensity and blue shifting of fluorescence emission within the visible spectrum. The vapoluminescent responses are found to be more sensitive with a limit of detection (LOD) of ?7 ppm and a wider dynamic range as compared to the vapochromic responses with a LOD of ?60 ppm for the detection of a model VOC: chloroform. Notably, all the PT illustrate an instantaneous recovery of colour and luminescence upon desorption of VOC. PT interaction with VOC of varying polarities was ascertained using density functional theory (DFT) and principal component analysis (PCA) methodologies. In summary, the polarity induced vapochromic and vapoluminescent properties of PT could yield a selective and sensitive vapochromic and fluorometric dual-mode VOC detection platform. © 2023Article Citation - WoS: 15Citation - Scopus: 15Sorafenib Loaded Zif-8 Metal-Organic Frameworks as a Multifunctional Nano-Carrier Offers Effective Hepatocellular Carcinoma Therapy(Elsevier, 2023) Mete, Derya; Yemeztaşlıca Yetişkin, Egehan; Şanlı Mohamed, GülşahHepatocellular carcinoma (HCC) is a primary malignant neoplasia of the liver and sorafenib is one of the most commonly used drugs in the treatment of HCC. Due to undesirable nature and side effects of sorafenib, nano-drug delivery systems are being developed. A member of metal-organic frameworks (MOFs), ZIF-8 offers a very suitable platform for drug transport and controlled drug release due to its zinc content and pH-sensitive, biodegradable in an acidic environment. In the present study, sorafenib was encapsulated in ZIF-8 material with 53.8% efficiency and 58% loading capacity (SRF@ZIF-8). Structural characterizations of synthesized ZIF-8 and SRF@ZIF-8 system were investigated in details. Drug release analysis exhibited a faster release profile at pH 5.0 compared to that of pH 7.4. The cytotoxic effects of sorafenib and zinc were investigated in HepG2 and HuH-7 cell lines in vitro. The results demonstrated that in addition to sorafenib, ZIF-8 provided zinc to the envi-ronment with its biodegradable structure resulted in an effective cytotoxic effect on HCC cells. The findings showed that a formulation combining zinc and sorafenib together was more effective in HCC treatment compared to sorafenib itself.Article Citation - WoS: 1Citation - Scopus: 1A Multi-Layered Graphene Based Gas Sensor Platform for Discrimination of Volatile Organic Compounds Via Differential Intercalation(Royal Society of Chemistry, 2023) Özkendir İnanç, Dilce; Ng, Zhi Kai; Başkurt, Mehmet; Keleş, Berfin; Vardar, Gökay; Şahin, Hasan; Tsang, Siu Hon; Palaniappan, Alagappan; Yıldız, Ümit Hakan; Teo, EhtSelective and sensitive detection of volatile organic compounds (VOCs) is of critical importance for environmental monitoring, disease diagnosis and industrial applications. Among VOCs, assay development for primary alcohols has captured significant research attention since their toxicity causes adverse effects on gastrointestinal and central nerve systems, resulting in irreversible blindness, and coma, and can be even fatal at high exposure levels. However, selective detection of primary alcohols is extremely challenging owing to the similarity in their molecular structure and characteristic groups. Herein, we have attempted to investigate the differential methanol (MeOH)-ethanol (EtOH) discriminative properties of single-layer, bi-layer, and multi-layer graphene morphologies. Chemiresistors fabricated using the three morphologies of graphene illustrate discriminative MeOH-EtOH responses, which is attributed to the phenomenon of differential intercalation of MeOH within layered graphene morphologies as compared to that of EtOH. This hypothesis is verified by density functional theory calculations, which revealed that the adsorption of EtOH molecules on the graphene surface is more energetically favorable as compared to that of MeOH molecules, thereby inhibiting their intercalation within the layered graphene morphologies. It is further evaluated that the degree of MeOH intercalation increases with increasing layers of graphene for obtaining differential MeOH-EtOH responses. Experimental results suggest possibilities to develop selective and sensitive MeOH assays fabricated using various graphene morphologies in a combinatorial sensor array format.Article Citation - WoS: 3Citation - Scopus: 3Synthesis and Antifungal and Antibacterial Bioactivities of Diborolanes Containing Arylamines(Elsevier, 2023) Aygün, Muhittin; Sevinçek, Resul; Özgener, Hüseyin; Bıyık, Hacı Halil; Metin, Kubilay; Şahin, Yüksel; Poyrazoğlu Çoban, Esra; Gürbüz, BurçinA good yield of 1,2-diarylamino-1,2-diborolanes 2 was obtained from the reaction of 1,2-dichloro-1,2-diborolane 1 and ArNHLi (an anilide). The structures of these new derivatives were characterized by nuclear magnetic resonance spectroscopy. The molecular structures of 2a and 2b were also determined using single-crystal X-ray diffraction. Antimicrobial activities of synthesized compounds against some Gram-positive and -negative bacteria and yeasts were determined. Some compounds were found to have strong antibacterial and antifungal properties, especially against the bacterium, S. pneumonia, which is the causative agent of pneumonia, and the fungus, C. albicans, which is the causative agent of candidiasis. The compounds 2a and 3 had a powerful effect (compound 2a and 3 = 1 μgmL−1) against S. pneumoniae ATCC 27336 bacteria. In addition, compounds 2a, 3 and 2f were observed to have strong effects (compound 2a, 3, 2f = 2 μgmL−1) against C. albicans ATCC 10231 and C. utilis ATCC 9950. The results obtained were found to be more effective than the MIC values (128–64 μgmL−1) of Streptomycin and Flukanozol drugs used for bacteria and yeasts. The results of our study show that the synthesized substances can be used for new drug applications that are being developed against infectious diseases in the pharmaceutical industry. © 2023 Elsevier B.V.Article Citation - WoS: 9Citation - Scopus: 11Pcr-Free Methodology for Detection of Single-Nucleotide Polymorphism With a Cationic Polythiophene Reporter(American Chemical Society, 2021) Yücel, Müge; Koç, Altuğ; UÜgenalp, Ayfer; Akkoç, Gün Deniz; Ceyhan, Metin; Yıldız, Ümit HakanThis study presents a nonamplification-based nucleic acid assay for the detection of single-nucleotide polymorphism (SNP) associated with familial Mediterranean fever (FMF) besides polymerase chain reaction (PCR)-based methodologies. The major objective is to show the potential of the proposed assay for rapid screening of FMF in a Mediterranean region of 400 million population. The assay relies on binding difference of specially designed wild and mutant primers to the target genomic DNA, followed by determination of unbound primers by quick titration of a cationic polythiophene reporter. The fluorescent reporter exhibits signal transition from 525 to 580 nm in the presence of unbound primers, and it correlates the binding affinity of label-free primers to the homozygous wild and mutant genomes. As a proof of concept, 26 real samples are studied relying on the ON and OFF fluorescence signals of the cationic polythiophene reporter. The results are analyzed by principal component analysis (PCA), which provides clear separation of healthy and patient individuals. The further analysis by support vector machine (SVM) classification has revealed that our assay converges to 96% overall accuracy. These results support that the PCR-free nucleic acid assay has a significant potential for rapid and cost-effective screening of familial Mediterranean fever.Article Citation - WoS: 1Citation - Scopus: 1First-Principles Investigation of Structural, Raman and Electronic Characteristics of Single Layer Ge3n4(Elsevier, 2022) Yayak, Yankı Öncü; Sözen, Yiğit; Tan, Fırat; Güngen, Deniz; Gao, Q.; Kang, J.; Yağmurcukardeş, Mehmet; Şahin, HasanBy means of density functional theory-based first-principle calculations, the structural, vibrational and electronic properties of single-layer Ge3N4 are investigated. Structural optimizations and phonon band dispersions reveal that single-layer ultrathin form of Ge3N4 possesses a dynamically stable buckled structure with large hexagonal holes. Predicted Raman spectrum of single-layer Ge3N4 indicates that the buckled holey structure of the material exhibits distinctive vibrational features. Electronic band dispersion calculations indicate the indirect band gap semiconducting nature of single-layer Ge3N4. It is also proposed that single-layer Ge3N4 forms type-II vertical heterostructures with various planar and puckered 2D materials except for single-layer GeSe which gives rise to a type-I band alignment. Moreover, the electronic properties of single-layer Ge3N4 are investigated under applied external in-plane strain. It is shown that while the indirect gap behavior of Ge3N4 is unchanged by the applied strain, the energy band gap increases (decreases) with tensile (compressive) strain. © 2021 Elsevier B.V.Article Citation - WoS: 5Citation - Scopus: 6Boosting Up Printability of Biomacromolecule Based Bio-Ink by Modulation of Hydrogen Bonding Pairs(Elsevier Ltd., 2020) Köksal, Büşra; Önbaş, Rabia; Başkurt, Mehmet; Şahin, Hasan; Arslan Yıldız, Ahu; Yıldız, Ümit HakanThis study describes low dose UV curable and bioprintable new bioink made of hydrogen bond donor-acceptor adaptor molecule 2-isocyanatoethyl methacrylate (NCO)modified gelatin (NCO-Gel). Our theoretical calculations demonstrate that insertion of 2-isocyanatoethyl methacrylate doubles the interaction energy (500 meV) between gelatin chains providing significant contribution in interchain condensation and self-organization as compared to methacrylic anhydride modified gelatin (GelMA). The NCO-Gel exhibits peak around 1720 cm?1 referring to bidentate hydrogen bonding between H-NCO and its counterpart O[dbnd]CN[sbnd]H. These strong interchain interactions drive chains to be packed and thereby facilitating UV crosslinking. The NCO-Gel is exhibiting a rapid, 10 s gelation process by the exposure of laser (3 W, 365 nm). The dynamic light scattering characterization also reveals that NCO-Gel has faster sol to gel transition as compared to GelMA depending on the UV curing time. The NCO-Gel was found to be more firm and mechanically strong that provides advantages in molding as well as bioprinting processes. Bioprinted NCO-Gel has shown sharp borders and stable 3D geometry as compared to GelMA ink under 10 s UV curing time. The cell viability tests confirm that NCO-Gel facilitates cell proliferation and supports cell viability. We foresee that NCO-Gel bioink formulation provides a promising opportunity when low dose UV curing and rapid printing are required. © 2020 Elsevier Ltd