GCRIS Repository Collection: Collection of Chemistry / Kimya Bölümü koleksiyonu
https://hdl.handle.net/11147/4072
Collection of Chemistry / Kimya Bölümü koleksiyonu
2024-03-29T00:03:43Z
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Development of chrono-spectral gold nanoparticle growth based plasmonic biosensor platform
https://hdl.handle.net/11147/14273
Title: Development of chrono-spectral gold nanoparticle growth based plasmonic biosensor platform
Authors: Sözmen, Alper Baran; Elveren, Beste; Erdoğan, Duygu; Mezgil, Bahadır; Baştanlar, Yalın; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu
Abstract: Plasmonic sensor platforms are designed for rapid, label-free, and real-time detection and they excel as the next generation biosensors. However, current methods such as Surface Plasmon Resonance require expertise and well-equipped laboratory facilities. Simpler methods such as Localized Surface Plasmon Resonance (LSPR) overcome those limitations, though they lack sensitivity. Hence, sensitivity enhancement plays a crucial role in the future of plasmonic sensor platforms. Herein, a refractive index (RI) sensitivity enhancement methodology is reported utilizing growth of gold nanoparticles (GNPs) on solid support and it is backed up with artificial neural network (ANN) analysis. Sensor platform fabrication was initiated with GNP immobilization onto solid support; immobilized GNPs were then used as seeds for chrono-spectral growth, which was carried out using NH2OH at varied incubation times. The response to RI change of the platform was investigated with varied concentrations of sucrose and ethanol. The detection of bacteria E.coli BL21 was carried out for validation as a model microorganism and results showed that detection was possible at 102 CFU/ml. The data acquired by spectrophotometric measurements were analyzed by ANN and bacteria classification with percentage error rates near 0% was achieved. The proposed LSPR-based, label-free sensor application proved that the developed methodology promises utile sensitivity enhancement potential for similar sensor platforms. © 2024 The Author(s)
2024-01-01T00:00:00Z
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A novel 2-aminophenalenone-based fluorescent probe designed for monitoring H2O2 for in vitro and in vivo bioimaging
https://hdl.handle.net/11147/14266
Title: A novel 2-aminophenalenone-based fluorescent probe designed for monitoring H2O2 for in vitro and in vivo bioimaging
Authors: Saygılı, Ecem; Ersöz Gülseven, Esra; Kıbrıs, Erman; Çakan Akdoğan, Gülçin; Üçüncü, Muhammed
Abstract: A 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.
2024-01-01T00:00:00Z
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Free-standing three-dimensional graphene scaffolds for protease functional assay
https://hdl.handle.net/11147/14267
Title: Free-standing three-dimensional graphene scaffolds for protease functional assay
Authors: Ng, Zhi Kai; Yan, Evelias; Goyal, Garima; Gudlur, Sushanth; Kanagavel, Deepankumar; Yıldız, Ümit Hakan; Tsang, Siu Hon; Alagappan, Palaniappan; Teo, Edwin Hang Tong
Abstract: Three-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 biomarkers of significant interest. Recombinant OmpT was employed as a model protease for validating the proposed 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 significant 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 re-quenching associated with the typical homogeneous assays based on graphene, yielding a limit of detection (LOD) of ∼ 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. © 2023 Elsevier B.V.
2024-01-01T00:00:00Z
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The soft nanodots as fluorescent probes for cell imaging: Analysis of cell and spheroid penetration behavior of single chain polymer dots
https://hdl.handle.net/11147/14255
Title: The soft nanodots as fluorescent probes for cell imaging: Analysis of cell and spheroid penetration behavior of single chain polymer dots
Authors: Yücel, Müge; Onbaş, Rabia; Arslan Yıldız, Ahu; Yıldız, Ümit Hakan
Abstract: This study describes the formation, size control, and penetration behavior of polymer nanodots (Pdots) consisting of single or few chain polythiophene-based conjugated polyelectrolytes (CPEs) via nanophase separation between good solvent and poor solvent of CPE. Though the chain singularity may be associated with dilution nanophase separation suggests that molecules of a good solvent create a thermodynamically driven solvation layer surrounding the CPEs and thereby separating the single chains even in their poor solvents. This statement is therefore corroborated with emission intensity/lifetime, particle size, and scattering intensity of polyelectrolyte in good and poor solvents. Regarding the augmented features, Pdots are implemented into cell imaging studies to understand the nuclear penetration and to differentiate the invasive characteristics of breast cancer cells. The python based red, green, blue (RGB) color analysis depicts that Pdots have more nuclear penetration ability in triple negative breast cancer cells due to the different nuclear morphology in shape and composition and Pdots have penetrated cell membrane as well as extracellular matrix in spheroid models. The current Pdot protocol and its utilization in cancer cell imaging are holding great promise for gene/drug delivery to target cancer cells by explicitly achieving the very first priority of nuclear intake. The penetration capability of cationic soft nanodots in to tumor models of breast cancer is demonstrated. The image analysis based on fluorescence intensity variation reveals the characteristics of translocation of nanodots in dense mediums such as tumor models.image
2024-01-01T00:00:00Z