Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Nitrate Sensing With Molecular Cage Ionophores: a Potentiometric Approach(Royal Soc Chemistry, 2025) Onder, Ahmet; Begar, Ferit; Kibris, Erman; Buyukcakir, Onur; Yildiz, Umit HakanNitrate ions are widespread environmental pollutants in water and soil, posing critical risks to both human health and ecosystems. This study introduces a molecular cage as a novel ionophore for potentiometric nitrate-selective ion-selective electrodes (ISEs) designed for enhanced specificity and sensitivity. Among six synthetic candidates, the electrode incorporating a 1,3,5-tri(p-hydroxyphenyl)benzene-based chlorotriazine pillared cage molecule (CAGE-1) exhibited superior performance, characterized by a linear response in the nitrate concentration range of 1.0 x 10-5 to 1.0 x 10-1 M, with a high coefficient of determination (R2 = 0.9971) and a slope of -53.1 +/- 1.4 mV dec-1. The electrode also achieved a limit of detection of 7.5 x 10-6 M. These findings highlight the potential of molecular cages as ionophores for nitrate sensing in environmental applications.Article Citation - WoS: 4Citation - Scopus: 5Near-Infrared Emissive Super Penetrating Conjugated Polymer Dots for Intratumoral Imaging in 3d Tumor Spheroid Models(Wiley, 2024) Karabacak, Soner; Coban, Basak; Yildiz, Ahu Arslan; Yildiz, Umit HakanThis study describes the formation of single-chain polymer dots (Pdots) via ultrasonic emulsification of nonionic donor-acceptor-donor type (D-A-D) alkoxy thiophene-benzobisthiadiazole-based conjugated polymers (Poly BT) with amphiphilic cetyltrimethylammonium bromide (CTAB). The methodology yields Pdots with a high cationic surface charge (+56.5 mV +/- 9.5) and average hydrodynamic radius of 12 nm. Optical characterization reveals that these Pdots emit near-infrared (NIR) light at a maximum wavelength of 860 nm owing to their conjugated polymer backbone consisting of D-A-D monomers. Both colloidal and optical properties of these Pdots make them promising fluorescence emissive probes for bioimaging applications. The significant advantage of positively charged Pdots is demonstrated in diffusion-limited mediums such as tissues, utilizing human epithelial breast adenocarcinoma, ATCC HTB-22 (MCF-7), human bone marrow neuroblastoma, ATCC CRL-2266 (SH-SY5Y), and rat adrenal gland pheochromocytoma, CRL-1721 (PC-12) tumor spheroid models. Fluorescence microscopy analysis of tumor spheroids from MCF-7, SH-SY5Y, and PC-12 cell lines reveals the intensity profile of Pdots, confirming extensive penetration into the central regions of the models. Moreover, a comparison with mitochondria staining dye reveals an overlap between the regions stained by Pdots and the dye in all three tumor spheroid models. These results suggest that single-chain D-A-D type Pdots, cationized via CTAB, exhibit long-range mean free path of penetration (approximate to 1 mu m) in dense mediums and tumors. The single chain near infrared (NIR) emissive Pdots with high cationic surface charge enable penetration in dense medium such as tumor spheroids. Both colloidal and optical properties of Pdots make them promising fluorescent probe in bioimaging. imageArticle 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.