GCRIS

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Development of Conducting Polymer-Based Fluorescence On/Off Biosensor for Biomolecule Analysis
(01. Izmir Institute of Technology, 2022) Arslantaş, Duygu; Arslan Yıldız, Ahu
Sensitive and selective detection of biomolecules and cells is essential for early diagnosis of diseases, prognosis monitoring, and effective therapy. This thesis aimed to develop a novel fluorescence ‘‘turn-on/off’’ biosensor for biomolecules and cells detection. In this study, cationic polythiophene derivative poly(1,4-dimethyl-1-(3-((4- methylthiophen-3-yl)oxy)propyl)piperazin-1-ium bromide) (PT–Pip) was used as an efficient fluorescence transduction element to discriminate proteins, mammalian cells, and amino acids for the first time. Initially, pH–dependent spectroscopic characterization of the PT–Pip was performed to monitor the conformational and optical changes. The pH sensitivity of the PT–Pip was demonstrated for the first time. Afterwards, the fluorescence ‘‘turn–off’’ phenomena were investigated in detail using citrate–capped gold nanoparticles as an efficient fluorescence quencher. Further, the interaction of target analytes such as proteins, mammalian cells, and amino acids with pre–quenched non–covalent PT–Pip–AuNP complexes was examined. Disruption of the binding equilibrium between PT–Pip and AuNP by analytes resulted in the selective displacement of PT–Pip, which generated signal output as a fluorescence ‘‘turn–on’’ mode. Consequently, for the sensitive detection of biomolecules and cells, chemical tongue sensor arrays were developed utilizing differential sensing approaches. PCA was used for the statistical evaluation of the multi–dimentional fluorescence response patterns. As a result, unique fingerprints were rapidly obtained by the direct sensing of proteins, ratiometric sensing of mammalian cells, and indirect sensing of amino acids. The combination of a differential sensing strategy with an appropriate multivariate statistical technique enabled the selective and sensitive detection and identification of proteins, mammalian cells, and amino acids.
Characterization of Conjugated Polyelectrolytes for Nucleic Acid Sensing, Gene Delivery and Imaging
(01. Izmir Institute of Technology, 2022) Yücel, Müge; Yıldız, Ümit Hakan; Yıldız, Ümit Hakan
In this thesis, cationic derivatives of poly(3-alkylmethoxythiophene) (PT) which are a class of conjugated polyelectrolytes (CPE), have been synthesized. PT has been polymerized via FeCl3 oxidative polymerization, were treated in a set of solvents to elaborate coil conformation of polymer chain in different physicochemical environment. Spectroscopic and scattering techniques have ascertained that ethylene glycol is a good solvent for PT regarding Flory-Huggins theory. The smaller interaction parameter of PT with respect to ethylene glycol than water drives a thermodynamically driven ultra-small particle (Pdot) formation in aqueous phase by a rapid nanophase separation between PTrich ethylene glycol and PT-poor water phase. All CPEs have been then employed to prepare single polymer chain polymer dots (Pdot) by “nanophase separation” method. As a next step, Pdots have been characterized in terms of optical and colloidal properties that they possess in the backbone conformations altered by solvation effect. Regarding their colloidal characteristic, translocation of Pdot into cancerous cells was analyzed compared to healthy cells by 2D cell culture and co-culture studies. It has reported that Pdots have ability to penetrate through nuclear envelope in hepatocellular carcinoma whereas accumulate around nucleus of healthy liver cells in cytoplasm. Additionally, Pdots were studied in breast cancer cell lines to understand the behavior of Pdot staining in 2D cell culture of invasive and non-invasive breast cancer types. The findings suggest that Pdots are prone to penetrate into the invasive cancerous cells attributed to the greater deformations on nucleus membrane of triple negative breast cancer cells. In a next application, the enhanced photophysical property of PT exhibited in ethylene glycol media allows PT to be utilized as a fluorescent probe for determination of single nucleotide polymorphism by a non-amplification-based protocol. Fluorescence emission at specific wavelengths resulted from very distinct conformations of PT chain is the key elements for the SNP detection assay. The evaluation of optical data obtained from the probe with principal component analysis proves the separation of healthy individuals from patients with an overall 96% accuracy.

Phd Degree / Doktora

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