Phd Degree / Doktora
Permanent URI for this collectionhttps://hdl.handle.net/11147/2869
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Doctoral Thesis Chemical Vapor Deposited Reusable Fluorescent Thin Film Sensor Nanoprobes for the Detection of Heavy Metal Ions(01. Izmir Institute of Technology, 2023) Karabıyık, Merve; Ebil, ÖzgençHeavy metal pollution has made a serious threat to the environment and human health day by day due to developing science, technology and industrial activities, therefore, the importance of selective detection of heavy metals has increased. Heavy metals gradually accumulate in the human body, especially via water sources. Among heavy metals, cadmium is one of the most carcinogenic ones and has harmful effects even in trace amounts. Despite it, detection studies of cadmium ion are very few. This thesis study focuses on the development of Initiated Chemical Vapor Deposition (iCVD) synthesized polymer thin film based quantum dot-nitroxide radical fluorescence sensor nanoprobe, which has a multi-use property and high durability, unlike sensor probes developed for single use in liquid media, and selective detection of Cd2+ ions in real water sources. By examining the effects of pH, concentration, solvent type and reaction time, the most suitable conditions to improve the interaction between Cd2+ ion and the newly developed sensor nanoprobe were investigated. The results proved that it is possible to detect the target ion easily even in complex environments where other heavy metal ions are present. Cd2+ ion detection limit with this proposed nanoprobe was found as 0.195 μM and high recovery percentage (>90%) obtained in standard addition method. In the multi-use study, it was confirmed that nanoprobe could be used repeatedly for the selective and sensitive detection of Cd2+ ion without being influenced by the content of daily water samples. This thesis is a great guide for new fluorescent sensor applications.Doctoral Thesis Two Dimensional Material Based Field Effect Transistor for Biosensing Applications(01. Izmir Institute of Technology, 2023) İnanç, Dilce; Yıldız, Ümit Hakan; Çelebi, CemThis thesis presents research on the use of two-dimensional material graphene as an area-effective transistor and its application in biological fields. The formation of wrinkled and flat structures on the surface of a single-layer graphene area-effective transistor, epitaxially grown for determining the bio-membrane dynamics of graphene, was examined using two different methods of deposition (thermal evaporation and pulsed electron accumulation) of a silicon dioxide (SiO2) layer. The investigation aimed to evaluate the pH and lipid bilayer formation performance of both wrinkled and flat GFETs. Increased sensitivity was determined through electrical measurements, as the oxide layer becomes thinner due to the existence of wrinkles, thus providing electrostatic coating on graphene. A sensor platform of chemiresistor type was developed for the differential determination of volatile organic compounds (VOCs) by synthesizing single-layer, bilayer, and multilayer graphene, enabling the analysis of ethanol (EtOH) and methanol (MetOH). Sensors produced using three different graphene morphologies demonstrated differential MeOH-EtOH responses attributed to the differential intercalation phenomenon in multilayer graphene morphologies when compared to ethanol. For the detection of VOCs such as acetone, ethanol, and hexane in human breath, a polymer nanofiber/multi-walled carbon nanotube or poly (3,4-ethylenedioxythiophene)/gold (Au) and iron oxide (Fe) hybrid bioelectronic interface was developed. Sensitivity studies were conducted by applying pure VOCs at different concentrations to the sensor platforms, and the behavior of the sensor platforms against interfering elements was evaluated by recharacterizing them under CO2 and humidity conditions. Considering the responses of MWCNT-PLLCL-Fe-based sensors to acetone, ethanol, and hexane, the tendency of water molecules to adhere to the Fe surface was shown to decrease water condensation on the conductive layer compared to other sensor configurations, indicating that the humidity effect was minimized in MWCNT-PLLCL-Fe-based sensors.Doctoral Thesis Development of Conducting Polymer-Based Fluorescence On/Off Biosensor for Biomolecule Analysis(01. Izmir Institute of Technology, 2022) Arslantaş, Duygu; Arslan Yıldız, AhuSensitive 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.Doctoral Thesis Preparation of Nanostructured Interface by Polymer Grafting on Various Solid Substrates for Biosensor Applications(Izmir Institute of Technology, 2021) Özenler, Sezer; Yıldız, Ümit HakanThis thesis presents the utilization, various applications, and characterization of the soft material-based coating formed on the gold surface with varying thickness and chemical properties resulting from the isocyanate-gold interaction. Theoretical calculations regarding the interaction of isocyanate with the gold surface revealed the character of the bond formed and the orientation of the functional groups on the surface. Results by X-ray photoelectron spectroscopy showed the tendency to shift to the high energy at N 1s and C 1s binding energies in the gold-interacting isocyanate group. In the next steps, the isocyanate-activated gold substrate was subjected to sequential incubation of 1,4-butanediol/hexamethylene diisocyanate, and thin-film formation was achieved by surface assisted (SurfAst) urethane polymerization. It was revealed with three different applications that a nano-porous polyurethane (PU) structure was formed on the gold substrate and could be postmodified by using SurfAst polymerization method. In the first application, modification with polyethylene glycol (PEG) was provided to obtain antifouling properties. The PEG-terminated PU structure on the gold surface was shown to reduce protein adhesion by approximately ten-fold. In the second application, SurfAst was applied on the 11-mercaptodecanoic acid incubated surface and grafting onto the poly (N-allyl-N-methyl-N-(3-((4-methylthiophen-3-yl)oxy)propyl) prop-2-en-1-aminium surface was characterized. As a result of PT grafting, PT nanowires with an average height of 100 nm, a width of 250 nm, and a length of 7 μm were obtained on the gold surface. In the last application, a soft nanogel was obtained by a reactive layer-layer (rLBL) coating method using the aza-Michael addition reaction of branched polyethyleneimine and polyester on the isocyanate functional surface. The mechanical and electrical permeability and coating properties of the nanogel layer were assessed. In conclusion, the high potential of isocyanate in surface activation has been demonstrated theoretically and experimentally. Effective modification of gold surfaces by polymer grafting with the SurfAst method and rLBL coating techniques has been achieved.Doctoral Thesis Development of a Plasmonic Biosensor for Detection of Exosomes(Izmir Institute of Technology, 2020) Taykoz, Damla; Bulmuş Zareie, Esma Volga; Tekin, Hüseyin CumhurThe aim of this work was to develop Localized Surface Plasmon Resonance (LSPR) surfaces for quantitative detection of exosomes from different sources. For this aim, gold nanorods (AuNRs) with a mean diameter of 40 nm with an aspect ratio of 2.9 were first synthesized and characterized. The self-assembly of AuNRs on glass wafers were optimized through several experiments. In parallel, PEGylation of cetrimonium bromide (CTAB) stabilized AuNRs was investigated using PEGs with three different molecular weights via LSPR, zeta potential and XPS techniques. PEGylated AuNRs were further self-assembled on silanized microscope slides as confirmed. Surface functionalization of AuNR patterned slides was performed using alkane thiol molecules having carboxylic acid and hydroxyl functional groups and confirmed via XPS, FTIR and zeta potential. Specific antibodies (Ab) were conjugated to the surface following two different methods, i.e. click and NHS/EDC chemistry. To perform click chemistry strategy, ImmuneLink® molecules were conjugated with Abs and the final conjugate was used to functionalize surfaces prepared beforehand using azide bearing molecules. The functionalization procedure was confirmed via XPS FTIR and LSPR spectroscopy. The orientation of the antibodies on the AuNRs patterned surfaces was investigated with LSPR in comparison with conventional EDC/NHS chemistry. The click-chemistry strategy proved to provide conjugation of antibodies through their Fc regions exposing Fab regions better for antigen recognition. Finally, surfaces functionalized with a variety of antibodies were used to detect first a pregnancy-associated protein, PLAP, and then exosomes obtained from human semen samples with pre-determined exosome concentrations. The LoD of the biosensor surfaces was found to be between 103-104 exosomes/mL and 5 ng/mL (0.3 pM) PLAP. Human breast cancer cell culture samples having an unknown concentration of exosomes were further analyzed using the newly developed LSPR biochips and the exosome concentration was determined as 108 exosomes/mL for MCF-7 cell line and 107 exosomes/mL for MDA-MB-231 cell line.