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Karabacak, Soner
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Karabacak,S.
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04.01. Department of Chemistry
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Sustainable Development Goals
1NO POVERTY
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2ZERO HUNGER
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3GOOD HEALTH AND WELL-BEING
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4QUALITY EDUCATION
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5GENDER EQUALITY
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6CLEAN WATER AND SANITATION
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7AFFORDABLE AND CLEAN ENERGY
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8DECENT WORK AND ECONOMIC GROWTH
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9INDUSTRY, INNOVATION AND INFRASTRUCTURE
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10REDUCED INEQUALITIES
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11SUSTAINABLE CITIES AND COMMUNITIES
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12RESPONSIBLE CONSUMPTION AND PRODUCTION
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Scholarly Output
7
Articles
4
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19860/1302
Supervised MSc Theses
1
Supervised PhD Theses
1
WoS Citation Count
21
Scopus Citation Count
25
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0
WoS Citations per Publication
3.00
Scopus Citations per Publication
3.57
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3
Supervised Theses
2
| Journal | Count |
|---|---|
| ACS Applied Materials & Interfaces | 1 |
| Advanced Science | 1 |
| Emerging Technologies in Biophysical Sciences: A World Scientific Reference: Volume 3: Emerging Technologies for Diagnostics | 1 |
| Nanomaterials | 1 |
| Sensors and Actuators, B: Chemical | 1 |
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7 results
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Now showing 1 - 7 of 7
Article Citation - WoS: 11Citation - Scopus: 12Colorimetric and Fluorometric Profiling of Advanced Glycation End Products(American Chemical Society, 2022) Ammanath, Gopal; Karabacak, Soner; Karabacak, Soner; Yıldız, Ümit Hakan; Boehm, Bernhard O.; Yıldız, Ümit Hakan; Alagappan, Palaniappan; Liedberg, Bo; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyProfiling of advanced glycation end products (AGEs) is an emerging area of clinical significance for disease diagnosis and prognosis. Typically, concentrations of AGEs are estimated in laboratories by trained personnel using sophisticated equipment. Herein, a facile approach for colorimetric and fluorometric profiling of AGEs is reported for rapid and on-site analysis. The concentrations of AGE levels in plasma are estimated via changes in optical properties of polythiophenes (PTs) upon interaction with aptamers (Apts) in the presence and in the absence of AGEs. To validate the proposed approach, glyceraldehyde-derived AGEs (AGE class 1 [AGE1]), the biomarker associated with cardiovascular diseases and diabetes, are used as a model system. Colorimetric analysis yielded linear responses for AGE1 for clinically relevant concentration ranges between 1.5 and 300 μg/mL with a limit of detection (LOD) of ∼1.3 μg/mL. Subsequently, an approach utilizing PTs with four different pendant groups in conjunction with four different Apts is demonstrated for qualitative colorimetric profiling and for quantitative fluorometric profiling of up to four AGEs in clinical matrices. Principal component analysis (PCA) of fluorometric responses of AGE-spiked samples yielded distinct responses for the different AGEs tested. Thus, the proposed approach ascertains rapid profiling of spiked AGEs in plasma samples without the requirement of preanalytical processing and advanced instrumentation, thereby facilitating on-site diagnosis.Article Citation - WoS: 1Citation - Scopus: 1Gadolinium and Polythiophene Functionalized Polyurea Polymer Dots as Fluoro-Magnetic Nanoprobes(MDPI, 2022) Karabacak, Soner; Palaniappan, Alagappan; Yıldız, Ümit Hakan; Karabacak, Soner; Gulyás, Balázs; Padmanabhan, Parasuraman; Yıldız, Ümit Hakan; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyA rapid and one-pot synthesis of poly 3-thiopheneacetic acid (PTAA) functionalized pol-yurea polymer dots (Pdots) using polyethyleneimine and isophorone diisocyanate is reported. The one-pot mini-emulsion polymerization technique yielded Pdots with an average diameter of ~20 nm. The size, shape, and concentration of the surface functional groups could be controlled by al-tering the synthesis parameters such as ultrasonication time, concentration of the surfactant, and crosslinking agent, and the types of isocyanates utilized for the synthesis. Colloidal properties of Pdots were characterized using dynamic light scattering and zeta potential measurements. The spherical geometry of Pdots was confirmed by scanning electron microscopy. The Pdots were post-functionalized by 1,4,7,10 tetraazacyclododecane-1,4,7,10-tetraacetic acid for chelating gadolinium nanoparticles (Gd3+) that provide magnetic properties to the Pdots. Thus, the synthesized Pdots possess fluorescent and magnetic properties, imparted by PTAA and Gd3+, respectively. Fluorescence spectroscopy and microscopy revealed that the synthesized dual-functional Gd3+-Pdots ex-hibited detectable fluorescent signals even at lower concentrations. Magnetic levitation experiments indicated that the Gd3+-Pdots could be easily manipulated via an external magnetic field. These findings illustrate that the dua-functional Gd3+-Pdots could be potentially utilized as fluorescent reporters that can be magnetically manipulated for bioimaging applications.Article Citation - WoS: 5Citation - Scopus: 4Polarity Induced Vapochromism and Vapoluminescence of Polythiophene Derivatives for Volatile Organic Compounds Classification(Elsevier, 2023) Karabacak, Soner; Yıldız, Ümit Hakan; Qun, David Lee Chao; Yağmurcukardeş, Mehmet; Ammanath, Gopal; Karabacak, Soner; Yeasmin, Sanjida; Yağmurcukardeş, Mehmet; Palaniappan, Alagappan; Liedberg, Bo; Yıldız, Ümit Hakan; 04.04. Department of Photonics; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyPolarity 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: 4Citation - Scopus: 5Near-Infrared Emissive Super Penetrating Conjugated Polymer Dots for Intratumoral Imaging in 3d Tumor Spheroid Models(Wiley, 2024) Arslan Yıldız, Ahu; Karabacak, Soner; Yıldız, Ümit Hakan; Yildiz, Umit Hakan; 04.01. Department of Chemistry; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 04. Faculty of Science; 01. Izmir Institute of TechnologyThis 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. imageDoctoral Thesis Synthesis and Characterization of Near-Infrared (nir) Emissive Conjugated Polymer Dots for Tumoroid Imaging(01. Izmir Institute of Technology, 2024) Karabacak, Soner; Yıldız, Ümit Hakan; Karabacak, Soner; Yıldız, Ümit Hakan; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyThis thesis describes the synthesis and characterization of near-infrared (NIR) emissive conjugated polymers and their polymer dots (Pdots). The Pdots were exploited to image the tumor cells and tumor spheroids. The penetration behavior of NIR emissive Pdots was characterized in five different tumor spheroid models. Three different polymerization techniques were tried to synthesize the NIR emissive polymers, namely oxidative, direct arylation, and Stille polymerization. The obtained NIR emissive polymers underwent structural and optical characterization. P1 was chosen as a model polymer to obtain Pdots from NIR emissive polymers for imaging tumoroids. Pdot preparation includes using ultrasonic emulsification to modify nonionic D-A-D type alkoxy thiophene-benzobisthiadiazole-based conjugated polymers (P1) with amphiphilic cetyltrimethylammonium bromide (CTAB). The technique yields Pdots with a significant positive surface charge of +56.5 mV ± 9.5 and an average hydrodynamic radius of 12 nm. Optical characterization reveals that these Pdots were found as emissive in the NIR region, with a maximum wavelength of 860 nm. These Pdots possess colloidal and optical properties that make them appropriate for use as fluorescence emissive probes in bioimaging applications. The advantageous use of positively charged Pdots has been proven in diffusion-limited settings such as tissues, specifically in certain tumor spheroid models produced from the tumoroid cell lines. After the fluorescence imaging analysis, the Pdots' emission intensity profile indicates that they have high penetration capability into the tumoroid models' center parts. The results show that Pdots with a single-chain donor-acceptor polymer structure that has been cationized with CTAB can penetrate through dense materials over about 1 μm. This provides valuable insights into the progression of targeted theranostic strategies in cancer therapy.Master Thesis Synthesis of Polythiophene-Polyurethane Soft Nanoparticles for Bioimaging Applications(Izmir Institute of Technology, 2020) Karabacak, Soner; Yıldız, Ümit Hakan; Yıldız, Ümit Hakan; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyIn this study, synthesis of fluorescent polythiophene and polyurethane soft nanoparticles carrying them was carried out for bioimaging applications. Conjugated polythiophenes and polyurethane derivatives were obtained by changing their structural properties such as size, charge, and group, and were characterized by nuclear magnetic resonance, infrared spectroscopy, dynamic functional light scattering, fluorescent microscopy, methods. In the study, changing characteristics of polyurethane nanoparticle materials were investigated depending on the synthesis conditions. Synthesis of polyurethane nanoparticles was carried out by miniemulsion polymerization technique and synthesized as nanosphere to be more controllable on nanoparticle size, morphology and stability. The sizes of the polyurethane nanospheres varied in the range from 10 to 500 nm. Polyelectrolyte-polyelectrolyte complexation was investigated using cationic polythiophene-anionic polythiophene for use in bioimaging applications. Synthesized conjugated polythiophenes are divided into two groups as anionic and cationic polythiophenes. In this thesis, three kinds of cationic polythiophene synthesis are included, but poly (1,4-dimethyl-1- (3- ((4-methylthiophene-3-yl) oxy) propyl) piperazine-1-ium bromide) (PT4) was used as cationic conjugated polythiophene in the studies. Anionic polythiophene acetic acid (PTAA) was used as a counter-charged polythiophene. In addition to these studies, dual-mode imaging agents were prepared, consisting of PTAA as fluorescent agent and gadolinium metals as magnetic agent. The bioimaging studies continued under conditions imitating biological systems, and the potential of the proposed bioimaging agents was investigated.Book Part Citation - Scopus: 3Advances and Future Perspective of Graphene Field Effect Transistors (gfets) for Medical Diagnostics and Point-Of Tools(World Scientific Publishing, 2022) İnanç, Dilce; Karabacak, Soner; Mutlu, Mustafa Umut; İnanç, Dilce; Karabacak, Soner; Mutlu, Mustafa Umut; Yıldız, Ümit Hakan; Yıldız, Ümit Hakan; 04.04. Department of Photonics; 04.01. Department of Chemistry; 03.09. Department of Materials Science and Engineering; 03. Faculty of Engineering; 04. Faculty of Science; 01. Izmir Institute of TechnologyRecently, major focus has been centered to enhance the capability of graphenebased devices and to facilitate utilization of graphene for biological applications by lowering its toxicity. In this chapter, from synthesis to applications, many of the conspicuous characteristics of graphene have been elaborately reviewed. We primarily focused on graphene-based field effect transistor (FET) for medical diagnostics and point-of-care applications. The device configurations and their application potential as well as sensing capability of various graphene FETs (GFETs) have been discussed. Here, we have also presented several aspects and advantages of GFETs in medical applications while discussing their pros and cons in commercialization. We address the advances and challenges for GFET-based sensing platforms for the medical applications and elaborate the combination strategy of GFETs with the existing commercial systems. © 2023 by World Scientific Publishing Co. Pte. Ltd.