Browsing by Author "Kibar, Gunes"

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Citation - WoS: 4
Citation - Scopus: 4
Aptamer decorated PDA@magnetic silica microparticles for bacteria purification
(Springer Wien, 2024) Kavruk, Murat; Babaie, Zahra; Kibar, Gunes; Cetin, Barbaros; Yesilkaya, Hasan; Amrani, Yassine; Ozalp, V. Cengiz; Basic Sciences; Nutrition and Dietetics; 07. School of Health Sciences; 08. Medical School; 01. Atılım University
One significant constraint in the advancement of biosensors is the signal-to-noise ratio, which is adversely affected by the presence of interfering factors such as blood in the sample matrix. In the present investigation, a specific aptamer binding was chosen for its affinity, while exhibiting no binding affinity towards non-target bacterial cells. This selective binding property was leveraged to facilitate the production of magnetic microparticles decorated with aptamers. A novel assay was developed to effectively isolate S. pneumoniae from PBS or directly from blood samples using an aptamer with an affinity constant of 72.8 nM. The capture experiments demonstrated efficiencies up to 87% and 66% are achievable for isolating spiked S. pneumoniae in 1 mL PBS and blood samples, respectively.
Citation - WoS: 1
Citation - Scopus: 1
Assessment of Anticancer Effects of Aloe Vera on 3D Liver Tumor Spheroids in a Microfluidic Platform
(Wiley, 2025) Tevlek, Atakan; Kibar, Gunes; Cetin, Barbaros; Basic Sciences; 08. Medical School; 01. Atılım University
The search for effective anticancer therapies has increasingly focused on natural compounds like Aloe vera, renowned for its therapeutic properties. This study investigates the anticancer properties of Aloe vera on 3D liver tumor spheroids via a PDMS-based microfluidic device, providing a more physiologically realistic model compared to traditional 2D cultures. HepG2 cells were cultivated to generate 3D spheroids on-chip, thereafter subjected to different concentrations of Aloe vera and the chemotherapeutic drug Doxorubicin to evaluate cytotoxic effects. The microfluidic system, validated by COMSOL simulations, facilitated continuous perfusion and real-time assessment of cell viability over a duration of 10 days. The results indicated that Aloe vera markedly diminished cell viability by triggering apoptosis at concentrations over 12.5 mg/mL. IC50 values were determined at 72 h: 25 +/- 0.10 mg/mL for Aloe vera and 5.47 +/- 0.03 mu g/mL for Doxorubicin in 2D cultures, but in 3D cultures, the IC50 values were 31.25 +/- 0.14 mg/mL for Aloe vera and 8.33 +/- 0.05 mu g/mL for Doxorubicin. This study underscores the promise of Aloe vera as a natural anticancer agent and illustrates the efficacy of microfluidic platforms for enhanced drug screening and customized medicine applications.
Citation - WoS: 7
Citation - Scopus: 8
Biosensor for Atp Detection Via Aptamer-Modified Pda@poss Nanoparticles Synthesized in a Microfluidic Reactor
(Springer Wien, 2024) Kibar, Gunes; Sahinoglu, O. Berkay; Kilincli, Betul; Erdem, E. Yegan; Cetin, Barbaros; Ozalp, V. Cengiz; Basic Sciences; 08. Medical School; 01. Atılım University
This study introduces aptamer-functionalized polyhedral oligomeric silsesquioxane (POSS) nanoparticles for adenosine triphosphate (ATP) detection where the POSS nanoparticles were synthesized in a one-step, continuous flow microfluidic reactor utilizing thermal polymerization. A microemulsion containing POSS monomers was generated in the microfluidic reactor which was designed to prevent clogging by using a continuous oil flow around the emulsion during thermal polymerization. Surfaces of POSS nanoparticles were biomimetically modified by polydopamine. The aptamer sequence for ATP was successfully attached to POSS nanoparticles. The aptamer-modified POSS nanoparticles were tested for affinity-based biosensor applications using ATP as a model molecule. The nanoparticles were able to capture ATP molecules successfully with an affinity constant of 46.5 mu\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\upmu $$\end{document}M. Based on this result, it was shown, for the first time, that microfluidic synthesis of POSS nanoparticles can be utilized in designing aptamer-functionalized nanosystems for biosensor applications. The integration of POSS in biosensing technologies not only exemplifies the versatility and efficacy of these nanoparticles but also marks a significant contribution to the field of biorecognition and sample preparation.
Citation - WoS: 6
Citation - Scopus: 7
Expanding the Role of Exosomes in Drug, Biomolecule, and Nanoparticle Delivery
(Pergamon-elsevier Science Ltd, 2025) Saka, Ongun Mehmet; Dora, Devrim Demir; Kibar, Gunes; Tevlek, Atakan; Basic Sciences; 08. Medical School; 01. Atılım University
Exosomes are nanoscale extracellular vesicles released by diverse cell types, serving essential functions in intercellular communication and physiological processes. These vesicles have garnered considerable interest in recent years for their potential as drug delivery systems, attributed to their natural origin, minimal immunogenicity, high biocompatibility, and capacity to traverse biological barriers, including the blood-brain barrier. Exosomes can be obtained from diverse biological fluids, rendering them accessible and versatile vehicles for therapeutic medicines. This study emphasizes the burgeoning significance of exosomes in drug administration, concentrating on their benefits, including improved stability, target selectivity, and the capacity to encapsulate various biomolecules, such as proteins, nucleic acids, and small molecules. Notwithstanding their potential applications, other problems remain, including as effective drug loading, industrial scalability, and the standardization of isolation methodologies. Overcoming these hurdles via new research is essential for fully harnessing the promise of exosomes in therapeutic applications, especially in the treatment of intricate diseases like cancer and neurological disorders.
Citation - WoS: 2
Citation - Scopus: 3
Microfluidic Rapid Isolation and Electrochemical Detection of S. Pneumonia Via Aptamer-Decorated Surfaces
(Elsevier, 2025) Babaie, Zahra; Kibar, Gunes; Yesilkaya, Hasan; Amrani, Yassine; Dogan, Soner; Tuna, Bilge G.; Cetin, Barbaros; Özalp, Veli Cengiz; 01. Atılım University
Background: S. pneumoniae is widely recognized as a leading cause of respiratory infections worldwide, often resulting in high mortality rates. However, the advent of microfluidic technologies has brought significant advancements, including the simplified, sensitive, cost-effective, and rapid approach to pneumococcal bacteremia detection. In this study, a microfluidic magnetic platform is presented for rapid isolation, and an electrode array is utilized for the electrochemical detection of S. pneumoniae. Aptamer-decorated surfaces were employed for both isolation and detection. For isolation, silica magnetic microparticles were synthesized and decorated with aptamer. Results: Isolation performance was assessed for phosphate-buffered saline (PBS) and blood samples for different concentrations of S. pneumoniae. Electrical impedance spectroscopy (EIS) with fabricated gold interdigitated electrodes (IDEs) decorated with aptamer was implemented for the detection of S. pneumoniae at different bacteria concentrations. The microfluidic platform performed bacteria isolation at comparable isolation efficiency with batch systems but at a much faster rate (isolation took about a minute, and the aptamer-decorated electrode array exhibited a limit of detection (LOD) at 962 CFU/mL and linear range between 104 and 107CFU/mL. Significance: Our method represents a significant advancement compared to previous reports. Our microfluidic platform can efficiently isolate 60 mu L of the bacteria sample within about one minute. The entire process takes about two minutes including the detection step. Furthermore, our method achieves a notable improvement in the detection limit for S. pneumoniae compared to conventional ELISA and magnetic microfluidics ELISA.
Ultrafast Green Synthesis of Superparamagnetic Hybrid Nanoparticle for Advanced Applications
(Wiley, 2025) Kibar, Gunes; 01. Atılım University
The integration of superparamagnetic iron oxide nanoparticles (SPIONs) into functional hybrid nanostructures remains a challenge, particularly in preserving their magnetic properties within composite frameworks. Herein, we present a rapid and environmentally friendly synthesis strategy for SPION-decorated polyhedral oligomeric silsesquioxane (POSS) nanoparticles. The process involves UV-induced polymerization to form POSS nanoparticles, followed by in situ SPION precipitation, with comprehensive characterization performed via SEM, FTIR, XRD, and VSM analyses. This approach enables the fabrication of hybrid nanoparticles (similar to 160 nm) within 5 min and subsequent SPION decoration in under an hour, ensuring (10 emu/g) superparamagnetic behavior. The developed method is highly scalable, efficient, and compatible with green chemistry principles, making it a promising platform for engineering advanced hybrid nanostructures. These nanoparticles hold significant potential for applications in biomedicine, catalysis, and next-generation material science.