Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 2Citation - Scopus: 2A Novel Phenalenone-Based Probe for Dual-Mode Hydrazine Detection(Elsevier Inc., 2025) Saygili, Ecem; Kibris, Erman; Gelen, Sultan Sacide; Eldem, Asli; Odaci, Dilek; Ucuncu, MuhammedDespite its toxic and carcinogenic nature, hydrazine (N2H4) remains a crucial compound in environmental and industrial applications. Its associated risks demand effective monitoring; however, conventional detection methods often fall short in sensitivity and accuracy, highlighting the need for innovative approaches. This study presents a novel turn-on probe based on phenalenone-phthalimide scaffold, 2-(1-oxo-1H-phenalen-6-yl)isoindoline-1,3-dione (6-AP-PI), specifically designed for N2H4 detection, offering a novel approach by combining fluorescence and electrochemical signals, thereby significantly enhancing detection performance. 6-AP-PI exhibits an exceptional selectivity and sensitivity toward N2H4 both in solution and cellular media, providing rapid signal enhancement (<1 min) and a low limit of detection (490 nM). Overall, this dual-mode design effectively addresses the limitations of traditional methods, enhancing both sensitivity and selectivity, positioning the 6-AP-PI probe as a promising tool for future health, safety, and environmental protection applications.Review Citation - WoS: 23Citation - Scopus: 24Microfluidic-Based Technologies for Diagnosis, Prevention, and Treatment of Covid-19: Recent Advances and Future Directions(Springer, 2023) Tarım, Ergün Alperay; Anıl İnevi, Müge; Özkan, İlayda; Keçili, Seren; Bilgi, Eyüp; Başlar, Muhammet Semih; Özçivici, Engin; Öksel Karakuş, Ceyda; Tekin, Hüseyin CumhurThe COVID-19 pandemic has posed significant challenges to existing healthcare systems around the world. The urgent need for the development of diagnostic and therapeutic strategies for COVID-19 has boomed the demand for new technologies that can improve current healthcare approaches, moving towards more advanced, digitalized, personalized, and patient-oriented systems. Microfluidic-based technologies involve the miniaturization of large-scale devices and laboratory-based procedures, enabling complex chemical and biological operations that are conventionally performed at the macro-scale to be carried out on the microscale or less. The advantages microfluidic systems offer such as rapid, low-cost, accurate, and on-site solutions make these tools extremely useful and effective in the fight against COVID-19. In particular, microfluidic-assisted systems are of great interest in different COVID-19-related domains, varying from direct and indirect detection of COVID-19 infections to drug and vaccine discovery and their targeted delivery. Here, we review recent advances in the use of microfluidic platforms to diagnose, treat or prevent COVID-19. We start by summarizing recent microfluidic-based diagnostic solutions applicable to COVID-19. We then highlight the key roles microfluidics play in developing COVID-19 vaccines and testing how vaccine candidates perform, with a focus on RNA-delivery technologies and nano-carriers. Next, microfluidic-based efforts devoted to assessing the efficacy of potential COVID-19 drugs, either repurposed or new, and their targeted delivery to infected sites are summarized. We conclude by providing future perspectives and research directions that are critical to effectively prevent or respond to future pandemics.Article Citation - WoS: 56Citation - Scopus: 55A Bodipy-Based Fluorescent Probe To Visually Detect Phosgene: Toward the Development of a Handheld Phosgene Detector(John Wiley and Sons Inc., 2018) Sayar, Melike; Karakuş, Erman; Güner, Tuğrul; Yıldız, Büşra; Yıldız, Ümit Hakan; Emrullahoğlu, MustafaA boron-dipyrromethene (BODIPY)-based fluorescent probe with a phosgene-specific reactive motif shows remarkable selectivity toward phosgene, in the presence of which the nonfluorescent dye rapidly transforms into a new structure and induces a fluorescent response clearly observable to the naked eye under ultraviolet light. Given that dynamic, a prototypical handheld phosgene detector with a promising sensing capability that expedites the detection of gaseous phosgene without sophisticated instrumentation was developed. The proposed method using the handheld detector involves a rapid response period suitable for issuing early warnings during emergency situations.Article Citation - WoS: 625Citation - Scopus: 698Flow Cytometry: Basic Principles and Applications(Taylor and Francis Ltd., 2017) Adan, Aysun; Alizada, Günel; Kiraz, Yağmur; Baran, Yusuf; Nalbant, AytenFlow cytometry is a sophisticated instrument measuring multiple physical characteristics of a single cell such as size and granularity simultaneously as the cell flows in suspension through a measuring device. Its working depends on the light scattering features of the cells under investigation, which may be derived from dyes or monoclonal antibodies targeting either extracellular molecules located on the surface or intracellular molecules inside the cell. This approach makes flow cytometry a powerful tool for detailed analysis of complex populations in a short period of time. This review covers the general principles and selected applications of flow cytometry such as immunophenotyping of peripheral blood cells, analysis of apoptosis and detection of cytokines. Additionally, this report provides a basic understanding of flow cytometry technology essential for all users as well as the methods used to analyze and interpret the data. Moreover, recent progresses in flow cytometry have been discussed in order to give an opinion about the future importance of this technology.Article Citation - WoS: 80Citation - Scopus: 82Electrophilic Cyanate as a Recognition Motif for Reactive Sulfur Species: Selective Fluorescence Detection of H2s(American Chemical Society, 2016) Karakuş, Erman; Üçüncü, Muhammed; Emrullahoğlu, MustafaAn ESIPT-based fluorescent dye, 3-hydroxyflavone, is chemically masked with an electrophilic cyanate motif in order to construct a fluorescent probe for cellular sulfur species. This novel probe structure, displays an extremely fast, highly sensitive and selective "turn-on" type fluorescent response toward H2S. We have also documented its utility for imaging of H2S in the living cells.Article Citation - WoS: 24Citation - Scopus: 24A Ratiometric Fluorescent Probe for Gold and Mercury Ions(John Wiley and Sons Inc., 2015) Üçüncü, Muhammed; Karakuş, Erman; Emrullahoğlu, MustafaA fluorescent probe that displays a ratiometric fluorescence response towards gold and mercury ions has been devised. Emitting at a relatively longer wavelength, the conjugated form of the fluorescent dye transforms in the presence of the gold or mercury ions into a new dye, the molecular structure of which lacks the conjugation and consequently emits at a distinctly shorter wavelength. A fluorescent probe that displays a ratiometric fluorescence response towards gold and mercury ions has been devised. Emitting at a relatively longer wavelength, the conjugated form of the fluorescent dye transforms in the presence of the gold or mercury ions into a new dye (see figure).Article Citation - WoS: 43Citation - Scopus: 43A Bodipy-Based Fluorescent Probe for the Differential Recognition of Hg(ii) and Au(iii) Ions(Royal Society of Chemistry, 2015) Cantürk, Ceren; Üçüncü, Muhammed; Emrullahoğlu, MustafaWe describe the design, synthesis and spectral behaviour of a fluorescent molecular sensor able to recognize Hg2+ and Au3+ ions via different emission modes. The molecular sensor is constructed on a single BODIPY dye appended with a semithio-carbazone functionality as a recognition motif.Article Citation - WoS: 6Citation - Scopus: 6Investigation of the Spontaneous Emission Rate of Perylene Dye Molecules Encapsulated Into Three-Dimensional Nanofibers Via Flim Method(Springer Verlag, 2014) Açıkgöz, Sabriye; Demir, Mustafa Muammer; Yapaşan, Ece; Kiraz, Alper; Ünal, Ahmet A.; İnci, Mehmet NaciThe decay dynamics of perylene dye molecules encapsulated in polymer nanofibers produced by electrospinning of polymethyl methacrylate are investigated using a confocal fluorescence lifetime imaging microscopy technique. Time-resolved experiments show that the fluorescence lifetime of perylene dye molecules is enhanced when the dye molecules are encapsulated in a three-dimensional photonic environment. It is hard to produce a sustainable host with exactly the same dimensions all the time during fabrication to accommodate dye molecules for enhancement of spontaneous emission rate. The electrospinning method allows us to have a control over fiber diameter. It is observed that the wavelength of monomer excitation of perylene dye molecules is too short to cause enhancement within nanofiber photonic environment of 330 nm diameters. However, when these nanofibers are doped with more concentrated perylene, in addition to monomer excitation, an excimer excitation is generated. This causes observation of the Purcell effect in the three-dimensional nanocylindrical photonic fiber geometry.Article Citation - WoS: 16Citation - Scopus: 19N,n-Dialkylaniline Tetraethynylethenes: a New Class of Chromophores Possessing an Emitting Charge-Transfer State. Experimental and Computational Studies(John Wiley and Sons Inc., 2001) Gobbi, Luca; Elmacı, Nuran; Lüthi, Hans Peter; Diederich, FrançoisThe photophysical properties of N,N-dimethylaniline- (DMA) substituted tetraethynylethene (TEE; 3,4-diethynylhex-3-ene-1,5-diyne) and related derivatives were investigated in a joint experimental and computational study. Measurements of the electronic emission spectra showed that these novel chromophores display a dual fluorescence which strongly depends on solvent polarity. Computational studies suggest that the twisted intramolecular charge-transfer state (TICT) model offers a possible explanation for the experimentally observed dual fluorescence. Time-dependent density functional calculations revealed that the initial excited state reached upon photoirradiation relaxes to a lower-energy TICT state in which either the dimethylamino group is twisted into an orthogonal position with respect to the remaining planar arylated TEE moiety or the entire DMA donor group takes an orthogonal orientation with respect to the rigid, planar TEE acceptor moiety. For the compounds investigated, the charge-transfer state responsible for the strongly solvent-dependent luminescence is directly connected with the initial excited state, namely, no crossing of states is involved.Article Citation - WoS: 3Fret Measurements Between Small Numbers of Molecules Identifies Subtle Changes in Receptor Interactions(SPIE, 2013) Özçelik, Serdar; Orr, Galya; Hu, Dehong; Chen, Chii-Shiarng; Reşat, Haluk; Harms, Greg S.; Opresko, Lee K.; John Wiley and Sons Inc., H. Steven; Colson, Steven D.Overexpression of HER2 alters the cellular behavior of EGF receptor (EGFR) and itself,with great implications on cell fate. To understand the molecular interactions underlying these alterations, we quantified the association between the two receptors by looking at efficiency changes in fluorescence resonance energy transfer (FRET) between a small number of molecules at the membrane of living cells. Human mammary epithelial (HME) cells expressing varying degrees of HER2 were studied, to identify and compare the degree of receptors interactions as a function of HER2 overexpression. A high resolution wide-field laser microscope combined with a high sensitivity cooled CCD camera was used to capture simultaneously donor and acceptor emissions. Alternating between green and red lasers every 80 msec, donor, FRET, and acceptor images were acquired and were used to calculate FRET efficiency. Automated image analysis was developed to create FRET efficiency maps from overlapping donor, acceptor and FRET images, and derive FRET efficiency histograms to quantify receptorreceptor interactions pixel by pixel. This approach enabled us to detect subtle changes in the average distance between EGFR molecules, and between EGFR and HER2. We found pre-existing EGFR homoassociations, and EGFR-HER2 heteroassociations in cells overexpressing HER2, and identified the changes in these interactions with ligand stimulation. These observations demonstrate the power of FRET measurements between small numbers of molecules in identifying subtle changes in molecular interactions in living cell.