Browsing by Subject "BODIPY"

Now showing 1 - 15 of 15

Open Access
A bifunctional photosensitizer for enhanced fractional photodynamic therapy: singlet oxygen generation in the presence and absence of light
(Wiley-VCH Verlag, 2016) Turan, I. S.; Yildiz, D.; Turksoy, A.; Gunaydin, G.; Akkaya, E. U.
The photosensitized generation of singlet oxygen within tumor tissues during photodynamic therapy (PDT) is self-limiting, as the already low oxygen concentrations within tumors is further diminished during the process. In certain applications, to minimize photoinduced hypoxia the light is introduced intermittently (fractional PDT) to allow time for the replenishment of cellular oxygen. This condition extends the time required for effective therapy. Herein, we demonstrated that a photosensitizer with an additional 2-pyridone module for trapping singlet oxygen would be useful in fractional PDT. Thus, in the light cycle, the endoperoxide of 2-pyridone is generated along with singlet oxygen. In the dark cycle, the endoperoxide undergoes thermal cycloreversion to produce singlet oxygen, regenerating the 2-pyridone module. As a result, the photodynamic process can continue in the dark as well as in the light cycles. Cell-culture studies validated this working principle in vitro.
Open Access
Cascading logic gates using ion signals generated by photolabile caged compounds
(2013) Atılgan, Ahmet
Caged compounds have attracted great attention due to their use in the elucidation of numerous biochemical processes. Photolabile caged compounds release covalently bound moieties upon exposure of ultraviolet light. Releasing the active species in such a controlled manner enables concentration of the molecules to be manipulated in spatiotemporal way. Getting inspired from the knowledge of cellular information transfer through second messenger systems which Ca and Zn ions play important role, we synthesized a photolabile caged Zn(II) compound so that we benefit from its controlled ion release feature, so as to integrate two molecular logic gates physically. For that reason, a molecular logic operation was designed and the released ion was used as information carrier from one logic gate to other. After proving its practicality, we tested same principle for higher molecular logic systems. To do that, photolabile caged Zn(II) compound and previously proved supermolecule with coupled AND logic gates were physically integrated. Results proved that photolabile caged Zn(II) compounds is a useful way to combine two separate logic gates by means of free zinc ions. From this point of view, the approach physical integration of molecular logic gates through a metal ion or compound might be a solution for building more complex molecular logic systems.
Open Access
Energy transfer, photosensitization and sensing with novel bodipy compounds and their supramolecular assemblies
(2017-06) Yeşilgül, Nisa
Fluorescent dyes have been used for decades in many applications due to their versatility, sensitivity and many other useful properties. Since their discovery in 1968, BODIPY dyes have come forward and have been used in many fields of research such as photodynamic therapy, anion/cation sensing, dye-sensitized solar cells. In this thesis, novel applications of fluorescent dyes, mainly based on BODIPY fluorophores are reported. In the first project, a photosensitizer derived from erythrosine attached to a luminol derivative is presented. The main purpose was to achieve photosensitization without requiring external excitation with light. In another project, we synthesized and characterized a series of heavy atom substituted BODIPY based photosensitizers. In a related study, the photophysical properties of a BODIPY based chemosensor substituted with benzo-21-crown-7 units were studied in the presence of various -diamino alkanes. Then, we designed a BODIPY based probe sensitive to bioreductive conditions known to be prevalent in hypoxic cancer cells. In the final chapter, we present a mechanically interlocked energy transfer cassette consisted of a distyryl-BODIPY acceptor and two donor units.
Open Access
An exploration of new avenues regarding deep tissue penetration and higher singlet oxygen efficiencies: novel near-IR photosensitizers for photodynamic therapy
(TÜBİTAK, 2019) Yeşilgül, Nisa; Kılıç, Bilal
A series of novel BODIPY-bearing electron-withdrawing groups at the meso position are reported here. According to the optical measurements, it may be clearly seen that the introduction of electron-donating groups into 3,5-positions and the presence of electron-withdrawing groups at the meso position of the BODIPY core resulted in spectacular bathochromic shifts (up to ~ 304 nm), and the projected photosensitizers had absorption bands in the therapeutic window of the electromagnetic spectrum (600–900 nm). The absorption maxima of compounds 4, 5, 6, and 7 were at 886 nm, 890 nm, 760 nm, and 761 nm, respectively. The singlet oxygen generation experiments revealed that compounds 6 and 7, with high singlet oxygen quantum yields (0.52 and 0.93, respectively), were excellent and promising candidates for photodynamic therapy. The singlet oxygen quantum yield of 0.93 was the highest reported value so far for BODIPY-based photosensitizers.
Open Access
Generation, storage and delivery of singlet oxygen by a multifunctional agent
(2017-04) Türksoy, Abdurrahman
Photodynamic therapy (PDT) relies on thephoto sensitized generation of sin- glet oxygen (by consuming dissolved oxygen) within tumortissues whose oxygen level is already low enough to make this treatment self-limiting. In certain ap- plications, hypoxia induced by photosensitizer is minimized by introducing light intermittently (fractionalPDT) in order to allow time for the replenishment of cellular oxygen, resulting in more effective treatment. In this particular study, we demonstrated that a photosensitizer with an attached 2-pyridone module to halogenated di-styryl BODIPY would be useful in fractional PDT. Upon illumi- nation of photosensitizer (PYR) with a light at specific wavelength in therapeutic window the endoperoxide of 2-pyridone isgenerated along with singlet oxygen. During the time required for replenishment of cellular oxygen the endoperoxide undergoes cycloreversion to produce singlet oxygen, regenerating the2-pyridonemoiety. Such mechanism enables continuation of photodynamic process in the dark, resulting improved fractional photodynamic thearpy drug validated by cell culture studies in vitro.
Open Access
A homogeneous system for photogeneration of hydrogen initiated by bodipy based photoinduced electron transfer
(2015-08) Atılgan, Hale
The key technology to fulfill the energy needs in the future is the generation of fuels by harvesting solar energy. Due to high abundance and low prices of cobalt, water-splitting (based on cobalt) method has received a lot of attention compared to noble metals. Several times cobaltoxime based catalysts were studied for proton reduction. In this project, our aim was to produce a homogeneous photocatalytic system for photogeneration of hydrogen with high efficiency. To do so, we synthesized ten integrated molecules in which we are making use of the highly quantum efficient and photostable BODIPY chromophore. After the synthesis and characterization of target molecules, we achieved to demonstrate hydrogen evolution with five of our molecules.
Open Access
Iron oxide/silica core-shell nanoparticles as rechargeable sources of singlet oxygen for synthetic applications
(2017-04) Yıldız, Deniz
In the rapidly developing world ofsynthetic chemistry, there is aconstant need for high-efficient catalyst. Besides this, reusable and easily removable catalysts are highly desired to reduce costs for environmentally friendly synthesis for both synthetic and manufacturing requirements. Magnetic nano particles (MNPs) are promising candidates for effortlessly removable structures due to their ability of being removed by magnetic field. Iron oxide nano particles have a well distin- guished place among MNPs since they have unique properties and they can be prepared and functionalized easily. Combination of photo sensitizers with MNPs is a new approach forsynthetic applications due to the fact that singlet oxygen is a reactive specie for various types of reactions. Herein, BODIPY with2-pyridone moiety on silica coated iron oxide nanoparticle is designed as a magnetically remov able nanostructure that cangenerate, store and release singlet oxygen. The efficiency is studied by the oxidation of organic sulfides to sulfoxides since they are at the core of many biological processes. Furthermore, thisdesign can produce recyclable and reusable catalysts for additional transformations with high efficieny.
Open Access
Metal ion release and signaling in molecular logic gate design
(2016-10) Uyar, Taha Bilal
Mimicking the biological structures is one of the main goals of the natural sciences, because processes are well-organized in nature despite its amazing complexity. On account of this, releasing metal ions at molecular level is a crucial topic owing to similar process in living organisms. In this thesis, we designed novel cage compounds for this purpose. Our novel cage molecule is activated with near-IR light while almost all of the cage compounds in the previous literature function in the UV region. Consequently, it is appropriate for using in biological systems. Release of zinc ions that has critical roles in human body successfully achieved by our novel compound in Part 2 of the thesis work. Molecular logic concept is one of the promising areas of chemistry. Today, electronic devices consists of silicon based circuits that process information by using binary logic. Molecular logic offers alternative for silicon based devices. Using molecules to process data is a promising idea in the fields from electronics to biotechnology. In part 3, we proposed AND gate whose inputs are pH and glutathione while the response is singlet oxygen which can be used to destroy cancer cells. It is possible to process much complicated information by combining more than one logic gate. In first part of the thesis study, we designed modular molecular logic gates by cascading of three logic gates via metal ion signals. In the last part, a fluorescent chemosensor was proposed for dopamine molecule, which is crucial in a number of biological processes at the human body.
Open Access
Nitroolefin functionalized bodipy dyes for protein labeling
(2013) Turgut, Hatice
Protein labeling has significant importance in terms of visualizing dynamics of proteins, cell-cell interactions, mechanisms of life cycles of proteins, etc. Proteins are labeled by either synthetic or natural molecules with purposes such as analysis of 3D structures, determination of turnover number, covalent modifications and tracking protein-protein interactions. In addition to this, sensing and signalling thiol groups have gained popularity recently. Nitroolefin groups on dyes are good Micheal acceptors which undergo fast and selective reaction with thiol moieties. With this knowledge, in this study, we aimed to obtain derivatives of BODIPY dyes having nitroolefin substituents on its different positions. Nitroolefin functionalization of BODIPY dyes was targeted to result in conjugation of nitroolefins with thiol groups such as those belonging to cysteine residues on proteins. Three different nitroolefin functionalized BODIPY dyes have been designed, synthesized and characterized successfully. Incorporating triethylene glycol (TEG) units onto BODIPYs increased water-solubility of the molecules. To prove bioconjugation of the dyes with proteins, absorbance and emission changes were recorded after reaction with both L-cysteine and Bovine Serum Albumin (BSA) and large spectral changes were obtained. The result suggests that nitroolefin functionalization of BODIPY dyes is a promising way to sense biological thiols and hence labeling proteins having thiol groups.
Open Access
Optimization of orthogonal reactions on bodipy dyes for one-pot synthesis of light harvesting dendrimers
(2013) Bekdemir, Ahmet
For more than a decade, synthetic organic chemistry has dealt with focusing on highly selective and efficient reactions that can proceed under mild conditions which would then be categorized under the term “orthogonal click chemistry”. These types of reaction have served number of applications for years as in peptide synthesis, homogeneous catalysis and development of supramolecular systems. On the other side, after a partial understanding of how photosynthetic bacteria and plants harvest solar radiation in order to carry their necessary carbon dioxide reduction reaction by converting light to chemical energy, artificial light harvesting systems have captivated a lot attention of scientists. Because today’s one of the biggest and inevitable problems is to discover/invent alternative energy sources/devices for future demands, these artificial light harvesting and solar concentrator systems are highly open for further development and optimization. However, like most other macromolecular systems, synthesis of these kind of devices should be straightforward so as to decrease the cost and to increase the efficiency. At this point, orthogonal click reactions, being mild and efficient synthetic models, can undoubtedly be worthwhile to consider as proper tools for easy preparation of light harvesting molecules. Here we propose a synthesis of thiol, Michael accepting groups, amine and isothiocyanate modified BODIPY dyes for light harvesting cascade preparation. Moreover, the optimization of Michael addition type thiol – ene reaction of these functionalized dyes has been discussed. Among methyl methacrylate, cyanoacetic acid and nitroolefin functionalizations, it was found that nitroolefin attached BODIPY dyes are the most reactive one. The achieved product has been investigated in terms of fluorescence and energy transfer.
Open Access
Photosensitization and controlled photosensitization with BODIPY dyes
(Elsevier, 2017) Türksoy, Abdurrahman; Yıldız, Deniz; Akkaya, Engin U.
Highly versatile BODIPY dyes proved themselves to be very useful as photosensitizers. These dyes can be derivatized to absorb essentially anywhere in the visible the near IR region of the spectrum. As a result of their diverse reactivity, singlet oxygen generation efficiency can be modulated very precisely, leading to a number of selective photosensitizers for photodynamic therapy. Among the biologically relevant modulators, glutathione concentration and pH received particular attention. In this review, we highlight modulatable BODIPY-based photodynamic photosensitizers, and various synthetically useful chemical reactions triggered by singlet oxygen and other reactive oxygen species generated by BODIPY-based photosensitizers.
Open Access
Rational design and synthesis of bodipy dyes for molecular sensing, light harvesting and photodynamic applications
(2014) Kütük, Tuğba Özdemir
BODIPY dyes have been addressed in many applications due to highly important features. These unique properties can be summarized as high photostability, high extinction coefficient, easy functionality, etc. Thus, tremendous studies have been published and, ion sensing, photodynamic therapy, dye-sensitized solar cells and light harvesting are some of the areas that BODIPY dyes have been utilized. In this thesis, BODIPY dyes were functionalized to be used for different concepts. In the first study, the main purpose was to seek for ion signaling differences of two isomeric tetra-styryl BODIPY dyes with charge donor ligand located at 1,7 versus 3,5 positions. Second work focuses on the light harvesting concept with the use of tetra-styryl BODIPY derivatives. Third study describes the coupling of energy transfer with internal charge transfer to monitor the alterations in intensity ratios, so, dynamic range of the fluorescent probe is improved. Design and synthesis of BODIPY dyes for detection of biological thiols in aqueous solution both chromogenically and fluorogenically was given in fourth study. Another biologically important molecule, hydrogen sulfide is selectively detected via BODIPY-based probe and depicted in the fifth study. In the sixth work, persistent luminescent nanoparticles are attached to BODIPY-based photosensitizer to activate the photodynamic action.
Open Access
Reaction-based BODIPY probes for selective bio-imaging
(Elsevier B.V., 2018) Kolemen, S.; Akkaya, E. U.
Complex intracellular environment of cells, which involves interaction of a large variety of bio-molecules, is a dynamic medium with full of important information that can be recovered as well as many unanswered questions. It is highly critical to image and track biologically relevant molecules in their native media without interfering with the regular cellular processes in order to gather as much data as possible to illuminate intricacies of the biological mechanisms. To that end, small-molecule fluorescent probes have been extensively developed during the last few decades with the help of current advances in imaging technologies. Although conventional probes utilizing non-covalent supramolecular interactions with the analyte of interest are successful, significant effort has been also put into the design of reaction-based probes (chemodosimeters). Chemodosimeters exploit selective reactions of analytes with fluorophores in attempt to improve the selectivity of the probes, address the limitations of former sensors and broaden the palette of useful probes. Various types of fluorophore scaffolds can be used in the design of chemodosimeters for visualization of different analytes. In this review, we highlight the 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) based chemodosimeters which have been used to image bio-thiols, reactive oxygen/nitrogen species, and gaseous molecules in living cells.
Open Access
Synthesis and characterization of novel ion sensor based on 2, 6-functionalized BODIPY structure
(2012) Uyar, Taha Bilal
Latest developments in chemistry of BODIPY make available synthesis of novel BODIPY based fluorescent chemosensors. Therefore, the design of novel chemosensors is attracting great attention in recent years. In this study, we functionalized 2 and 6 positions of BODIPY choromophore to understand that binding of different metal ions how affect the absorption and emission spectrums of BODIPY. We used three metal ions which are important in environment and biological systems and these are Hg (II), Zn (II) and Ca ions. Binding of these metal ions to azo crown ether is which attached BODIPY caused large changes in absorption and emission spectrums according to photoinduced electron transfer (PET) and internal charge transfer (ICT) mechanism.
Open Access
Synthesis of BODIPY conjugates towards multimodal therapeutic applicaitons
(2016-08) Okeev, Darika
Photodynamic therapy (PDT) is a promising and developing strategy to treat various types of cancers. Either on its own, or combined with surgical interference, it provides easy treatment without destructive side effects of chemotherapy. Its success is straightly dependent on the presence of singlet oxygen (SO) in the tumor tissues. Upon the activation of the photosensitizer, SO gets produced, harming the surrounding tissues. The destructive effect can be increased by a simultaneous treatment with a cytotoxic cancer drug. In this project, we have combined a BODIPY photosensitizer and a Camptothecin (CPT) drug moiety with a (Z)-1,2-bis(alkyl-thio)ethane linker to produce a macromolecule with higher destructive power for tumors. Upon irradiation with a light source, it is expected of the BODIPY sensitizer to convert triplet ground state oxygen to singlet excited state, which then would react with the linker to release CPT.