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Publication Metadata only (Bis)phosphonic acid-functionalized poly(ethyleneimine)- poly(amido amine)s for selective in vitro transfection of osteosarcoma cells(Amer Chemical Soc, 2021) Güven, Melek Naz; Altuncu, Seçkin; Konca, Yeliz Utku; Avcı, Duygu; N/A; Department of Chemistry; Demirci, Gözde; Acar, Havva Funda Yağcı; Master Student; Faculty Member; Department of Chemistry; Graduate School of Sciences and Engineering; College of Sciences; N/A; 178902Osteosarcoma is aggressive bone cancer, whose treatment has not changed significantly for the past few decades. Although gene therapy methods have emerged as potential treatment routes, the need for efficient and nontoxic gene delivery systems targeting osteosarcoma cells remains a challenge. High-molecular-weight poly(ethyleneimine)s (PEIs) are used as universal transfection agents; however, they cause significant cytotoxicity. on the other hand, poly(amido amine)s (PAAs) are biocompatible, biodegradable polymers with promising transfection efficiency, which should be improved further. In this paper, we combined low-molecular-weight branched PEI (1800 Da) and PAA macromers functionalized with various amounts of (bis)phosphonic acid groups and pentanol (via 5-amino-1-pentanol (AP)). The (bis)phosphonic acid groups on these polymers (PAEIs) are intended to facilitate bone targeting. The molecular weights of the PAEI polymers were between 2600 and 8600 g/mol. Their cytotoxicities and green fluorescence protein (GFP) transfection efficiencies were tested on an osteosarcoma cell line (U-2 OS cells), which is challenging to transfect, and healthy muscle cells (C2C12). Both the cytotoxicity and transfection efficiency of PAEIs were affected by the phosphonic acid (via APA, 2-aminoethyl phosphonic acid) or bisphosphonic acid (via ALE, sodium alendronate) content of the polymers. PAEIs are more cytocompatible than both linear and branched 25 kDa PEI. ALE-containing PAEIs provided better transfection than APA-containing ones. The most efficient PAEI polymer, containing a 0.7:0.3 AP/ALE ratio, displayed a transfection efficiency that was five times higher than that of 25 kDa PEI with dramatically better cytocompatibility. This is comparable to FuGENE, but PAEI is more advantageous in selective transfection of the U-2 OS. This set of polymers may be promising candidates for targeted gene therapy of osteosarcoma.Publication Metadata only 3D printed biodegradable polyurethaneurea elastomer recapitulates skeletal muscle structure and function(American Chemical Society (ACS), 2021) Gokyer, Seyda; Berber, Emine; Vrana, Engin; Orhan, Kaan; Abou Monsef, Yanad; Guvener, Orcun; Zinnuroglu, Murat; Oto, Cagdas; Huri, Pinar Yilgor; Department of Chemistry; Department of Chemistry; Yılgör, Emel; Yılgör, İskender; Researcher; Faculty Member; Department of Chemistry; College of Sciences; College of Sciences; N/A; 24181Effective skeletal muscle tissue engineering relies on control over the scaffold architecture for providing muscle cells with the required directionality, together with a mechanical property match with the surrounding tissue. Although recent advances in 3D printing fulfill the first requirement, the available synthetic polymers either are too rigid or show unfavorable surface and degradation profiles for the latter. In addition, natural polymers that are generally used as hydrogels lack the required mechanical stability to withstand the forces exerted during muscle contraction. Therefore, one of the most important challenges in the 3D printing of soft and elastic tissues such as skeletal muscle is the limitation of the availability of elastic, durable, and biodegradable biomaterials. Herein, we have synthesized novel, biocompatible and biodegradable, elastomeric, segmented polyurethane and polyurethaneurea (TPU) copolymers which are amenable for 3D printing and show high elasticity, low modulus, controlled biodegradability, and improved wettability, compared to conventional polycaprolactone (PCL) and PCL-based TPUs. The degradation profile of the 3D printed TPU scaffold was in line with the potential tissue integration and scaffold replacement process. Even though TPU attracts macrophages in 2D configuration, its 3D printed form showed limited activated macrophage adhesion and induced muscle-like structure formation by C2C12 mouse myoblasts in vitro, while resulting in a significant increase in muscle regeneration in vivo in a tibialis anterior defect in a rat model. Effective muscle regeneration was confirmed with immunohistochemical assessment as well as evaluation of electrical activity produced by regenerated muscle by EMG analysis and its force generation via a custom-made force transducer. Micro-CT evaluation also revealed production of more muscle-like structures in the case of implantation of cell-laden 3D printed scaffolds. These results demonstrate that matching the tissue properties for a given application via use of tailor-made polymers can substantially contribute to the regenerative outcomes of 3D printed tissue engineering scaffolds.Publication Metadata only 3D printed poly(lactic acid) scaffolds modified with chitosan and hydroxyapatite for bone repair applications(Elsevier, 2020) N/A; N/A; N/A; N/A; Department of Chemistry; Department of Chemical and Biological Engineering; Department of Chemistry; Nazeer, Muhammad Anwaar; Önder, Özgün Can; Sevgili, İlkem; Yılgör, Emel; Kavaklı, İbrahim Halil; Yılgör, İskender; PhD Student; PhD Student; PhD Student; Researcher; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; College of Sciences; N/A; N/A; N/A; N/A; 40319; 241813D printed poly(lactic acid) (PLA) scaffolds surface modified with chitosan (CS) and hydroxyapatite (HA) to produce a novel bioactive composite scaffold is reported. Excellent mechanical properties of PLA, the bioactivity of CS, and osteogenic characteristics of HA are combined to fabricate composite scaffolds using a simple desktop 3D printer. Scaffolds were characterized through attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray (EDX) spectroscopy, X-ray diffraction (XRD) and water contact angle measurements before and after modification. Formic acid was used as a solvent to prepare stable CS/HA dispersions and was found to be a suitable solvent for producing PLA/CS/HA composites. Surface properties of modified scaffolds were superior in terms of hydrophilicity and bioactivity, which resulted in enhanced attachment and proliferation of human osteosarcoma cells in vitro compared to the unmodified PLA scaffolds.Publication Metadata only 3D printing of cytocompatible gelatin-cellulose-alginate blend hydrogels(Wiley-V C H Verlag Gmbh, 2020) Erkoc, Pelin; Uvak, Ileyna; Odeh, Yazan Nitham; Akdogan, Ozan; Odeh, Yazan Nitham; Akdogan, Ozan; N/A; Department of Chemistry; Department of Chemical and Biological Engineering; Nazeer, Muhammad Anwaar; Batool, Syeda Rubab; Kızılel, Seda; PhD Student; Researcher; Faculty Member; Department of Chemistry; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; 283763D bioprinting of hydrogels has gained great attention due to its potential to manufacture intricate and customized scaffolds that provide favored conditions for cell proliferation. Nevertheless, plain natural hydrogels can be easily disintegrated, and their mechanical strengths are usually insufficient for printing process. Hence, composite hydrogels are developed for 3D printing. This study aims to develop a hydrogel ink for extrusion-based 3D printing which is entirely composed of natural polymers, gelatin, alginate, and cellulose. Physicochemical interactions between the components of the intertwined gelatin-cellulose-alginate network are studied via altering copolymer ratios. The structure of the materials and porosity are assessed using infrared spectroscopy, swelling, and degradation experiments. The utility of this approach is examined with two different crosslinking strategies using glutaraldehyde or CaCl2. Multilayer cylindrical structures are successfully 3D printed, and their porous structure is confirmed by scanning electron microscopy and Brunauer-Emmett-Teller surface area analyses. Moreover, cytocompatibility of the hydrogel scaffolds is confirmed on fibroblast cells. The developed material is completely natural, biocompatible, economical, and the method is facile. Thus, this study is important for the development of advanced functional 3D hydrogels that have considerable potential for biomedical devices and artificial tissues.Publication Metadata only A comparative study on the effect of monodisperse Au and Ag nanoparticles on the performance of organic photovoltaic devices(Elsevier, 2021) Kacus, Hatice; Sevim, Melike; Biber, Mehmet; Baltakesmez, Ali; Aydogan, Sakir; Department of Chemistry; Metin, Önder; Faculty Member; Department of Chemistry; College of Sciences; 46962The monodisperse Au (similar to 5 nm) and Ag (similar to 3 nm) nanoparticles used in this study were obtained using surfactant-assistant solvothermal methods and characterized by XRD TEM and SEM. Then, these nanoparticles were embedded into the P3HT:PCBM photoactive layer at different ratios and the effects of the nanoparticles on the performance of the organic solar cells have been studied by varying the loading percent of the NPs in the range of 0.5-2 wt%. The best solar cell composition was determined to be 1 wt% for Au NPs and 0.5 wt% for Ag NPs. Optical absorption spectrum of P3HT:PCBM, P3HT:PCBM:AuNPs and P3HT:PCBM:AgNPs active layers were obtained using UV-visible spectroscopy. The J-V plots of ITO/PEDOT:PSS/P3HT:PCBM/LiF/Al solar cells having 1.10(-6) m(2) OSC area and with different Au NPs and Ag NPs loading ratios in the P3HT:PCBM were obtained under air mass (AM) 1.5G illumination. Open circuit voltage, short-circuit current density, fill factor, and power conversion efficiency of the OSC were calculated. The highest PCE values were obtained as 3.35% for Au NPs and as 3.50% for Ag NPs doped devices. This increase in PCEs was explained by a plasmonic effect that stems from the metallic NPs.Publication Metadata only A facile synthesis of mesoporous graphitic carbon nitride supported palladium nanoparticles as highly effective and reusable catalysts for Stille coupling reactions under mild conditions(Royal Soc Chemistry, 2020) N/A; Department of Chemistry; N/A; Department of Chemistry; Department of Chemistry; Kalay, Erbay; Çetin, Sultan; Kölemen, Safacan; Metin, Önder; Researcher; PhD Student; Faculty Member; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Sciences; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; 59456; N/A; 272051; 46962The development of a Stille coupling protocol that is operable under moderate conditions without using a base is highly required for the synthetic organic chemistry community, which requires an efficient nanocatalyst. In this respect, addressed herein is a facile one-pot synthesis of mesoporous graphitic carbon nitride (mpg-CN) supported Pd NPs, denoted as mpg-CN/Pd hereafter, and investigation of their catalytic activity in Stille cross-coupling reactions for the first time. It has been demonstrated that mpg-CN nanosheets can serve as not only a support material but also a stabilizer for the generation of 4.5 nm Pd NPs. The ecofriendly generated heterogeneous nanocatalyst was characterized by TEM, XRD, XPS, BET surface area and ICP-MS analysis. The mpg-CN/Pd nanocatalysts showed high activity in the Stille coupling reaction of a variety of electron-deficient and electron-rich aryl iodides/bromides and two different organostannanes with a wide substrate scope to afford the corresponding biaryls without using any bases and additional ligands under relatively mild conditions. The catalyst can be easily recovered from the reaction medium by centrifugation. It can be reused at least 5 times without any loss of activity.Publication Metadata only A facile synthesis of monodisperse cobalt–ruthenium alloy nanoparticles as catalysts for the dehydrogenation of morpholine borane and the hydrogenation of various organic compounds(Royal Soc Chemistry, 2022) Can, Hasan; Can, Sumeyra; Ebiri, Rustem; Department of Chemistry; Metin, Önder; Faculty Member; Department of Chemistry; College of Sciences; 46962Herein we report a novel wet-chemical protocol for the composition-controlled synthesis of monodisperse cobalt-ruthenium (CoRu) alloy NPs and their catalysis in the hydrolytic dehydrogenation of morpholine borane (MB) for chemical hydrogen storage and the hydrogenation of various organic compounds using MB as a hydrogen source. Monodisperse CoRu NPs with an average particle size of 1.7 +/- 0.6 nm at three different alloy compositions were prepared by the presented novel protocol that comprises the reduction of in situ formed ruthenium(iii) oleate complex with dicobalt octacarbonyl (Co-2(CO)(8)) in the presence of oleylamine (OAm). Next, as-synthesized CoRu alloy NPs were supported on carbon black (VC) and reduced graphene oxide (rGO) to study their catalysis in the dehydrogenation of MB and the transfer hydrogenation of various organic compouns bearing unsaturated functional groups (nitro, nitrile and carbonyl) using MB as a hydrogen source, respectively. VC-CoRu nanocatalysts exhibited a higher catalytic activity in hydrogen generation from the hydrolysis of MB with an initial turnover frequency (TOF) of 95 mol H-2*(mol (Co + Ru) min)(-1) while rGO-CoRu nanocatalysts showed better catalytic performance in the transfer hydrogenation reactions. All tested unsatured organic compounds (30 examples in total) are converted into corresponding hydrogenated products with the yields reaching up to 99% under mild conditions.Publication Metadata only A hydrogen peroxide responsive resorufin-based phototheranostic agent for selective treatment of cancer cells(Elsevier Sci Ltd, 2021) Department of Chemistry; Department of Chemistry; Almammadov, Toghrul; Kölemen, Safacan; Researcher; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Koç University Boron and Advanced Materials Application and Research Center (KUBAM) / Koç Üniversitesi Bor ve İleri Malzemeler Uygulama ve Araştırma Merkezi (KUBAM); College of Sciences; College of Sciences; N/A; 272051Enhanced selectivity towards cancer cells is one of the most essential features sought in new generation photodynamic therapy (PDT) agents in order to minimize the side effects on healthy cells and to improve the efficacy of the treatment. In this direction, one promising approach is to design activatable photosensitizers, which tend to stay in an OFF state and get activated only in cancer cells with tumor-associated stimuli. Based on this idea, herein we introduced a hydrogen peroxide (H2O2) activatable iodinated resorufin (RR-1) as a redshifted, water soluble and cancer cell selective photosensitizer. RR-1 exhibited high singlet oxygen quantum yield in aqueous solutions upon reacting with H2O2 and induced selective photocytotoxicity in colorectal (HCT116) and triple negative breast (MDA MB-231) cancer cells, which contain high level of reactive oxygen species (ROS). Additionally, fluorescence signal of the iodo-resorufin core was restored upon cleavage of the cage unit in these cancer cells. In contrast, very low photocytotoxicity and negligible fluorescence enhancement were observed in normal fibroblast (NIH-3T3) cells. RR-1 not only marks the first example of a H2O2 activatable resorufin-based photosensitizer but also represents the first ever resorufin-based theranostic agent. We anticipate that iodo-resorufin scaffold can be easily modified with different masking units towards realization of highly selective and efficient phototheranostic agents for treatment of various cancer cells.Publication Metadata only A leucine aminopeptidase activatable photosensitizer for cancer cell selective photodynamic therapy action(Elsevier Sci Ltd, 2021) N/A; N/A; N/A; Department of Chemistry; N/A; Department of Physics; Department of Chemistry; Department of Chemistry; Arslan, Büşra; Bilici, Kübra; Demirci, Gözde; Almammadov, Toghrul; Khan, Minahil; Sennaroğlu, Alphan; Acar, Havva Funda Yağcı; Kölemen, Safacan; Master Student; PhD Student; Master Student; Researcher; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Physics; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Boron and Advanced Materials Application and Research Center (KUBAM) / Koç Üniversitesi Bor ve İleri Malzemeler Uygulama ve Araştırma Merkezi (KUBAM); Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; College of Sciences; N/A; N/A; N/A; N/A; N/A; 23851; 178902; 272051Activity based photosensitizers (PS) continue to attract great attention as they enable selective photodynamic therapy action on cancer cells while sparing normal cells even under light irradiation. Sensitivity to specific enzymes that are differentially overexpressed in cancer cells is crucial in the design of activatable PSs. In this direction, we report here, for the first time, a leucine aminopeptidase (LAP) activatable PDT agent (HCL), which is a red-shifted, water soluble and photostable brominated hemicyanine derivative. HCL was activated by endogenous LAP enzyme selectively in A549 (lung) and HCT116 (colon) cancer cells containing high LAP levels and induced effective photocytotoxicity with negligible dark toxicity. Furthermore, the fluorescence of the parent bromo-hemicyanine core was restored upon LAP-based activation in cancer cells. On the other side, no remarkable phototoxicity or fluorescence turn-on was detected in healthy L929 cells. Thus, HCL serves as an effective and tumour associated LAP-sensitive phototheranostic agent. We believe different cancer-associated analytes can be utilized in combination with near-IR absorbing scaffolds in the scope of activatable PDT designs to enrich the tumour-selective PS arsenal.Publication Open Access A near-infrared benzothiazole-based chemodosimeter for rapid and selective detection of hydrogen sulfide(Turkish Chemical Society / Türkiye Kimya Derneği, 2021) Department of Chemistry; Kölemen, Safacan; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Boron and Advanced Materials Application and Research Center (KUBAM) / Koç Üniversitesi Bor ve İleri Malzemeler Uygulama ve Araştırma Merkezi (KUBAM); College of Sciences; 272051Hydrogen sulfide (H2S) is a biologically relevant gaseous molecule, which involves in a wide variety of physiological and pathological processes. Thus, detection of H2S is highly valuable in order to clarify its complex roles. In this study, a new benzothiazole-based donor-acceptor type H 2S selective chemodosimeter (HP-1) was synthesized and its H2S detection capabilities were investigated in aqueous solutions. HP-1 exhibited a red-shifted absorption signal at 530 nm and a near-infrared (NIR) fluorescence peak at 680 nm as a result of enhanced intramolecular charge transfer (ICT) in the presence of H2S, which enabled a selective and very rapid ratiometric fluorescent detection. HP-1 was also showed to be highly sensitive toward H2S with a very low limit of detection value.