Glioblastoma multiforme’ ye karşı DNA aptamerlerinin in vitro seçilimi.

Aptamer probes for specific recognition of glioblastoma multiforme were generated using a repetitive and broad cell-SELEX-based procedure without negative selection. The 454 sequencing technology was used to monitor SELEX, and bioinformatics tools were used to identify aptamers from high throughput data. A group of aptamers were generated that can bind to target cells specifically with dissociation constants (K d ) in the nanomolar range. Selected aptamers showed high affinity to different types of glioblastoma cell lines, while showing little or no affinity to other cancer cell lines. The aptamers generated in this study have potential use in different applications, such as probes for diagnosis and devices for targeted drug delivery, as well as tools for molecular marker discovery for glioblastomas.Ph.D. - Doctoral Progra

Mercimek kotiledon petiollerinde rejenerasyon ve transformasyon sistemlerinin optimizasyonu.

In this study, optimization of a transformation and regeneration system via indirect organogenesis in cotyledonary petiole tissue of lentil (Lens culinaris Medik.) was investigated. Eight different medium types differing in their plant growth regulator compositions were employed to examine the callus induction potency of cotyledonary petiole. Except two, all other tested medium yielded more than 80% callus induction. Nine different medium types were studied to test the potencies of callus structures for shoot induction. Only the callus induced in medium H (1 mg/L Zeatin riboside + 1 mg/L Naphthalane acetic acid) yielded shoots at 8 to 40 % frequency. The most responsive medium was MS basal medium with no growth regulators. Also five and three different medium types were employed to examine callus induction potency of epicotyl tissues respectively. Each medium type yielded 90% callus induction. Only the callus induced in medium H yielded shoots At 6 to 26% frequency. Preliminary studies were carried out for somatic embryogenesis in cotyledonary petiole. Effects of salicylic acid on somatic embryogenesis were also investigated. Salicylic acid at 200æM was found to enhance the percentage of somatic embryos by 25 % and reduce the necrosis 24 %. However none of the globular and heart shape embryos were able to regenerate. Transient GUS expression efficiencies of roots, shoot tips, and cotyledonary petioles were tested after Agrobacterium-mediated transformation. Transformation frequencies were 26, 74, and 38 % for cotyledonary petiole, shoot tips, and roots respectively.M.S. - Master of Scienc

Label-free G-Quadruplex aptamer and Thioflavin-T based turn-off fluorescent detection of ethanolamine

WOS:000489191200004A label free aptasensor based on G-quadruplex forming ethanolamine aptamers and Thioflavin T was developed for the selective and sensitive detection of ethanolamine. The detection system consists of DNA aptamers with four GGG repeats forming a G-quadruplex that Thioflavin T can easily bind to causing high fluorescence emission intensity because of its fluorescence molecular rotor nature. In the presence of ethanolamine, binding of aptamer to its target induces conformational changes causing the separation of Thioflavin T from the complex with a dramatic decrease in fluorescence intensity of reaction mixture. This fluorescence aptasensor has a convenient sensitivity and selectivity with a detection limit of 641 mu M to measure ethanolamine directly in contaminated water samples in a wide linear range. Furthermore this method avoids all complicated modification and labelling steps and thus offers a simple, fast, and cost efficient solution for ethanolamine detection

Inhibition of cell migration and invasion by ICAM-1 binding DNA aptamers

WOS:000681225200010PubMed ID: 34038704Cancer is the second leading cause of death worldwide and most of the cancer-related deaths result from metastasis. As expressed on the surface of various cancer cell types, intercellular adhesion molecule-1 (ICAM-1) has been shown to play a role in the attachment, invasion and migration of tumor cells. In this study, DNA aptamers were generated against ICAM-1 by cell-SELEX and protein SELEX method using ICAM-1(+) CHO-ICAM-1 cells and ICAM-1 protein, respectively. The pools obtained at the end of the 10th round of both SELEX were sequenced and the most enriched sequences were characterized for their binding behaviors and affinities to ICAM-1(+) CHO-ICAM-1 and ICAM-1(−) MIA PaCa-2 cells. Moreover, the inhibition abilities of sequences on migration and invasion were measured. The seven aptamer sequences were obtained selectively binding to CHO-ICAM-1 cells with Kd values in the ranging from 13.8 to 47.1 nM. Four of these aptamers showed inhibition in both migration and invasion of CHO-ICAM-1 cells at least 61%. All these results suggested that these aptamers have potential to detect specifically ICAM-1 expressing tumor cells and inhibit migration and invasion by blocking ICAM-1 related interactions of circulating tumor cells

Domuz Jelatinine Özgü DNA Aptamerlerinin Seçilimi ve Karakterizasyonu

Aptamerler farklı hedeflere yüksek etkin ve özgünlükte bağlanabilen DNA ve RNA moleküllerdir. Bu çalışmada domuz jelatininin algılanmasında kullanılmak üzere DNA aptamerleri geliştirilmiştir. Aptamerlerin seçilimi için tekrarlı, negatif seçilim bulunan bir SELEX metodu takip edilmiş ve kütüphaneler bu yolla zenginleştirilmiştir. Zenginleştirilen kütüphaneler tarafımızca modifiye edilmiş bir metagenomik dizileme metodu kullanılarak yeni nesil dizileme sistemi Miseq ile dizilenmiş ve elde edilen yüksek hacimli veriden aday aptamer dizileri uygun biyoinformatik araçlar kullanılarak belirlenmiştir. Floresan modifiye olarak üretilen aday DNA aptameri domuz jelatinine karşı yüksek afinite göstermekte balık ve sığır jelatinine görece düşük afinite ile bağlanmaktadır. Bu çalışmada geliştirilen aptamer gıda tağşişlerinin belirlenmesi için kullanılacak sensörlerin geliştirilmesinde potansiyel algılama ajanı olarak kullanılabilecektir

Selection of DNA aptamers to Streptococcus pneumonia and fabrication of graphene oxide based fluorescent assay

WOS:000441368000014PubMed:29964028Pneumococci are one of the leading causes of infections throughout the world causing problems mainly in children, elderly, and immune-deficient patients. In recent years antibiotic resistant Streptococcus pneumoniae strains become widespread. Therefore simple, rapid, and specific detection methods are needed for public health. In this study, DNA aptamer probes against S. pneumoniae were selected using bacterial Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and these probes were integrated in to a graphene oxide (GO) based fluorescent assay. Among the tested aptamers three candidates Lyd-1, Lyd-2 and Lyd-3 showed K-d values of 844.7 +/- 123.6, 1984.8 +/- 347.5, and 661.8 +/- 111.3 nM, respectively. These candidates showed binding affinity to S. pneumoniae and no specific binding to the bacteria used in negative selection. The binding of aptamers were showed by fluorescence spectroscopy and flow cytometry. GO based label-free fluorescent assay developed using Lyd-3 aptamer had a unique detection limit of 15 cfu mL(-1) . Thus we believe that the selected aptamers and fabricated GO based assay has potential to be used in the detection of S. pneumoniae. Selected aptamers selectively bind to S. pneumonia with anti-pneumococcal potential and holds great potential to be used as molecular probes for identifying and targeting.Scientific and Technological Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [114S856]This work was supported by the Scientific and Technological Research Council of Turkey [Project No. 114S856]

Evaluation of anticancer activities of novel facile synthesized calix[n]arene sulfonamide analogs

WOS:000499232500005Here, new calixarene sulfonamide analogs were synthesized from the reaction of chlorosulfonated calix[n]arene (n: 4, 6, and 8) with N,N′-dimethylethylenediamine or ethylenediamine for the first time and an excellent calixarene sulfonamide analog showing potent and selective cytotoxic activity on some cancer cell lines were discovered. Cytotoxicity of the prepared calix[n]arene sulfonamide analogs towards both cancer and healthy cell lines was assessed by performing cell growth inhibition assays. In cytotoxicity assay results, it was observed that while sulfonamide analog based calix[4]arene (9) was not affecting the growth of epithelial cell lines (HEK), and it was especially effective on inhibiting the growth of some human cancer cell lines (MCF-7 and MIA PaCa-2). These results highlight that sulfonamide analog–based calix [4] arene (9) can be further studied as a potential anticancer agent

A label-free G-quadruplex and ThT mediated fluorescent sensor for detection of Cu2+ from water samples

A facile and label-free detection method based on the formation of the G-quadruplex structure of Thioflavin T and a DNA sequence was developed for rapid and sensitive detection of copper (Cu2+) ion. The DNA sequence with many guanine (G) repeats has the potential to form a G-quadruplex structure and exhibits high selectivity to Cu2+. ThT promotes the formation of the G-quadruplex structure resulting in high fluorescence intensity because of its fluorescence molecular rotor characteristic. As opposed to, when the DNA sequence binds to its target in the presence of Cu2+, conformational changes occur, resulting in ThT dissociation and a substantial decrease in fluorescence intensity. By virtue of this change, unlabeled, low-cost, sensitive, and selective detection of Cu2+ was achieved and not interfered by many other ions. The proposed method has high sensitivity and selectivity, with a detection limit of 30.7 nM, allowing it to directly measure Cu2+ in contaminated water samples in a wide linear range from 0.1 to 100 µM with a high recovery rate

Nanotechnology in food and agriculture

Due to their extraordinary properties, nanoparticles have enormous applications in different fields. Nanotechnology is an obstructive field and has a potential with developed methods to change the current scenario of the food and agricultural industry. Developments and innovations in nanotechnology like nanosensors, nanopesticides, nanofertilizers, nanoencapsulation, and active packaging, facilitated the transformations in food and agriculture sectors. In this chapter, the most recent applications of nanotechnology in food and agriculture and the safety issues of nanomaterials in processing and packaging are discussed. Nanotechnology exhibits promising potentials to be widely utilized in every aspect of food and agriculture. Therefore, the rapid progress of nanotechnology will be helpful to facilitate the development of agriculture and the food sector. © 2020 Nova Science Publishers, Inc. All rights reserved

Development of Aptamers for Targeted Drug Delivery to Glioblastoma Multiforme Brain Tumors

Bu çalışmada glioblastoma multiforme’yi özel olarak tanıyan aptamer probları negatif seçilim yapılmadan tekrarlı hücre SELEX’i temelli bir prosedürün kullanılmasıyla oluşturulmuştur. Seçilim sonrasında 454 sekanslama teknolojisi SELEX yöntemini izlemek için, biyoenformatik araçlar ise yüksek kapasiteli verilerden yararlanılarak aptamerleri tanımlamak için kullanılmıştır. Özellikle hedef hücreye bağlanabilen ve nanomolar düzeyinde ayrılma sabitine (Kd) sahip bir grup aptamer üretilmiştir. Seçilen aptamerler glioblastoma hücre hattına ait farklı türlere yüksek bağlanma eğilimi gösterirken, diğer kanser hücre hatlarına az ya da hiç bir bağlanma göstermemektedir. Bu çalışmada üretilen aptamerler glioblastoma hücreleri için moleküler işaretleyici keşfi için araç olmanın yanı sıra teşhis için kullanılan prob ve hedeflenmiş ilaç dağıtımı gibi farklı uygulama alanlarında kullanılma potensiyeline sahiptirler.In this study aptamer probes for specific recognition of glioblastoma multiforme were generated using a repetitive and broad cell-SELEX-based procedure without negative selection. The 454 sequencing technology was used to monitor SELEX, and bioinformatics tools were used extensively to identify aptamers from high throughput data. A group of aptamers were generated that can bind to target cells specifically with dissociation constants (Kd) in the nanomolar range. Selected aptamers showed high affinity to different types of glioblastoma cell lines, while showing little or no affinity to other cancer cell lines. The aptamers generated in this study is used as tools in some applications. First of all they were used as recognition elements for their specific target in microscopy. They displayed a distinct binding on their target with observable microscopy images. Also preliminary experiments are carried out with a selected aptamer to be used as drug delivery vehicl