Yazar "Kavruk, Murat" seçeneğine göre listele

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    Antibiotic loaded nanocapsules functionalized with aptamer gates for targeted destruction of pathogens
    (Royal Soc Chemistry, 2015) Kavruk, Murat; Çelikbıçak, Ömer; Özalp, Veli Cengiz; Borsa, Barış Ata; Hernandez, Frank J.; Bayramoğlu, Gülay; Arıca, Yakup
    In this study, we designed aptamer-gated nanocapsules for the specific targeting of cargo to bacteria with controlled release of antibiotics based on aptamer-receptor interactions. Aptamer-gates caused a specific decrease in minimum inhibitory concentration (MIC) values of vancomycin for Staphylococcus aureus when mesoporous silica nanoparticles (MSNs) were used for bacteria-targeted delivery.
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    Aptamers in medical diagnosis
    (Pan Stanford Publishing Pte. Ltd., 2016) Özalp, Veli Cengiz; Kavruk, Murat; Dilek, Özlem; Bayraç, Abdullah Tahir
    Aptamers have been increasingly applied in biomedical field as a class of biorecognition elements that possess many advantages such as high specificity and binding affinity, easy synthesis, easy modification, small size, non-toxicity and good stability. Many diseases like cancer exhibit cellular aberrations at morphological and molecular levels. Medical diagnosis based on molecular features can be highly specific and extremely sensitive when proper recognition molecule and an efficient signal transduction system are employed. However, bioanalysis of human diseases at the molecular level is an extremely challenging field because effective probes to identify and recognize biomarkers of diseases are not readily available. Traditional bio-recognition molecule, antibody has been exploited to develop excellent diagnosis assays in many formats, but antibodies are insufficient to match the requirements of fast and portable biosensors for point-of-care applications, which are at high demand in pathogenic bacteria detection as well as other diseases like cancer. Aptamers are short single-stranded oligonucleotides, which can be selected from random combinatorial library by SELEX in vitro. This relatively new biorecognition agent has superior intrinsic characteristics for biosensor development. In this review, we first present major aptamer selection technologies and the main formats of biosensors, which were frequently employed in aptasensor development. Then, the current state of aptamers as applied to medical diagnosis was discussed for specifically cancer and pathogen diagnosis. Finally, an overview of aptamer-nanomaterials conjugates was presented in many applications such as diagnosis, bioimaging, and theranostics.
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    Aptamers: Molecular tools for medical diagnosis
    (Bentham Science Publ Ltd, 2015) Özalp, Veli Cengiz; Kavruk, Murat; Dilek, Özlem; Bayraç, Abdullah Tahir
    Aptamers have been increasingly applied in biomedical field as a class of biorecognition elements that possess many advantages such as high specificity and binding affinity, easy synthesis, easy modification, small size, non-toxicity and good stability. Many diseases like cancer exhibit cellular aberrations at morphological and molecular levels. Medical diagnosis based on molecular features can be highly specific and extremely sensitive when proper recognition molecule and an efficient signal transduction system are employed. However, bioanalysis of human diseases at the molecular level is an extremely challenging field because effective probes to identify and recognize biomarkers of diseases are not readily available. Traditional bio-recognition molecule, antibody has been exploited to develop excellent diagnosis assays in many formats, but antibodies are insufficient to match the requirements of fast and portable biosensors for point-of-care applications, which are at high demand in pathogenic bacteria detection as well as other diseases like cancer. Aptamers are short single-stranded oligonucleotides, which can be selected from random combinatorial library by SELEX in vitro. This relatively new biorecognition agent has superior intrinsic characteristics for biosensor development. In this review, we first present major aptamer selection technologies and the main formats of biosensors, which were frequently employed in aptasensor development. Then, the current state of aptamers as applied to medical diagnosis was discussed for specifically cancer and pathogen diagnosis. Finally, an overview of aptamer-nanomaterials conjugates was presented in many applications such as diagnosis, bioimaging, and theranostics.
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    Label-free lateral flow assay for Listeria monocytogenes by aptamer-gated release of signal molecules
    (Academic Press Inc Elsevier Science, 2019) Taşbaşı, B. Büşra; Güner, Buket C.; Sudağıdan, Mert; Uçak, Samet; Kavruk, Murat; Özalp, Veli Cengiz
    Lateral flow assay (LFA) type of biosensors have been popular due to cost-effectiveness and easy-interpretation for instant results, most common examples of applications being pregnancy tests, food safety or medical diagnostics. There are several examples of reports with high sensitivity, including pre-concentration of the sample by magnetic pull-down. However, sensitivity and direct detection designs with aptamers has been a limiting factor for developing aptamers-based LFA assays. In this study, we report a lateral flow design based on aptamer-gated silica nanoparticles to develop high sensitivity and direct bacterial assay by shifting aptamers-target interaction to conjugation pad. Aptamer-gated silica nanoparticles-based biosensors were reported for their high sensitivity, specificity and label-free detection for small molecules and whole cells. This label-free strategy for LFA can determine L. monocytogenes in minced chicken matrix at less than 5 min with a limit of detection (LOD) of 53 cells in one mL samples.
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    Nanocapsules in biomedicine promises and challenges
    (Scrivener Publishing Llc, 2015) Hernandez, Frank J.; Kavruk, Murat; Hernandez, Luiza I.; Özalp, Veli Cengiz
    With the recent advances in nanotechnology, in the past decade, the ways of doing biomedicine have been reshaped considerably. Nanometer-size structures (nanoparticles, nanowires, nanocapsules, etc.) are used in biosensing, molecular imaging, diagnosis and therapies, based on their exceptionally diverse properties. Properties such as size, morphology, aggregation propensity, functionalization, biocompatibility, and biodegradability are being continuously optimized to maximize their biomedical efficacy. Among these nanostructures, nanocapsules are the next-generation approach promising to control "cellular health," by programming the release of cargo to the target cell or organ based on endogenous (e.g. enzymes and pH) or external (light, magnetic field, ultrasound) stimuli. Nanocapsules are a class of porous polymeric or inorganic particles in the nanometer range, with tunable features such as pore diameter, pore topology, diverse surface properties, and loading efficiencies that can be easily tailored to several biomedical applications. However, the use of nanocapsules in the biomedicine field is still in its infancy. Most studies have been performed in silico or in cell lines, and just very few studies have been done in animal models of disease. This chapter focuses on those studies where nanocapsules have been well characterized in vitro and in vivo, with the potential to be translated into the clinic. Moreover, this chapter also offers an overview of the recent advances in nanocapsule-based approaches for cancer therapy.
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    NanoKeepers: Stimuli responsive nanocapsules for programmed specific targeting and drug delivery
    (Royal Soc Chemistry, 2014) Hernandez, Frank J.; Hernandez, Luiza I.; Kavruk, Murat; Arıca, Yakup M.; Bayramoğlu, Gülay; Borsa, Barış Ata; Özalp, Veli Cengiz
    Bacterial resistance is a high priority clinical issue worldwide. Thus, an effective system that rapidly provides specific treatment for bacterial infections using controlled dose release remains an unmet clinical need. Herein, we report on the Nano Keepers approach for the specific targeting of S. aureus with controlled release of antibiotics based on nuclease activity.
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    Nanoparticle embedded enzymes for improved lateral flow sensors
    (Royal Soc Chemistry, 2013) Özalp, Veli Cengiz; Zeydanlı, Uğur S.; Lunding, Anita; Kavruk, Murat; Öz, M. Tufan; Eyidoğan, Füsun; Öktem, Huseyin A.
    In this study, combining the nanoparticle embedded sensors with lateral flow assays, a novel strategy for ensuring the quality of signalling in lateral flow assays (LFAs) was developed. A LFA for reactive oxygen species (ROS) is reported that is based on horse radish peroxidase (HRP) which is co-entrapped with Texas Red dextran inside porous polyacrylamide nanoparticles. In this system, enzymes are protected in the porous matrix of polyacrylamide which freely allows the diffusion of the analyte. The sensor is rapid and sensitive for quantification of hydrogen peroxide concentrations. A test solution of hydrogen peroxides was quantified with this novel LFA-ROS sensor to obtain a linear range between 1 and 25 mM. Nanoparticle embedding of enzymes is proposed here as a general strategy for developing enzyme-based lateral flow assays, eliminating adverse effects associated with biological samples.
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    Pathogen detection by core-shell type aptamer-magnetic preconcentration coupled to real-time PCR
    (Academic Press Inc Elsevier Science, 2014) Özalp, Veli Cengiz; Bayramoğlu, Gülay; Kavruk, Murat; Keskin, Batuhan B.; Öktem, Hüseyin A.; Arıca, M. Yakup
    The presence of pathogenic bacteria is a major health risk factor in food samples and the commercial food supply chain is susceptible to bacterial contamination. Thus, rapid and sensitive identification methods are in demand for the food industry. Quantitative polymerase chain reaction (PCR) is one of the reliable specific methods with reasonably fast assay times. However, many constituents in food samples interfere with PCR, resulting in false results and thus hindering the usability of the method. Therefore, we aimed to develop an aptamer-based magnetic separation system as a sample preparation method for subsequent identification and quantification of the contaminant bacteria by real-time PCR. To achieve this goal, magnetic beads were prepared via suspension polymerization and grafted with glycidylmethacrylate (GMA) brushes that were modified into high quantities of amino groups. The magnetic beads were decorated with two different aptamer sequences binding specifically to Escherichia coli or Salmonella typhimurium. The results showed that even 1.0% milk inhibited PCR, but our magnetic affinity system capture of bacteria from 100% milk samples allowed accurate determination of bacterial contamination at less than 2.0 h with limit of detection around 100 CFU/mL for both bacteria in spiked-milk samples. (C) 2013 Elsevier Inc. All rights reserved.
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    Portable bioactive paper-based sensor for quantification of pesticides
    (Hindawi Ltd, 2013) Kavruk, Murat; Özalp, Veli Cengiz; Öktem, Hüseyin Avni
    A paper-based biosensor was developed for the detection of the degradation products of organophosphorus pesticides. The biosensor quantifies acetylcholine esterase inhibitors in a fast, disposable, cheap, and accurate format. We specifically focused on the use of sugar or protein stabilizer to achieve a biosensor with long shelf-life. The new biosensor detected malathion with a detection limit of 2.5 ppm in 5 min incubation time. The operational stability was confirmed by testing 60 days storage at 4 degrees C when glucose was used as stabilizer.