Researcher:
Demir, Enis

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Master Student

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Enis

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Demir

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Demir, Enis

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2009 - 200912010 - 20121

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Researcher Of Publications: search.filters.isAuthorOfPublication.a092aac6-cc82-4af6-82ec-6b9eebb7c21b

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    Gold nanoparticle-assisted AFM study of DNA damage and repair
    (2009) N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; N/A; N/A; Kızılel, Seda; Kavaklı, İbrahim Halil; Demir, Enis; Asımgil, Hande; Faculty Member; Faculty Member; Master Student; PhD Student; Department of Chemical and Biological Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 28376; 40319; N/A; N/A
    The purpose of this research is to investigate gold nanoparticles as a potential scaffold for the characterization of DNA damage and repair using atomic force microscopy (AFM) techniques. The procedure consists of functionalizing the surface of gold nanoparticles with DNA which are then immobilized onto amine modified silicon or glass surfaces. Our objective is to examine various lesions in individual DNA molecules and follow in the AFM their direct reversal by DNA repair enzymes. In order to achieve this goal DNA repair proteins such as photolyase (repairs UV damaged thymine dimers in DNA using blue-light energy) is used as damage markers and imaged in complexes with DNA by AFM in order to locate and identify the damage sites. Force spectroscopy measurements will determine the mechanical Fingerprints of various types of DNA damage caused by UV and gamma radiation and directly follow damage reversal in the presence of the repair activities. AFM images will be further compared with in vitro photoreactivation assay results.
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    PublicationOpen Access
    Investigation of real-time photorepair activity on DNA via surface plasmon resonance
    (Public Library of Science, 2012) Department of Chemical and Biological Engineering; Kızılel, Rıza; Demir, Enis; Azizoğlu, Selimcan; Asımgil, Hande; Kavaklı, İbrahim Halil; Kızılel, Seda; Researcher; Master Student; N/A; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; N/A; N/A; N/A; N/A; 40319; 28376
    The cyclobutane pyrimidine dimer (CPD) and 6-4 lesion formations along with the specific breaks on strands are the most common type of DNA damage caused by Ultraviolet light (UV) irradiation. CPD photolyase I and II construct two subfamilies of flavoproteins, which have recognition and repair capabilities of CPD sites on both single stranded (ssDNA) and double stranded DNA (dsDNA) with the aid of blue light energy. The other types of flavoprotein family consist of cryptochromes (CRY) that act as photoreceptors in plants, or circadian rhythm regulators in animals. Recent findings showed that a specific type of Cryptochrome-Drosophila, Arabidopsis, Synechocystis, Human (CRY-DASH) has photorepair activity on ssDNA. In this work, real-time interactions between CRY-DASH and ss/dsDNA as well as the interactions between Vibrio cholerae photolyase (VcPHR) and ss/dsDNA were investigated using Surface Plasmon Resonance (SPR). The interactions were then characterized and compared in order to investigate the effect of different types of flavoprotein on UV damaged ss/dsDNA. SPR results confirm the specific binding of VcPHR and CRY-DASH with UV treated DNA. This study is the first instance to quantify the interactions of UV treated and untreated DNA with flavoproteins.