Researcher:
Asımgil, Hande

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Hande

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Asımgil

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Asımgil, Hande

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Researcher Of Publications: search.filters.isAuthorOfPublication.2331826e-ce0a-4f1f-b953-665178389281

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    Purification and characterization of five members of photolyase/cryptochrome family from cyanidioschyzon merolae
    (Elsevier Ireland Ltd, 2012) N/A; Department of Chemical and Biological Engineering; Asımgil, Hande; Kavaklı, İbrahim Halil; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 40319
    The photolyase/cryptochrome family is a large family of flavoproteins that possess different functions and use blue light as an energy source. Photolyases repair UV-induced DNA damage, whereas cryptochromes regulate the growth and development of plants in a blue-light dependent manner. In this paper, we report the characterization of five genes the photolyase/cryptochrome family from the red algae Cyanidioschyzon merolae. Phylogenetic analysis indicated that one gene is close to the (6-4) photolyase, 3 to the cryptochrome-dash (CRY-DASH), and one gene is an independent clade. We investigated the diversity and similarity of the enzymes' biochemical and photochemical properties. Both biochemical and complementation assays indicated that one of the CRY-DASH genes (CmPHR6) is not involved in the repair of either ssDNA or dsDNA. In addition, we isolated the first known (6-4) photolyase from C. merolae, the most primitive photosynthetic organism, which will give evolutionary insights into this protein family. (C) 2011 Elsevier Ireland Ltd. All rights reserved.
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    Detection of interaction constants between biological clock proteins by Surface Plasmon Resonance
    (AIChE, 2012) Çakır, Bilal; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; N/A; Department of Chemical and Biological Engineering; Kızılel, Seda; Kavaklı, İbrahim Halil; Gidon, Doğan; Asımgil, Hande; Kızılel, Rıza; Kepsütlü, Burcu; Demirer, Gözde Sultan; Faculty Member; Faculty Member; Undergraduated Student; PhD Student; Researcher; Master Student; Undergraduated Student; Department of Chemical and Biological Engineering; College of Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; 28376; 40319; N/A; N/A; 114475; N/A; N/A
    Organisms adopt their behaviors and physiology to the appropriate time of the day to anticipate daily environmental changes and the circadian clock regulates their daily rhythms. In mammals, the clock is present in essentially every cell. A heterodimer of CLOCK and BMAL1 proteins binds to the E-box in Per and Cry promoters and activates their transcription. In this work, we have purified core clock proteins and characterized the affinity of previously identified clock-relevant transcription factors. We have investigated the mechanism of the clock complex and the interactions of clock proteins with and without DNA using Surface Plasmon Resonance (SPR). Kinetic parameters determined from real time data bring a solid insight into the interactions of the clock proteins with their cognate promoter.
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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
    CRY1-CBS binding regulates circadian clock function and metabolism
    (Wiley, 2021) Growe, Jacqueline; Selby, Christopher P.; Rhoades, Seth D.; Malik, Dania; Francey, Lauren J.; Sancar, Aziz; Kruger, Warren D.; Hogenesch, John B.; Weljie, Aalim; Anafi, Ron C.; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; N/A; Kayıtmazbatır, Sibel Çal; Öner, Haşimcan; Asımgil, Hande; Kavaklı, İbrahim Halil; PhD Student; Faculty Member; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; N/A; N/A; 40319
    Circadian disruption influences metabolic health. Metabolism modulates circadian function. However, the mechanisms coupling circadian rhythms and metabolism remain poorly understood. Here, we report that cystathionine beta-synthase (CBS), a central enzyme in one-carbon metabolism, functionally interacts with the core circadian protein cryptochrome 1 (CRY1). In cells, CBS augments CRY1-mediated repression of the CLOCK/BMAL1 complex and shortens circadian period. Notably, we find that mutant CBS-I278T protein, the most common cause of homocystinuria, does not bind CRY1 or regulate its repressor activity. Transgenic Cbs(Zn/Zn) mice, while maintaining circadian locomotor activity period, exhibit reduced circadian power and increased expression of E-BOX outputs. CBS function is reciprocally influenced by CRY1 binding. CRY1 modulates enzymatic activity of the CBS. Liver extracts from Cry1(-/-) mice show reduced CBS activity that normalizes after the addition of exogenous wild-type (WT) CRY1. Metabolomic analysis of WT, Cbs(Zn/Zn), Cry1(-/-), and Cry2(-/-) samples highlights the metabolic importance of endogenous CRY1. We observed temporal variation in one-carbon and transsulfuration pathways attributable to CRY1-induced CBS activation. CBS-CRY1 binding provides a post-translational switch to modulate cellular circadian physiology and metabolic control.
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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.