Investigation of Real-Time Photorepair Activity on DNA via Surface Plasmon Resonance

Kizilel, Rıza; Demir, Enis; Azizoglu, Selimcan; Asımgi, Hande; Kavaklı, İbrahim Halil; Kızılel, Seda

doi:10.1371/journal.pone.0044392

Cited by 5 publications

(7 citation statements)

References 43 publications

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“…During SPR experiments, the baseline drift was carefully monitored in order not to exceed 1 RU per minute so that higher accuracies would be obtained. The flow rate of 50 µl/min was selected for the experiments to minimize mass transport limitation (Schuck, ; Kizilel et al ., ; Azizoglu et al ., ). SPR data is analyzed with QDAT Data analysis tool, and the best fit curves were established using one‐to‐one simple reaction model.…”

Section: Resultsmentioning

confidence: 98%

Quantification of interactions among circadian clock proteins via surface plasmon resonance

2014

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Circadian clock is an internal time keeping system recurring 24 h daily rhythm in physiology and behavior of organisms. Circadian clock contains transcription and translation feedback loop involving CLOCK/NPAS2, BMAL1, Cry1/2, and Per1/2. In common, heterodimer of CLOCK/NPAS2 and BMAL1 binds to EBOX element in the promoter of Per and Cry genes in order to activate their transcription. CRY and PER making heterodimeric complexes enter the nucleus in order to inhibit their own BMAL1-CLOCK-activated transcription. The aim of this study was to investigate and quantify real-time binding affinities of clock proteins among each other on and off DNA modes using surface plasmon resonance. The pairwise interaction coefficients among clock proteins, as well as interaction of PER2, CRY2, and PER2 : CRY2 proteins with BMAL1 : CLOCK complex in the presence and absence of EBOX motif have been investigated via analysis of surface plasmon resonance data with pseudo first-order reaction kinetics approximation and via nonlinear regression curve fitting. The results indicated that CRY2 and PER2, BMAL1, and CLOCK proteins form complexes in vitro and that PER2, CRY2 and PER2 : CRY2 complex have similar affinities toward BMAL1 : CLOCK complex. CRY2 protein had the highest affinity toward EBOX complex, whereas PER2 and CRY2 : PER2 complexes displayed low affinity toward EBOX complex. The quantification of the interaction between clock proteins is critical to understand the operation mechanism of the biological clock and to address the behavioral and physiological disorders, and it will be useful for the design of new drugs toward clock-related diseases.

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Section: Resultsmentioning

confidence: 98%

Quantification of interactions among circadian clock proteins via surface plasmon resonance

2014

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“…Phylogenetic analyses of more than 250 photolyase/cryptochrome family members have revealed several major classes (Fig. 2) (Asimgil & Kavakli, 2012;Kavakli et al, 2017;Ozturk, 2017;Ozturk et al, 2008). These include Class I CPD photolyase, Class II CPD photolyase, Class III CPD photolyase, (6-4) photolyase and single-strand specific DNA photolyases (previously known as DASH-CRY).…”

Section: Cryptochrome/photolyase Protein Familymentioning

confidence: 99%

“…However, a subsequent study with a CRY-DASH from Vibrio cholerae (VcCRY1) showed photolyase activity, where VcCRY1 specifically repairs ssDNA but not dsDNA (Selby & Sancar, 2006). It is interesting to note that these types of proteins found in multiple copies form in algae (Asimgil & Kavakli, 2012;Chaves et al, 2011) and their functions are reviewed in (Noordally & Millar, 2015).…”

Section: Cryptochrome/photolyase Protein Familymentioning

confidence: 99%

DNA repair by photolyases

Kavaklı

Öztürk

Gül

2019

Advances in Protein Chemistry and Structural Biology

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Photolyases belong to the cryptochrome/photolyase protein family (CPF) which perform different functions such as DNA repair, circadian photoreceptor, and transcriptional regulation. Photolyase protein is a DNA repair enzyme that repairs UV-induced DNA damages of cyclobutane pyrimidine dimer (CPD) and pyrimidine-pyrimidone (6-4) photoproducts using blue-light as an energy source. This enzyme is a flavoprotein containing two chromophores: flavin adenine dinucleotide (FAD) as a cofactor and a photoantenna such as methenyltetrahydrofolate (MTHF). The FAD is essential for catalysis DNA repair. MTHF absorbs photons from the blue light spectrum and transfers energy to FAD to increase the repair efficiency of the enzyme. Phylogenetic analysis in which amino acid sequences of several hundreds of CPF members are used suggests that they form more classes than we have considered so far. In this chapter, we discussed structure-functions and reaction mechanisms of different classes of photolyases. Table of Contents 1. Introduction 2. Cryptochrome/Photolyase protein family 2.1 Cofactors of the Photolyases 2.2 The crystal structure of the photolyase 2.3 Reaction Mechanism of DNA repair Mediated by CPD Photolyase 2.4 Reaction mechanisms of DNA repair mediated by (6-4) and other classes of the photolyases 3. Conclusion 4. Acknowledgment 5.References

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“…Our recent work using surface plasmon resonance to measure the affinity of photolyases to DNA during the active repair period has indicated that VcCRY1 exhibits high affinity toward damaged ssDNA rather than dsDNA (Table ). This observation may explain why CRY‐DASH cannot repair dsDNA.…”

Section: A Single‐strand Dna Repair Enzyme: Cryptochrome Dash (Cry‐dash)mentioning

confidence: 99%

The Photolyase/Cryptochrome Family of Proteins as DNA Repair Enzymes and Transcriptional Repressors

Kavaklı

Barış

Tardu

et al. 2017

Photochem & Photobiology

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Light is a very important environmental factor that governs many cellular responses in organisms. As a consequence, organisms possess different kinds of light-sensing photoreceptors to regulate their physiological variables and adapt to a given habitat. The cryptochrome/photolyase family (CPF) includes photoreceptors that perform different functions in different organisms. Photolyases repair ultraviolet-induced DNA damage by a process known as photoreactivation using photons absorbed from the blue end of the light spectrum. On the other hand, cryptochromes act as blue light circadian photoreceptors in plants and Drosophila to regulate growth and development. In mammals, cryptochromes have lightindependent functions and are very important transcriptional regulators that act at the molecular level as negative transcriptional regulators of the circadian clock. In this review, we highlight current knowledge concerning the structural and functional relationships of CPF members.

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Investigation of Real-Time Photorepair Activity on DNA via Surface Plasmon Resonance

Cited by 5 publications

References 43 publications

Quantification of interactions among circadian clock proteins via surface plasmon resonance

Quantification of interactions among circadian clock proteins via surface plasmon resonance

DNA repair by photolyases

The Photolyase/Cryptochrome Family of Proteins as DNA Repair Enzymes and Transcriptional Repressors

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