1. Thermodynamics of the multi-stage DNA lesion recognition and repair by formamidopyrimidine-DNA glycosylase using pyrrolocytosine fluorescence—stopped-flow pre-steady-state kinetics
- Author
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Lev N. Krasnoperov, Olga S. Fedorova, Nikita A. Kuznetsov, and Yuri N. Vorobjev
- Subjects
Models, Molecular ,DNA Repair ,DNA damage ,DNA repair ,Biology ,Genome Integrity, Repair and Replication ,Fluorescence ,DNA-formamidopyrimidine glycosylase ,chemistry.chemical_compound ,Cytosine ,Genetics ,AP site ,Furans ,Guanosine ,Formamidopyrimidine DNA glycosylase ,Base excision repair ,DNA ,Kinetics ,Biochemistry ,chemistry ,DNA-Formamidopyrimidine Glycosylase ,DNA glycosylase ,Biophysics ,Thermodynamics ,DNA Damage - Abstract
Formamidopyrimidine-DNA glycosylase, Fpg protein from Escherichia coli, initiates base excision repair in DNA by removing a wide variety of oxidized lesions. In this study, we perform thermodynamic analysis of the multi-stage interaction of Fpg with specific DNA-substrates containing 7,8-dihydro-8-oxoguanosine (oxoG), or tetrahydrofuran (THF, an uncleavable abasic site analog) and non-specific (G) DNA-ligand based on stopped-flow kinetic data. Pyrrolocytosine, highly fluorescent analog of the natural nucleobase cytosine, is used to record multi-stage DNA lesion recognition and repair kinetics over a temperature range (10–30°C). The kinetic data were used to obtain the standard Gibbs energy, enthalpy and entropy of the specific stages using van’t Hoff approach. The data suggest that not only enthalpy-driven exothermic oxoG recognition, but also the desolvation-accompanied entropy-driven enzyme-substrate complex adjustment into the catalytically active state play equally important roles in the overall process.
- Published
- 2012