Thermodynamics of the multi-stage DNA lesion recognition and repair by Formamidopyrimidine-DNA glycosylase using pyrrolocytosine fluorescence - Stopped-flow pre-steady-state kinetics
Document Type
Article
Publication Date
8-1-2012
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. © The Author(s) 2012.
Identifier
84867298594 (Scopus)
Publication Title
Nucleic Acids Research
External Full Text Location
https://doi.org/10.1093/nar/gks423
e-ISSN
13624962
ISSN
03051048
PubMed ID
22584623
First Page
7384
Last Page
7392
Issue
15
Volume
40
Grant
10-04-00070
Fund Ref
Russian Foundation for Basic Research
Recommended Citation
Kuznetsov, Nikita A.; Vorobjev, Yuri N.; Krasnoperov, Lev N.; and Fedorova, Olga S., "Thermodynamics of the multi-stage DNA lesion recognition and repair by Formamidopyrimidine-DNA glycosylase using pyrrolocytosine fluorescence - Stopped-flow pre-steady-state kinetics" (2012). Faculty Publications. 18145.
https://digitalcommons.njit.edu/fac_pubs/18145
