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Thermodynamic analysis of fast stages of specific lesion recognition by DNA repair enzymes

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Abstract

The methodology of determination of the thermodynamic parameters of fast stages of recognition and cleavage of DNA substrates is described for the enzymatic processes catalyzed by DNA glycosylases Fpg and hOGG1 and AP endonuclease APE1 during base excision repair (BER) pathway. For this purpose, stopped-flow pre-steady-state kinetic analysis of tryptophan fluorescence intensity changes in proteins and fluorophores in DNA substrates was performed at various temperatures. This approach made it possible to determine the changes of standard Gibbs free energy, enthalpy, and entropy of sequential steps of DNA-substrate binding, as well as activation enthalpy and entropy for the transition complex formation of the catalytic stage. The unified features of mechanism for search and recognition of damaged DNA sites by various enzymes of the BER pathway were discovered.

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Abbreviations

APE1:

human AP endonuclease

AP site:

apurinic-apyrimidinic site

aPu:

2-aminopurine

Cpy :

pyrrolocytosine

Fpg:

formamidopyrimidine-DNA glycosylase from E. coli

F-site:

(2R,3S)-2-(hydroxymethyl)-3-hydroxytetrahydrofuran

hOGG1:

human 8-oxoguanine-DNA glycosylase

oxoG:

7,8-dihydro-8-oxoguanosine nucleoside

oxoGua:

7,8dihydro-8-oxoguanine base

tC°:

1,3-diaza-2-oxophenoxazine

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  1. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia

    N. A. Kuznetsov & O. S. Fedorova

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Original Russian Text © N. A. Kuznetsov, O. S. Fedorova, 2016, published in Biokhimiya, 2016, Vol. 81, No. 10, pp. 1410–1426.

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Kuznetsov, N.A., Fedorova, O.S. Thermodynamic analysis of fast stages of specific lesion recognition by DNA repair enzymes. Biochemistry Moscow 81, 1136–1152 (2016). https://doi.org/10.1134/S0006297916100114

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