TY - JOUR

T1 - Thermodynamics of the DNA repair process by endonuclease VIII

AU - Kladova, O. A.

AU - Kuznetsov, N. A.

AU - Fedorova, O. S.

PY - 2019/1/1

Y1 - 2019/1/1

N2 - In the present work, a thermodynamic analysis of the interaction between endonuclease VIII (Endo VIII) and model DNA substrates containing damaged nucleotides, such as 5,6-dihydrouridine and 2-hydroxymethyl- 3-hydroxytetrahydrofuran (F-site), was performed. The changes in the fluorescence intensity of the 1,3-diaza-2-oxophenoxazine (tCO) residue located in the complementary chain opposite to the specific site were recorded in the course of the enzyme-substrate interaction. The kinetics was analyzed by the stopped-flow method at different temperatures. 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, were calculated. The comparison of the kinetic and thermodynamic data characterizing the conformational transitions of enzyme and DNA in the course of their interaction made it possible to specify the nature of the molecular processes occurring at the stages of substrate binding, recognition of the damaged base, and its removal from DNA.

AB - In the present work, a thermodynamic analysis of the interaction between endonuclease VIII (Endo VIII) and model DNA substrates containing damaged nucleotides, such as 5,6-dihydrouridine and 2-hydroxymethyl- 3-hydroxytetrahydrofuran (F-site), was performed. The changes in the fluorescence intensity of the 1,3-diaza-2-oxophenoxazine (tCO) residue located in the complementary chain opposite to the specific site were recorded in the course of the enzyme-substrate interaction. The kinetics was analyzed by the stopped-flow method at different temperatures. 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, were calculated. The comparison of the kinetic and thermodynamic data characterizing the conformational transitions of enzyme and DNA in the course of their interaction made it possible to specify the nature of the molecular processes occurring at the stages of substrate binding, recognition of the damaged base, and its removal from DNA.

KW - DNA glycosylase

KW - Kinetic mechanism

KW - Pre-steady-state kinetics

KW - Thermodynamics

KW - pre-steady-state kinetics

KW - thermodynamics

KW - LESION RECOGNITION

KW - BINDING

KW - kinetic mechanism

UR - http://www.scopus.com/inward/record.url?scp=85065515897&partnerID=8YFLogxK

UR - https://www.elibrary.ru/item.asp?id=37312867

U2 - 10.32607/20758251-2019-11-1-29-37

DO - 10.32607/20758251-2019-11-1-29-37

M3 - Article

AN - SCOPUS:85065515897

VL - 11

SP - 29

EP - 37

JO - Acta Naturae

JF - Acta Naturae

SN - 2075-8251

IS - 1

ER -