Thermodynamics of the DNA repair process by endonuclease VIII

O. A. Kladova; N. A. Kuznetsov; O. S. Fedorova

doi:10.32607/20758251-2019-11-1-29-37

Thermodynamics of the DNA repair process by endonuclease VIII

Переведенное название: Термодинамические параметры взаимодействия эндонуклеазы VIII с поврежденной ДНК

O. A. Kladova, N. A. Kuznetsov, O. S. Fedorova

Результат исследования: Научные публикации в периодических изданиях › статья › рецензирование

5 Цитирования (Scopus)

Аннотация

Проведен термодинамический анализ взаимодействия эндонуклеазы VIII (Endo VIII) с модель ными ДНК, содержащими поврежденные нуклеотиды, такие, как 5,6-дигидроуридин и 2-гидроксиметил-3-гидрокситетрагидрофуран (F-сайт). Методом «остановленного потока» при разных температурах с реги страцией изменений интенсивности флуоресценции остатка 1,3-диаза-2-оксофеноксазина, расположенного в комплементарной цепи напротив специфического сайта, проведен анализ кинетики фермент-субстратного взаимодействия. Рассчитаны изменения стандартной свободной энергии Гиббса, энтальпии и энтропии для последовательных стадий ферментативного процесса, а также образования переходного состояния в каталитической стадии. Совокупный анализ кинетических и термодинамических данных о конформационных превращениях фермента Endo VIII и ДНК, протекающих в ходе их взаимодействия, позволил дета лизировать природу молекулярных процессов, происходящих на стадиях связывания субстрата, узнавания поврежденного основания и его удаления из ДНК

Переведенное название	Термодинамические параметры взаимодействия эндонуклеазы VIII с поврежденной ДНК
Язык оригинала	английский
Страницы (с-по)	29-37
Число страниц	9
Журнал	Acta Naturae
Том	11
Номер выпуска	1
DOI	https://doi.org/10.32607/20758251-2019-11-1-29-37
Состояние	Опубликовано - 1 янв 2019

ГРНТИ

34 БИОЛОГИЯ

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

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title = "Thermodynamics of the DNA repair process by endonuclease VIII",

abstract = "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.",

keywords = "DNA glycosylase, Kinetic mechanism, Pre-steady-state kinetics, Thermodynamics, pre-steady-state kinetics, thermodynamics, LESION RECOGNITION, BINDING, kinetic mechanism",

author = "Kladova, {O. A.} and Kuznetsov, {N. A.} and Fedorova, {O. S.}",

year = "2019",

month = jan,

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doi = "10.32607/20758251-2019-11-1-29-37",

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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

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