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Protein binding has a large effect on radical mediated DNA damage.

ABSTRACT: Oxidative DNA damage is important in aging and a variety of diseases. Significant advances have been made in our understanding of the chemistry of radical mediated DNA damage. These studies have been carried out on DNA in the absence of proteins. However, in cells DNA is typically bound by proteins such as in chromatin and transiently by proteins that regulate biochemical processes. How and whether protein binding affects DNA radical reactivity is not well understood. The effect of the DNA binding protein Hbb on the reactivity of the 5-(2'-deoxyuridinyl)methyl radical (1) and 5-(2'-deoxycytidinyl)methyl radical (2) was studied. Hbb bends DNA and disrupts base stacking at the sites of kinking. The reactivity of 1 and 2 are significantly affected when they are generated at the kinking site in the presence of Hbb. The increased conformational mobility of the radicals results in significantly higher yields of DNA interstrand cross-links. These studies provide the first specific data on how protein binding affects the reactivity of a DNA radical and bring us closer to understanding oxidative DNA damage in cells.

SUBMITTER: Peng X

PROVIDER: S-EPMC2829750 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature

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Protein binding has a large effect on radical mediated DNA damage.

Peng Xiaohua X Pigli Ying Z YZ Rice Phoebe A PA Greenberg Marc M MM

Journal of the American Chemical Society 20080909 39

Oxidative DNA damage is important in aging and a variety of diseases. Significant advances have been made in our understanding of the chemistry of radical mediated DNA damage. These studies have been carried out on DNA in the absence of proteins. However, in cells DNA is typically bound by proteins such as in chromatin and transiently by proteins that regulate biochemical processes. How and whether protein binding affects DNA radical reactivity is not well understood. The effect of the DNA bindi ...[more]

PMID: 18778053

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Project description:Breakage of one strand of DNA is the most common form of DNA damage. Most damaged DNA termini require end-processing in preparation for ligation. The importance of this step is highlighted by the association of defects in the 3'-end processing enzyme tyrosyl DNA phosphodiesterase 1 (TDP1) and neurodegeneration and by the cytotoxic induction of protein-linked DNA breaks (PDBs) and oxidized nucleic acid intermediates during chemotherapy and radiotherapy. Although much is known about the repair of PDBs in the nucleus, little is known about this process in the mitochondria. We reveal that TDP1 resolves mitochondrial PDBs (mtPDBs), thereby promoting mitochondrial gene transcription. Overexpression of a toxic form of mitochondrial topoisomerase I (TOP1mt*), which generates excessive mtPDBs, results in a TDP1-dependent compensatory up-regulation of mitochondrial gene transcription. In the absence of TDP1, the imbalance in transcription of mitochondrial- and nuclear-encoded electron transport chain (ETC) subunits results in misassembly of ETC complex III. Bioenergetics profiling further reveals that TDP1 promotes oxidative phosphorylation under both basal and high energy demands. It is known that mitochondrial dysfunction results in free radical leakage and nuclear DNA damage; however, the detection of intermediates of radical damage to DNA is yet to be shown. Consequently, we report an increased accumulation of carbon-centered radicals in cells lacking TDP1, using electron spin resonance spectroscopy. Overexpression of the antioxidant enzyme superoxide dismutase 1 (SOD1) reduces carbon-centered adducts and protects TDP1-deficient cells from oxidative stress. Conversely, overexpression of the amyotrophic lateral sclerosis-associated mutant SOD1G93A leads to marked sensitivity. Whereas Tdp1 knockout mice develop normally, overexpression of SOD1G93A suggests early embryonic lethality. Together, our data show that TDP1 resolves mtPDBs, thereby regulating mitochondrial gene transcription and oxygen consumption by oxidative phosphorylation, thus conferring cellular protection against reactive oxygen species-induced damage.

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Protein binding has a large effect on radical mediated DNA damage.

Publications

Protein binding has a large effect on radical mediated DNA damage.

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