Effects of base sequence on the removal of DNA damage by nucleotide excision repair mechanisms in vitro

Polycyclic Aromatic Hydrocarbons (PAHs) constitute a class of well known environmental pollutants. Benzo[a]pyrene is a typical and extensively studied representative of PAHs. Once it enters the human body, the metabolically generated reactive intermediates can bind to native DNA thus forming bulky adducts such as BPDE-dG or BPDE-dA adducts. If not removed by cellular defense mechanisms, these adducts can cause mutations and cancer.;One of the critical lines of defense of the human body to these environmental carcinogens is DNA repair, specifically by the nucleotide excision repair (NER) mechanism that removes bulky DNA adducts. The structural features of different DNA lesions that elicit the response of the NER damage recognition system has been a subject of interest. In this work, I have studied the removal of (+)-trans-anti-B[a]PDE-dG lesions embedded in different sequence contexts by bacterial and mammalian nucleotide excision repair mechanisms in vitro. The aim of my projects was to (1) study the effects of bases flanking the modified bases that contribute to differences in the recognition and repair of certain families of lesions, and (2) to provide insights into the repair mechanisms that govern efficient or inefficient repair.;I employed both the bacterial NER system and human Hela cell-free extracts to investigate the effects of neighboring bases on the removal of (+)- trans-anti-B[a]PDE-N2-dG lesions in GG mutation hotspots and TG*T and CG*C sequence contexts. I demonstrated that both the prokaryotic and eukaryotic NER machineries recognize differences in the distortions of the structural properties of DNA duplexes that are influenced by sequence context and by the stereochemical properties of the lesions. The weakened Watson-Crick hydrogen bonding 5'-flanking the lesion provides the strongest signal, followed by a flexible kink/bend. The hypothesis that the base in the complementary strand opposite to the modified base is required for NER has also been investigated. Previous work indicated that the full complementary strand is a requirement for successful NER. However, our results do not support the notion that the deletion of the partner cytosine opposite the adduct G* abolishes NER activity, and a revised mechanism of the recognition of DNA lesions is proposed here.