Description
- Abstract:
- Repair of damaged DNA is indispensable for not only cellular, but also organismal survival. Nucleobase lesions, which arise from endogenous or exogenous sources of damage, are repaired through the base excision repair (BER) pathway. Packaging of nuclear DNA into chromatin presents an obstacle for the recognition of the damage by glycosylases and completion of the pathway. The most basic unit of DNA packaging is the nucleosome core particle (NCP), which consists of 145-147 base pairs of DNA wrapped around a core of eight histone proteins (2 copies each of H2A, H2B, H3, and H4) with a central dyad axis of pseudosymmetry. Comparison of activity of the three members of the uracil DNA glycosylase (UDG) superfamily in the excision of uracil (U) from an out-facing lesion in the dyad region of an NCP substrate reveals that the high levels of activity that are observed for UDG are not universal to the two other members of this superfamily, thymine DNA glycosylase (TDG) and single-strand selective monofunctional uracil DNA glycosylase (SMUG1). As such, the potential modulation of TDG activity through mimicking acetylation of its N-terminus was investigated. While the effects of acetylation analogues are subtle on short oligonucleotides, they are amplified on the NCP, with three analogues approaching full excision of U. While investigations of glycosylase activity on single sites within the NCP yield important information, these results cannot be generalized necessarily to all sites, leading to an examination of the activity of the glycosylase human oxoguanine glycosylase 1 (OGG1) in excision of 8-oxoG throughout the NCP. This study uses a population of substrates that contain 8-oxoG substitutions for G throughout the sequence. The development of this technique led to investigations into the repair of U and eA throughout the NCP. Computational techniques comparing the repair of these three lesions reveal structural elements of the NCP determined by other methods. With these studies, we strive to understand the mechanisms governing and influencing repair of nucleobase lesions. A more thorough understanding of these mechanisms will provide insight into the interplay of cellular metabolism, DNA repair, and mutation in both pathological and physiological contexts.
- Notes:
- Thesis (Ph. D.)--Brown University, 2022
Citation
Tarantino, Mary Elizabeth,
"TDG, NCP, and other TLAs (Three Letter Abbreviations) of DNA BER: Initiation of DNA Base Excision Repair in Nucleosome Core Particles"
(2022).
Molecular Biology, Cell Biology, and Biochemistry Theses and Dissertations.
Brown Digital Repository. Brown University Library.
https://repository.library.brown.edu/studio/item/bdr:3bqyss2u/
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Molecular Biology, Cell Biology, and Biochemistry Theses and Dissertations
Theses and Dissertations for the Molecular Biology, Cell Biology, and Biochemistry department....