Proteins that recognize and repair structural abnormalities in DNA are essential for preserving the integrity of genetic information. Dysfunction of systems that repair and control the cellular response to DNA damage contribute to a significant proportion of all cancers. On the other hand, fortification of DNA repair systems can bring about increased resistance to the cytotoxic and mutagenic effects of DNA damaging agents: up- regulation of DNA repair systems presents a serious problem in cancer chemotherapy, because it allows transformed cells to bypass the cytotoxic effects of therapeutic DNA-alkylating agents. These factors have all contributed to an intense impetus to obtain a more complete understanding of the workings of DNA repair systems. Although the function of many DNA repair proteins has been described at a biochemical level, a real gap in our understanding exists with respect to the structural basis for these complex functions. The fundamental issue of how repair proteins distinguish aberrant bases in DNA from their normal counterparts, which are often closely related in structure, remains poorly understood. Notwithstanding significant advances in defining the overall mechanism of some DNA repair proteins, including the identification of catalytic residues, the integration of these disparate facts into a robust description of enzymatic function is generally lacking. In no small part, the lack of structural information on DNA repair stems from the very nature of enzymatic catalysis itself: enzymes typically bind their substrates only for the fleeting instant during which the chemistry transpires, thus offering little opportunity to glimpse the intermediates that lie along the reaction pathway. To address this problem, we have taken a synthetic and mechanism-based approach toward dissecting substrate recognition from catalysis by DNA repair proteins. The immediate goal of this program is to obtain stable complexes of DNA repair proteins bound to substrate-like molecules, and to solve the structures of these molecules at high resolution. Ultimately, we aim to understand in detail the function of DNA repair proteins. The present study will focus on a prominent class of repair proteins, DNA glycosylases, which catalyze the hydrolytic excision of damaged bases from DNA. Two distinct mechanistic avenues will be explored toward selective ablation of catalysis while leaving substrate recognition intact: one involves destabilization of the transition state for glycosidic bond hydrolysis; the other involves mimicry of the transition state. Although the objectives of this study are firmly rooted in basic science, the molecules to be generated in this study have potential practical value: inhibition of DNA repair proteins may substantially increase the potency of chemotherapeutic drugs or radiation therapy , perhaps allowing lower dosages or abbreviated regimens to be used.
