Nucleotide and Base Excision Repair

University Of Calif-Lawrenc Berkeley Lab, Berkeley CA

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Abstract

The Project (Nucleotide Excision Repair and Base Excision Repair) focuses on[unreadable] understanding the interactions of key proteins with DNA substrates and partner proteins critical for functional[unreadable] DNA excision repair complexes. Our goal is to leverage structural and biochemical studies of the repair[unreadable] endonuclease ERCC1-XPF and of DNA ligase to illuminate the coordination of the multi-step reaction[unreadable] pathways that comprise Nucleotide Excision Repair (NER) and the completion of B_ase Excision Repair[unreadable] (NER). Defects in DNA excision repair proteins and pathways result in increased rates of mutation,[unreadable] chromosomal breakage, and an increased incidence of cancers. Distortions of the helical structure of DNA[unreadable] are specifically recognized by repair enzymes and can be read out in a way that does not depend on the[unreadable] chemical identity of the damage. This generalized strategy enables one enzyme to initiate the repair of a[unreadable] variety of lesions in DNA. Moreover, interactions with other DNA binding and repair proteins provide[unreadable] additional biological specificity and contribute to the efficiency of repair. Although the enzymatic activities[unreadable] constituting the basic NER and BER pathways are known, it remains to be determined how these activities[unreadable] are coordinated into a multi-step reaction pathway by the physical interactions within enzyme-DNA[unreadable] complexes catalyzing the excision repair of DNA damage. Structural analyses of the relevant enzyme-DNA[unreadable] complexes will reveal distinct conformational states of the enzymes and their DNA substrates corresponding[unreadable] to different steps of the repair reaction. Low-resolution structures and conformations derived from x-ray[unreadable] scattering in solution will complement high-resolution images of the repair complexes that can be[unreadable] crystallized. In this way, the dynamic assembly and disassembly of multi-protein complexes catalyzing DNA[unreadable] repair will be characterized. We propose to test and develop these hypotheses by investigating specific[unreadable] excision repair components as follows: 1) Catalytic Substrate specificity of XPF-ERCC1, and related DNA[unreadable] structure-specific nucleases; 2) Damage senses by XPA that recruits XPFERCC1 to NER complexes; 3) Catalytic selectivity of DNA ligases; Nick-sensing and DNA repair; 4) Interactions of DNA Ligase I with DNA sliding clamps; and 5) Interactions of ligase I with the clamp loaders.