We are studying the structural organization of DNA repair complexes that excise DNA damage and the functional consequences of disrupting these protein-protein interactions by mutation and small molecule inhibitors. Alternative pathways of repair are available for many types of DNA damage, and posttranslational modifications generated in response to DNA damage control the differential assembly of repair complexes, providing a mechanism for regulating pathway choice. Cancer-associated defects in DNA maintenance activities can be exploited therapeutically by targeting the remaining repair activities with mechanism-based inhibitors. Our work focuses on the mechanisms of repairing DNA single strand breaks generated by the base excision and nucleotide excision repair pathways. We are studying the physical assembly of DNA damage excision complexes in vitro and in cultured cells, and the mechanism of coupling DNA cleavage to end processing and ligation. Small angle x-ray scattering of purified DNA repair complexes reveals dynamic conformational states that we propose are important for handoffs of DNA repair intermediates to successive enzymes in a pathway. High resolution crystal structures and small molecule screening experiments are being used to predict and identify inhibitors of repair protein interactions, which are candidates for anti-tumor therapies and serve as reversible chemical probes of cellular physiology during DNA damage responses. This integrated approach takes advantage of the broad expertise of investigators in Projects 1, 2, and 6 for assays and biological materials, as well as the unique capabilities of the Expression and Molecular Biology Core and the Structural Cell Biology Core of the SBDR Program to produce proteins and structurally evaluate repair complexes.

Public Health Relevance

The Achilles'heel of all cancer cells is their defect in DNA repair and cell cycle checkpoints that can kill tumor cells by causing them to enter cell division before repair is complete. Thus, many cancers are treated by radiation and chemotherapies to overload repair in tumor cells but not in normal cells, which are better protected by redundant repair pathways and functioning cell cycle checkpoints. SBDR will comprehensively characterize DNA repair circuits to reveal tumor vulnerabilities that are key to short-circuiting DNA repair and specifically killing cancer cells while not harming better-protected normal cells.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Program Projects (P01)
Project #
2P01CA092584-11
Application #
8153344
Study Section
Special Emphasis Panel (ZCA1-RPRB-0 (M1))
Program Officer
Pelroy, Richard
Project Start
2001-09-27
Project End
2016-08-31
Budget Start
2011-09-14
Budget End
2012-08-31
Support Year
11
Fiscal Year
2011
Total Cost
$2,981,000
Indirect Cost
Name
Lawrence Berkeley National Laboratory
Department
Biology
Type
Organized Research Units
DUNS #
078576738
City
Berkeley
State
CA
Country
United States
Zip Code
94720
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Dungrawala, Huzefa; Bhat, Kamakoti P; Le Meur, Rémy et al. (2017) RADX Promotes Genome Stability and Modulates Chemosensitivity by Regulating RAD51 at Replication Forks. Mol Cell 67:374-386.e5
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Sugitani, Norie; Voehler, Markus W; Roh, Michelle S et al. (2017) Analysis of DNA binding by human factor xeroderma pigmentosum complementation group A (XPA) provides insight into its interactions with nucleotide excision repair substrates. J Biol Chem 292:16847-16857
Aceytuno, R Daniel; Piett, Cortt G; Havali-Shahriari, Zahra et al. (2017) Structural and functional characterization of the PNKP-XRCC4-LigIV DNA repair complex. Nucleic Acids Res 45:6238-6251
Ma, Chu Jian; Kwon, Youngho; Sung, Patrick et al. (2017) Human RAD52 interactions with replication protein A and the RAD51 presynaptic complex. J Biol Chem 292:11702-11713
Tsutakawa, Susan E; Thompson, Mark J; Arvai, Andrew S et al. (2017) Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Nat Commun 8:15855
Shi, Yuqian; Hellinga, Homme W; Beese, Lorena S (2017) Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I. Proc Natl Acad Sci U S A 114:6010-6015
Woodrick, Jordan; Gupta, Suhani; Camacho, Sharon et al. (2017) A new sub-pathway of long-patch base excision repair involving 5' gap formation. EMBO J 36:1605-1622

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