DNA repair enzymes detect damaged DNA bases in the dramatically different contexts of naked duplex DNA as well as nucleosomes and chromatin. These fascinating and essential molecular recognition processes require dynamic motions of the DNA base pairs to expose damaged bases to the enzyme, and also, facilitated diffusion of the enzyme along the DNA chain so that stretches of the DNA chain can be meticulously interrogated in a single bimolecular encounter event. A fundamental understanding of damage recognition in the contexts of naked DNA and nucleosomes requires a paradigm system that is especially amenable to study using a wide variety of biophysical tools. One such system is the uracil base excision repair pathway (UBER). This multienzyme pathway is initiated by the enzyme uracil DNA glycosylase (UNG), which efficiently locates and excises uracil bases from DNA. The biomedical relevance of UBER arises from the central role of this pathway in the adaptive immune response, in providing innate immunity against viruses, and in mediating the therapeutic effects of fluoropyrimidine anticancer drugs. In addition, aberrant UBER has been related to carcinogenesis. The characterization of the molecular nature of these interactions provides the basis for identifying new targets for biomedical intervention in the immune response, cancer therapy and viral pathogenesis. The focus of this proposal is to: (1) Elucidate the mechanism and molecular interactions that allow human UNG to execute intramolecular facilitated transfer between uracil sites in duplex DNA. Using NMR paramagnetic relaxation enhancement (PRE) methods, we will characterize transient and poorly populated binding modes of hUNG to nonspecific and specific DNA that are important for intramolecular site transfer. Based on unique structural insights, we will mutate specific residues on UNG, and make discrete perturbations of functional groups on the DNA, to uncover enzyme-DNA interactions important for intramolecular transfer. (2) Elucidate the role of nucleosomal DNA dynamics in uracil excision by hUNG. We will use newly conceived NMR and biophysical methods to explore the dynamic properties of DNA in mononucleosomes for the first time, and we will elucidate the mechanism by which UNG locates and repairs uracil sites imbedded in nucleosomal DNA. (3) Determine the mechanism and efficiency of intramolecular facilitated transfer by hUNG between uracil sites embedded in nucleosomes. The significance and mechanism of intramolecular site transfer in the context of mononucleosomes will be elucidated using novel biophysical and chemical approaches. In particular, we will discern whether the nucleosome surface provides a pathway for intramolecular transfer, whether the DNA scaffold is the primary conduit, or if site location occurs by diffusion from bulk solution.

Public Health Relevance

The biomedical relevance of uracil base excision repair (UBER) arises from the central role of this pathway in the adaptive immune response, in providing innate immunity against viruses, and in mediating the therapeutic effects of fluoropyrimidine anticancer drugs. In addition, aberrant UBER has been related to carcinogenesis. The characterization of the molecular interactions in this pathway provides the basis for identifying new targets for biomedical intervention in the immune response, cancer therapy and viral pathogenesis.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM056834-16
Application #
8136286
Study Section
Macromolecular Structure and Function E Study Section (MSFE)
Program Officer
Marino, Pamela
Project Start
1998-02-01
Project End
2014-08-31
Budget Start
2011-09-01
Budget End
2012-08-31
Support Year
16
Fiscal Year
2011
Total Cost
$376,675
Indirect Cost
Name
Johns Hopkins University
Department
Pharmacology
Type
Schools of Medicine
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21218
Rodriguez, Gaddiel; Esadze, Alexandre; Weiser, Brian P et al. (2017) Disordered N-Terminal Domain of Human Uracil DNA Glycosylase (hUNG2) Enhances DNA Translocation. ACS Chem Biol 12:2260-2263
Weiser, Brian P; Stivers, James T; Cole, Philip A (2017) Investigation of N-Terminal Phospho-Regulation of Uracil DNA Glycosylase Using Protein Semisynthesis. Biophys J 113:393-401
Esadze, Alexandre; Rodriguez, Gaddiel; Cravens, Shannen L et al. (2017) AP-Endonuclease 1 Accelerates Turnover of Human 8-Oxoguanine DNA Glycosylase by Preventing Retrograde Binding to the Abasic-Site Product. Biochemistry 56:1974-1986
Hansen, Erik C; Ransom, Monica; Hesselberth, Jay R et al. (2016) Diverse fates of uracilated HIV-1 DNA during infection of myeloid lineage cells. Elife 5:
Cravens, Shannen L; Stivers, James T (2016) Comparative Effects of Ions, Molecular Crowding, and Bulk DNA on the Damage Search Mechanisms of hOGG1 and hUNG. Biochemistry 55:5230-42
Seamon, Kyle J; Bumpus, Namandjé N; Stivers, James T (2016) Single-Stranded Nucleic Acids Bind to the Tetramer Interface of SAMHD1 and Prevent Formation of the Catalytic Homotetramer. Biochemistry 55:6087-6099
Cravens, Shannen L; Schonhoft, Joseph D; Rowland, Meng M et al. (2015) Molecular crowding enhances facilitated diffusion of two human DNA glycosylases. Nucleic Acids Res 43:4087-97
Seamon, Kyle J; Stivers, James T (2015) A High-Throughput Enzyme-Coupled Assay for SAMHD1 dNTPase. J Biomol Screen 20:801-9
Seamon, Kyle J; Sun, Zhiqiang; Shlyakhtenko, Luda S et al. (2015) SAMHD1 is a single-stranded nucleic acid binding protein with no active site-associated nuclease activity. Nucleic Acids Res 43:6486-99
Hansen, Erik C; Seamon, Kyle J; Cravens, Shannen L et al. (2014) GTP activator and dNTP substrates of HIV-1 restriction factor SAMHD1 generate a long-lived activated state. Proc Natl Acad Sci U S A 111:E1843-51

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