The research program described in this proposal relies largely on organic chemistry to improve our understanding of how nucleic acids are oxidatively damaged, a fundamentally important biomedical research topic. Nucleic acid oxidation plays important roles in human disease and is an important tool in biotechnology. It is involved in the etiology of cancer, but is also the source of the cytotoxicity of g-radiolysis and many chemotherapeutics used to treat this complex disease. DNA damage also plays a role in aging and a variety of other ailments, including cardiovascular and neurodegenerative diseases. In addition, RNA oxidation has been implicated in neurodegenerative diseases. Nucleic acid oxidation is also a valuable tool for detecting biopolymer structure, noncovalent interactions between molecules, and the kinetics of RNA folding. Our goal is to undertake fundamental research to develop a detailed understanding of how nucleic acids are oxidatively damaged, and to apply the knowledge gained in these investigations to the design of research tools and possible therapeutic agents. Our general approach utilizes organic synthesis to independently generate reactive intermediates that are involved in nucleic acid damage. This method simplifies studies on nucleic acid damage by controlling which reactive intermediates are produced and where they are generated. We will use this approach to build upon our own related research and be the first to study how DNA is damaged in nucleosomes (Aim 2). We will also address how one of the most important DNA lesions, OxodG, is produced (Aim 1). Building upon observations made during the previous funding period, we will explore the role of nucleobase radicals in RNA oxidation and determine whether this can be used to learn more about its structure in hydroxyl radical (OH7) cleavage experiments (Aim 3). Finally, Aim 4 builds upon our proof of principle experiments to develop a family of nucleotide analogues that are radiosensitizing agents and form interstrand cross-links in DNA selectively under hypoxic conditions. In summary, the project combines organic chemistry and biochemistry to increase our understanding of fundamentally important chemical processes that occur in living organisms.

Public Health Relevance

Nucleic acid damage pathways are important chemical processes that significantly impact human health. These chemical processes are associated with aging and a variety of diseases, such as cancer. They are also useful tools in biotechnology. Understanding nucleic acids are damaged enhances our molecular level understanding of the etiology of diseases, as well as the various treatments for which nucleic acids are the target, and provides the impetus for the design of therapeutic agents and biotechnology tools.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM054996-14
Application #
8387782
Study Section
Synthetic and Biological Chemistry A Study Section (SBCA)
Program Officer
Fabian, Miles
Project Start
1997-07-01
Project End
2015-11-30
Budget Start
2012-12-01
Budget End
2013-11-30
Support Year
14
Fiscal Year
2013
Total Cost
$319,368
Indirect Cost
$116,718
Name
Johns Hopkins University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21218
Hou, Dianjie; Greenberg, Marc M (2014) DNA interstrand cross-linking upon irradiation of aryl halide C-nucleotides. J Org Chem 79:1877-84
San Pedro, Joanna Maria N; Greenberg, Marc M (2014) 5,6-Dihydropyrimidine peroxyl radical reactivity in DNA. J Am Chem Soc 136:3928-36
Zhou, Chuanzheng; Greenberg, Marc M (2014) DNA damage by histone radicals in nucleosome core particles. J Am Chem Soc 136:6562-5
Sloane, Jack L; Greenberg, Marc M (2014) Interstrand cross-link and bioconjugate formation in RNA from a modified nucleotide. J Org Chem 79:9792-8
Taverna Porro, Marisa L; Greenberg, Marc M (2013) DNA double strand cleavage via interstrand hydrogen atom abstraction. J Am Chem Soc 135:16368-71
San Pedro, Joanna Maria N; Greenberg, Marc M (2013) Photochemical control of DNA structure through radical disproportionation. Chembiochem 14:1590-6
Bar-Shir, Amnon; Liu, Guanshu; Liang, Yajie et al. (2013) Transforming thymidine into a magnetic resonance imaging probe for monitoring gene expression. J Am Chem Soc 135:1617-24
Weng, Liwei; Horvat, Sonia M; Schiesser, Carl H et al. (2013) Deconvoluting the reactivity of two intermediates formed from modified pyrimidines. Org Lett 15:3618-21
Bar-Shir, Amnon; Liu, Guanshu; Greenberg, Marc M et al. (2013) Synthesis of a probe for monitoring HSV1-tk reporter gene expression using chemical exchange saturation transfer MRI. Nat Protoc 8:2380-91
Cadet, Jean; Loft, Steffen; Olinski, Ryszard et al. (2012) Biologically relevant oxidants and terminology, classification and nomenclature of oxidatively generated damage to nucleobases and 2-deoxyribose in nucleic acids. Free Radic Res 46:367-81

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