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.
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.
|Paul, Rakesh; Greenberg, Marc M (2016) Mechanistic Studies on RNA Strand Scission from a C2'-Radical. J Org Chem 81:9199-9205|
|Cheng, Bokun; Zhou, Qingxuan; Weng, Liwei et al. (2016) Identification of proximal sites for unwound DNA substrate in E. coli topoisomerase I with oxidative crosslinking. FEBS Lett :|
|Greenberg, Marc M (2016) Pyrimidine Nucleobase Radical Reactivity in DNA and RNA. Radiat Phys Chem Oxf Engl 1993 128:82-91|
|Pidugu, Lakshmi S; Flowers, Joshua W; Coey, Christopher T et al. (2016) Structural Basis for Excision of 5-Formylcytosine by Thymine DNA Glycosylase. Biochemistry 55:6205-6208|
|Taverna Porro, Marisa L; Greenberg, Marc M (2015) Double-strand breaks from a radical commonly produced by DNA-damaging agents. Chem Res Toxicol 28:810-6|
|Panja, Subrata; Paul, Rakesh; Greenberg, Marc M et al. (2015) Light-Triggered RNA Annealing by an RNA Chaperone. Angew Chem Int Ed Engl 54:7281-4|
|Rudra, Arnab; Hou, Dianjie; Zhang, Yonggang et al. (2015) Bromopyridone Nucleotide Analogues, Anoxic Selective Radiosensitizing Agents That Are Incorporated in DNA by Polymerases. J Org Chem 80:10675-85|
|Weng, Liwei; Zhou, Chuanzheng; Greenberg, Marc M (2015) Probing interactions between lysine residues in histone tails and nucleosomal DNA via product and kinetic analysis. ACS Chem Biol 10:622-30|
|Paul, Rakesh; Greenberg, Marc M (2015) Rapid RNA strand scission following C2'-hydrogen atom abstraction. J Am Chem Soc 137:596-9|
|Paul, Rakesh; Greenberg, Marc M (2014) Independent generation and reactivity of uridin-2'-yl radical. J Org Chem 79:10303-10|
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