The long term goal of this research is to understand how nucleic acids are oxidatively damaged, and to use this knowledge to design new therapeutic candidates and research tools. Nucleic acid oxidation is important in the etiology and treatment of disease. For instance, ionizing radiation causes cancer and destroys tumor cells by damaging DNA. Nucleic acid oxidation is also an important biotechnology tool. For instance, hydroxyl radical cleavage is useful for determining RNA structure and folding dynamics, as well as for determining nucleic acid binding interactions;These studies will be accomplished using synthetic and physical organic chemistry, biochemistry, as well as molecular and cellular biology. We pursue a complementary two-fold experimental approach. We study reaction mechanism by designing molecules that enable us to independently generate reactive intermediates at defined sites in oligonucleotides. In addition, when our mechanistic studies provide the appropriate impetus, we synthesize molecules that capitalize upon these discoveries. The proposed research encompasses the following goals: 1. Design and study in vitro and in cells of mechanism-based radiosensitizing agents that produce DNA interstrand cross-links. 2. Determine the repair of a novel family of interstrand cross-links in vitro and in E. coli. 3. Examine the reactivity of the radical resulting from C5'-hydrogen atom abstraction in DNA. This radical is produced by a variety of antitumor agents and is a major source of cleavage resulting from reaction with hydroxyl radical. 4. Explore the ability of nucleobase radical adducts in RNA to produce direct strand breaks. 5. Design molecules that will exploit electron transfer in DNA as a means for producing interstrand cross- links. Relevance to public health: Oxidative nucleic acid damage plays an important role in aging, as well as the etiology and treatment of genetic diseases, such as cancer. Nucleic acid oxidation is also an invaluable research tool in biotechnology (e.g. probing nucleic acid structure and folding dynamics), which is in turn used to study human disease. Hence, this fundamental research is valuable to understanding the etiology and treatment of diseases such as cancer. Furthermore, the application of the knowledge gleaned from this research provides the starting point for potentially new therapeutics and research tools.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Special Emphasis Panel (ZRG1-BCMB-B (02))
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Fabian, Miles
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Johns Hopkins University
Schools of Arts and Sciences
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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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