Nucleic acid oxidation encompasses myriad chemical processes, notably ionizing radiation and chronic inflammation, which are at the heart of a variety of diseases and aging. DNA oxidation is recognized as a contributing factor in an increasing number of diseases, including cancer, cardiovascular, and most recently triplet repeat diseases (e.g. Huntington's disease). RNA oxidation is also associated with neurodegenerative diseases. Nucleic acid damage is a double-edged sword because cancer is treated by ?-radiolysis and drugs that oxidatively damage DNA. Furthermore, nucleic acid oxidation is used to study nucleic acid structure, noncovalent binding, and RNA folding, and is an important tool in biotechnology. 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. 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 propose to use this approach to be the first to independently generate reactive intermediates in DNA that are produced by the direct effect of ionizing radiation and that are involved in electron transfer (Aims 1 & 2). We will explore the rol that protein radicals in nucleosomes play in DNA damage (Aim 3). We also propose to advance our understanding of a novel mechanism for DNA double-strand cleavage that we discovered during the previous funding period (Aim 4). This could lead to the development of molecules that produce double- strand breaks via a single oxidation event. Finally, Aim 5 builds upon our 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, and potentially improve human health.

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 how 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.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Synthetic and Biological Chemistry A Study Section (SBCA)
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Fabian, Miles
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Johns Hopkins University
Schools of Arts and Sciences
United States
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Zheng, Liwei; Greenberg, Marc M (2018) Traceless Tandem Lesion Formation in DNA from a Nitrogen-Centered Purine Radical. J Am Chem Soc 140:6400-6407
Sun, Huabing; Zheng, Liwei; Greenberg, Marc M (2018) Independent Generation of Reactive Intermediates Leads to an Alternative Mechanism for Strand Damage Induced by Hole Transfer in Poly(dA-T) Sequences. J Am Chem Soc 140:11308-11316
Sun, Huabing; Taverna Porro, Marisa L; Greenberg, Marc M (2017) Independent Generation and Reactivity of Thymidine Radical Cations. J Org Chem 82:11072-11083
Zheng, Liwei; Greenberg, Marc M (2017) DNA Damage Emanating From a Neutral Purine Radical Reveals the Sequence Dependent Convergence of the Direct and Indirect Effects of ?-Radiolysis. J Am Chem Soc 139:17751-17754
Zheng, Liwei; Lin, Lu; Qu, Ke et al. (2017) Independent Photochemical Generation and Reactivity of Nitrogen-Centered Purine Nucleoside Radicals from Hydrazines. Org Lett 19:6444-6447
Cheng, Bokun; Zhou, Qingxuan; Weng, Liwei et al. (2017) Identification of proximal sites for unwound DNA substrate in Escherichia coli topoisomerase I with oxidative crosslinking. FEBS Lett 591:28-38
Zheng, Liwei; Griesser, Markus; Pratt, Derek A et al. (2017) Aminyl Radical Generation via Tandem Norrish Type I Photocleavage, ?-Fragmentation: Independent Generation and Reactivity of the 2'-Deoxyadenosin- N6-yl Radical. J Org Chem 82:3571-3580
Greenberg, Marc M (2016) Reactivity of Nucleic Acid Radicals. Adv Phys Org Chem 50:119-202
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

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