USING THE CHEMISTRY OF IRON(II) TO STUDY DNA STRUCTURE

Boston University, Boston MA

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Abstract

As a convenient source of the hydroxyl radical ( OH), the EDTA complex of iron(II) has found wide use in chemical probe experiments of nucleic acid structure. The hydroxyl radical is also produced by ionizing radiation, and as such is the proximal agent in radiation-induced DNA damage. The long-term goal of this project is to understand in detail the chemistry of the hydroxyl radical with DNA and RNA. This information will be put to use in elucidating DNA and RNA structure in solution, as well as in attaining a deeper understanding of radiation damage to DNA and its repair. The Specific Aims of the present application are: (1) to use deuterium kinetic isotope effect experiments to determine, at an atomic level of detail, which deoxyribose hydrogens of DNA react with the hydroxyl radical, and how DNA structure affects this reactivity. Similar new information on hydroxyl radical reactivity using deuterium isotope effect experiments will also be obtained for RNA. (2) to study the structure and dynamics of DNA having a single- stranded gap in its backbone. The single-nucleoside strand gap is the lesion produced by ionizing radiation, so deeper knowledge of its structure and dynamics will help in understanding how DNA damage-repair proteins recognize such lesions in the genome. (3) the hydroxyl radical will be used as a chemical probe of the structure of curved adenine- tract DNA which has been substituted with chemically-modified nucleic acid bases. The high resolution and structural sensitivity of the hydroxyl radical will be used to determine structural details of these DNA molecules in solution.