Mass spectrometry Studies on Radical Reactions of DNA

Purdue University West Lafayette, West Lafayette IN

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Abstract

[unreadable] DESCRIPTION (provided by applicant): The action of many non-hydrolytic DNA cleaving drugs is believed to be based on reactive phenyl radicals that abstract hydrogen atoms from deoxyribose in DNA. Various issues relating to this process, including the drug's binding site on DNA and the mechanism of radical formation, are being addressed by scientists to advance the rational design of better antitumor and antiviral drugs. However, the key part of the process, the reaction of the radical intermediate with DNA, remains unexplored. Although information on the factors that control this reaction is critically needed for drug design, nearly nothing is known about the radical intermediates formed from drugs because of severe experimental difficulties in studying such highly reactive species. Our goal is to learn how to control the reactivity and intrinsic selectivity of a radical warhead by structural changes. We have developed a novel experimental approach based on mass spectrometry to study biologically relevant radical reactions. The method involves attaching a charged group to a radical of interest for manipulation in an FT-ICR mass spectrometer wherein small neutral biomolecules are introduced by laser-induced acoustic desorption. This proposal presents a continuation for a four-year project that involved 1) purchase and set-up of the necessary instrumentation, 2) demonstration of the feasibility of the approach, 3) examination of known systems to show that the method yields data relevant to neutral radicals and solution conditions, and 4) collection of kinetic reactivity data that provided several novel structure/reactivity relationships that are likely to advance the design of better non-hydrolytic DNA cleavers. The most important areas of future work include (1) developing structure/reactivity relationships for more complex systems, (2) exploring the selectivity of different radicals toward various sites in small oligonucleotides, (3) examining the reactivity of the radicals toward peptides to model protein damage, and (4) based on the insights gained in the above studies, developing a general thermochemistry-based reactivity paradigm that provides general predictive power. This paradigm will be ultimately employed to design target-specific radical warheads that can be generated photolytically for site-specific tumor.