Fundamentals of Excess Electron Transport in Biologically Relevant Systems

Title of Document FUNDAMENTALS OF EXCESS ELECTRON TRANSPORT IN BIOLOGICALLY RELEVANT SYSTEMS Amethist Shajary Finch Doctor of Philosophy, 2008 Directed By: Professor Steven E. Rokita Department of Chemistry and Biochemistry Thymine dimers are premutagenic lesions that form via ultraviolet irradiation of DNA. While the distribution of thymine dimers is non-random, it is also not yet predictable. Thymine dimer accumulation is likely to be controlled by both its formation and reversion. Formation of thymine dimers occurs via direct excitation of thymine residues, while the reversion is governed by both direct and indirect photochemical processes. The Rokita lab previously determined that charge transport from surrounding DNA sequences affect the accumulation of UV-induced thymine dimers in DNA. This dissertation focuses on the variable efficiency of both direct and indirect pathways affecting thymine dimer distribution. Thymine dimer accumulation is dependent upon sequence and conformation. The conformational dependence was used to study the kinetic versus thermodynamic control of thymine dimer accumulation in natural systems. In this system, no difference was observed in the accumulation of thymine dimer in free vs. constrained DNA. Therefore, the anticipated studies on the reversibility of thymine dimer formation still await a suitable system that does respond to DNA conformation. A model system was also used to concurrently investigate the effect of local sequence on thymine dimer accumulation. Excess electron transport in DNA is also important in modulating the overall accumulation of thymine dimers. The parameters affecting excess electron transport were investigated with a model system based on electron transfer from an aromatic amine to bromouridine. Electrons injected into duplex DNA by the aromatic amine migrate through the stacked nucleotides to the bromouridine acceptor covalently attached to the DNA. Modifications of the intervening nucleotide sequence previously allowed for the study of distance dependence, sequence dependence, and directionality of excess electron transfer reactions. This system was used here to determine if a polaron type mechanism was operative in excess electron transport in analogy to such observations in hole transfer. At least for the systems examined in this work, a polaron type mechanism does not appear operative for excess electron transfer. In order to determine if excess electron transport efficiency is dependent on the reduction potential of the aromatic amine, the redox potentials of a variety aromatic amine were determined. These aromatic amines differed by the addition of electron donating groups and π conjugation. Preliminary studies in this final model system with an aromatic amine of strong reduction potential showed no difference in excess electron transport when compared to the aromatic amine with a weaker reduction potential. FUNDAMENTALS OF EXCESS ELECTRON TRANSPORT IN BIOLOGICALLY RELEVANT SYSTEMS By Amethist Shajary Finch Dissertation submitted to the Faculty of the Graduate School of the University of Maryland, College Park, in partial fulfillment of the requirements for the degree of Doctor of Philosophy 2008