Excited State Dynamics of Nucleobases, and Structure and Dynamics of Melanin

Abstract

Two of the most important classes of natural heterocycles are nitrogen containing nucleic acid bases (purines and pyrimidines), and indoles. Purines and pyrimidines are building blocks of our genetic information carrier deoxyribonucleic acid (DNA). Indole plays functionally important roles as structural units present in proteins and the biopigment melanin. This thesis presents structural and photodynamical studies on these two important macromolecules of life. DNA bases are highly photostable under ultraviolet radiation due to the ultrafast sub-picosecond (ps) lifetimes of electronic excited states associated with their absorption band centered at ~260 nm. With a combination of resonance Raman (RR) intensity analysis and quantum chemical computation, I have demonstrated that sub-100 femtosecond (fs) dynamics leads to distinct structural distortions in purines following photon absorption to two different singlet states, La (~260 nm) and Bb (~210 nm). These instantaneous distortions do not lie along photochemically active, lesion-forming coordinates. Melanins are an important class of biomacromolecules that are known to have versatile functionalities, e.g., acting as natural sunscreen to the entire animal kingdom, pattering and radical scavengers. They also have important technological applications. Unfortunately, the structure is not completely understood. I have obtained spectroscopic evidences that help in deriving an integrated kinetic model of enzymatic and non-enzymatic melanin formation. Using density functional theory (DFT), novel eumelanin fundamental building blocks that are inspired by experimentally detected small oligomers are proposed. Merits and demerits of these structural scaffolds in explaining several experimental observables of melanin are discussed vis-à-vis other reported models. Using a bottom-up approach and three-dimensional topographic imaging with atomic force microscopy (AFM), I have demonstrated that synthetic melanin has an organizational hierarchy that is similar to that present in natural melanin.