Catalytic RNAs are responsible for essential physiological functions in organisms. For example, leading models for the origin of life suggest that life began with an RNA-World, where RNA played structural, genetic, and catalytic roles. Perturbation of pKa values can favor a particular ionization state of a nucleobase at biological pH and control the function of the nucleic acid. While Watson-Crick base pairing typically shifts the pKa of nucleobases away from neutrality, certain bases may have pKa’s that are shifted towards physiological pH. This thesis details various computational and experimental efforts to identify and characterize the presence of such ionized base pairs. A database of known A+•C wobble pairings was compiled and analyzed. Small DNA oligonucleotides were synthesized to probe the pKa shift of guanine in the presence of a cationic base utilizing UV-Visible pH dependent titrations. Raman spectroscopy was employed to determine differences in signal intensity from different electrostatic states of guanine. Surface Enhanced Raman Spectroscopy (SERS) was investigated as an alternative to in-solution Raman analysis and Raman crystallography. This thesis lays groundwork for future experiments in elucidating functional and structural roles of ionized bases in nucleic acids.
