UC San Diego

The diversity and complexity of life on this planet is based on a narrow selection of organic molecules. One approach towards understanding the emergence and evolution of life is to address questions concerning the particular selection of these biochemical building blocks. The five nucleobases of DNA and RNA, also known as the genetic alphabet, are among the archetypal examples of nature's selection. The origin of these canonical bases is the subject of this dissertation. The work begins with a detailed discussion and assessment of selection pressures that could have shaped the chemical and biological evolution of the alphabetic bases. This is followed by the introduction of a new hypothetical selection pressure that could have occurred after the transition from the RNA to the DNA world. The pressure is based on the differences in N-glycosidic bond stabilities between RNA and DNA and the consequences of their hydrolytic rupture. A systematic investigation on the comparative stability of N-glycosyl bonds (via hydrolytic deglycosylation experiments) in modified, alternative and damaged nucleosides was undertaken. Kinetics studies were performed under the same conditions to measure relative changes in N-glycosyl destabilization based on differences in ribo and deoxyribo -glycosidic bonds. Thermodynamic activation parameters were obtained to help explain the observed rate enhancements and relative rates of hydrolysis. A low to mild acidic pH based kinetics study was also undertaken to compare how the deoxynucleosides varied in their relative stabilities. Implications for the occurrence of modified bases in DNA, the exclusion of certain surrogate bases, and for the composition of the genetic alphabet are discussed