Synthesis, investigation and application of modified nucleic acids

Modified nucleic acids were synthesized both as a target and as a tool. Modified RNA was synthesized containing the modified nucleotide pseudouridine. In order to realize this oligonucleotide, the synthetic organic chemistry of the nucleoside pseudouridine was explored. Methods were developed to allow the synthesis of pseudouridine in a minimal number of steps from commercially available starting materials. Next, the methodology of pseudouridine phosphoramidite synthesis was explored including methods to incorporate this nucleoside into oligonucleotides that allow deprotection under neutral conditions. Finally, a series of pseudouridine containing oligonucleotides were synthesized by using the chemistry of Dr. Scaringe. These oligonucleotides were studied to determine the effect of pseudouridylation on the overall structure.;In the second part of the investigation, modified nucleic acids were applied to the development of a nucleic-acid-based therapeutic. Modified DNAs were synthesized containing backbone and 3' modifications in an attempt to improve their performance as a therapeutic. These oligonucleotides were evaluated in vitro and in cell culture to assess the potential to down-regulate Bcl-2 in a follicular small cleaved cell lymphoma cell line and stimulate apoptosis.