Gamma-PNA Chemical Building Blocks: Methodoly Development, Synthesis and Application

The research described in this thesis focuses on the synthesis of chemical building blocks of an important class of nucleic acid mimic, called gamma peptide nucleic acid (γPNA). γPNA offers an attractive nucleic acid platform for
biological and biotechnological applications, as molecular tools for basic research as well as possible therapeutic and diagnostic reagents. These studies were undertaken in attempts to determine the optimal route for preparing γPNA
monomers on large-scale and with high optical purity, suitable for automated solid-phase oligo synthesis.
Chapter I provide a historical perspective on the field. In Chapter II we compare the optical purity of γPNA monomers prepared by various synthetic routes. Out of the various methods examined, the Mitsunobu coupling scheme
provides the highest optically purity. We used 19F-NMR spectroscopic tool to determine the optical purity of the monomers. A detailed, systematic study was
performed to determine the source and the extent of epimerization in each of the synthetic routes. The effects of epimerized monomers on the helical conformation as well as the binding affinity of γPNA oligomers were also investigated. In Chapter III we describe the development of a new synthetic scheme for preparing (R)-Fmoc MPγPNA monomers. In order to expedite the exploration of
γPNA as molecular tools and reagents for basic research in biology and medicine, an automated, parallel solid-phase synthesis of γPNA oligomers is necessary. However, the current Boc solid-phase synthesis (SPS) strategy is not suitable for automation. In this work we report the first synthetic methodology for synthesizing optically-pure (R)-Fmoc-MPγPNA monomers based on the Mitsunobu coupling strategy. In Chapter IV we describe a new synthetic route for preparing both (R)-and (S)-Fmoc MPγPNA monomers starting from a commercially available and
relatively cheap L-Serine. Even though the Mitsunobu route to synthesizing (R)-Fmoc-MPγPNA monomers is a rather simple, it is not suitable for large scale synthesis. Recognition of this obstacle, we devised a simple but yet robust procedure for synthesizing optically-pure (R)- and (S)-Fmoc-MPyPNA chemical building blocks. The synthetic flexibility and versatility of this methodology is also amendable for preparing (S)-Fmoc-MPyPNA monomers, using the same starting material. Owing to its recognition orthogonality with the right-handed conformer, the left-handed γPNA offers an attractive and unique platform for
organizing molecular self-assembly, especially for in vivo applications where enzymatic degradation and inadvertent binding hybridization of probes to the host‘s genetic materials (i.e. DNA and RNA) are of concern. The methodology development in the synthesis of γPNA monomers described in this thesis could have a significant impact on the overall research of γPNA. The findings on the optical purity of the monomers and their effects on
binding affinity have important implication not only on the synthesis of γPNA building blocks but also on the development of other chiral reagents. The work described herein on the development of a new synthetic route for preparing (R)- and (S)-Fmoc MPγPNA monomers will pave the road for future development and exploration of γPNA in biology and medicine.