Synthesis and properties of modified nucleic acids and analogues

This thesis focused on the development of nucleic acids analogs that have the potential to serve as biomolecular tools or are capable of artificial regulation of gene expression. More specifically, the research centered on nucleobase modified peptide nucleic acid (PNA) and DNA. The goal of this thesis was to: (i) develop synthetic routes to modified PNA in order to produce oligomers with new and improved physical and biophysical properties; (ii) improve the synthesis methods of PNA and discover new methods for PNA synthesis; (iii) design and synthesize fluorescent PNA and DNA nucleobases capable of increased hydrogen bonding interactions.;Additionally, a convertible nucleobase based on orotic acid was developed that was modified by a post-synthetic reaction. The convertible nucleobase allowed for the rapid synthesis of a series of modified oligomers with various substituents. The C5-substituted convertible nucleobase was also investigated and found to be stabilizing and endowed PNA with solubilising and cationic groups.;A new phenylpyrrolocytosine derivative, boPhpC, has been designed to selectively interact with guanine and has been evaluated in peptide nucleic acid where it imparts increased selective binding affinity for complementary oligonucleotides. The modified nucleobase also possesses an exceptionally high fluorescence quantum yield that is responsive to hybridization. The synthesis of second generation phenylpyrrolocytosine derivatives has been accomplished in order to increase binding affinity.;Finally a pyrrolocytosine substituted with indole-3-acetamide was synthesized. This compound has a very high fluorescent quantum yield in organic solvents but its fluorescence decreases in an aqueous environment.;Towards these goals, a simple and practical synthesis of the benzyl, allyl, and 4-nitrobenzyl esters of N-[2-(Fmoc)aminoethyl]glycine is described starting from the known N-(2-aminoethyl)glycine. These esters were used in the synthesis of peptide nucleic acid monomers possessing bis-N-Boc-protected nucleobase moieties on the exocyclic amino groups of ethyl cytosin-1-ylacetate, ethyl adenin-9-ylacetate and ethyl (O6-benzylguanin-9-yl)acetate. The Fmoc/bis- N-Boc-protected monomers were successfully used in the Fmoc-mediated solid-phase peptide synthesis of mixed sequence 10-mer PNA oligomers and are shown to be a viable alternative to the currently used Fmoc/Bhoc-protected peptide nucleic acid monomers. The synthesis of a Boc protected pseudoisocytosine PNA monomer and its subsequent incorporation into a PNA oligomer by Fmoc-based chemistry was also achieved.;Keywords. peptide nucleic acid, PNA, convertible nucleobases, phenylpyrrolocytosine, fluorescence quantum yield, hybridization, binding affinity, indole, nucleic acid.