Twisted intercalating nucleic acids (TINA) in guanosine-rich oligonucleotides : a thesis submitted in the partial fulfilment of the requirements for the degree of Doctor of Philosophy in Chemistry, Massey University, Palmerston North, New Zealand.

Abstract

The main role in the structural diversity of DNA molecules belongs to guanosines due to their array of hydrogen bond donors and acceptors, large aromatic surface and ability to adopt syn or anti conformations. These properties lead to the formation of various DNA topologies such as triplexes or G-quadruplexes by guanosine-rich oligonucleotides. For a long time these secondary structures were mainly considered to be a fascinating phenomenon with little practical use; it was subsequently realised that these structures are likely to be formed under physiological conditions and therefore might be involved in many important biological processes, including genome recombination, telomere stability and regulation of gene expression. Thus, there is a growing interest in development and control of these non-traditional nucleic acid structures. Although the secondary structures of nucleic acids can be controlled to a certain extent by the careful design of oligonucleotide sequence this strategy alone is not always sufficient. In this thesis we investigated how to control the assemblies of guanosine-rich oligonucleotides using a novel tool, twisted intercalating nucleic acids (TINAs). The incorporation of pyrene-containing TINA monomers into guanosine-rich oligonucleotides led to the formation of stable triplexes or G-quadruplexes depending on the position of TINA monomers. In the light of our results, we have established a set of rules that helps to create a desired structure of guanosine-rich oligonucleotides using TINA molecules. In the second half of the thesis we focused on expanding the functionality of TINA conjugated oligonucleotides. In terms of fluorescence, we synthesised several fluorescently-silent triplex-forming oligonucleotides (TFOs) equipped with a dye at different positions in the DNA. Fluorescence properties were strongly dependent on the position of the dye. These fluorescently silent TFOs showed up to an 18-fold increase in fluorescent intensity upon triplex formation. These findings lay the foundation for the future design of artificial DNA sequences for expanding the repertoire of DNA secondary structures and function.