Targeting DNA secondary structures using chemically modified oligonucleotides : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Chemistry, Massey University, Palmerston North, New Zealand. EMBARGOED to 7 July 2024.

Abstract

Chemical modifications bring in additional features to oligonucleotides (ONs), including enhanced stability against nucleases, increased binding affinity towards DNA or RNA, improved cellular uptake, etc. This Thesis describes several strategies and chemical modifications used for targeting DNA duplexes and G-quadruplexes. We introduced a pyrene analogue, (R)-1-O-[2-(1-pyrenylethynyl)phenylmethyl]-glycerol, called ortho-TINA (twisted intercalating nucleic acid) monomer into a native duplex DNA. The affinity of ortho-TINA modified strands was low to each other, whereas the affinity of ortho-TINA sequence towards complementary DNA was increased. This property of ortho-TINA duplex was applied for targeting native duplexes in a sequence-specific manner using a process called dual duplex invasion (DDI). The speed of DDI is increased with the increased number of ortho-TINA pairs present in the duplex, as well as with the rise of temperature from 4 to 37 ℃. However, DDI against duplexes longer than the probe is compromised. To improve the kinetics of DDI, we designed and synthesised DNA probes with zwitterionic moieties, 4‐(trimethylammonium)butylsulfonyl phosphoramidate groups (N+), in which the negatively charged phosphate is neutralised by the positively charged quaternary amine.--Shortened abstract