Cancer results from the accumulation of genetic mutations in a normal cell that ultimately result in the expression (or overexpression) of oncogenes. The design of drugs having high affinity for specific DNA sequences or structural motifs is vital to gaining a better understanding of gene expression and to the development of new cancer treatments that are based on turning off oncogene expression. This dissertation presents studies of the binding of two ligand families, Berenil (DMZ), and ruthenium polypyridyl complexes (RPCs), to B-DNA and G-quadruplex (G4) DNA. The structureunction relationships for the interaction of these ligand families with DNA were probed by functional group substitution, truncation, or modification of the DMZ amidine groups, and by changing one of the RPC ruthenium ligands from phenanthroline to dipyridophenazine (dppz) or tetraazatetrapyrido-pentacene (tatpp), and lastly by adding a second Ru(Phen)2 core to the tatpp bridging ligand. Removal of one or both amidine groups from DMZ drastically reduces its binding to both B-DNA and G4-DNA. DMZ analogs in which one amidine was replaced by an alkyne group were synthesized with the expectation that the additional π-bonding character of the alkyne group would increase G4 affinity. All of the DMZ alkyne compounds were found to bind preferentially to G4-DNA (over B-DNA) and a few of these compounds demonstrated significant anticancer activity. RPCs with progressively longer ruthenium bound ligands were found to bind with differing affinities to B-DNA and G4-DNA. Monoruthenium RPCs exhibited a preference for binding to B-DNA, while binding the diruthenium RPC to G4-DNA was more complicated exhibiting both tighter and a weaker binding modes in comparison to the B-DNA complex. The diruthenium complex was found to bind more tightly to G4-DNA by approximately 3 kcal mol-1. The binding of small molecules to DNA resulting in the disruption of oncogene transcription represents a powerful approach to the treatment of cancer.

Bibliography: leaves 178-195.

This thesis reports the synthesis, characterisation and DNA binding of a number of novel ruthenium(II) complexes. Four mononuclear complexes were synthesised. These complexes were resolved using a large scale extraction procedure employing the chiral TRISPHAT anion. The racemic mononuclear complexes containing halogenated ligands were used in the synthesis of the racemic dinuclear complexes. Resolved mononuclear complexes were also used to stereo-selectively synthesise enantiomers of their respective dinuclear complexes. All metal complexes were characterised using fluorescence spectroscopy. Resolved metal complexes were further characterised using CD spectroscopy to determine their molar rotation coefficients and optical purity. Preliminary DNA binding studies were conducted using the racemic dinuclear complexes and their mononuclear equivalent. Titration experiments with calf thymus-DNA were used to determine the DNA binding constant and binding site size. Samples containing a higher NaCl concentration (100 mM) slightly improved the oligonucleotide spectrum resolution, but not to an extent where a complex binding model could be determined. Attempts to determine DNA binding preferences of the dinuclear complexes with oligonucleotides which contain two-adenine bulge sites using a 96-well a fluorescence plate reader were attempted, but were unsuccessful. Samples containing a higher NaCl concentration (100 mM) slightly improved the oligonucleotide spectrum resolution, but not to an extent where a complex binding model could be determined. Attempts to determine DNA binding preferences of the dinuclear complexes with oligonucleotides which contain two-adenine bulge sites using a 96-well a fluorescence plate reader were attempted, but were unsuccessful. / Doctor of Philosophy (PhD)

Bibliography: leaves 178-195. / xiv, 195 leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Chemistry, 2001

"January 2004" / Bibliography: leaves 163-184. / v, 184 leaves : ill. (some col.), photos ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, School of Chemistry and Physics, Discipline of Chemistry, 2004

Thesis (Ph.D.)--McMaster University, 2006. / Supervisor: Yingfy Li. Includes bibliographical references (leaves 151-167).

Thesis (Ph.D.)--University of Western Sydney, 2008. / A thesis presented to the University of Western Sydney, College of Health and Science, School of Biomedical and Health Sciences, in fulfilment of the requirements for the degree of Doctor of Philosophy. Includes bibliographies.

Thesis (M. Sc.) (Hons.) -- University of Western Sydney, 2002. / A thesis presented to the University of Western Sydney in partial fulfilment of the rquirements for the degree of Master of Science (Honours), February, 2002. Includes bibliographical references.

Thesis (M.Sc.) (Hons)--University of Western Sydney, 2008. / A thesis presented to the University of Western Sydney, College of Health and Science, School of Biomedical and Health Sciences, in fulfilment of the requirements for the degree of Master of Science (Honours). Includes bibliographies.

In the 1980's, Nicholas Farrell developed a range of structurally distinct multinuclear Pt complexes that form long-range interstrand crosslinks (IXLs) in DNA. The dinuclear complex [{trans-PtCl2(NH3)}2-µ-(H2N(CH2)6NH2)]2+ (1,1/t,t) was the first of this series to show promising results, however, it was the trinuclear complex [{trans-PtCl2(NH3)}2-µ-trans-Pt(NH3)2(H2N(CH2)6NH2)2]4+ (1,0,1/t,t,t or BBR3464) that was chosen for clinical trials based on significantly increased cytotoxicity compared to 1,1/t,t and cisplatin. Molecular biology experiments have shown that 1,1/t,t exclusively forms IXLs in DNA in the 5'¿ 5' direction, whilst 1,0,1/t,t,t can form IXLs in both the 5'¿5' and 3'¿3' directions. Previously, 2D [1H,15N] HSQC NMR has been used to study the formation of 5'–5' 1,4–GG IXLs. The formation of 3'–3' 1,4–GG IXLs have been studied as part of this thesis. More recently, Pt complexes such as [{trans–PtCl2(NH3)}2{H2N(CH2)6(NH2(CH2)2NH2)(CH2)6NH2}]4+ (1,1/t,t–6,2,6) and [{trans–PtCl2(NH3)}2{H2N(CH2)6(NH2)(CH2)6NH2}]3+ (1,1/t,t–6,6), where the charged central Pt moiety of 1,0,1/t,t,t is replaced by a polyamine linker, have been developed in the Farrell group and show increased potency compared to 1,0,1/t,t,t. The complex 1,1/t,t 6,2,6 is a lead candidate currently undergoing Phase I clinical trials. Prior to the work presented in this thesis, little was known about the aquation chemistry or kinetics of DNA binding of these novel complexes. Reported in Chapter 3 is the study of the formation of 3'–3' 1,4–GG IXLs by both 1,0,1/t,t,t and 1,1/t,t in the duplex 5' {d(TATACATGTATA)2} (33–14XL) (pH 5.4, 298K). A combination of 1D 1H and 2D [1H, 15N] HSQC NMR experiments was used to directly compare the results with the stepwise formation of the 5'–5' 1,4–GG IXL with the previously studied duplex, 5' {d(ATATGTACATAT)2} (55–14XL), under the same conditions. Preassociation as well as aquation were similar, however, differences were observed at the monofunctional binding step with evidence for numerous monofunctional adducts. Both reactions did not yield a single 3'–3' 1,4–GG IXL, rather several adducts that could not be characterised. Molecular dynamics simulations of the 3'–3' 1,4–GG IXLs showed highly distorted lesions that may have implication in cellular repair processes.