Brogden, Anna Leigh; (2006) The Holliday junction as a therapeutic target: Synthetic and structural studies of the interactions of small molecules with nucleic acid structures. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

This work describes the interactions of small molecules with nucleic acid structures. Chapter 1 is concerned with the structure of DNA and goes on to explain the structure of the DNA Holliday junction, an intermediate in homologous recombination. Chapter 2 explains why the DNA Holliday junction is a potential therapeutic target for small molecules in the disruption of certain pathways utilizing homologous recombination. Chapter 3 goes on to describe the process of ligand design with the development of the bis(9-aminoacridine-4-carboxamides) as potential junction binders. Chapter 4 is concerned with DNA crystallography as a method to examine small molecule binding to nucleic acid structures. Chapter 5 presents Structure 1: the first structural evidence of a small synthetic molecule non-covalently cross-linking two DNA duplexes. The asymmetric unit consists of one DNA duplex containing an intercalated acridine-4-carboxamide chromophore at each of the two CG steps. The other half of each ligand is bound to another DNA molecule in a symmetry related manner, with the alkyl linker threading through the minor grooves. The two crystallographically independent ligand molecules adopt distinct side chain interactions, forming hydrogen bonds to either O6 or N7 on the major groove face of guanine, in contrast with the semi-disordered state of mono-intercalators bound to the same DNA molecule. The complex described here suggests a possible explanation for the inconsistent behaviour of 6-carbon linked bis-acridines in previous assays of DNA bis-intercalation. Chapter 6 presents Structure 2: the first example of non-covalent small molecule binding to the DNA Holliday junction. The bis-acridine molecule; compound 2, binds across the centre of the junction, and the two adenines either side of the junction cross-over, are replaced by the acridine chromophores. These line up with adjacent thymine bases and form stacking interactions with the pyrimidine bases above and below. The linker lies across the junction centre in the major groove and the side chains attached to each chromophore thread through into the minor grooves, forming hydrogen bonding interactions with the surrounding DNA bases. This structure represents a starting point for the design and synthesis of new ligands capable of binding to the DNA Holliday junction in preference to any other DNA structure. The disruption or stabilisation of Holliday junctions could eventually lead to the inhibition or prevention of inappropriate homologous recombination, a new direction in the targeting of tumour cells utilising HR as a means to maintain immortality. Chapter 7 lists the experimental results for both the synthetic and the crystallographic techniques.

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