Supramolecular assembly and metal-coordination in G-quadruplex structures : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Chemistry, Massey University, Manawatu, New Zealand
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Date
2014
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Massey University
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Abstract
G-quadruplexes are supramolecular structures formed from the self association of guaninerich
oligonucleotides. They consist of stacks of G-quartets, each of which is made of four
guanine bases arranged in a cyclic, planar array and held together through hydrogen
bonding. Recent evidence has suggested G-quadruplexes have a biological role. Telomeric
DNA, which has been linked to cancer formation and ageing, is capable of forming a variety
of G-quadruplex structures. This observation has led to the development of a number of drug
candidates that are currently undergoing clinical trials. Although G-quadruplex structure can
be controlled to a certain extent by the careful selection of oligonucleotide sequence, this
strategy alone is not always sufficient to allow predictable assembly to occur. To address this
problem, we investigated metal-coordinating nucleotides as a method of controlling the
predictable assembly of G-quadruplexes. Our research was focused on the use of 1,2,4-
triazole and cytosine nucleotides in the formation of base pairs and base quartets; their
ability to coordinate transition metal ions was examined.
We investigated a variety of intramolecular and intermolecular G-quadruplex assemblies
modified with triazole nucleotides, each providing a different environment for metal
coordination. We found that 1,2,4-triazole nucleotides were not capable of forming either
base pairs or quartets. We were not able to find evidence of a direct interaction between
triazole nucleotides and metal-ions under the conditions studied.
The stabilisation of a DNA duplex by coordination of silver(I) ions to cytosine nucleotides
was observed. However, this interaction was not useful in directing the assembly of a Gquadruplex
structure. In most cases we found that the presence of transition metal ions had
a negative impact on the stability of G-quadruplex structures, and that destabilisation
occurred before metal coordination could be observed.
Our investigations into the metal-coordinating properties of a 3+1 G-quadruplex based on
the 3htel sequence have highlighted the significance of the Watson-Crick base pair formed in
this assembly. In the absence of this base pair, the G-quadruplex is completely destabilised,
however, evidence suggests the formation of a G-triplex instead.
Although we did not observe G-quadruplex assembly directed by metal-coordinating
nucleotides, the contents of this thesis may be considered as a basis for the further
development of supramolecular oligonucleotide assemblies.
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Keywords
G-quadruplexes, Ssupramolecular oligonucleotide assemblies, Metal-coordinating nucleotides, Triazole nucleotides