Investigating the binding mode of azide labelled derivatives of Hoechst 33258 by NMR, UV-Vis and IR spectroscopy

This thesis describes attempts to develop a method for studying the dynamics of dsDNA: small molecule ligand association and dissociation through 2D-IR spectroscopy. The strategy employed was to synthesise azide-bearing derivatives of the archetypal minor groove binding ligand, Hoechst 33258, with the azide acting as a reporter functional group. Chapter 1 describes both the state of the art, and also what is unknown regarding the processes of association and dissociation of small molecules from dsDNA, and how this project aims to gain a fuller understanding of the dynamics of association between dsDNA and a small molecule MGB. The clinical significance of minor groove binders is also discussed. Chapter 2 describes the synthesis of two azide-bearing derivatives of H33258 through an amide coupling strategy, and the significant problems encountered with the purification of these compounds. Future alternative pathways to these compounds are proposed. An investigation into the spectroscopic properties of the azide functional groups in the free compounds is also presented. Chapter 3 describes the investigation of the utility of the azide functional group through a comparative study of the thermal dissociation of these compounds from dsDNA. It was found that the utility of the azide was dependent on the position of the azide within the molecule, and is sensitive to the changes in solvation of the minor groove of dsDNA. One compound in particular exhibited a marked change in both the shape and the intensity of the azide absorption band and was commensurate with the melting temperature, Tm of the complex. Chapter 4 describes the investigation into the structural origins of the marked difference in the azide absorption band of one MGB when in complex with a dsDNA oligomer through structural characterization of this complex by NMR spectroscopy. It was found that the azide functional group is in close proximity to the exocyclic amine of guanosine, and this specific interaction is proposed to give rise to the observed changes in the azide absorption band. The orientation of the molecule was found to be opposite to that reported for H33258, a reason why this is the case is also proposed.

Name dc:type.qualificationname

phd

Level dc:type.qualificationlevel

doctoral-pg

Grantor dc:publisher.institution

University of Strathclyde

Year dc:date.issued

2016

Author dc:creator

• May, John

DOI

10.48730/c1dc-mc58

Identifier

T14525

Author Identifier

201255025

OAI identifier oai:identifier

oai:strathclyde:xp68kg29t