Exploring the dynamic landscape of small molecule-DNA binding

  • Lennart Ramakers

Student thesis: Doctoral Thesis


Deoxyribonucleic acid (DNA) is a fundamental component in all living organisms found in Nature. Although both the double-helix structure of this biomolecule and the fact that it stores all the genetic information required by the organism to survive are well understood there are still aspects related to this molecule which are not as clear. Particularly the interactions underpinning the formation of complexes between other molecules, such as proteins, and DNA remain unclear. One of these is the process underlying the formation of small molecule-DNA complexes. Such complexes are known to form via interactions between these small molecules and the DNA minor groove, it has proven to be complicated to develop a set of rational rules for the synthesis of binders to target particular DNA sequences. Such rules are complicated by the complex molecular environment found within the DNA minor groove as well as the role of the spine of hydration found within this groove. Another aspect of the behaviour of DNA which has attracted a lot of attention is related to the mechanism underlying the melting of short DNA sequence. It is important to gain a better understanding of these mechanisms as this process is thought to be important in DNA transcription, replication and repair as well as being important for the application and development of DNA scaffolds. Additionally, it is thought that understanding the impact of binding on this transition could be used to gain further insights into the interactions underpinning these complexes.Here, FT-IR, ultrafast IR pump-probe and two-dimensional infrared (2D-IR) spectroscopy have been applied to investigate the interactions underpinning the formation of small molecule-DNA. Utilising a specifically designed minor groove binding ligand, incorporating an azide moiety as a non-natural IR probe, the questions outlined above were addressed. The spectroscopy of the of azides and the DNA bases were initially studied separately, in order to gain the understanding of the spectroscopy of these vibrational modes necessary to maximise the information extracted from the DNA complexes. From the initial investigation of the asymmetric azide stretch of benzyl azide, a model compound, it was found that this mode could be used to determine the electrostatic potential and hydrogen bonding strength of the local environment. In the case of the DNA base modes, it was found that both changes in the structure of the duplex, due to alterations in the sequence and the binding of an archetypical minor groove binder, Hoechst 33258, could be reliably extracted. For the binding of Hoechst 33258, these modes reveal details about the interactions underpinning the formation of complexes with both its target and a sub-optimal DNA sequences. The insights gained were then brought together to study the complexes formed between DNA and the specially-designed ligand. This allowed both the interactions underlying these complexes and the nature of the water in the minor groove to be explored. Finally, these new spectroscopic methods were then utilised to begin to reveal details of the melting transition of these DNA duplexes and the impact on melting of ligand binding.
Date of Award18 May 2018
Original languageEnglish
Awarding Institution
  • University Of Strathclyde
SponsorsUniversity of Strathclyde & EPSRC (Engineering and Physical Sciences Research Council)
SupervisorNeil Hunt (Supervisor) & Glenn Burley (Supervisor)

Cite this