Ultrafast infrared spectroscopy investigation of DNA-ligand interactions

Student thesis: Doctoral Thesis

Abstract

Two-dimensional infrared spectroscopy (2D-IR) is a label-free analysis method that can provide structural insight into biological processes by uncovering the coupling between the intrinsic, vibrational modes of a molecule. Technological advancements in the last decade have drastically reduced acquisition times for 2D-IR spectra from several hours down to seconds, enabling researches to perform 2D-IR experiments with unprecedented samples sizes and complexity. This thesis applies 2D-IR spectroscopy as a high-throughput analysis method to study non-covalent binding of small molecules to minor grooves of DNA duplex structures. Minor groove binding to DNA is relevant in the development of potential new therapeutics that target specific DNA sequences to influence a biological process. The conception of a 2D-IR screening experiment will therefore allow for an assessment of sequence-specific ligand interactions across multiple different binding sites. Minor groove binding of two different types of ligands are investigated in this thesis. Application of the 2D-IR method in the context of screening is first assessed in a proof of-concept by studying the interaction of a well-established DNA stain, Hoechst 33258, across a set of different dsDNA sequences. In the following chapter, 2D-IR spectroscopyis applied again to study the interaction of three new types of hairpin polyamide ligands, screened across a set of different minor grooves. The final chapter revisits the Hoechst 33258 system to investigate the impact of minor groove binding at non-equilibrium conditions using a laser-induced temperature jump. This chapter is part of preliminary work to develop a temperature-jump, 2D-IR experiment in the future.
Date of Award5 Mar 2020
Original languageEnglish
Awarding Institution
  • University Of Strathclyde
SponsorsUniversity of Strathclyde
SupervisorNeil Hunt (Supervisor) & Matthew Baker (Supervisor)

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