Expanding the DNA binding repertoire of pyrrole-imidazole polyamids

  • Giacomo Padroni

Student thesis: Doctoral Thesis

Abstract

Pyrrole-Imidazole (Py-Im) hairpin polyamides are a programmable class of compounds that bind in the minor groove of double-stranded DNA (dsDNA). The hairpin conformationenables sufficient flexibility to form a side-by-side arrangement within the minor groove of target dsDNA sequences. An Im-Py pair discriminates G over C, A and T, whereas a Py-Pypair binds A and T over C and G. The possibility to target specific dsDNA sequences enables polyamides to modulate gene expression by the disruption of transcription factors such as the androgen receptor, over expressed in prostate cancer. A current limitation of the biological applications of Py-Im polyamides is their variable cell permeability profile. Im-richpolyamides tend to have reduced cellular and nuclear uptake in eukaryotic cells. Although modifications to the periphery of the polyamide scaffold have been explored at length, there has been limited studies on tuning the physicochemical properties of the G-recognising Imunit.This thesis describes the preparation and the evaluation of the binding mode of hairpin polyamides with Im units replaced by a series of 5-substituted 2-amino-4-carboxylic thiazole(Nt) building blocks. Chapter 1 introduces the endogenous and exogenous DNA recognition by protein and small molecules, the modulation of gene expression using Py-Im polyamides and the limitations of this approach. Chapter 2 describes the preparation of the building blocks and the optimisation of the solid phase synthesis of hairpin polyamides containing Nt units. These optimised conditions were used for the preparation of a suite of 8-ring polyamides incorporating Nt in different positions of the polyamide scaffold. Expanding the DNA binding repertoire of Pyrrole-Imidazole polyamides Chapter 3 describes the evaluation of the binding mode of Nt-containing polyamides using a combination of biophysical and biochemical methods. The 5-isopropyl substituted Nt (iPrNt) building block was identified as an alternative to Im for targeting G when incorporated at theN-terminus of the polyamide scaffold. Chapter 4 describes the structural characterisation of three selected polyamides binding to their dsDNA target sequence using NMR spectroscopy and molecular dynamics. This study reveals that the polyamide containing iPrNt at the N-terminus induces a greater compression of the major groove compared to the Im-containing analogue. Finally, Chapter 5 reflects on the work of this thesis and offers some perspective of the future development of Py-Im polyamides as gene expression modulators.
Date of Award1 Apr 2018
LanguageEnglish
Awarding Institution
  • University Of Strathclyde
SponsorsUniversity of Strathclyde
SupervisorGlenn Burley (Supervisor) & Craig Jamieson (Supervisor)

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