Synthesis and Structural Studies of Cyclic Py-Im Polyamides

Abstract

The work presented in this thesis is focused on the molecular recognition of DNA by minor groove binding polyamides. Methods and strategies for the solution-phase synthesis of hairpin and cyclic pyrrole-imidazole polyamides are presented with optimized protocols requiring little to no chromatography. These synthetic strategies have led to the design of cyclic polyamides targeted to the androgen response element and are shown to be biologically active and cell permeable in cell culture experiments in addition their binding affinities rival that of most polyamide architectures. The structural elucidation of an α-amino-turn-linked cyclic polyamide is presented at 1.17 A resolution providing insight into the detailed molecular recognition process and allosteric modulation responsible for the inhibition of transcription factor-DNA binding. Additionally, structural elucidation of a β-amino-turn-linked cyclic polyamide, highlighting the conformational differences compared to the α-amino-turn linked structure is presented. A structural basis for the inability of polyamides to bind dsRNA is also proposed based on biophysical, structural, and modeling data. In addition to these studies a new class of programmable oligomers targeting the DNA sequence 5’-WGGGGW-3’ were shown to inhibit DNA binding of the Nf-kB transcription factor by EMSA gel shift. Compounds synthesized in this study were found to possess unique fluorescent properties with the ability to modulate their fluorescence by binding their targeted dsDNA, leading to sequence specific fluorescent detection reagents. Efforts toward the templated-assembly of polyamides using higher-order DNA structure (NCP) are also reported and the development of a new pro-fluorescent class of heterocycle, which has the potential to be used as a chemical reporter of ligation events is described.