Synthesis of Novel N-Substituted Polyamide Porphyrins and Characterization of Ruthenium Complexes and Hemiporphyrazines as Potential G-quadruplex Stabilizers

The primary goal of this work was to synthesize and characterize potential G-quadruplex (GQ) ligands. This thesis is divided into three parts: a synthesis section dedicated to creating new porphyrin GQ stabilizers and two characterization sections dedicated to in-depth screening and assessment of the GQ-binding properties of two classes of molecules, ruthenium complexes and hemiporphyrazines. The synthesis section aimed to modify the porphyrin N-methyl mesoporphyrin IX (NMM), which is a very selective GQ binder, with amides at its periphery in hopes of improving its GQ binding affinity while maintaining its selectivity. Seven new amide derivatives were prepared. As NMM\u27s high GQ selectivity is mostly due to its N-methyl group, the synthesis of other N-modified porphyrins was also attempted but was largely unsuccessful. The second section of this thesis aimed to investigate the abilities of hexacoordinate ruthenium complexes to bind GQs. The interactions of these complexes with GQs have been previously characterized by past members of our lab by UV/Vis titrations, Job plots, and fluorescence titrations, and we sought to answer lingering questions about the complexes\u27 binding stoichiometries to Tel22 as well as how they affected GQ conformations upon binding. We were able to determine that most Ru complexes bound GQs in a 1:1 and 2:1 stoichiometry, with several binding in a 3:1 stoichiometry. We were also able to determine that most of the Ru complexes did induce some conformational change in the GQ upon binding, although the exact nature of this change was not obvious. Finally, we screened a set of hemiporphyrazines and related molecules for their abilities to stabilize GQ structures, as this class of molecules has not been previously studied with GQ DNA. One molecule, cyclohexylcyanine, emerged as a very selective and promising GQ stabilizer. We hope to use the insights gained from these experiments to establish the structural basis for a ligand\u27s selectivity and GQ-stabilizing properties in order to inform the targeted synthesis of novel GQ ligands

Interactions Of Ruthenium(II) Polypyridyl Complexes With Human Telomeric DNA

Eight [Ru(bpy)₂L]²⁺ and three [Ru(phen)₂L]²⁺ complexes (where bpy = 2,2′-bipyridine and phen = 1,10-phenanthroline are ancillary ligands, and L = a polypyridyl experimental ligand) were investigated for their G-quadruplex binding abilities. Fluorescence resonance energy transfer melting assays were used to screen these complexes for their ability to selectively stabilize human telomeric DNA variant, Tel22. The best G-quadruplex stabilizers were further characterized for their binding properties (binding constant and stoichiometry) using UV–vis, fluorescence spectroscopy, and mass spectrometry. The ligands\u27 ability to alter the structure of Tel22 was determined via circular dichroism and PAGE studies. We identified me₂allox as the experimental ligand capable of conferring excellent stabilizing ability and good selectivity to polypyridyl Ru(II) complexes. Replacing bpy by phen did not significantly impact interactions with Tel22, suggesting that binding involves mostly the experimental ligand. However, using a particular ancillary ligand can help fine-tune G-quadruplex-binding properties of Ru(II) complexes. Finally, the fluorescence “light switch” behavior of all Ru(II) complexes in the presence of Tel22 G-quadruplex was explored. All Ru(II) complexes displayed “light switch” properties, especially [Ru(bpy)₂(diamino)]²⁺, [Ru(bpy)₂(dppz)]²⁺, and [Ru(bpy)₂(aap)]2²⁺ Current work sheds light on how Ru(II) polypyridyl complexes interact with human telomeric DNA with possible application in cancer therapy or G-quadruplex sensing