Date of Award

Spring 2014

Document Type

Thesis

Terms of Use

© 2014 Navin C. Sabharwal. All rights reserved. This work is freely available courtesy of the author. It may only be used for non-commercial, educational, and research purposes. For all other uses, including reproduction and distribution, please contact the copyright holder.

Degree Name

Bachelor of Arts

Department

Chemistry & Biochemistry Department

First Advisor

Liliya A. Yatsunyk

Abstract

G-quadruplex (GQ) DNA is a non-canonical DNA structure thought to form throughout the human genome. Because the stabilization of quadruplexes formed in the telomeres and in the promoters of oncogenes may prevent the spread of cancer cells, there is great interest in developing and studying molecules that may bind to and stabilize these unique DNA structures. This thesis investigates the interactions between porphyrins and GQ DNA with the goal of determining how strongly and selectively porphyrins can stabilize the quadruplex structure. There is also great interest in developing luminescent probes for GQ structures to allow for their detection in vivo. Because porphyrins are also known to fluoresce intensely in the presence of quadruplex DNA, this thesis also investigates the extent to which porphyrins may be used as fluorescent probes for quadruplexes in the cell. The first chapter focuses on N-methylmesoporphyrin IX (NMM), a porphyrin that has been shown to bind selectively to quadruplex DNA over other DNA structures. NMM is especially unique because it binds selectively to parallel quadruplexes over other quadruplex topologies. Given that NMM has also been shown to display a selective increase in fluorescence in the presence of quadruplexes over duplex structures, we wished to systematically investigate the effect of secondary DNA structure on NMM fluorescence. Results indicate that NMM displays a selective fluorescence increase in the presence of parallel GQs over single-stranded DNA, double-stranded DNA, i-motif structures, anti-parallel GQs, and mixed hybrid GQs. NMM is also found to probe parallel quadruplexes even in the presence of excess duplex DNA, and thus has promise a selective fluorescent probe for parallel GQs. Fluorescence lifetime studies indicate solvent exclusion as the mechanism for NMM's fluorescence enhancement. The second chapter investigates the interactions between the Pt(II) and Pd(II) derivatives of 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4), a well- examined GQ ligand. These porphyrins are of interest because of their square planar geometry; the lack of axial-ligands on the metal center could potentially facilitate stronger binding and intercalation between the quartets. Moreover, Pt(II) complexes are known to have powerful luminescent properties, so Pt(II)-TMPyP4, like NMM, may have promise a fluorescent probe. Results indicate that the two porphyrins bind tightly to the human telomeric GQ in a high ratio and stabilize the GQ extremely well at low ligand concentrations. Pt(II)-TMPyP4 is found to display selective fluorescence enhancement in the presence of GQs over duplex structures, but is not as selective as NMM. Finally, the third chapter presents preliminary work examining the interactions between 5,10,15,20-tetrakis((N-spermido)benzamide)porphyrin (TCPPSpm4), a tentacle porphyrin with long side chains, and the human telomeric GQ. The results of this project, which is currently ongoing, suggest that the porphyrin stabilizes the GQ well and with good affinity. The results also seem to suggest a high ligand:GQ binding ratio and potentially cooperative binding to the GQ, although further work is needed to confirm these hypotheses.

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