Investigation of Porphyrins as Potential G-Quadruplex Stabilizing Ligands and Fluorescent Probes

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\u27s 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

Interactions Between Spermine-Derivatized Tentacle Porphyrins And The Human Telomeric DNA G-Quadruplex

G-rich DNA sequences have the potential to fold into non-canonical G-Quadruplex (GQ) structures implicated in aging and human diseases, notably cancers. Because stabilization of GQs at telomeres and oncogene promoters may prevent cancer, there is an interest in developing small molecules that selectively target GQs. Herein, we investigate the interactions of meso-tetrakis-(4-carboxysperminephenyl)porphyrin (TCPPSpm4) and its Zn(II) derivative (ZnTCPPSpm4) with human telomeric DNA (Tel22) via UV-Vis, circular dichroism (CD), and fluorescence spectroscopies, resonance light scattering (RLS), and fluorescence resonance energy transfer (FRET) assays. UV-Vis titrations reveal binding constants of 4.7 × 10⁶ and 1.4 × 10⁷ M⁻¹ and binding stoichiometry of 2–4:1 and 10–12:1 for TCPPSpm4 and ZnTCPPSpm4, respectively. High stoichiometry is supported by the Job plot data, CD titrations, and RLS data. FRET melting indicates that TCPPSpm4 stabilizes Tel22 by 36 ± 2 °C at 7.5 eq., and that ZnTCPPSpm4 stabilizes Tel22 by 33 ± 2 °C at ~20 eq.; at least 8 eq. of ZnTCPPSpm4 are required to achieve significant stabilization of Tel22, in agreement with its high binding stoichiometry. FRET competition studies show that both porphyrins are mildly selective for human telomeric GQ vs duplex DNA. Spectroscopic studies, combined, point to end-stacking and porphyrin self-association as major binding modes. This work advances our understanding of ligand interactions with GQ DNA

N-Methylmesoporphyrin IX Fluorescence As A Reporter Of Strand Orientation In Guanine Quadruplexes

Guanine quadruplexes (GQ) are four-stranded DNA structures formed by guanine-rich DNA sequences. The formation of GQs inhibits cancer cell growth, although the detection of GQs invivo has proven difficult, in part because of their structural diversity. The development of GQ-selective fluorescent reporters would enhance our ability to quantify the number and location of GQs, ultimately advancing biological studies of quadruplex relevance and function. N-methylmesoporphyrin IX (NMM) interacts selectively with parallel-stranded GQs; in addition, its fluorescence is sensitive to the presence of DNA, making this ligand a possible candidate for a quadruplex probe. In the present study, we investigated the effect of DNA secondary structure on NMM fluorescence. We found that NMM fluorescence increases by about 60-fold in the presence of parallel-stranded GQs and by about 40-fold in the presence of hybrid GQs. Antiparallel GQs lead to lower than 10-fold increases in NMM fluorescence. Single-stranded DNA, duplex, or i-motif, induce no change in NMM fluorescence. We conclude that NMM shows promise as a turn-on\u27 fluorescent probe for detecting quadruplex structures, as well as for differentiating them on the basis of strand orientation

Investigation Of The Interactions Between Pt(II) And Pd(II) Derivatives Of 5,10,15,20-Tetrakis (N-Methyl-4-Pyridyl) Porphyrin And G-Quadruplex DNA

G-quadruplexes are non-canonical DNA structures formed by guanine-rich DNA sequences that are implicated in cancer and aging. Understanding how small molecule ligands interact with quadruplexes is essential both to the development of novel anticancer therapeutics and to the design of new quadruplex-selective probes needed for elucidation of quadruplex biological functions. In this work, UV–visible, fluorescence, and circular dichroism spectroscopies, fluorescence resonance energy transfer (FRET) melting assays, and resonance light scattering were used to investigate how the Pt(II) and Pd(II) derivatives of the well-studied 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) interact with quadruplexes formed by the human telomeric DNA, Tel22, and by the G-rich sequences from oncogene promoters. Our results suggest that Pt- and PdTMPyP4 interact with Tel22 via efficient π–π stacking with a binding affinity of 106–107 M−1. Under porphyrin excess, PtTMPyP4 aggregates using Tel22 as a template; the aggregates reach maximum size at [PtTMPyP4]/[Tel22] ~8 and dissolve at [PtTMPyP4]/[Tel22] ≤ 2. FRET assays reveal that both porphyrins are excellent stabilizers of human telomeric DNA, with stabilization temperature of 30.7 ± 0.6 °C for PtTMPyP4 and 30.9 ± 0.4 °C for PdTMPyP4 at [PtTMPyP4]/[Tel22] = 2 in K+ buffer, values significantly higher as compared to those for TMPyP4. The porphyrins display modest selectivity for quadruplex vs. duplex DNA, with selectivity ratios of 150 and 330 for Pt- and PdTMPyP4, respectively. This selectivity was confirmed by observed ‘light switch’ effect: fluorescence of PtTMPyP4 increases significantly in the presence of a variety of DNA secondary structures, yet the strongest effect is produced by quadruplex DNA