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Open Access Dissertation

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Mary T. Rodgers


The chemical difference between DNA and RNA nucleosides is their 2′-hydrogen versus 2′-hydroxyl substituents. The 2′-O-methylation is common among natural posttranscriptional modifications of RNA. The structures and relative glycosidic bond stabilities of the protonated forms of the 2′-O-methylated nucleosides, 2′-O-methyladenosine (Adom), 2′-O-methylguanosine (Guom), 2′-O-methycytidine (Cydm), 2′-O-methyluridine (Urdm), and 5,2′-O-dimethyluridine (Thdm) are examined using two complementary tandem mass spectrometry approaches, infrared multiple photon dissociation (IRMPD) action spectroscopy and energy-resolved collision-induced dissociation (ER-CID). Theoretical calculations are also performed to predict the structures and relative stabilities of stable low-energy conformations of the protonated forms of the 2′-O-methylated nucleosides and their infrared spectra in the gas phase.

Low-energy conformations of protonated 2′-O-methylated nucleosides highly parallel to those found for the protonated forms of the canonical DNA and RNA nucleosides. Importantly, the preferred site of protonation, nucleobase orientation, and sugar puckering are preserved among the DNA, RNA and 2′-O-methylated variants of the protonated nucleosides. The 2′-substituent does however influence hydrogen-bond stabilization as the 2′-O-methyl and 2′-hydroxyl substituents enable a hydrogen-bonding interaction between the 2′- and 3′-substituents, whereas a 2′-hydrogen atom does not. Furthermore, 2′-O-methylation reduces the number of stable low-energy hydrogen-bonded conformations possible, and importantly inverts the preferred polarity of this interaction versus that of the RNA analogues. Trends in the CID50% values extracted from survival yield analyses of the 2′-O-methylated and canonical DNA and RNA forms of the protonated nucleosides are employed to elucidate their relative glycosidic bond stabilities. Overall, the glycosidic bond stabilities of all protonated nucleosides follow the order: [dNuo+H]+ < [Nuo+H]+ < [Nuom+H]+, except for guanine nucleosides.

Cisplatin is one of the most successful metal-based anticancer agents. This compound is also used to target RNA for exploration of new binding sites for future drugs. Seeking to discover alternative reactivity, amino acid-linked platinum complexes are being investigated and used as potential anticancer drug and for targeting and probing RNA. To gain a better understanding of the binding mechanism and assist in the optimization of chemical probing and drug design applications, experimental and theoretical studies of a series of amino acid-linked platinum complexes are being pursued. Glyplatin (glycine-linked cisplatin analogue) is examined first for its structural simplicity and to enable backbone effects to be separated from sidechain effects on the structure and reactivity. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments are performed on Glyplatin to characterize its structure and guide the selection of the most effective hybrid theoretical approach for determining its structure and IR spectrum. The simplicity of the Glyplatin system allows a wide variety of density functionals, treatments of the Pt center including the use of all-electron basis sets vs valence basis sets combined with an effective core potential (ECP), and basis sets for all other atoms to be evaluated at a reasonable computational cost. Present results suggest that the B3LYP/mDZP/def2-TZVP hybrid method can be effectively employed for structural and IR characterization of more complex amino acid-linked cisplatin complexes and their nucleic acid derivatives.

Based on theoretical guidance obtained from the Glyplatin work, deprotonated and sodium cationized arginine-, lysine-, and ornithine- linked cisplatin complexes are investigated both experimentally and theoretically. Quasimolecular forms of platinum complexes examined are [(ArgH)PtCl2], [(Arg)PtCl2+Na]+, [(LysH)PtCl2], [(Lys)PtCl2+Na]+, [(OrnH)PtCl2], [(Orn)PtCl2+Na]+. IRMPD action spectroscopy experiments and complementary electronic structure calculations are performed for these platinum complexes to elucidate the binding mode of the amino acid to the Pt center and determine how that binding is influenced by the local environment when pH or ionic strength change. By comparing the predicted IR spectra for various stable conformations of each form of platinum complex to the corresponding measured IRMPD spectra, trends of the binding mode of amino acids to the Pt metal center can be determined. Binding of Arg to the Pt center is found to involve backbone amino group and carboxylate moiety (NO binding mode), whereas Lys binds to Pt via two binding modes: backbone amino and carboxylate moieties (NO binding mode) and backbone and sidechain amino groups (NNs binding mode). The NNs binding mode is the only dominant binding mode of Orn binding to Pt that has been accessed in the IRMPD experiment.

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