DNA photocleaving reagents are a unique class of molecules that display the ability to cleave DNA, causing strand breaks, upon exposure to an irradiation source. In terms of biological applications, achieving excitation through a two-photon absorption event provides for unique benefits that can be useful in such applications as photodynamic therapy and cell viability studies. Thus, this thesis pertains to the study of a class of photocleaving reagents that have been shown to become excited through a twophoton process during irradiation with a pulsed femtosecond laser at 775 nm. N-(Alkoxy)pyridinethiones were selected as possible oxygen-based radical generators upon irradiation at two-photon wavelengths. Experiments were carried out with pBR 322 plasmid DNA to determine if these N-(alkoxy)pyridinethiones could cause strand cleavage and if so how efficient they are in doing so. Several compounds were found to be effective DNA strand cleavers when irradiated at two-photon wavelengths, displaying the utility of two-photon excitation in biological studies. Rationale is suggested for the observed variation in cleaving efficiency based on inherent properties of the generated radicals. A second study was done to measure the two-photon cross section of the compound N-(anthracenoyloxy)pyridinethione. The two-photon cross section was found by measuring the fraction of substrate remaining after specific periods of femtosecond laser irradiation at 775 nm, and the two-photon cross section was found to be 0.051 GM.

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In vitro, G-rich sequences form highly stable secondary structures known as G-Quadruplexes. These structures have been characterized by circular dichroism nuclear magnetic resonance and X-ray crystallography; although their detection in vivo has remained elusive. Due to the biological implication of a transisent and polymorphic secondary structure forming within the hypothetical G-Quadruplex forming regions, there is growing interest to understand their in vivo molecular dynamics. / text

This thesis reports the synthesis of new near infrared dyes in three chapters. The first two chapters outline the synthetic procedure for synthesizing mono- and pentamethine cyanine dyes. The initial chapter encompasses the synthesis of asymmetric monomethine dyes with red-shifted optical properties. The second chapter involves the synthesis and assessment of new symmetrical quinolin-4-yl and phenanthridin-6-yl pentamethine dyes as potential oxidative DNA cleavage agents. The last chapter of the thesis details the synthesis and evaluation of new phenoxizinum dyes as contrast agents for insulunomia, a pancreatic cancer. Furthermore, all new compounds were characterized via NMR and their coherent optical properties were obtained.

(Chemical Equation Presented) Torn genes: DNA tetramers containing the 2-deoxyribonolactone (dL) lesion have been isolated by HPLC from d(CGCG) and d(pCGCG) films irradiated with X-rays. Upon treatment with spermine as a catalyst, the dL-containing tetramers decompose to 5-methylene-2-furanone (5-MF; see scheme), a characteristic product of dL decomposition. Hence, 5-MP can be used to quantify dL lesions in DNA.

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