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This master thesis is focused on theoretical study of the Cy3 and Cy5 dyes and their interactions with DNA. The main aim was to find the mot populated conformations of the Cy3-DNA and Cy5-DNA complexes. A comparison with the experimental structure was also done and the influence of the cyanine dyes on the conformational changes of the DNA chain was evaluated.

This thesis outlines two projects that examine interactions between DNA and cyanine dyes: 1) Investigation of monomethine cyanine dye through the synthesis and optical characteristics with a goal to synthetically manipulate these systems to develop a fluorescent biological probe. Several asymmetric and one symmetrical monomethine cyanine dyes were synthetically prepared and their optical properties versus structural changes were explored. Representative dyes were selected for spectroscopically investigating DNA binding to enhance existing probe designs. 2) Early stage development of a non-metalated photosensitizer for photodynamic therapy (PDT) by screening experimentally derived cleavage activities of a number of polymethine cyanine dyes with various adjoining heterocycles. Structural characteristics of these dyes which promoted cleavage in the dark were identified and eliminated to allow for more selective photo-induced cleavage to enhance the candidacy of these compounds as photosensitizing agents. All compounds were purified through recrystallization or column chromatography and were characterized via 1H and 13C nuclear magnetic resonance (NMR). Compounds from the first chapter were further characterized using mass spectrometry.

Near-infrared (NIR) fluorescence imaging has emerged as an attractive non-invasive approach for direct visualization of diseases which depends on the development of stable, highly specific and sensitive optical probes. The NIR region of the electronic spectrum offers a reduction in the background autofluorescence and an increase in the tissue penetration depth. Cyanine dyes have often been considered promising contrast optic agents owing to their photophysical properties. Herein the synthesis of various penta- and heptamethine benzothiazole cyanine dyes has been described and their in vivo imaging efficacy was determined. Varying functionalities on the benzothiazole aromatic ring and changing substituents on the benzothiazolium nitrogen atom reflected subsequent changes in the imaging pattern and have resulted in the development of promising brain targeting agents.

The use of fluorescent imaging probes for the real time detection of cellular malfunctions, such as enzyme over expression has shown promise. Fluorescent dyes with absorption and emission values below 600 nm are limited in their in vivo applications due to high background auto-fluorescence and low resolution images. Employing near infrared (NIR) fluorophores such as cyanine dyes can overcome this disadvantage. Cyanine dyes can be synthesised using solution or solid-phase techniques with the use of solution phase chemistry allowing for larger scale and higher yielding reactions. Utilising a selection of functional groups and varying polymethine chain lengths a cyanine dye library with tuneable absorption and emission wavelengths was synthesised. This thesis gives the first detailed examples of how modifications on heptamethine cyanine dyes alter their cellular uptake and cellular toxicity. Furthermore, a NIR fluorescent microsphere is reported as well as NIR functionalised microspheres with the ability to be tracked within cells. Additional lines of work involved the synthesis of a fluorescent sensor for the visualisation of bacteria. Aminopeptidases are present within the peptidoglycan cell wall of Gram negative bacteria and therefore can be targeted for real time detection of bacteria to aid in the detection of infectious diseases. A coumarin based probe is reported which detects aminopeptidase in gram negative bacteria in vitro.

This thesis begins with a brief review about the role and importance of the small molecules containing fluorine atoms in medicine and imaging. Then, the first part of the thesis will discuss the synthesis, purification and characterization of pentamethine cyanine dyes. The structure identification of the final dyes is done by using 1H NMR, 13C NMR, 19F NMR, and mass spectrometry. The studies performed after full characterization were the determination of optical and physicochemical properties. After these properties were performed, the fluorophores were evaluated to be good candidates for in vivo testing.

Photodynamic therapy (PDT) is a cancer treatment method in which a photosensitizer, light of a particular wavelength, and also oxygen are used to destroy cancerous cells. Cancer cells absorb the photosensitizing agent which is injected into the body, and it is triggered to cause cell destruction upon absorption of light. This occurs because of the excitation of the photosensitizer produces reactive oxygen species that induce a cascade of cellular and molecular events in the body. Photosensitizing agents that can photo-cleave DNA at long wavelengths are highly demanded in PDT, because the long wavelengths of light can penetrate through tissue deeply compared to visible light. While most of the photosensitizers are activated at wavelengths less than 690 nm, penetration of light continues to increase at increasing wavelengths. In this thesis, photosensitizers that can be activated to oxidize DNA with long wavelengths of light will be discussed. Using quinoline cyanine dyes, here we report the first example of DNA photocleavage at a wavelength of light above 800 nm.

Near-infrared (NIR) fluorescence imaging has emerged as an attractive non-invasive approach for direct visualization of diseases which depends on the development of stable, highly specific and sensitive optical probes. The NIR region of the electronic spectrum offers a reduction in the background autofluorescence and an increase in the tissue penetration depth. Cyanine dyes have often been considered promising contrast optic agents owing to their photophysical properties. Herein the synthesis of various penta- and heptamethine benzothiazole cyanine dyes has been described and their in vivo imaging efficacy was determined. Varying functionalities on the benzothiazole aromatic ring and changing substituents on the benzothiazolium nitrogen atom reflected subsequent changes in the imaging pattern and have resulted in the development of promising brain targeting agents.

The use of cyanine dyes in bioanalytical applications has become a widely explored topic of interest in chemistry. Their ability to absorb and fluoresce in the UV-visible and near-infrared region of the electromagnetic spectrum benefits their use as imaging probes and fluorescent labels due to the reduced auto-fluorescence from biological molecules. The behavior of these dyes lies in their structure which consists of two nitrogen containing heterocycles joined by an electron deficient polymethine bridge that allows specific energy transitions to occur. The first portion of this work aims to explore dye functionality for analytical applications regarding the non-covalent labeling of bovine serum albumin. The second portion of the work explores dye interactions with human serum albumin in biological membrane mimetic environments using the ternary system of sodium dioctyl sulfosuccinate (AOT) in water and n-heptane.

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.