Fluorescent Nucleobase Analogues and their use for Investigating DNA Interactions

Doctoral thesis, 2014

Ever since unravelling the structure of DNA, an expanding research field has emerged with ongoing efforts dedicated to increase our understanding of the molecule of life. Since the natural nucleobases are virtually non-emissive, it has been a challenge for decades to ‘light up’ DNA/RNA in order to investigate their properties utilizing fluorescence techniques. This thesis focuses on fluorescent nucleobase analogues (FBAs) as probes for fluorescently labeling DNA and investigating its interactions, for example, with proteins. These artificial nucleobases attempt to closely mimic the characteristics of natural bases, while introducing fluorescence properties to the system. The first part of this work comprises the characterization of both new and established FBAs. Photophysical and base-mimicking properties of two fluorescent adenine analogues, triazole adenine (AT) and quadracyclic adenine (qA) are presented. Both exhibit promising features compared to the widely used commercially available adenine mimic 2-aminopurine (2-AP). Even though AT shows promising emission as a monomer and in certain DNA surroundings, it destabilizes the B-DNA duplex structure, most likely due to its C8-triazole extension. In order to overcome this effect, a new family of triazole adenine analogues extended on the 7-position was synthesized and photophysically characterized. The second thoroughly characterized adenine analogue, qA, is moderately fluorescent both as a monomer and inside DNA but in contrast to AT, the two-ring extension on qA is suggested to be well accommodated in the major groove and renders the DNA-duplex unperturbed or even stabilized, depending on the surrounding sequence. Finally, the photostability of tC, an already established FBA of the tricyclic cytosine family, was investigated. The latter yields a single photoproduct with a decreased fluorescence, which destabilizes DNA duplexes. In the second part of this work, the tricyclic cytosine FBA FRET-pair, tCO-tCnitro was applied in exploring the role of the mammalian transcription factor A in mitochondrial transcription. Furthermore, it was called upon to help resolve the order of events in which the different components of the transcription machinery initiate transcription.