Electronic Thesis and Dissertation Repository


Master of Science




Robert H. E. Hudson


Pyrrolocytosine (pC) derivatives are used in the study of nucleic acid structure, function and in the design of the hybridization probes. They have unique properties including small size and Watson-Crick base pairing capability and impressive fluorescent properties. However, they exhibit variation in the fluorescence properties upon incorporation into single-stranded DNA and double-stranded DNA.

This study analyzes the effect of the nearest neighbours on the fluorescence properties of phenylpyrrolocytosine (PhpC) and provides a guide to the proper design of the PhpC containing fluorescent probes. Moreover, the possibility of photoinduced electron transfer (PET) as the underlying mechanism of the unusual photophysical behavior of PhpC in response to different nearest neighbours is investigated by measurement of the redox potentials of the PhpC. Furthermore, the possibility of the fluorescence resonance energy transfer (FRET) between PhpC and p-NO2-PhpC for potential utilization in the design of molecular beacons is investigated by fluorescence studies.