Electronic Thesis and Dissertation Repository


Master of Science




Robert H. E. Hudson


This thesis reports work in the area of modified nucleosides for potential use as molecular probes in nucleic acid chemistry. These heterocyclic base surrogates that are capable of canonical base pairing have use in the study of nucleic acid conformation, as reporters of the state of hybridization.[1]

The synthesis of a 5-phenylpyrrolocytidine was attempted in order to compare its properties with its 6-substituted pyrrolocytidine counterpart. Unfortunately, the 5-substituted pyrrolocytidine was not achieved.

The synthesis of five nucleosides based on the pyrrolocytidine scaffold was reported. Their synthesis was achieved through the tandem Sonogashira/annulations reaction between 5-iodocytidine derivatives and terminal alkynes to yield the bicyclic nucleoside pyrrolocytidine.

Photophysical studies were performed to determine possible FRET pairs to be used as molecular beacons and Stern-Volmer plots were used to determine how effective each quencher was at reducing the fluorescence intensity of the fluorophores. The molar absorptivity of a 6-DABCYL mimic pyrrolocytidine was determined and compared with the universal quencher DABCYL.