Electronic Thesis and Dissertation Repository


Master of Science




Dr. Robert Hudson


Progress toward the synthesis of molecular beacons containing analogs of the universal quencher 4-(4'-dimethylaminophenylazo)benzoic acid (DABCYL) has been made. A synthetic methodology has been developed for the differential labeling of a PNA molecular beacon with quencher and fluorophore moieties. A DABCYL analog diarylazo compound and three small fluorescent molecules have been derivatized with terminal alkyne groups for incorporation into azide-decorated PNA oligomers by on-resin “click” chemistry. An optimized on-resin procedure was used to determine the viability of the fluorophores and quencher for incorporation into PNA.

The synthesis of a pyrrolocytidine phosphoramidite containing a diarylazo DABCYL analog moiety was undertaken with the aim of incorporation into a DNA molecular beacon by standard phosphoramidite chemistry. While the phosphoramidite was not achieved, an unprecedented addition of the dimethoxytrityl protecting group to the electron-rich pyrrolocytidine heterocycle was observed and a mechanism for its formation is proposed.