Progress Toward Synthesis of Molecular Beacons Incorporating DABCYL Analog Quenchers

Christie M. Ettles, The University of Western Ontario

Abstract

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.