Synthesis of a fluorescent PNA monomer containing 5-((9H-fluoren-2-yl)ethynyl)uracil

Pyrimidine nucleobases bearing 5-phenylethynyl substitution represent compact and intrinsically fluorescent nucleobases. Such nucleobases are capable of selective recognition of a complementary base and may fluorimetrically report on hybridization events. Our past work has demonstrated that the fluorescence of 5-phenylethynyluracils is sensitive to substitution on the phenyl ring, however these are relatively weak fluorophores. We currently are pursuing the functionalization of the phenyl group of these modified nucleobases in order to further improve their fluorescence response, increase their aqueous solubility and stabilize hybrids formed with complementary nucleic acids. As an example of this work, we have synthesized the 5-((9H-fluoren-2-yl)ethynyl)uracil PNA monomer that will be incorporated into oligomers using Fmoc-based chemistry. Initial evaluation of the fluorescence of the 5-((9H-fluoren-2-yl)ethynyl)uracil derivative shows that the fluorescence intensity is approximately 50 times greater than a similar 5-phenylethynyluracil derivative when under identical conditions.