Synthesis of DNA Building Blocks With Thiazole Fluorophores for Fluorescent Readout by Excimers and Energy Transfer

Two new charged DNA building blocks were synthesized with thiazole orange (TO) and dibenzothiazole (DB) as fluorescent DNA base surrogates. They promote excimer formation and energy transfer within DNA architectures, because they were incorporated as fluorophore pairs into oligonucleotides such that they interact in an interstrand and intrastrand orientation upon hybridization. Both excimer formation and energy transfer result not only in fluorescence intensity changes, but also in pronounced redshifted emission. In addition, DB was investigated as an energy donor with TO as well as cyanovinylenes and aminonaphthalimides as energy acceptors in DNA. These combinations render DB as a versatile fluorophore for DNA detection and imaging. Such sensitive fluorescent probes basically enable sequence-specific detection of nucleic acids not only through changes in fluorescence intensity but also by emission color as readout.