Quencher-free linear beacon systems containing 2-ethynylfluorenone-labeled 2′-deoxyuridine units

In this study we synthesized the 2-ethynylfluorenone-containing deoxyuridine derivative UFO and incorporated it at the central positions of oligodeoxynucleotides (ODNs) in an attempt to develop a new type of quencher-free linear beacon probe and to understand the effect of functionalization of the fluorene scaffold on the photophysical properties of the fluorescent ODNs. Herein, we describe our photophysical studies of UFO DNA probes and their application to single-nucleotide polymorphism typing.