Highly efficient quencher-free molecular beacon systems containing 2-Ethynyldibenzofuran- and 2-Ethynyldibenzothiophene-Labeled 2′-Deoxyuridine units

We have prepared two fluorescent DNA probes-U^DBF and U^DBT, containing 2-ethynyldibenzofuran and 2-ethynyldibenzothiophene moieties, respectively, covalently attached to the base dU-and incorporated them in the central positions of oligodeoxynucleotides (ODNs) so as to develop new types of quencher-free linear beacon probes and investigate the effect of functionalization of the fluorene scaffold on the photophysical properties of the fluorescent ODNs. The ODNs containing adenine flanking bases (FBs) displayed a selective fluorescence "turn-off" response to mismatched targets with guanine bases; this suggests that these probes could be used as base-discriminating fluorescent nucleotides. On the other hand, we observed a "turn-on" response to matched targets when the U^DBF and U^DBT units of ODNs containing pyrimidine-based FBs were positioned opposite the four natural nucleobases. In particular, an ODN incorporating U^DBT and cytosine FBs has potential use in single-nucleotide polymorphism typing.