Design of a fluorescent probe for DNA/RNA imaging

We report new on-off fluorescent DNA probes. We used the fluorescence quenching by the exciton coupling effect of thiazole orange dyes to achieve turning off of fluorescence. Aggregation of dyes tethered to a single nucleotide in DNA dramatically changes the photophysical properties of the dyes, as demonstrated by the large spectral shifts relative to the absorption of the monomeric dyes binding to DNA. The photophysically designed DNA showed strong emission when it hybridized with the target strand, whereas the emission was suppressed strongly in the single-stranded state. The present approach using an excitonic interaction exhibits a quenching ability that is high enough to work as an on-off probe, and also includes many advantages quite different from conventional assays.