In-Stem-Labeled Molecular Beacons for Distinct Fluorescent Color Readout

Molecular beacons typically contain a fluorophore and a quencher at the 3' and 5' end of the hairpin stem. Here, the authors incorporated a FRET pair internally into a stem. This design led to well-separated emission bands, a high contrast between duplex and hairpin, and enhanced an signal-to-noise ratio. Although not trivial to implement, I am wondering if this could also be applied to the detection of other DNA assembly events, e.g., the hairpin chain reaction.