A molecular beacon begins as a stem-and-loop structure. The sequences at the ends of the probe match and bind, creating the stem, while the rest of the probe is unmatched and unbound, creating the loop. While folded this way, the fluorophore at one end of the probe is next to the quencher at the other end. When the probe binds to a single-stranded DNA template, the structure unfolds, separating the quencher from the dye and allowing fluorescence.
