What is a scorpion primer?
Scorpion primers are structurally and functionally related to molecular beacons, but serve also as probes in the PCR reaction. Scorpion primers have self-complementary sequences that form a 5´-terminal stem-loop structure, with the loop sequence complementary to the amplicon sequence, which follows the primer sequence. The 3´-end serves as the probe. The stem region is labelled with a reporter fluorophor and a quencher. In the first step, the primer is extended, yielding a single-stranded template for the reverse primer in the second step. The stem then opens and the loop binds to the product, separating reporter and quencher. The reverse extension is blocked by a hexethylene glycol group. This ensures that the reporter of the scorpion probe remains quenched in unspecific products (e.g. primer dimmers).ScorpionsTM is a trademark of DxS.
