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| Scorpions are bi-functional molecules containing a PCR primer covalently linked to a probe. The fluorophore in the probe interacts with a quencher which reduces fluorescence. During a PCR reaction the fluorophore and quencher are separated which leads to an increase in light output from the reaction tube. There are two formats for Scorpions. The diagram below shows the bi-molecular Scorpion format. The alternative is known as the unimolecular format in which an integral stem loop sequence is used to bring the quencher close to the fluorophore. |
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Elements of a Scorpions Primer
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Step 1 - The Scorpions primer is extended on target DNA
Step 2 - The extended primer is heat denatured and the quencher disassociates 
Step 3 - As it cools the extended Scorpion undergoes an internal rearrangement and begins to fluoresce in a target specific manner. Unextended primer is quenched 
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| Scorpions are described more fully in Whitcombe, D., Theaker J., Guy, S.P., Brown, T., Little, S. (1999) - Detection of PCR products using self-probing amplicons and flourescence. Nature Biotech 17, 804-807. |
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