Dark quencher
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A quencher is a non-fluorescent dye that absorbs light but does not emit it. it is used in molecular biology in conjunction with regular fluorophores: when they are within range no emissions are detected but when they are separated the flourophore's emission is detected.
[edit] SNP Genotyping Example
An example of its use is SNP genotyping, often a hairpin loop with a fluorophore and quencher at the base of the stem is used: a unlabelled SNP specific PCR primer (one of many) with a specific 5' tail binds to the sequence to be probed, the taq polymerase extends the sequence that will have a specific 5' end dependent on the SNP (insensitive to polymorphisms upstream of the SNP in question), in the next run a primer, complementary to that tail, with a haipin loop is extended, in the next run the elongation of the complementary strand will linearise the hairpin separating the fluorophore and quencer. Another use is in FRET.
[edit] Examples of dark quenchers
Dabcyl (dimethylaminoazosulphonic acid) absorbs in the green spectrum and is often used with flourescein. Iowa black FQ absorbs in the green-yellow part of the spectrum. Iowa black RQ blocks in the orange-red part of the spectrum.
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