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 in Taqman or invader assay, SNP genotyping methods. for example 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. An alternative to using quenchers is by using FRET where the combination of two dyes gives a signal.

[edit] Examples of dark quenchers

Dabcyl (dimethylaminoazosulphonic acid) absorbs in the green spectrum and is often used with flourescein. (Dabsyl has a nearly identical absorption but has a sulphonyl choride to form more stable conjugates, instead of a succinimidyl ester). Qxl quenchers from Anaspec span the full visible spectrum. Iowa black FQ absorbs in the green-yellow part of the spectrum. Iowa black RQ blocks in the orange-red part of the spectrum. QSY dyes are well described in invitrogen's handbook[1].