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When a fluorescent dye is excited at a particular wavelength, it is promoted to an excited state. In the absence of a quencher, the excited dye emits light in returning to the ground state. When a quencher is present, the excited fluorophore can return to the ground state by transferring its energy to the quencher without the emission of light. This is fluorescence quenching.
Quenching depends on the ability of the fluorophore to transfer energy to the quencher without the emission of light. Collisional quenchers do this by partaking in close molecular interactions with the fluorophore, e.g. aromatic stacking. The quenching efficiency of collisional quenchers, in contrast to FRET quenchers, is not strongly wavelength-dependent. Also, collisional quenching is only efficient at very short distances and is particularly useful in hairpin loop structures such as molecular beacons and scorpions.
Dabcyl is the original dark fluorescence quencher, and was used historically with common fluorophores including FAM, HEX, ROX and JOE in molecular beacons and scorpion primers.
Figure 1 | The collisional fluorescence quencher Dabcyl
Table 1 ⎪ Dabcyl and quenchers
| Name | λmax / nm (absorption) | Appox. quenching range / nm | E at λmax | Compatible fluorophores |
|---|---|---|---|---|
| Dabcyl | 478 | 400-550 | 32 000 | - |
| Dinitrophenyl (DNP) | 349 | - | 18 000 | - |
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