FRET fluorescence quenchers

Contents

Background

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, while the quencher is promoted to its excited state.

FRET quenching depends on the ability of the fluorophore to transfer energy to the quencher. In order for this to happen, the emission spectrum of the fluorophore must overlap with the absorption spectrum of the quencher. In order for a quencher to quench fluorescence from several different fluorophores, it must therefore have a wide absorption spectrum and a high extinction coefficient.

Standard fluorophores return from the excited state to the ground state with the emission of light. The overall process of excitation, transfer, and emission to a second fluorophore is called fluorescence resonance energy transfer (FRET). Dark quenchers return from the excited state to the ground state via non-radiative decay pathways, without the emission of light. This is also a FRET mechanism but there is no secondary emission of light.

Black hole quenchers (BHQs)

The black hole quenchers (BHQs) are sold by Biosearch Technologies.

Table 1Black hole quenchers (BHQs)

Nameλmax / nm (absorption)Appox. quenching range / nmE at λmaxCompatible fluorophores
BHQ0493430-52034 000-
BHQ1534480-58034 000FAM, TET, JOE, HEX, Oregon Green®
BHQ2579550-65038 000TAMRA, ROX, Cyanine-3, Cyanine-3.5
BHQ3672620-73042 700Cyanine-5, Cyanine-5.5
Structures of Black Hole Quenchers (BHQs)

Figure 1 | Structures of Black Hole Quenchers (BHQs)

Atto quenchers

Table 2Atto quenchers

Nameλmax / nm (absorption)Appox. quenching range / nmE at λmaxCompatible fluorophores
ATTO 540Q542530-560105 000-
ATTO 580Q586560-610110 000-
ATTO 612Q615600-630115 000-

See also

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