Quenching (fluorescence)

[8][9] Many dyes undergo self-quenching, which can decrease the brightness of protein-dye conjugates for fluorescence microscopy,[10] or can be harnessed in sensors of proteolysis.

FRET is based on classical dipole-dipole interactions between the transition dipoles of the donor and acceptor and is extremely dependent on the donor-acceptor distance, R, falling off at a rate of 1/R6.

FRET also depends on the donor-acceptor spectral overlap (see figure) and the relative orientation of the donor and acceptor transition dipole moments.

[12] Dexter electron transfer is a short-range phenomenon that falls off exponentially with distance (proportional to e−kR where k is a constant that is the inverse of the sum of both van der Waals radius of the atom over 2 [13]) and depends on spatial overlap of donor and quencher molecular orbitals.

Collisional quenching occurs when the excited fluorophore experiences contact with an atom or molecule that can facilitate non-radiative transitions to the ground state.

Two samples of quinine dissolved in water with a violet laser (left) illuminating both. Typically quinine fluoresces blue, which is visible in the right sample. The left sample contains chloride ions which quench quinine's fluorescence, so the left sample does not fluoresce visibly (the violet light is just scattered laser light).
Donor emission and quencher absorption spectral overlap
Comparison of static and dynamic quenching mechanisms