AAT Bioquest

What is the mechanism of dynamic quenching?

Posted January 13, 2023


During dynamic quenching, there is an interaction between two light sensitive molecules: an acceptor and a donor. The donor fluorophore transfers energy to the acceptor which then may emit light itself or absorb the energy fully; electron excitation occurs before the quenching process. In the Forster mechanism, non-radiative dipole-dipole coupling occurs, in which a negatively charged polar region of a molecule can pass an electron to a positively charged region of another molecule or itself. This occurs at distances of approximately 10 nm but becomes more likely the closer dipoles are to one another; occurs at a rate of the inverse of the distance to the sixth power.     

In the Dexter mechanism, donor and acceptor molecules come close enough that their electron orbitals overlap. This allows for the excited electron of the donor molecule to be transported to an unoccupied orbital of the acceptor molecule; it then becomes its ground state. At that same moment, an electron is transferred from the acceptor to the donor molecule, also in its ground state. 

An excited dimer (Exciplex) is composed of two molecules with excited electrons or excimers. An excimer is a very shortly existing molecule consisting of either two similar monomers or heterodimeric molecules; the combination of two excimers creates the exciplex. When electrons return to their ground state, this creates the emission of light and thereby fluorescence. When the complex splits up, it releases a longer wavelength (lower energy) of light. An excimer cannot exist if both monomers are in the ground-state. Thus, a dimer or heterodimer has to have an inert group and an excited group or element. An exciplex binds covalently to a target molecule, to fluorescence that is being quenched, and the resulting chemical system is known as the charge transfer complex. This complex is responsible for starting the quenching process.

Additional resources

Mechanisms of Quenching of Alexa Fluorophores by Natural Amino Acids

Förster Resonance Energy Transfer (FRET)

Tide Quencher Dyes

DABCYL succinimidyl ester [4-((4-(Dimethylamino)phenyl)azo)benzoic acid, succinimidyl ester] *CAS 146998-31-4*