Fluorescence quenching

Introduction
Quenching of fluorescence is a physiochemical discipline that decreases fluorescent intensity of light emitting molecules. There are two different ways of quenching: static and dynamic quenching. It is to be mentioned that there is a difference between quenching and decrease of fluorescence due to the high state of molecular excitement or chemical changes of dye (like oxydation).

Static Quenching
Static quenching (or contact quenching) of fluorescence is, when a Fluorphor (F) and a Quencher (Q) are creating a complex (FQ) which is not fluorescent. The chemical equation therefore is: F + Q ⇌ FQ

The chemical equilibrium (Ks) between the Fluorphor, the Quencher and the complex FQ is formed by the law of mass action and equal to the Stern-Volmer-constant (Ksv). There [FQ] stands for the concentration of the complex FQ, [F] for the concentration of the loose Fluorfor and [Q] for the loose Quencher.

The Stern-Volmer-equation describes the dependence of the fluorescent intensity of a fluorescent dye on the concentration of an quenching material (Quencher). It was created by the two physical chemists Otto Stern and Max Volmer in 1919. There F0 is the fluorescent intensity of the fluorescent dye without the quencher, F is the fluorescent intensity of fluorescent dye with the quencher. Ks stands for the Stern-Volmer-constant and [Q] for the concentration of the quencher.

Dynamic Quenching
are non-radioactive, short-range quenching methods that occur between two light-sensitive molecules (called donor and acceptor fluorophores). Exchange of electrons between donor and acceptor fluorophore happens non-radioactively – without releasing of photons during the process. Dynamic quenching methods, explained further are: Förster Energy Transfer, Dexter Energy Transfer and Ecxiplex.

Förster Energy Transfer
is a non-radioactive phenomenon in which donor fluorophore transmits electron(s) to acceptor fluorophore without coming in direct contact. Fluorescence Resonance Energy Transfer (FRET) is a technique for measuring distance between two light sensitive molecules; it relies on Förster energy transfer principle. Since this process is so distance-dependent, using of it has become almost exclusively biology-driven. The most useful application is measuring the size of large molecules. A donor-acceptor pair of fluorophores is attached to a big molecule and length is measured over the time that passes while donor transmits energy to the acceptor. Application: Information is gathered only in case if no conformational changes occur to the subject molecule. If the shape or size of molecule is compromised, then information gathered will be useful for analyzing dynamical protein-based processes occurring between two fluorophores attached to the subject. Today, this technique is widely applied in many fields such as single-molecule experiments, molecular motors, biosensors and DNA mechanical movements.

Dexter Energy Transfer
similarly to Förster Energy Transfer, is a non-radioactive and short range process; though by principle and range they are different. Dexter Energy transfer happens only when two chemical groups (by fluorophores- intermolecular) or two parts (fluorophores-intramolecular) of a chemical group collide and exchange electrons bilaterally. Ground-State group (G) might come into contact with Excited, fluorescent group (E) and take away the electrons that account for fluorescence. Dexter energy transfer stands out as it requires a so-called “Wavefunction Overlap” between two fluorophores, in other terms; - atoms on molecules or chemical groups need to overlap their electron clouds. The energy transferring electron will travel from donor to acceptor and occupy acceptor’s leas occupied orbital. Energy Transfer results in donor’s returning from excited to ground state and acceptor’s maintaining the ground state due to greater electronegativity it has. Now that the energy is transferred there are no fluorophores that are excited and emit light, and we can say that the quenching process (decreasing of light emission) has happened. Application: Dexter energy transfer had been acclaimed as one of premier phenomena upon which photochemistry relied. Nowadays its application is more popular in emissions fields, in such as energy converters and organic LED’s

Exciplex
An Excimer is a very shortly existing molecule, either dimeric (consisting of two similar monomers A-A) or heterodimeric (consisting of two different monomers A-B). An Excimer cannot exist if both monomers are in ground-state phase. Therefore a dimer or a heterodimer has to consist of an inert group or element (with full octet; e.g. a noble gas) and an excited group or element. “Exciplex” (short for excited complex) is the other name for a heterodimeric excimer. Quenching process performed by Exciplexes relies heavily upon their “CT” (charge-transfer) character. An exciplex binds covalently to a target molecule, fluorescence of which needs to be quenched, and the resultant chemical entity is referred to as the “Charge Transfer Complex”. In The charge transfer complex itself, starts the quenching process. A CT complex is also called “Electron-Donor-Acceptor complex”; this means that a CT complex may be created by two fluorophores and a molecule, or be present in one large molecule as its two different parts providing the charge transfer capability. Fluorophores usually ought to bind to a large fluorescent macromolecule in order to form a CT complex and start decreasing its fluorescence. Unpaired electrons on the ends of both, - fluorophores and the macromolecule form covalent bonds (spin-pairs) and the energy dissipated by covalent bonds tends to decrease the CT complex energy as well as its fluorescence. The Process causes CT complex to stabilize and therefore is often called “CT Stabilization”. In another scenario, where donor-acceptor functionality is present within a macromolecule itself, the simple electron transfer happens after fluorescence is given off at a point at which molecule can no longer maintain its stable conformation and “performs” CT in order to stabilize. Application: This form of quenching and forming covalent bonds is of particular interest to fields of biology that rely on fluorescence spectroscopy techniques mainly as, and for most research means. There exists evidence indicating that CT stabilization leads to a conical intersection (concentration electrical energy in the center) of subject molecules of quenching, which is useful for analyzing electrical and dynamical activity data gathered during quenching and other chem ical processes that a subject molecule undergoes.

Medical Applications
Quenching is a really good visible physical phenomenon, that's why it is used as an indicator for molecular processes.

If DNA strand is hybridising with an opposite strand it gets quite linear and stiff. Fluorphor and Quencher are attached to the ends. If the bases are paring correctly the Fluorphor and Quencher disconnect and the quenching stops.
 * Indicator for DNA hybridisation

The ends of short DNA fragments (telomer sequence), connected with a fluorescent dye and quencher through a covalent bond, are divided in a solution. The dye is producing light. If the there are any potassium-ions present, the DNA fragment is wrapping around the potassium-ion and the endings are touching each other. The fluorescence is quenched (lightning stops).
 * Indicator for Potassium-ions

On a Rubidium complex one can show the level of oxygen saturation depending on the level of quenching.
 * Indicator of loose Oxygen