Fluorophore brightness

Considerations for Labeling Biomolecules with Fluorophores Brightness of Fluorophore... 

Umezawa K, Matsui A, Nakamura Y, Citterio D, Suzuki K (2009) Bright, color-tunable fluorescent dyes in the Vis/NIR region establishment of new tailor-made multicolor fluorophores based on borondipyrromethene. Chem Eur J 15 1096—1106... 

The quantum yield (Q) represents the ratio between the number of photons absorbed and photons emitted as fluorescence. It is a measure of brightness of the fluorophore and represents the efficiency of the emission process. The determination of absolute quantum yield for a fluorophore is experimentally difficult. Therefore, usually relative quantum yield values are determined. To measure the relative quantum yield of a fluorophore, the sample is compared to a standard fluorophore with an established quantum yield that does not show variations in the excitation wavelength [5, 6]. 

It is possible to make FRET measurements using much simpler and less mathematically intense measurement methods. If the excitation light were not to excite the acceptor fluorophore directly, the acceptor should only emit light when the two fluorophores are in close enough proximity for FRET. In addition, the brightness of the donor should also be reduced because the lifetime should be... 

The fast, sensitive, reliable, and reproducible detection of (bio)molecules including quantification as well as biomolecule localization, the measurement of their interplay with one another or with other species, and the assessment of biomolecule function in bioassays as well as in vitro and in vivo plays an ever increasing role in the life sciences. The vast majority of applications exploit extrinsic fluorophores like organic dyes, fluorescent proteins, and also increasingly QDs, as the number of bright intrinsic fluorophores emitting in the visible and NIR is limited. In the near future, the use of fluorophore-doped nanoparticles is also expected to constantly increase, with their applicability in vivo being closely linked to the intensively discussed issue of size-related nanotoxicity [88]. 

To increase the speed of the TIRF-based kinetic techniques, the perturbation can be optical rather than chemical. If the evanescent wave intensity is briefly flashed brightly, then some of the fluorophores associated with the surface will be photobleached. Subsequent exchange with unbleached dissolved fluorophores in equilibrium with the surface will lead to a recovery of fluorescence, excited by a continuous but much attenuated evanescent wave. The time course of this recovery is a measure of the desorption kinetic rate k2. This technique1-115) is called TIR/FRAP (or TIR/FPR) in reference to fluorescence recovery after photobleaching (or fluorescence photobleaching recovery). 

TIRF is an experimentally simple technique for selective excitation of fluorophores on or near a surface. It can be set up on a standard upright or inverted microscope, preferably but not necessarily with a laser source, or in a nonmicroscopic custom setup or commercial spectrofluorimeter. In a microscope, the TIRF setup is compatible and rapidly interchangeable with bright-field, dark-field, phase contrast, and epi-illumination and accommodates a wide variety of common microscope objectives without alteration. 

Brightness. Brighmess of a fluorophore is proportional to the product of the molar absorption coefficient at the excitation wavelength times its quantum yield. This is the theoretical value, but in practice it can be much reduced by fluorescent quenching on interaction with other labels on the protein or DNA surfaces. Sulfonic acid groups on the aromatic rings of cyanines reduce this interaction, giving very much improved protein fluorescence. 

Fluorescent compounds are sensitive to changes in their chemical environment. Alterations in media pH, buffer components, solvent polarity, or dissolved oxygen can affect and quench the quantum yield of a fluorescent probe (Bright, 1988). The presence of absorbing components in solution that absorb light at or near the excitation wavelength of the fluorophore will have the effect of decreasing luminescence. In addition, noncovalent interactions of the probe with other components in solution can inhibit rotational freedom and quench fluorescence. 

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