Fluorophores polarity affects

Any factor that affects the size or shape of a molecule, the hindered movement of a fluorophore within a molecule, or the energy transfer within the molecule will affect the measured depolarization of its fluorescence emission. Therefore, the conformation of humic fractions in solution can be studied as a function of pH, ionic strength, temperature, and other factors by depolarization measurements. The principle of the method is that excitation of fluorescent samples with polarized light stimulates... 

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. 

The extinction coefficients and quantum yields of many fluorophores depend on the microenvironment. For example, pH can affect either Cexc or (f). Fluorescein is fluorescent at pH 8 but is almost nonfluorescent at pH 6. Also there are fluorophores that are sensitive to solvent polarity. Dansyl and 7-nitrobenz-2-oxa-l,3-diazole (NBD) are much more fluorescent in hydrocarbon environments than in water. Other fluorophores are sensitive to the microviscosity. The cyanine label Cy3 is significantly more fluorescent in viscous solvents and when bound to proteins and DNA compared to when it is in water. Cyanines and rhodamines, on the other hand, are not sensitive to polarity or pH changes between 4 and 11. 

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