Interactions Between Chromophores and their Microenvironment

The chromophore environment can affect the spectral position of the absorption and emission bands, the absorption and emission intensity (eM, r), and the fluorescence lifetime as well as the emission anisotropy, e.g., in the case of rigid matrices or hydrogen bonding. Changes in temperature typically result only in small spectral shifts, yet in considerable changes in the fluorescence quantum yield and lifetime. This sensitivity can be favorably exploited for the design of fluorescent sensors and probes [24, 51], though it can unfortunately also hamper quantification from simple measurements of fluorescence intensity [116], The latter can be, e.g., circumvented by ratiometric measurements [24, 115], 

For both organic dyes and QDs, bioconjugation often leads to a decrease in fluorescence quantum yield and thus typically also in emission lifetime. Parameters that can affect label fluorescence are the chemical nature and the length of the spacer and, at least for organic dyes, the type of neighboring biomolecules like oligonucleotides or amino acids in the bioconjugated form. 

Generally, the knowledge of microenvironment effects greatly simplifies label choice. This is an advantage of organic dyes as the spectroscopic properties of many 

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