Fluorophores quenchers properties

Because of the variety of substances which act as quenchers, one can frequently identify fluorophore-quencher combinations for a desired purpose. It is important to note that not all fluorophores are quenched by all the substances listed above. This fact occasionally allows selective quenching of a given fluorophore. The occurrence of quenching depends upon the mechanism, which in turn depends upon the chemical properties of the individual molecules. Detailed analysis of the mechanism of quenching is complex. In this chapter we will be concerned primarily with the type of quenching, that is, whether quenching is diffusive or static in nature. Later in this chapter, we describe biochenucal applications of quenching. 

When compared to fluorescent proteins, fluorophores and quenchers of fluorescence (short quenchers) are small molecules with sizes varying from 1 to 10 A. They are the main building blocks for constructing small molecule FRET probes. As molecular entities, they might influence the performance of the probe to a great extent. Their fluorescent properties will determine the sensitivity and dynamic range of the sensor. The success of the probe for a specific application will depend on the selection of the right fluorophores... 

Table 1 The physical properties of the main fluorophores and fluorescent quenchers reported in this article ...

Ksv characterizes the accessibility of the fluorophore to the quencher while the bimolecular quenching constant kq characterize the diffusion properties of the quencher. 

In the time window between the absorption and emission of a photon, a number of molecular processes can occur. They concern either (a) the fluorophore itself (its rotational and translational diffusion, conformational changes, transition between electronic states differing in dipole moment) or (b) molecules in its immediate vicinity (reorganization of the solvent shell, diffusion of quenchers, etc.). All these processes influence the fluorescence properties (position and shape of the emission band, quantum yield, decay time, etc.). In most cases, both the fluorophore and the surrounding molecules participate in the process and fluorescence characteristics are in fact influenced by their mutual interactions. Figure 3 shows a survey of important... 

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