Fluorescence microscopy fluorophore choice

Just as for any other fluorescence microscopy technique, the choice of the fluorescent probe is of significant importance for PCS. Drops in the autocorrelations curves can occur as a result of photophysical and photochemical processes. In particular, the contribution of saturation effects and triplet blinking has been investigated [97, 98] and the rates of intersystem crossing and triplet decay as well as the excitation cross section of fluorophores could be determined [12]. In addition, antibunching is determined by the photophysics of the fluorophore. Therefore, the choice of appropriate dyes is essential to obtain meaningful results. Apart from that, the fluorescent probe should also serve as a selective label to... 

Perhaps the most well-recognized fluorescent dye for detection of DNA hybridization is ethidium bromide (EtBr). EtBr is a cationic phenanthridinium compound that can bind to DNA by intercalation. This dye has an excitation maxima at 518 nm when bound to double-stranded DNA (dsDNA). Excitation of EtBr is often done by use of an argon ion laser, making this fluorophore a viable choice for applications in optical sensors as well as confocal scanning laser microscopy and fluorometry [41]. The structure of ethidium bromide is shown in Fig. 6. 

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