Fluorescent nucleic acid base analogues

The use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent probemolecule close to the site of examination in the nucleic acid-containing system of interest withmerely a minimal perturbation to the natural structure makes fluorescent base analogues highlyattractive. In recent years, there has been a growing interest in developing novel candidates inthis group of fluorophores for utilization in various investigations. This review describes thedifferent classes of fluorophores that can be used for studying nucleic acid-containing systems,with an emphasis on choosing the right kind of probe for the system under investigation.It describes the characteristics of the large group of base analogues that has an emission that issensitive to the surrounding microenvironment and gives examples of investigations in whichthis group of molecules has been used so far. Furthermore, the characterization and useof fluorescent base analogues that are virtually insensitive to changes in their microenvironmentare described in detail. This group of base analogues can be used in several fluorescenceinvestigations of nucleic acids, especially in fluorescence anisotropy and fluorescence resonanceenergy transfer (FRET) measurements. Finally, the development and characterization of the firstnucleic base analogue FRET pair, tCO–tCnitro, and its possible future uses are discussed