Fluorescence correlation spectroscopy to study the degradation of oligonucleotides, both naked and complexed, to cationic carriers

The degradation of double-labeled oligonucleotides (ONs) was followed by the disappearance of Fluorescence Energy Transfer between the rhodamine green and Cy5 fluorophores attached to the 3′ and 5′ end of the oligonucleotides. The fluorescence intensities after rhodamine green excitation were recorded using the ultra-sensitive detectors of a dual-color FCS setup. The ratio of the Cy5 to rhodamine green fluorescence showed to give accurate information on the integrity of the oligonucleotides and could be easily used to follow the degradation of naked or complexed double-labeled oligonucleotides, both in buffer and in living cells.