Terminal excimer and exciplex fluorescence a sensitive oligonucleotide probe

The development of a new sensitive, safe and easy to use exciplex probes system for the detection of DNA is of relevant importance. The aim of this study was to develop a fluorescence- based technique to work in homogenous, and then heterogeneous assays systems. Exciplex signal with DNA hybridisation were determined in solution using fluorescence measurements and complementary fluorophore-labeled oligonucleotides. One oligonucleotide probe, was labeled with a 5′-terminal pyrene, and the other was labelled with 3′-terminal naphthalene. The juxtaposition of the two labels in double-stranded complexes, results in a strong exciplex signal at a longer wavelength (∼ 480nm) thereby providing the means to differentiate single-stranded DNA from double-stranded DNA. Since measurements were based on fluorescence, DNA denaturation and association could be monitored routinely at low DNA concentrations. The importance of the presence of various counter cations (Na+, K+ and Mg2+) on exciplex signal intensity was evaluated. The results obtained represent the first case of an oligonucleotide terminally located probe system based on exciplex fluorescence emission.