A novel fluorescent tag for labelling of some antisense oligonucleotides

A new versatile fluorescent tag, 4-acetylamino-1,8-naphthalimido-N-caproic acid (NCA) has been synthesized and characterized, and the optimal conditions for the maximum fluorescence using this tag allow a sensitivity level of 10(-9) mol/l. Useful fluorescence is observed upon covalent linking of this tag via its activated carboxy end to an alkylamino moiety, activated by the use of carbonyldiimidazole and hexamethylenediamine at the 5'-termini of an octamer, d(TCTTGCTC), a 33-mer, and a 41-mer complementary to the tat initiator of the HIV-1 genome. A new method for the generation of alkylamino function at the 5'-termini of oligonucleotides by the use of N-(4-bromobutyl) phthalimide is also described. The variation in fluorescence with respect to alteration of chain length of the oligonucleotides has also been studied. The fluorescence exhibited by these oligodeoxynucleotide (ODN)-NCA conjugates suggests that they may have a potential application as experimental tools in medicine and molecular biology.