Fluorophores for labeling of DNA/RNA fragments

Three fluorescent tags, viz. 4-acetylamino-(N-caproyl)-1,8-naphthalimide, 4-acetylamino-(N-p-carboxyphenyl)-1,8-naphthalimide and 4-acetylamino-1,8-naphthalic anhydride have been synthesized starting from acenaphthene. These were characterized by chromatographic and spectroscopic studies and their relative fluorescence assessed under different conditions. An octamer d(TCTTGCTC) complementary to tat initiator of HIV-1, SK 102(+), a 33-mer and SK 19(+), a 41-mer complementary to a highly conserved region of HIV-1 genome were synthesized. 4-Acetylamino-(N-caproyl)-1, 8-naphthalimide was tagged via its carboxyl function to the 5'-end of these oligonucleotides by generating aliphatic amino function through the reaction of 5'-hydroxyl with carbonyldiimidazole and subsequently with hexamethylenediamine. The resultant labelled oligonucleotides were purified by HPLC on RPC C18 column and showed significant fluorescence.