Synthesis and purification of a novel DNA intercalator-oligonucleotide conjugate

A novel DNA intercalator-oligonucleotide conjugate, naphthyl imide-substituted oligonucleotide, was synthesized by S-alkylation reaction, and then purified by HPTLC. The synthetic compounds were identified by HPLC and ultraviolet absorption spectrophotometer. In order to improve the coupling reaction and decrease the side-reaction, the optimal concentration of K⁺ for the synthesis should be higher than that of thiophosphate oligonucleotide but lower than that of N- (6-hexanoxyl)-3-nitro-1, 8-naphthyl imide. The solution, isopropanol/H₂O/ammonia (5:3:1, v/v), was elucidated to be the optimal mobile phase for purification. It was shown that potassium ion concentration plays an important role in the coupling reaction. The yield was increased from 20% to 40-50% by controlling K⁺concentration. Isopropanol/H2O/ammonia (5:3:1, v/v) proved to be the optimal mobile phase for purification.