Targeting of nucleic acid junctions: Addressing to a branch point an oligodeoxynucleotide conjugated with an intercalator

Abstract

It is possible to enhance targeting of a DNA stem flank domain with a complementary DNA when it is conjugated with diphenyl ether at the branch point. The nucleoside 2'-deoxy-5-methyl-N4-(4-phenoxy-phenyl)cytidine (5) was synthesized from thymidine by tritylation, acetylation, amination via 2,4,6-trimethylbenzenesulfonyl activation and subsequent de-protection. When a three-way junction is formed with a bulged nucleoside 5 at the branch point, the thermal melting temperature was increased by 9°C when compared with wild-type DNA. When hybridizing to one of the flanks at a stem allowing coaxial stacking to the stem, modification at the branch point resulted in ΔT(m) = 5.8°C. For targeting to RNA the results were more ambiguous. RNase H activity was observed in some cases when an intercalating aromatic ring was addressed at the branch point. RNase H activity was observed even for a short 7mer ODN.