Nucleosides and nucleotides. 208. alternate-strand triple-helix formation by the 3 '-3 '-linked oligodeoxynucleotides with the anthraquinonyl group at the junction point

The synthesis of 3 ' -3 ' -linked oligodeoxynucleotides (ODNs) with the ant hraquinonyl group at the junction point is described. The ODNs were synthes ized on a DNA synthesizer using a controlled pore glass (CPG) carrying pent aerythritol that has an intercalator at one of the four hydroxymethyl group s. Stability of the triplexes with the target duplexes was studied by therm al denaturation. The 3 ' -3 ' -linked ODNs with the anthraquinonyl group en hanced the thermal stability of the triplexes when compared with those with out the intercalator and the unmodified nonamer 10. It was found that the O DNs 12 and 13 carrying the anthraquinonyl groups can form thermally stable triplexes by skipping two or three extra base pairs between two binding dom ains of the target duplexes. The ability of the 3 ' -3 ' -linked ODNs to in hibit cleavage of the target DNA 22 by the restriction enzyme Hind III was tested. It was found that the 3 ' -3 ' -linked ODN 16 with the anthraquinon yl group at the junction point inhibited the cleavage by the enzyme more ef fectively than the nonamer 14 and the 3 ' -3 ' -linked ODN 15 without the i ntercalator.