Synthesis of new functionalized nucleic acids by the pentaerythritol linker.

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The 3'-3'-linked oligodeoxynucleotides (ODNs) by pentaerythritol with an intercalator at the junction point is that can form the parallel triplexes with the duplex target by Hoogsteen hydrogen bonds were synthesized. Stability of the triplexes with the target duplexes was studied by thermal denaturation. The 3'-3'-linked ODNs with the anthraquinonyl group enhanced the thermal stability of the triplexes when compared with those without the intercalator and the unmodified nonamer. It was found that the ODNs carrying the anthraquinonyl groups can form thermally stable triplexes by skipping two or three extra base pairs between two binding domains of the target duplexes. The 3'-3'-linked ODN with the anthraquinonyl group at the junction point inhibited the cleavage by the enzyme Hind III more effectively.We also synthesized the 3'-3'-linked TFOs that can form the antiparallel triplexes with the duplex DNA target by reverse Hoogsteen hydrogen bonds. The alternate-strand triplexes were significantly stabilized by linking the TFO fragments with the pentaerythritol linker. And, unlike the alternate-strand triplexes composed of the pyrimidine motif, the terminal ammonium ion of the aminobutyl-linker and the intercalator of the TFOs did not contribute to the stability of the alternate-strand triplex comprised of the purine motif.