Nucleosides and nucleotides. 218. Alternate-strand triple-helix formation by the 3'-3'-linked oligodeoxynucleotides using a purine motif.
In this paper, we describe the synthesis of the 3'-3'-linked TFOs that can form the antiparallel triplexes with the duplex DNA target by reverse Hoogsteen hydrogen bonds. Stability of the alternate-strand triplexes between these TFOs and the target DNAs was investigated using the electrophoretic mobility shift assay (EMSA). It was found that 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. We also tested the ability of the 3'-3'-linked TFOs to inhibit cleavage of the duplex DNA target 17 by the restriction enzyme EcoT14I and found that the 3'-3'-linked TFOs 12 and 13 inhibited the cleavage by the enzyme more effectively than the unlinked decamer 8. Thus, the TFOs linked with pentaerythritol may be useful as the antigene oligonucleotide to the DNA targets, which have alternating oligopyrimidine-oligopurine sequences.
Hoshika
Shuichi
S
Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
Ueno
Yoshihito
Y
Matsuda
Akira
A
D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D009705:Nucleosides / Q000737:chemistry*; D009711:Nucleotides / Q000737:chemistry*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011685:Purine Nucleotides / Q000737:chemistry
D009692:Nucleic Acid Heteroduplexes; D009705:Nucleosides; D009711:Nucleotides; D009838:Oligodeoxyribonucleotides; D011685:Purine Nucleotides; C051802:triplex DNA; D004247:DNA