Triplex-forming oligonucleotides (TFOs) are sequence-specific DNA-binding agents, but their recognizable duplexes are limited to homopurine/homopyrimidine sequences because of interruption of pyrimidine base in the purine strand. This problem has not been fully solved despite numerous studies. We have previously reported that the novel nucleoside analogues (WNA: W-shaped nucleoside analogues), WNA-betaT and WNA-betaC, can recognize a TA and a CG interrupting sites to form triplexes with high stability and selectively, respectively. However, further investigations have shown that the triplex formation using the WNA derivatives is dependent on its neighbouring bases of the TFOs. In this study, the new WNA analogues having a variety aromatic ring were synthesized to evaluate effects on sequence dependency. And it was found that changes in the substituent of aromatic ring of WNA derivatives altered the binding selectivity and stability in the triplex formation.
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