We have previously reported DNA triplexes containing the unnatural base triad G-PPI·C3, in which PPI is an indole-fused cytosine derivative incorporated into DNA duplexes and C3 is an abasic site in triplex-forming oligonucleotides (TFOs) introduced by a propylene linker. In this study, we developed a new unnatural base triad A-ψ·CR1 where ψ and CR1 are base moieties 2′-deoxypseudouridine and 5-substituted deoxycytidine, respectively. We examined several electron-withdrawing substituents for R1 and found that 5-bromocytosine (CBr) could selectively recognize ψ. In addition, we developed a new PPI derivative, PPIMe, having a methyl group on the indole ring in order to achieve selective triplex formation between DNA duplexes incorporating various Watson–Crick base pairs, such as T-A, C-G, A-ψ, and G-PPIMe, and TFOs containing T, C, CBr, and C3. We studied the selective triplex formation between these duplexes and TFOs using UV-melting and gel mobility shift assays.
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