DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and selective triplexes

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·C^R1 where ψ and C^R1 are base moieties 2′-deoxypseudouridine and 5-substituted deoxycytidine, respectively. We examined several electron-withdrawing substituents for R1 and found that 5-bromocytosine (C^Br) could selectively recognize ψ. In addition, we developed a new PPI derivative, PPI^Me, 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-PPI^Me, and TFOs containing T, C, C^Br, and C3. We studied the selective triplex formation between these duplexes and TFOs using UV-melting and gel mobility shift assays.