Design of the new recognition molecules for the formation of triplex helix DNA at any predetermined sites.

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Since triplex formation within the major groove of duplex DNA has been proposed as a selective method for specific inhibition of gene expression at a predetermined sequence, a major concern has been to overcome its intrinsic limitation that triplexes are formed only toward homopurine-homopyrimidine sequences of the duplex. That is, pyrimidine bases within the homopurine strand of the duplex inhibit triplex formation; therefore, efforts have been focused on development of a non-natural base structure to stabilize triplexes at such interrupting sites. Nevertheless, triplex formation at any DNA sequence has remained a challenging theme.In this approach, we focused on an antiparallel triplex formed with purine-rich triplex-forming oligonucleotides (TFO), because the antiparallel triplexes are formed under physiological conditions with higher stability than the parallel ones with pyrimidine TFOs.We designed a new general structure of nucleoside analogs bearing an aromatic part for stacking, a base for Hoogesteen hydrogen bonds, and a [3.3.0]bicycooctane structure to fix fix the two former components. The newly designed molecule was named the W-shaped nucleic acid (WNA) after its shape. In the antiparallel orientation, the purine base is expected to form two Hoogesteen hydrogen bonds toward the target purine base within a pyrimidine strand of the duplex, and an aromatic may play a role to maintain stacking interaction of the TFO continuously through the new nucleoside analog.In conclusion, we have revealed that the new W-shaped nucleic acid derivative WNA-bT exhibits high stabilization effect toward a TA interrupting site with high selectivity. In addition, WNA-bC showed selective stabilization toward the duplex having a CG interrupting site. Thus, the new WNA analogs would become new candidates for the formation of non-natural type triplexes with high selectivity and affinity to a TA and to a CG interrupting site.