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

由于在双链DNA的主要凹槽内形成三联体已被提出作为一种选择性方法，在预定序列上特异性抑制基因表达，因此主要关注的是克服其固有的局限性，即三联体仅在双链的同嘌呤-同嘧啶序列上形成。即，双链的同嘌呤链内的嘧啶碱基抑制三链的形成；因此，人们一直致力于开发一种非天然碱基结构来稳定这些中断位点的三联体。然而，任何DNA序列的三联体形成仍然是一个具有挑战性的主题。在这种方法中，我们重点研究了由富含嘌呤的三聚体形成的反平行三聚体，因为反平行三聚体是在生理条件下形成的，比由嘧啶TFO形成的平行三聚体具有更高的稳定性。我们设计了一种新的核苷类似物的通用结构，其中包含一个用于堆叠的芳香部分，一个用于Hoogesteen氢键的碱基，以及一个用于固定前两个成分的[3.3.0]双环辛烷结构。新设计的分子以其形状命名为w形核酸（WNA）。在反平行方向上，嘌呤碱基有望在双链的嘧啶链内与目标嘌呤碱基形成两个Hoogesteen氢键，并且芳香族可能通过新的核苷类似物持续维持TFO的堆叠相互作用。总之，我们揭示了新的w型核酸衍生物WNA-bT对TA中断位点具有高选择性的高稳定作用。此外，WNA-bC对具有CG中断位点的双链表现出选择性稳定。因此，新的WNA类似物将成为形成对TA和CG中断位点具有高选择性和亲和力的非天然型三联体的新候选物。

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.