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

设计新的识别分子，用于在任何预定位点形成三螺旋 DNA。

• 批准号: 13672218
• 负责人: SASAKI Shigeki
• 金额: $ 2.24万
• 依托单位: Kyushu University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2001
• 资助国家: 日本
• 起止时间: 2001 至 2002
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-13672218/
• 关键词: triplex DNA; artificial nucleobase analog; antigene; recognition of duplex sequence; inhibition of gene expression; recognition molecule; expansion of triplex code; genome-targeting chemistry; 三本鎖DNA; Hoogsteen水素結合; オリゴヌクレオチド; アンチセンス; バイオテクノロジ

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.

由于已提出在双链体DNA的大沟内形成三链体作为在预定序列特异性抑制基因表达的选择性方法，因此主要关注的是克服其固有的局限性，即三链体仅朝向双链体的高嘌呤-高嘧啶序列形成。也就是说，双链体的高嘌呤链内的嘧啶碱基抑制三链体形成;因此，努力集中在开发非天然碱基结构以在这种中断位点稳定三链体。尽管如此，任何DNA序列上的三链体形成仍然是一个具有挑战性的主题。在这种方法中，我们重点关注由富含嘌呤的三链体形成寡核苷酸（TFO）形成的反平行三链体，因为反平行三链体是在生理条件下形成的。比与嘧啶TFO形成的平行三链体具有更高的稳定性。我们设计了一种新的带有芳香部分的核苷类似物的通用结构用于堆叠，Hoogesteen氢键的基础，和[3.3.0]双环辛烷结构以固定前两个组分。新设计的分子以其形状命名为W形核酸（WNA）。在反平行取向中，嘌呤碱基预期在双链体的嘧啶链内朝向靶嘌呤碱基形成两个Hoogesteen氢键，并且芳香族可以发挥作用以通过新的核苷类似物连续地维持TFO的堆积相互作用。我们已经揭示了新的W形核酸衍生物WNA-bT对TA中断位点表现出高选择性的高稳定效果。此外，WNA-bC显示出对具有CG中断位点的双链体的选择性稳定。因此，新的WNA类似物将成为用于形成对TA和CG中断位点具有高选择性和亲和力的非天然型三链体的新候选物。

项目成果

Sasaki, Shigeki: "Active Oligonucleotides Incorporating Alkylating Agent as Potential Sequence-and Base Selective Modifier of Gene Expression,"Eur. J. Phar. Sci.. 13(1). 43-51 (2001)

Sasaki，Shigeki：“结合烷基化剂的活性寡核苷酸作为基因表达的潜在序列和碱基选择性修饰剂”，Eur。

Nagatsugi, Fumi, Tokuda, Natsuko, Maeda, Minoru, Sasaki, Shigeki: "A New Reactive Nucleoside Analog for Highly Reactive and Selective Cross-linking Reaction to Cytidine Under Neutral Conditions"Bioorg & Med.Chem Lett.. 11(19). 2577-2579 (2001)

Nagatsugi、Fumi、Tokuda、Natsuko、Maeda、Minoru、Sasaki、Shigeki：“一种新的反应性核苷类似物，可在中性条件下与胞苷进行高度反应性和选择性交联反应”Bioorg

Sasaki, S., Yamauchi, H., Nagatsugi, F., Takahashi, R., Taniguchi, Y., Minoru M.: "W-Shape Nucleic Acid (WNA) for Selective Formation of Non-Natural Anti-Parallel Triplex Including a TA Interrupting Site"Tetrahedron Letters. 42(39). 6915-6918 (2001)

Sasaki, S.、Yamauchi, H.、Nagatsugi, F.、Takahashi, R.、Taniguchi, Y.、Minoru M.：“用于选择性形成非天然反平行三链体的 W 形核酸（WNA），包括

Yosuke Taniguchi, Ryo Takahashi, Keiichi Kodama, Yusuke Senko, Minoru Maeda, Shigeki Sasaki: "Selective formation of non-natural type triplexes containing TA interrupting sites with the TFO incorporating W-shape nucleic acid (WNA) analogs"Nucleic Acids Re

Yosuke Taniguchi、R​​yo Takahashi、Keiichi Kodama、Yusuke Senko、Minoru Maeda、Shigeki Sasaki：“使用掺有 W 形核酸 (WNA) 类似物的 TFO 选择性形成含有 TA 中断位点的非天然型三链体”Nucleic Acids Re

Sasaki, Shigeki; Yamauchi, Hiroyuki; Nagatsugi, Fumi; Takahashi, Ryo; Taniguchi, Yosuke; Minoru Maeda.: "W-Shape Nucleic Acid (WNA) for Selective Formation of Non-Natural Anti-Parallel Triplex Including a TA Interrupting Site."Tetrahedron Letters.. 42(39)

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