Design and Synthesis of New Recognition Molecules for the Sequence-Selective Triple Helical DNA Formation

序列选择性三螺旋 DNA 形成的新型识别分子的设计与合成

• 批准号: 07672269
• 负责人: SASAKI Shigeki
• 金额: $ 1.47万
• 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: 1995
• 资助国家: 日本
• 起止时间: 1995 至 1996
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-07672269/
• 关键词: triple helix; triplex; DNA; non-natural base; nucleic acid; hydrogen bonding; 3重鎖DNA; トリプルヘリックス; 遺伝発現制御

The triplex formation between the duplex and a single strand DNA has been shown to inhibit transcription at the specific DNA site, and expected as a new biological tool and a new therapeutic method in the so-called antigene strategy. However, native oligonucleotides can form triplexes only within the major groove of the homopurine-homopyrimidine stretch of DNA,and the triplex is destabilized either at a TA or a CG interrupting site. Thus, for expansion of the target DNA sequence, several groups have been attempting to develop non-native nucleobases for binding a TA or a CG base pair, but these problems have not yet been generally solved. We have designed new nucleobase 1 (BIG or B) to form a base triplet with a CG base pair selectively through Hoogsteen-type hydrogen bonds. In this study, we synthesized the oligonucleotide incorporating the non-native base 1 (B), with which we have investigated triplex formation with several duplex DNAs. As a result, it has been demonstrated that the oligonucleotide incorporating 1 forms triplexes by recognizing a CG base pair within a homopurine-homopyrimidine motif. In addition, it has been also revealed that the new non-native base (2) can stabilize a triplex at a CG site more selectively than 1, and that the selective triplex formation at a TA site is enabled by the new non-native base (3). To our knowledge, these new bases are the first ones that form nonnative-type triplexes selectively with comparable stability with native-type triplexes. Therefore, these non-native bases (1,2,3) will become potential candidates to expand the target sequence containing CG and TA interrupting sites.

双链DNA与单链DNA之间形成的三链结构可以抑制特定DNA位点的转录，有望在所谓的抗基因策略中成为一种新的生物工具和治疗方法。然而，天然寡核苷酸只能在DNA的高嘌呤-高嘧啶延伸的主槽内形成三链，并且三链在TA或CG中断位点处不稳定。因此，为了扩大靶DNA序列，几个小组一直试图开发用于结合TA或CG碱基对的非天然核苷酸碱基，但这些问题尚未得到普遍解决。我们设计了新的碱基1(BIG或B)，通过Hoogsteen氢键选择性地与CG碱基对形成碱基三重态。在这项研究中，我们合成了含有非天然碱基1(B)的寡核苷酸，并用它研究了几个双链DNA的三链形成。结果，已经证明了含有1的寡核苷酸通过识别高嘌呤-高嘧啶基序中的CG碱基对而形成三链。此外，还揭示了新的非天然碱基(2)比1更有选择性地稳定CG位点的三链，而TA位点的选择性三链的形成是由新的非天然碱基(3)实现的。据我们所知，这些新碱基是第一个选择性地形成非本土型三联体的碱基，具有与本土型三联体相当的稳定性。因此，这些非天然碱基(1，2，3)将成为扩展含有CG和TA中断位点的靶序列的潜在候选者。

项目成果

Sasaki,Shigeki: "A New Application of a Peptide Library to Identify Selective Interaction Between Small Peptides in an Attempt to Develop Recognition Molecules toward Protein Surface" Tetrahedron Lett.37(1). 85-88 (1996)

Sasaki、Shigeki：“肽库的新应用，用于识别小肽之间的选择性相互作用，试图开发蛋白质表面的识别分子”Tetrahedron Lett.37(1)。

Fumi Nagatsugi: "Design and Synthesis of New Cross-Linking Agents" Nucleic Acids, Symp. Series. 34. 171-172 (1995)

Fumi Nagatsugi：“新型交联剂的设计与合成”核酸，Symp。

Nakashima, Shouji ; Matsuura, Naoko ; Nagatsugi, Fumi ; Maeda, Minoru ; Sasaki, Sasaki: "The New Artificial Nucleobases for the Selective Formation of the Non-Natural Type Triple Complex with T-A and C-G Base Pairs" Nucleic Acids, Symp.Ser.35. 105-106 (19

中岛，庄二；

Mizushima,Tohru: "Molecular Design of Inhibvitors of in Vito oriC DNA Replication Based on the Potential to Block the ATP Binding of DnaA Protein" J.Biol.Chem.,. 271(4). 25178-25183, (1996)

Mizushima，Tohru：“基于阻断 DnaA 蛋白 ATP 结合潜力的体外 oriC DNA 复制抑制剂的分子设计”J.Biol.Chem.,。

Mizushima,Tohru: "Molecular Design of Inhibitors of in Vitro oriC DNA Replication Based on the Potential to Block the ATP Binding of DnaA Protein" J.Biol.Chem.,. 271(41). 25178-25183 (1996)

Mizushima,Tohru：“基于阻断 DnaA 蛋白 ATP 结合潜力的体外 oriC DNA 复制抑制剂的分子设计”J.Biol.Chem.,。