3'-O-tert-butyldimethylsilyl-2'-deoxy-5'-O-(4,4'-dimethoxytrityl)-2'-piperazino-2',3'-secouridine | 1120329-65-8

• 分子结构分类: 有机化合物 - 苯类化合物 - 三苯基化合物
• 英文名称: 3'-O-tert-butyldimethylsilyl-2'-deoxy-5'-O-(4,4'-dimethoxytrityl)-2'-piperazino-2',3'-secouridine
• 英文别名: 1-[(1R)-1-[(2R)-1-[bis(4-methoxyphenyl)-phenylmethoxy]-3-[tert-butyl(dimethyl)silyl]oxypropan-2-yl]oxy-2-piperazin-1-ylethyl]pyrimidine-2,4-dione
• CAS: 1120329-65-8
• 化学式: C₄₀H₅₄N₄O₇Si
• 分子量: 730.977
• InChiKey: BRTLERIPGRLFRI-ZEEKBPLESA-N

计算性质

• 辛醇/水分配系数(LogP)：
  5.37
• 重原子数：
  52
• 可旋转键数：
  17
• 环数：
  5.0
• sp3杂化的碳原子比例：
  0.45
• 拓扑面积：
  111
• 氢给体数：
  2
• 氢受体数：
  9

反应信息

• 作为反应物：
  描述：

  3'-O-tert-butyldimethylsilyl-2'-deoxy-5'-O-(4,4'-dimethoxytrityl)-2'-piperazino-2',3'-secouridine 在 吡啶 、 吡啶盐酸盐 、 triethylamine tris(hydrogen fluoride) 作用下， 以 四氢呋喃 、 二氯甲烷 为溶剂， 反应 6.0h， 生成 2'-deoxy-5'-O-(4,4'-dimethoxytrityl)-2'-(4-(9-fluorenylmethoxycarbonyl)piperazino)-2',3'-secouridine
  参考文献：
  名称：

  Thermodynamic and biological evaluation of a thrombin binding aptamer modified with several unlocked nucleic acid (UNA) monomers and a 2′-C-piperazino-UNA monomer

  摘要：

  Thrombin binding aptamer is a DNA 15-mer which forms a G-quadruplex structure and possess promising anticoagulant properties due to specific interactions with thrombin. Herein we present the influence of a single 2'-C-piperazino-UNA residue and UNA residues incorporated in several positions on thermodynamics, kinetics and biological properties of the aptamer. 2'-C-Piperazino-UNA is characterized by more efficient stabilization of quadruplex structure in comparison to regular UNA and increases thermodynamic stability of TBA by 0.28-0.44 kcal/mol in a position depending manner with retained quadruplex topology and molecularity. The presence of UNA-U in positions U3, U7, and U12 results in the highest stabilization of G-quadruplex structure (Delta Delta G degrees(37) = -1.03 kcal/mol). On the contrary, the largest destabilization mounting to 1.79 kcal/mol was observed when UNA residues were placed in positions U7, G8, and U9. Kinetic studies indicate no strict correlation between thermodynamic stability of modified variants and their binding affinity to thrombin. Most of the studied variants bind thrombin, albeit with decreased affinity in reference to unmodified TBA. Thrombin time assay studies indicate three variants as being as potent as TBA in fibrin clotting inhibition. (C) 2011 Elsevier Ltd. All rights reserved.

  DOI：

  10.1016/j.bmc.2011.06.087
• 作为产物：
  描述：

  哌嗪 、 以 乙醇 为溶剂， 反应 2.0h， 以441 mg的产率得到3'-O-tert-butyldimethylsilyl-2'-deoxy-5'-O-(4,4'-dimethoxytrityl)-2'-piperazino-2',3'-secouridine
  参考文献：
  名称：

  解锁的核酸三联吡啶单体的合成和核酸双链体中二价金属离子的结合

  摘要：

  本文中，我们介绍了含有解锁核酸（UNA）吡啶吡啶单体的修饰寡核苷酸的合成和热稳定性研究。将该单体掺入DNA双链体的两条链中，可在添加或撤出二价金属离子时进行可逆的热稳定性调节。这种现象的可能解释是两个三联吡啶单元与金属离子之间的链间络合。该系统可用于基于DNA杂交的纳米级设备的开发。

  DOI：

  10.1021/jo9019978

文献信息

• Thermodynamic and biological evaluation of a thrombin binding aptamer modified with several unlocked nucleic acid (UNA) monomers and a 2′-C-piperazino-UNA monomer
  作者：Troels B. Jensen、Jonas R. Henriksen、Bjarne E. Rasmussen、Lars M. Rasmussen、Thomas L. Andresen、Jesper Wengel、Anna Pasternak

  DOI：10.1016/j.bmc.2011.06.087

  日期：2011.8

  Thrombin binding aptamer is a DNA 15-mer which forms a G-quadruplex structure and possess promising anticoagulant properties due to specific interactions with thrombin. Herein we present the influence of a single 2'-C-piperazino-UNA residue and UNA residues incorporated in several positions on thermodynamics, kinetics and biological properties of the aptamer. 2'-C-Piperazino-UNA is characterized by more efficient stabilization of quadruplex structure in comparison to regular UNA and increases thermodynamic stability of TBA by 0.28-0.44 kcal/mol in a position depending manner with retained quadruplex topology and molecularity. The presence of UNA-U in positions U3, U7, and U12 results in the highest stabilization of G-quadruplex structure (Delta Delta G degrees(37) = -1.03 kcal/mol). On the contrary, the largest destabilization mounting to 1.79 kcal/mol was observed when UNA residues were placed in positions U7, G8, and U9. Kinetic studies indicate no strict correlation between thermodynamic stability of modified variants and their binding affinity to thrombin. Most of the studied variants bind thrombin, albeit with decreased affinity in reference to unmodified TBA. Thrombin time assay studies indicate three variants as being as potent as TBA in fibrin clotting inhibition. (C) 2011 Elsevier Ltd. All rights reserved.
• Synthesis of an Unlocked Nucleic Acid Terpyridine Monomer and Binding of Divalent Metal Ion in Nucleic Acid Duplexes
  作者：Kasper K. Karlsen、Troels B. Jensen、Jesper Wengel

  DOI：10.1021/jo9019978

  日期：2009.11.20

  Herein we present the synthesis and thermal stability studies of modified oligonucleotides containing an unlocked nucleic acid (UNA) terpyridine monomer. Incorporation of this monomer into both strands of a DNA duplex allowed reversible thermal stability modulation upon addition or withdrawal of divalent metal ions. A likely explanation of this phenomenon is interstrand complexation between two terpyridine

  本文中，我们介绍了含有解锁核酸（UNA）吡啶吡啶单体的修饰寡核苷酸的合成和热稳定性研究。将该单体掺入DNA双链体的两条链中，可在添加或撤出二价金属离子时进行可逆的热稳定性调节。这种现象的可能解释是两个三联吡啶单元与金属离子之间的链间络合。该系统可用于基于DNA杂交的纳米级设备的开发。