3'-O-<4''-((N-dansyl)-5'''-aminopent-1-yl-oxy)-5''-methoxy-2''-nitrophenylmethyl>-5'-O-(tert-butyldiphenylsilyl)thymidine | 221895-91-6

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 核苷和核苷酸类似物
• 英文名称: 3'-O-<4''-((N-dansyl)-5'''-aminopent-1-yl-oxy)-5''-methoxy-2''-nitrophenylmethyl>-5'-O-(tert-butyldiphenylsilyl)thymidine
• CAS: 221895-91-6
• 化学式: C₅₁H₆₁N₅O₁₁SSi
• 分子量: 980.224
• InChiKey: ROYRQIWBURZZQK-PBQAQGAHSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  6.96
• 重原子数：
  69.0
• 可旋转键数：
  21.0
• 环数：
  7.0
• sp3杂化的碳原子比例：
  0.37
• 拓扑面积：
  193.56
• 氢给体数：
  2.0
• 氢受体数：
  13.0

反应信息

• 作为反应物：
  描述：

  3'-O-<4''-((N-dansyl)-5'''-aminopent-1-yl-oxy)-5''-methoxy-2''-nitrophenylmethyl>-5'-O-(tert-butyldiphenylsilyl)thymidine 在 四丁基氟化铵 作用下， 以 四氢呋喃 为溶剂， 反应 0.75h， 生成 3'-O-<4''-((N-dansyl)-5'''-aminopent-1-yl-oxy)-5''-methoxy-2''-nitrophenylmethyl>thymidine 5'-O-triphosphate
  参考文献：
  名称：

  Syntheses of Nucleosides Designed for Combinatorial DNA Sequencing

  摘要：

  Nucleoside triphosphates I with 3'-O-blocking groups that are both photolabile and fluorescent were required to investigate the viability of a strategy for sequencing DNA in a combinatorial fashion (see Figure 1). Four compounds were prepared to realize this goal. Two of them, 14a and 14t, had dansyl-functionalized, 3'-O-(2"-nitrobenzyl) ether groups, while the other two, 18a and 18t, had similar pendant carbonate groups. Tests for incorporation of these analogues were performed by using five different DNA replicating enzymes, but the analogues were not incorporated. These results were surprising in view of the fact that previous studies had shown that 3'-O-(2"-nitrobenzyl)adenosine triphosphate II was incorporated by Bst DNA polymerase I. However, molecular simulations with the coordinates of a T7 polymerase crystal structure as a model demonstrates that analogues 14a, 14t, 18a and 18t are too large to fit into the enzyme active site, whereas accommodation of the unsubstituted 2-nitrobenzyl compound II is much less demanding. We conclude that both the nucleoside triphosphates and the DNA polymerase enzyme must be modified if the proposed DNA sequencing scheme is to be viable.

  DOI：

  10.1002/(sici)1521-3765(19990301)5:3<951::aid-chem951>3.0.co;2-g
• 作为产物：
  描述：

  1-<(N-allyloxycarbonyl)-5'-aminopent-1-yl-oxy>-4-(hydroxymethyl)-2-methoxy-5-nitrobenzene 在 四(三苯基膦)钯 4-二甲氨基吡啶 、 sodium hydroxide 、 四溴化碳 、 四丁基氢氧化铵 、 水 、 二乙胺 、 三乙胺 、 三苯基膦 、 sodium iodide 作用下， 以 四氢呋喃 、 氯仿 、 乙酸乙酯 、 N,N-二甲基甲酰胺 为溶剂， 反应 24.25h， 生成 3'-O-<4''-((N-dansyl)-5'''-aminopent-1-yl-oxy)-5''-methoxy-2''-nitrophenylmethyl>-5'-O-(tert-butyldiphenylsilyl)thymidine
  参考文献：
  名称：

  Syntheses of Nucleosides Designed for Combinatorial DNA Sequencing

  摘要：

  Nucleoside triphosphates I with 3'-O-blocking groups that are both photolabile and fluorescent were required to investigate the viability of a strategy for sequencing DNA in a combinatorial fashion (see Figure 1). Four compounds were prepared to realize this goal. Two of them, 14a and 14t, had dansyl-functionalized, 3'-O-(2"-nitrobenzyl) ether groups, while the other two, 18a and 18t, had similar pendant carbonate groups. Tests for incorporation of these analogues were performed by using five different DNA replicating enzymes, but the analogues were not incorporated. These results were surprising in view of the fact that previous studies had shown that 3'-O-(2"-nitrobenzyl)adenosine triphosphate II was incorporated by Bst DNA polymerase I. However, molecular simulations with the coordinates of a T7 polymerase crystal structure as a model demonstrates that analogues 14a, 14t, 18a and 18t are too large to fit into the enzyme active site, whereas accommodation of the unsubstituted 2-nitrobenzyl compound II is much less demanding. We conclude that both the nucleoside triphosphates and the DNA polymerase enzyme must be modified if the proposed DNA sequencing scheme is to be viable.

  DOI：

  10.1002/(sici)1521-3765(19990301)5:3<951::aid-chem951>3.0.co;2-g