3'-amino-N4-benzoyl-2',3'-dideoxy-5'-O-(4,4'-dimethoxytrityl)cytidine | 170236-31-4

• 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'-amino-N4-benzoyl-2',3'-dideoxy-5'-O-(4,4'-dimethoxytrityl)cytidine
• 英文别名: 3'-amino-N4-benzoyl-5'-O-(4,4'-dimethoxytrityl)-2',3'-dideoxycytidine；N(4)-benzoyl-3'-amino-5'-(4,4'-dimethoxytrityl)-2',3'-dideoxycytidine；3'-Amino-n4-benzoyl-2',3'-dideoxy-5'-o-dmt-cytidine；N-[1-[(2R,4S,5S)-4-amino-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]oxolan-2-yl]-2-oxopyrimidin-4-yl]benzamide
• CAS: 170236-31-4
• 化学式: C₃₇H₃₆N₄O₆
• 分子量: 632.716
• InChiKey: DQVBUEBFFZSSSM-VOTWKOMSSA-N

物化性质

• 密度：
  1.27±0.1 g/cm3(Predicted)

计算性质

• 辛醇/水分配系数(LogP)：
  5
• 重原子数：
  47
• 可旋转键数：
  11
• 环数：
  6.0
• sp3杂化的碳原子比例：
  0.22
• 拓扑面积：
  125
• 氢给体数：
  2
• 氢受体数：
  7

反应信息

• 作为反应物：
  描述：

  3'-amino-N4-benzoyl-2',3'-dideoxy-5'-O-(4,4'-dimethoxytrityl)cytidine 在 二氯乙酸 作用下， 以 二氯甲烷 为溶剂， 反应 0.33h， 以91%的产率得到3’-amino-N⁴-benzoyl-2’,3’-dideoxycytidine
  参考文献：
  名称：

  Synthesis of N3′-P5′-linked Phosphoramidate DNA by Nonenzymatic Template-Directed Primer Extension

  摘要：

  A fast and accurate pathway for nonenzymatic RNA replication would simplify models for the emergence of the RNA world from the prebiotic chemistry of the early earth. However, numerous difficulties stand in the way of an experimental demonstration of effective nonenzymatic RNA replication. To gain insight into the necessary properties of potentially self-replicating informational polymers, we have studied several model systems based on amino-sugar nucleotides. Here we describe the synthesis of N3'-P5'-linked phosphoramidate DNA (3'-NP-DNA) by the template-directed polymerization of activated 3'-amino-2',3'-dideoxyribonucleotides. 3'-NP-DNA is an interesting model because of its very RNA-like A-type duplex conformation and because activated 3'-amino-2',3'-dideozyribonucleotides are much more reactive than the corresponding activated ribonucleotides. In contrast to our previous studies with 2'-amino-2',3'-dideoxyribonucleotides (for which G and C but not A and T exhibit efficient template copying), we have found that all four canonical 3'-amino-2',3'-dideoxyribonucleotides (G, C, A, and T) polymerize efficiently on RNA templates. RNA templates are generally superior to DNA templates, and oligo-ribo-T templates are superior to oligo-ribo-U templates, which are the least efficient of the RNA homopolymer templates. We have also found that activation of 3'-aminonucleotides with 2-methylimidazole results in a ca. 10-fold higher polymerization rate relative to activation with imidazole, an observation that parallels earlier findings with ribonucleotides. We discuss the implications of our experiments for the possibility of self-replication in the 3'-NP-DNA and RNA systems.

  DOI：

  10.1021/ja311164j
• 作为产物：
  描述：

  3'-azido-N4-benzoyl-5'-O-(4,4'-dimethoxytrityl)-2',3'-dideoxycytidine 在 palladium on activated charcoal 、 氢气 、 碳酸氢钠 作用下， 以 乙醇 、 水 为溶剂， 反应 6.0h， 以93%的产率得到3'-amino-N4-benzoyl-2',3'-dideoxy-5'-O-(4,4'-dimethoxytrityl)cytidine
  参考文献：
  名称：

  3'-Amino-2'，3'-Dideoxynucleosides，它们的5'-Monophosphates和3'-Aminoterminal Oligodeoxynucleotide Primers的便捷合成

  摘要：

  从脱氧核苷开始，通过叠氮化物以五至六步制备含有四个规范核碱基（A / C / G / T）中任何一个的5'-保护的3'-氨基-2'，3'-二脱氧核苷。对于嘧啶，合成途径涉及脱水核苷的亲核打开。对于嘌呤，原位氧化/还原序列，然后与二苯基-2-吡啶基膦和叠氮化钠的Mitsunobu反应，以高收率和纯度提供了3'-叠氮核苷。对于固相合成氨基末端寡核苷酸，氨基核苷通过新型六氟戊二酸接头与受控孔玻璃相连。这些支持物通过常规的DNA链组装和氨水一步脱保护/释放，以高产率和高纯度提供了3'-氨基末端引物。如此制备的引物在无酶化学引物延伸中成功进行了测试，这是一种用于基因分型和标记的廉价方法。还制备了3'-氨基-2'，3'-二脱氧核苷的受保护的5'-单磷酸酯，为制备标记的或光敏性受保护的单体用于化学引物延伸提供了起始原料。

  DOI：

  10.1021/jo8018889

文献信息

• New oligonucleotide derivatives as unreactive substrate analogues and potential inhibitors of human apurinic/apyrimidinic endonuclease APE1
  作者：Nikita A. Kuznetsov、Maxim S. Kupryushkin、Tatyana V. Abramova、Alexandra A. Kuznetsova、Anastasia D. Miroshnikova、Dmitry A. Stetsenko、Dmitrii V. Pyshnyi、Olga S. Fedorova

  DOI：10.1039/c5mb00692a

  日期：——

  Human apurinic/apyrimidinic endonuclease APE1 is one of the key enzymes of base excision DNA repair system. Main biological function of APE1 is the hydrolysis of the phosphodiester bond on the...

  人嘌呤/嘧啶内切核酸酶APE1是碱基切除DNA修复系统的关键酶之一。APE1的主要生物学功能是水解磷酸二酯键。
• Synthesis of Dinucleoside (N3‘→MeP5‘) Methanephosphonamidates
  作者：Barbara Nawrot、Milena Sobczak、Slawomir Antoszczyk

  DOI：10.1021/ol0259084

  日期：2002.5.1

  [structure: see text] Three different approaches were used for the synthesis of dinucleoside methanephosphonamidates [3'-NH-P(O)(CH3)O-5'], starting from dichloromethylphosphine or dichloromethanephosphonate as the phosphorus-containing moiety. 5'-DMT-3'-amino-3'-deoxythymidine and N(4)-benzoyl-5'-DMT-3'-amino-2',3'-dideoxycytidine were used as the aminonucleoside precursors and the respective 3'-protected

  [结构：见正文]从二氯甲基膦或二氯甲烷膦酸酯作为含磷部分开始，使用了三种不同的方法合成二核苷甲烷膦酸酯[3'-NH-P（O）（CH3）O-5']。5'-DMT-3'-氨基-3'-脱氧胸苷和N（4）-苯甲酰基-5'-DMT-3'-氨基-2'，3'-二脱氧胞苷用作氨基核苷前体，各自的3'保护的核苷（胸苷或N（4）-苯甲酰基-2'-脱氧胞苷）作为5'-羟基试剂。
• Synthesis of 2‘,3‘-Dideoxyribonucleoside-3‘-<i>N</i>-(2-oxo-1,3,2-oxathiaphospholanes) and Their Reactions with 5‘-OH Nucleosides and Fluoride Ion
  作者：Janina Baraniak、Dariusz Korczyñski、Wojciech J. Stec

  DOI：10.1021/jo982240r

  日期：1999.6.1
• Synthesis of N3′-P5′-linked Phosphoramidate DNA by Nonenzymatic Template-Directed Primer Extension
  作者：Shenglong Zhang、Na Zhang、J. Craig Blain、Jack W. Szostak

  DOI：10.1021/ja311164j

  日期：2013.1.16

  A fast and accurate pathway for nonenzymatic RNA replication would simplify models for the emergence of the RNA world from the prebiotic chemistry of the early earth. However, numerous difficulties stand in the way of an experimental demonstration of effective nonenzymatic RNA replication. To gain insight into the necessary properties of potentially self-replicating informational polymers, we have studied several model systems based on amino-sugar nucleotides. Here we describe the synthesis of N3'-P5'-linked phosphoramidate DNA (3'-NP-DNA) by the template-directed polymerization of activated 3'-amino-2',3'-dideoxyribonucleotides. 3'-NP-DNA is an interesting model because of its very RNA-like A-type duplex conformation and because activated 3'-amino-2',3'-dideozyribonucleotides are much more reactive than the corresponding activated ribonucleotides. In contrast to our previous studies with 2'-amino-2',3'-dideoxyribonucleotides (for which G and C but not A and T exhibit efficient template copying), we have found that all four canonical 3'-amino-2',3'-dideoxyribonucleotides (G, C, A, and T) polymerize efficiently on RNA templates. RNA templates are generally superior to DNA templates, and oligo-ribo-T templates are superior to oligo-ribo-U templates, which are the least efficient of the RNA homopolymer templates. We have also found that activation of 3'-aminonucleotides with 2-methylimidazole results in a ca. 10-fold higher polymerization rate relative to activation with imidazole, an observation that parallels earlier findings with ribonucleotides. We discuss the implications of our experiments for the possibility of self-replication in the 3'-NP-DNA and RNA systems.
• Convenient Syntheses of 3′-Amino-2′,3′-dideoxynucleosides, Their 5′-Monophosphates, and 3′-Aminoterminal Oligodeoxynucleotide Primers
  作者：Ralf Eisenhuth、Clemens Richert

  DOI：10.1021/jo8018889

  日期：2009.1.2

  5′-Protected 3′-amino-2′,3′-dideoxynucleosides containing any of the four canonical nucleobases (A/C/G/T) were prepared via azides in five to six steps, starting from deoxynucleosides. For pyrimidines, the synthetic route involved nucleophilic opening of anhydronucleosides. For purines, an in situ oxidation/reduction sequence, followed by a Mitsunobu reaction with diphenyl-2-pyridylphosphine and sodium

  从脱氧核苷开始，通过叠氮化物以五至六步制备含有四个规范核碱基（A / C / G / T）中任何一个的5'-保护的3'-氨基-2'，3'-二脱氧核苷。对于嘧啶，合成途径涉及脱水核苷的亲核打开。对于嘌呤，原位氧化/还原序列，然后与二苯基-2-吡啶基膦和叠氮化钠的Mitsunobu反应，以高收率和纯度提供了3'-叠氮核苷。对于固相合成氨基末端寡核苷酸，氨基核苷通过新型六氟戊二酸接头与受控孔玻璃相连。这些支持物通过常规的DNA链组装和氨水一步脱保护/释放，以高产率和高纯度提供了3'-氨基末端引物。如此制备的引物在无酶化学引物延伸中成功进行了测试，这是一种用于基因分型和标记的廉价方法。还制备了3'-氨基-2'，3'-二脱氧核苷的受保护的5'-单磷酸酯，为制备标记的或光敏性受保护的单体用于化学引物延伸提供了起始原料。