5'-O-4,4'-dimethoxytrityl-3'-O-tertbutyldimethylsilyl-4-O-triisopropylphenylsulfonyl thymidine | 242475-43-0

• 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: 5'-O-4,4'-dimethoxytrityl-3'-O-tertbutyldimethylsilyl-4-O-triisopropylphenylsulfonyl thymidine
• 英文别名: [1-[(2R,4S,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-[tert-butyl(dimethyl)silyl]oxyoxolan-2-yl]-5-methyl-2-oxopyrimidin-4-yl] 2,4,6-tri(propan-2-yl)benzenesulfonate
• CAS: 242475-43-0
• 化学式: C₅₂H₆₈N₂O₉SSi
• 分子量: 925.271
• InChiKey: PMTTWWRSUYRWBL-WEDPTRSYSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  11.39
• 重原子数：
  65
• 可旋转键数：
  18
• 环数：
  6.0
• sp3杂化的碳原子比例：
  0.46
• 拓扑面积：
  131
• 氢给体数：
  0
• 氢受体数：
  9

反应信息

• 作为反应物：
  描述：

  5'-O-4,4'-dimethoxytrityl-3'-O-tertbutyldimethylsilyl-4-O-triisopropylphenylsulfonyl thymidine 在 4-二甲氨基吡啶 、 四丁基氟化铵 、 三乙胺 作用下， 以 四氢呋喃 、 吡啶 为溶剂， 反应 15.5h， 生成 N⁴-(N²-acetamidoureido)-5'-O-4,4'-dimethoxytrityl-5-methyl-2'-deoxycytidine
  参考文献：
  名称：

  Synthesis and Triplex Forming Properties of Pyrimidine Derivative Containing Extended Functionality

  摘要：

  Two pyrimidine nucleosides have been synthesized containing extended hydrogen bonding functionality. In one case the side chain is based upon semicarbazide and in the second monoacetylated carbohydrazide was employed. DNA sequences;sequences could be prepared using both analogue nucleosides in a reverse coupling protocol, and provided that the normal capping step was eliminated and that the iodine-based oxidizing solution was replaced with one based upon 10-camphorsulfonyl oxaziridine. Both derivatives exhibited moderate effects in targeting selectively C-G base pairs embedded within a polypurine target sequence.

  DOI：

  10.1080/07328319908044841
• 作为产物：
  描述：

  2,4,6-三异丙基苯磺酰氯 、 5'-O-(4,4'-dimethoxytrityl)-3'-O-(t-butyldimethylsilyl)-2'-deoxythymidine 在 4-二甲氨基吡啶 、 三乙胺 作用下， 以 二氯甲烷 为溶剂， 反应 18.0h， 以52%的产率得到5'-O-4,4'-dimethoxytrityl-3'-O-tertbutyldimethylsilyl-4-O-triisopropylphenylsulfonyl thymidine
  参考文献：
  名称：

  Synthesis and Triplex Forming Properties of Pyrimidine Derivative Containing Extended Functionality

  摘要：

  Two pyrimidine nucleosides have been synthesized containing extended hydrogen bonding functionality. In one case the side chain is based upon semicarbazide and in the second monoacetylated carbohydrazide was employed. DNA sequences;sequences could be prepared using both analogue nucleosides in a reverse coupling protocol, and provided that the normal capping step was eliminated and that the iodine-based oxidizing solution was replaced with one based upon 10-camphorsulfonyl oxaziridine. Both derivatives exhibited moderate effects in targeting selectively C-G base pairs embedded within a polypurine target sequence.

  DOI：

  10.1080/07328319908044841

文献信息

• Intermolecular 'cross-torque': the N4-cytosine propargyl residue is rotated to the 'CH'-edge as a result of Watson-Crick interaction
  作者：O. Domingo、I. Hellmuth、A. Jaschke、C. Kreutz、M. Helm

  DOI：10.1093/nar/gkv285

  日期：2015.6.23

  Propargyl groups are attractive functional groups for labeling purposes, as they allow CuAAC-mediated bioconjugation. Their size minimally exceeds that of a methyl group, the latter being frequent in natural nucleotide modifications. To understand under which circumstances propargyl-containing oligodeoxynucleotides preserve base pairing, we focused on the exocyclic amine of cytidine. Residues attached to the exocyclic N4 may orient away from or toward the Watson–Crick face, ensuing dramatic alteration of base pairing properties. ROESY-NMR experiments suggest a uniform orientation toward the Watson–Crick face of N4-propargyl residues in derivatives of both deoxycytidine and 5-methyl-deoxycytidine. In oligodeoxynucleotides, however, UV-melting indicated that N4-propargyl-deoxycytidine undergoes standard base pairing. This implies a rotation of the propargyl moiety toward the ‘CH’-edge as a result of base pairing on the Watson–Crick face. In oligonucleotides containing the corresponding 5-methyl-deoxycytidine derivative, dramatically reduced melting temperatures indicate impaired Watson–Crick base pairing. This was attributed to a steric clash of the propargyl moiety with the 5-methyl group, which prevents back rotation to the ‘CH’-edge, consequently preventing Watson–Crick geometry. Our results emphasize the tendency of an opposing nucleic acid strand to mechanically rotate single N4-substituents to make way for Watson–Crick base pairing, providing no steric hindrance is present on the ‘CH’-edge.

  炔丙基是极具吸引力的标记官能团，因为它们可以进行 CuAAC 介导的生物连接。它们的大小比甲基小得多，后者在天然核苷酸修饰中很常见。为了了解在什么情况下含丙炔的寡去氧核苷酸能保持碱基配对，我们重点研究了胞苷的外环胺。连接到外环 N4 的残基可能会偏离或朝向 Watson-Crick 面，从而导致碱基配对特性发生巨大变化。ROESY-NMR 实验表明，在脱氧胞苷和 5-甲基脱氧胞苷的衍生物中，N4-丙炔基残基统一朝向沃森-克里克面。然而，在寡脱氧核苷酸中，紫外线熔解表明 N4-丙炔基脱氧胞苷会发生标准碱基配对。这意味着由于沃森-克里克面上的碱基配对，丙炔分子向'CH'边旋转。在含有相应的 5-甲基脱氧胞苷衍生物的寡核苷酸中，熔化温度的急剧下降表明 Watson-Crick 碱基配对受到了影响。这归因于丙炔基与 5-甲基基团的立体冲突，它阻止了向'CH'边的反向旋转，从而阻碍了 Watson-Crick 几何结构。我们的研究结果表明，如果'CH'边上不存在立体阻碍，对立的核酸链倾向于机械旋转单个 N4-取代基，为沃森-克里克碱基配对让路。