N⁴-benzoyl-5'-O-(4,4'-dimethoxytrityl)-3'-O-(N,N-diisopropylamino)-[4-[N-methyl-N-(2,2,2-trifluoroacetyl)amino]butoxy]phosphinyl-2'-deoxycytidine

• 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: N⁴-benzoyl-5'-O-(4,4'-dimethoxytrityl)-3'-O-(N,N-diisopropylamino)-[4-[N-methyl-N-(2,2,2-trifluoroacetyl)amino]butoxy]phosphinyl-2'-deoxycytidine
• 英文别名: N-[1-[(2R,4S,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-[[di(propan-2-yl)amino]-[4-[methyl-(2,2,2-trifluoroacetyl)amino]butoxy]phosphanyl]oxyoxolan-2-yl]-2-oxopyrimidin-4-yl]benzamide
• 化学式: C₅₀H₅₉F₃N₅O₉P
• 分子量: 962.016
• InChiKey: GMRCJEZCWHAATF-VXZGYNRXSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  8.4
• 重原子数：
  68
• 可旋转键数：
  22
• 环数：
  6.0
• sp3杂化的碳原子比例：
  0.4
• 拓扑面积：
  141
• 氢给体数：
  1
• 氢受体数：
  13

反应信息

• 作为产物：
  描述：

  4-羟基-N-甲基丁烷酰胺 在 四氮唑 、 lithium aluminium tetrahydride 、 三氯化磷 作用下， 以 乙醚 、 二氯甲烷 、 乙腈 、 Petroleum ether 为溶剂， 反应 91.0h， 生成 N⁴-benzoyl-5'-O-(4,4'-dimethoxytrityl)-3'-O-(N,N-diisopropylamino)-[4-[N-methyl-N-(2,2,2-trifluoroacetyl)amino]butoxy]phosphinyl-2'-deoxycytidine
  参考文献：
  名称：

  The 4-[N-Methyl-N-(2,2,2-trifluoroacetyl)amino]butyl Group as an Alternative to the 2-Cyanoethyl Group for Phosphate Protection in the Synthesis of Oligodeoxyribonucleotides

  摘要：

  The 4-[N-methyl-N-(2,2,2-trifluoroacetyl)amino]butyl group for phosphate protection in the synthesis of oligodeoxyribonucleotides has been developed to completely prevent nucleobase alkylation by acrylonitrile that could potentially occur upon deprotection of the traditional 2-cyanoethyl phosphate protecting group. The properties of this new phosphate protecting group were evaluated using the model phosphotriester 9. The mechanism of phosphate deprotection was studied by treating 9 with concentrated NH4OH. NMR analysis,of the deprotection reaction demonstrated that cleavage of the N-trifluoroacetyl group is rate-limiting. The resulting phosphotriester intermediate 13 was also shown to undergo rapid cyclodeesterification to produce O,O-diethyl phosphate 15 and N-methylpyrrolidine -16 (Scheme 2). Given the facile removal of the 4-[N-methyl-N-(2,2,2-trifluoroacetyl)amino]butyl phosphate protecting group under mild basic conditions, its utilization in oligonucleotide synthesis began with the preparation of the deoxyribonucleoside phosphoramidites 4a-d (Scheme 3). The coupling efficiency of 4a-d and conventional a-cyanoethyl deoxyribonucleoside phosphoramidites 24a-d was then compared in the solid-phase synthesis of the 20-mer d(ATCCGTAGCTAAGGTCATGC). As previously observed in the deprotection of 9, the 4-[N-methyl,N-(2,2,2-trifluoroacetyl)amino]butyl phosphate protecting groups were easily and completely removed from the oligonucleotide by using either concentrated NH4OH or pressurized ammonia gas. Analysis of the deprotected oligomer by polyacrylamide gel electrophoresis (Figure 3) indicated that the phosphoramidites 4a-d are as efficient as the 2-cyanoethyl phosphoramidites 24a-d in the synthesis of the 20-mer. Furthermore, following digestion of the crude 20-mer by snake venom phosphodiesterase and bacterial alkaline phosphatase, HPLC analysis showed complete hydrolysis to individual nucleosides and no detectable nucleobase modification.

  DOI：

  10.1021/jo990835w

文献信息

• The 4-[<i>N</i>-Methyl-<i>N</i>-(2,2,2-trifluoroacetyl)amino]butyl Group as an Alternative to the 2-Cyanoethyl Group for Phosphate Protection in the Synthesis of Oligodeoxyribonucleotides
  作者：Andrzej Wilk、Andrzej Grajkowski、Lawrence R. Phillips、Serge L. Beaucage

  DOI：10.1021/jo990835w

  日期：1999.10.1

  The 4-[N-methyl-N-(2,2,2-trifluoroacetyl)amino]butyl group for phosphate protection in the synthesis of oligodeoxyribonucleotides has been developed to completely prevent nucleobase alkylation by acrylonitrile that could potentially occur upon deprotection of the traditional 2-cyanoethyl phosphate protecting group. The properties of this new phosphate protecting group were evaluated using the model phosphotriester 9. The mechanism of phosphate deprotection was studied by treating 9 with concentrated NH4OH. NMR analysis,of the deprotection reaction demonstrated that cleavage of the N-trifluoroacetyl group is rate-limiting. The resulting phosphotriester intermediate 13 was also shown to undergo rapid cyclodeesterification to produce O,O-diethyl phosphate 15 and N-methylpyrrolidine -16 (Scheme 2). Given the facile removal of the 4-[N-methyl-N-(2,2,2-trifluoroacetyl)amino]butyl phosphate protecting group under mild basic conditions, its utilization in oligonucleotide synthesis began with the preparation of the deoxyribonucleoside phosphoramidites 4a-d (Scheme 3). The coupling efficiency of 4a-d and conventional a-cyanoethyl deoxyribonucleoside phosphoramidites 24a-d was then compared in the solid-phase synthesis of the 20-mer d(ATCCGTAGCTAAGGTCATGC). As previously observed in the deprotection of 9, the 4-[N-methyl,N-(2,2,2-trifluoroacetyl)amino]butyl phosphate protecting groups were easily and completely removed from the oligonucleotide by using either concentrated NH4OH or pressurized ammonia gas. Analysis of the deprotected oligomer by polyacrylamide gel electrophoresis (Figure 3) indicated that the phosphoramidites 4a-d are as efficient as the 2-cyanoethyl phosphoramidites 24a-d in the synthesis of the 20-mer. Furthermore, following digestion of the crude 20-mer by snake venom phosphodiesterase and bacterial alkaline phosphatase, HPLC analysis showed complete hydrolysis to individual nucleosides and no detectable nucleobase modification.