4-(2-cyanoethyl)seleno-5'-O-(4,4'-dimethoxytriphenylmethyl)thymidine | 937376-82-4

• 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: 4-(2-cyanoethyl)seleno-5'-O-(4,4'-dimethoxytriphenylmethyl)thymidine
• 英文别名: 3-[1-[(2R,4S,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-hydroxyoxolan-2-yl]-5-methyl-2-oxopyrimidin-4-yl]selanylpropanenitrile
• CAS: 937376-82-4
• 化学式: C₃₄H₃₅N₃O₆Se
• 分子量: 660.628
• InChiKey: CYUJRKAEVMPDOD-OJDZSJEKSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  3.89
• 重原子数：
  44
• 可旋转键数：
  12
• 环数：
  5.0
• sp3杂化的碳原子比例：
  0.32
• 拓扑面积：
  114
• 氢给体数：
  1
• 氢受体数：
  7

反应信息

• 作为反应物：
  描述：

  4-(2-cyanoethyl)seleno-5'-O-(4,4'-dimethoxytriphenylmethyl)thymidine 、 2-氰乙基N,N-二异丙基氯亚磷酰胺 在 二异丙胺 作用下， 以 二氯甲烷 为溶剂， 以92%的产率得到4-(2-cyanoethyl)seleno-5'-O-(4,4'-dimethoxytriphenylmethyl)thymidine 3'-O-(2-cyanoethyl)diisopropylaminophosphoramidite
  参考文献：
  名称：

  Oxygen Replacement with Selenium at the Thymidine 4-Position for the Se Base Pairing and Crystal Structure Studies

  摘要：

  The T-A and C-G base pairing and stacking allow the formation of the stable DNA duplex structure for genetic information storage, transcription, and replication. To replace the oxygen of the nucleotide nucleobases with selenium for the studies of the base-pair recognition, the duplex stability, and the nuclei acid crystal structures, we have synthesized for the first time the 4-Se thymidine phosphoramidite and incorporated it into oligonucleotides via solid-phase synthesis with high coupling yield (99%). The Se modification on the nucleobase is relatively stable under the elevated temperature. Using the dU(Se) (2'-Se-dU) to facilitate the crystallization, we have successfully crystallized the DNA containing the 4-Se-T substitution and determined its structure at 1.50 A resolution. The UV-melting and X-ray crystal structure studies have indicated that the Se substitution on the nucleobase does not cause a significant structure perturbation, the large Se atom on the thymine can be successfully accommodated by the DNA duplex, and the Se-mediated hydrogen bond (longer than the usual hydrogen bond) is formed within the modified T-A base pair. In addition, the Se derivatization on the nucleobases further facilitates X-ray crystal structure determination of nucleic acids and their protein complexes via Se MAD phasing.

  DOI：

  10.1021/ja0680919
• 作为产物：
  描述：

  保护胸苷 在 triethylamine tris(hydrogen fluoride) 、 三氯氧磷 作用下， 以 四氢呋喃 、 乙腈 为溶剂， 反应 4.75h， 生成 4-(2-cyanoethyl)seleno-5'-O-(4,4'-dimethoxytriphenylmethyl)thymidine
  参考文献：
  名称：

  Oxygen Replacement with Selenium at the Thymidine 4-Position for the Se Base Pairing and Crystal Structure Studies

  摘要：

  The T-A and C-G base pairing and stacking allow the formation of the stable DNA duplex structure for genetic information storage, transcription, and replication. To replace the oxygen of the nucleotide nucleobases with selenium for the studies of the base-pair recognition, the duplex stability, and the nuclei acid crystal structures, we have synthesized for the first time the 4-Se thymidine phosphoramidite and incorporated it into oligonucleotides via solid-phase synthesis with high coupling yield (99%). The Se modification on the nucleobase is relatively stable under the elevated temperature. Using the dU(Se) (2'-Se-dU) to facilitate the crystallization, we have successfully crystallized the DNA containing the 4-Se-T substitution and determined its structure at 1.50 A resolution. The UV-melting and X-ray crystal structure studies have indicated that the Se substitution on the nucleobase does not cause a significant structure perturbation, the large Se atom on the thymine can be successfully accommodated by the DNA duplex, and the Se-mediated hydrogen bond (longer than the usual hydrogen bond) is formed within the modified T-A base pair. In addition, the Se derivatization on the nucleobases further facilitates X-ray crystal structure determination of nucleic acids and their protein complexes via Se MAD phasing.

  DOI：

  10.1021/ja0680919

文献信息

• WO2008/80060
  申请人：——

  公开号：——

  公开（公告）日：——
• Oxygen Replacement with Selenium at the Thymidine 4-Position for the Se Base Pairing and Crystal Structure Studies
  作者：Jozef Salon、Jia Sheng、Jiansheng Jiang、Guexiong Chen、Julianne Caton-Williams、Zhen Huang

  DOI：10.1021/ja0680919

  日期：2007.4.1

  The T-A and C-G base pairing and stacking allow the formation of the stable DNA duplex structure for genetic information storage, transcription, and replication. To replace the oxygen of the nucleotide nucleobases with selenium for the studies of the base-pair recognition, the duplex stability, and the nuclei acid crystal structures, we have synthesized for the first time the 4-Se thymidine phosphoramidite and incorporated it into oligonucleotides via solid-phase synthesis with high coupling yield (99%). The Se modification on the nucleobase is relatively stable under the elevated temperature. Using the dU(Se) (2'-Se-dU) to facilitate the crystallization, we have successfully crystallized the DNA containing the 4-Se-T substitution and determined its structure at 1.50 A resolution. The UV-melting and X-ray crystal structure studies have indicated that the Se substitution on the nucleobase does not cause a significant structure perturbation, the large Se atom on the thymine can be successfully accommodated by the DNA duplex, and the Se-mediated hydrogen bond (longer than the usual hydrogen bond) is formed within the modified T-A base pair. In addition, the Se derivatization on the nucleobases further facilitates X-ray crystal structure determination of nucleic acids and their protein complexes via Se MAD phasing.