5-azido-5′-(4,4′-dimethoxytrityl)-2′-deoxyuridine | 1574218-86-2

• 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-azido-5′-(4,4′-dimethoxytrityl)-2′-deoxyuridine
• CAS: 1574218-86-2
• 化学式: C₃₀H₂₉N₅O₇
• 分子量: 571.59
• InChiKey: LWJGZUMNWPPUKC-OYUWMTPXSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  4.15
• 重原子数：
  42.0
• 可旋转键数：
  10.0
• 环数：
  5.0
• sp3杂化的碳原子比例：
  0.27
• 拓扑面积：
  160.77
• 氢给体数：
  2.0
• 氢受体数：
  9.0

反应信息

• 作为反应物：
  描述：

  5-azido-5′-(4,4′-dimethoxytrityl)-2′-deoxyuridine 在 吡啶 、 copper(ll) sulfate pentahydrate 、 二异丙基铵盐四氮唑 、 sodium ascorbate 作用下， 以 二氯甲烷 、 水 、 叔丁醇 为溶剂， 反应 17.0h， 生成 3′-O-(P-(2-cyanoethoxy)-N,N′-diisopropylaminophosphinyl)-5′-O-(4,4′-dimethoxytrityl)-5-((4-phenyl)-1,2,3-triazol-1-yl)-2′-deoxyuridine
  参考文献：
  名称：

  High-Affinity RNA Targeting by Oligonucleotides Displaying Aromatic Stacking and Amino Groups in the Major Groove. Comparison of Triazoles and Phenyl Substituents

  摘要：

  Three 5-modified 2'-deoxyuridine nucleosides were synthesized and incorporated into oligonucleotides and compared with the previously published 5-(1-phenyl-1,2,3-triazol-4-yl)-2'-deoxyuridine monomer W. The introduction of an aminomethyl group on the phenyl group led to monomer X, which was found to thermally stabilize a 9-mer DNA:RNA duplex, presumably through the partial neutralization of the negative charge of the backbone. By also taking advantage of the stacking interactions in the major groove of two or more of the monomer X, an extremely high thermal stability was obtained. A regioisomer of the phenyltriazole substituent, that is the 5-(4-phenyl-1,2,3-triazol-1-yl)-2'-deoxyuridine monomer Y, was found to destabilize the DNA:RNA duplex significantly, but stacking in the major groove compensated for this when two to four monomers were incorporated consecutively. Finally, the 5-phenyl-2'-deoxyuridine monomer Z was incorporated for comparison, and it was found to give a more neutral influence on duplex stability indicating less efficient stacking interactions. The duplexes were investigated by CD spectroscopy and MD simulations.

  DOI：

  10.1021/jo4025896
• 作为产物：
  描述：

  5-azido-2′-deoxyuridine 、 4,4'-双甲氧基三苯甲基氯 在 吡啶 作用下， 反应 14.0h， 以42%的产率得到5-azido-5′-(4,4′-dimethoxytrityl)-2′-deoxyuridine
  参考文献：
  名称：

  High-Affinity RNA Targeting by Oligonucleotides Displaying Aromatic Stacking and Amino Groups in the Major Groove. Comparison of Triazoles and Phenyl Substituents

  摘要：

  Three 5-modified 2'-deoxyuridine nucleosides were synthesized and incorporated into oligonucleotides and compared with the previously published 5-(1-phenyl-1,2,3-triazol-4-yl)-2'-deoxyuridine monomer W. The introduction of an aminomethyl group on the phenyl group led to monomer X, which was found to thermally stabilize a 9-mer DNA:RNA duplex, presumably through the partial neutralization of the negative charge of the backbone. By also taking advantage of the stacking interactions in the major groove of two or more of the monomer X, an extremely high thermal stability was obtained. A regioisomer of the phenyltriazole substituent, that is the 5-(4-phenyl-1,2,3-triazol-1-yl)-2'-deoxyuridine monomer Y, was found to destabilize the DNA:RNA duplex significantly, but stacking in the major groove compensated for this when two to four monomers were incorporated consecutively. Finally, the 5-phenyl-2'-deoxyuridine monomer Z was incorporated for comparison, and it was found to give a more neutral influence on duplex stability indicating less efficient stacking interactions. The duplexes were investigated by CD spectroscopy and MD simulations.

  DOI：

  10.1021/jo4025896

文献信息

• Three new double-headed nucleotides with additional nucleobases connected to C-5 of pyrimidines; synthesis, duplex and triplex studies
  作者：Pawan Kumar、Pawan K. Sharma、Jonas Hansen、Lukas Jedinak、Charlotte Reslow-Jacobsen、Mick Hornum、Poul Nielsen

  DOI：10.1016/j.bmc.2015.12.043

  日期：2016.2

  In the search for double-coding DNA-systems, three new pyrimidine nucleosides, each coded with an additional nucleobase anchored to the major groove face, are synthesized. Two of these building blocks carry a thymine at the 5-position of 20-deoxyuridine through a methylene linker and a triazolomethylene linker, respectively. The third building block carries an adenine at the 6-position of pyrrolo-20-deoxycytidine through a methylene linker. These double-headed nucleosides are introduced into oligonucleotides and their effects on the thermal stabilities of duplexes are studied. All studied double-headed nucleotide monomers reduce the thermal stability of the modified duplexes, which is partially compensated by using consecutive incorporations of the modified monomers or by flanking the new double-headed analogs with members of our former series containing propyne linkers. Also their potential in triplex-forming oligonucleotides is studied for two of the new double-headed nucleotides as well as the series of analogs with propyne linkers. The most stable triplexes are obtained with single incorporations of additional pyrimidine nucleobases connected via the propyne linker. (c) 2016 Elsevier Ltd. All rights reserved.