5-[3-(6-dimethylaminonaphthalen-2-yl)-3-hydroxy-1-propyn-1-yl]-3'O,5'O-bis(tert-butyldimethylsilyl)-2'-deoxyuridine | 891492-02-7

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 嘧啶核苷
• 英文名称: 5-[3-(6-dimethylaminonaphthalen-2-yl)-3-hydroxy-1-propyn-1-yl]-3'O,5'O-bis(tert-butyldimethylsilyl)-2'-deoxyuridine
• 英文别名: 5-[3-(6-dimethylamino-2-naphthyl)-3-hydroxy-2-propynyl]-3'O,5'O-bis(tert-butyldimethylsilyl)-2'-deoxyuridine；5-[6-dimethylamino-2-(1-hydroxypropynyl)naphthalene]-2'-deoxy-3',5'-O-(tert-butyldimethylsilyl)uridine
• CAS: 891492-02-7
• 化学式: C₃₆H₅₃N₃O₆Si₂
• 分子量: 680.004
• InChiKey: CPVFGSDJURHJRM-CQHGWOHYSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  6.54
• 重原子数：
  47.0
• 可旋转键数：
  8.0
• 环数：
  4.0
• sp3杂化的碳原子比例：
  0.56
• 拓扑面积：
  106.02
• 氢给体数：
  2.0
• 氢受体数：
  8.0

反应信息

• 作为反应物：
  描述：

  5-[3-(6-dimethylaminonaphthalen-2-yl)-3-hydroxy-1-propyn-1-yl]-3'O,5'O-bis(tert-butyldimethylsilyl)-2'-deoxyuridine 在 palladium on activated charcoal 四丙基高钌酸铵 、 4 A molecular sieve 、 氢气 、 N-甲基吗啉氧化物 作用下， 以 甲醇 、 二氯甲烷 为溶剂， 反应 10.0h， 生成 5-(6-propionyl-2-dimethylaminonaphthalene)-3'O,5'O-bis(tert-butyldimethylsilyl)-2'-deoxyuridine
  参考文献：
  名称：

  PRODAN-Conjugated DNA:  Synthesis and Photochemical Properties

  摘要：

  A solvatochromic fluorophore, PRODAN, has been used as a microenvironment-sensitive reporter. Based on the chemistry of PRODAN, we designed and synthesized four novel fluorescent nucleosides, X-PDN (X = U, C, A, and G), to which a PRODAN fluorophore was attached at pyrimidine C5 or purine C8. The fluorescent nucleosides sensitively varied the Stokes shift values depending on the orientational polarizability of the solvent. The X-PDN incorporated into DNA also changed the Stokes shift values depending on the DNA structure. In particular, the excitation spectrum of the X-PDN-containing duplex shifted to a longer wavelength and gave a smaller Stokes shift value when the base opposite X-PDN could form a Watson-Crick base pair with X-PDN. A lower energy excitation of X-PDN-containing DNA resulted in a strong fluorescence emission selective to the Watson-Crick pairing base. This unique photochemical character was applicable to the efficient typing of single-nucleotide polymorphisms of genes.

  DOI：

  10.1021/ja069156a
• 作为产物：
  描述：

  6-dimethylamino-2-(3-trimethylsilyl-1-hydroxy-2-propynyl)naphthalene 在 四(三苯基膦)钯 copper(l) iodide 、 sodium methylate 、 三乙胺 作用下， 以 甲醇 、 N,N-二甲基甲酰胺 为溶剂， 反应 2.0h， 生成 5-[3-(6-dimethylaminonaphthalen-2-yl)-3-hydroxy-1-propyn-1-yl]-3'O,5'O-bis(tert-butyldimethylsilyl)-2'-deoxyuridine
  参考文献：
  名称：

  Synthesis and fluorescence properties of dimethylaminonaphthalene–deoxyuridine conjugates as polarity-sensitive probes

  摘要：

  The design of probes for monitoring various structures and dynamics of DNA and its surroundings is an important step in understanding biological events accompanying interbiomolecular interaction. We have developed novel fluorescent nucleosides in which the uracil base and the fluorophore are tethered by rigid linkers. They show unique absorption and fluorescence emission spectra. Nucleoside 2 is a fluorophore with high CT character and the fluorescence is very sensitive to solvent polarity. Nucleoside 3 shows absorption and emission maxima with longer wavelength due to extension of the DAN-conjugate system. These fluorophore-deoxyuridine conjugates with unique fluorescence properties would work as reporter probes sensitive to the change in microenvironment around specific sites of DNA. (c) 2007 Elsevier Ltd. All rights reserved.

  DOI：

  10.1016/j.tet.2006.09.113

文献信息

• Prodan-containing nucleotide and use thereof
  申请人：Okamoto Akimitsu

  公开号：US20060142311A1

  公开（公告）日：2006-06-29

  A compound represented by formula (1): wherein R 1 is a substituent represented by formula (2): wherein R 2 is ═O or —NH 2 , with the proviso that when R 2 is ═O, H is attached to the 1-position N of the pyrimidine ring, and the bond between the 1-position N and the 6-position C is a single bond; or a substituent represented by formula (3): wherein R 3 is —OH, ═O, or —NH 2 , with the proviso that when R 3 is —OH or —NH 2 , R 4 is H; when R 3 is ═O, R 4 is —NH 2 ; and when R 3 is ═O, H is attached to the 1-position N of the purine ring, and the bond between the 1-position N and the 6-position C is a single bond.

  一种由式（1）表示的化合物：其中R1是由式（2）表示的取代基：其中R2为 ═O或—NH2，但是当R2为═O时，H附着在嘧啶环的1位N上，并且1位N和6位C之间的键为单键；或者由式（3）表示的取代基：其中R3为—OH，═O或—NH2，但是当R3为—OH或—NH2时，R4为H；当R3为═O时，R4为—NH2；当R3为═O时，H附着在嘌呤环的1位N上，并且1位N和6位C之间的键为单键。