5-(6-propionyl-2-dimethylaminonaphthalene)-2'-deoxyuridine | 891492-05-0

• 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-(6-propionyl-2-dimethylaminonaphthalene)-2'-deoxyuridine
• 英文别名: 5-PRODAN-2'-deoxyuridine；5-[3-[6-(dimethylamino)naphthalen-2-yl]-3-oxopropyl]-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione
• CAS: 891492-05-0
• 化学式: C₂₄H₂₇N₃O₆
• 分子量: 453.495
• InChiKey: XWKPBVNDQDKBDA-BHDDXSALSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  1.4
• 重原子数：
  33
• 可旋转键数：
  7
• 环数：
  4.0
• sp3杂化的碳原子比例：
  0.38
• 拓扑面积：
  119
• 氢给体数：
  3
• 氢受体数：
  7

反应信息

• 作为反应物：
  描述：

  5-(6-propionyl-2-dimethylaminonaphthalene)-2'-deoxyuridine 在 四氮唑 作用下， 以 吡啶 、 乙腈 为溶剂， 反应 4.5h， 生成 5-(6-propionyl-2-dimethylaminonaphthalene)-5'O-(4,4'-dimethoxytrityl)-2'-deoxyuridine 3'O-(2-cyanoethyl)-N,N-diisopropylphosphoramidite
  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-(二甲基氨基)-2-萘醛 在 palladium on activated charcoal 、 copper(l) iodide 、 四(三苯基膦)钯 正丁基锂 、 四丙基高钌酸铵 、 4 A molecular sieve 、 四丁基氟化铵 、 氢气 、 sodium methylate 、 N-甲基吗啉氧化物 、 三乙胺 作用下， 以 四氢呋喃 、 甲醇 、 正己烷 、 二氯甲烷 、 N,N-二甲基甲酰胺 为溶剂， 反应 28.5h， 生成 5-(6-propionyl-2-dimethylaminonaphthalene)-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

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。
• PRODAN-Conjugated DNA:  Synthesis and Photochemical Properties
  作者：Kazuki Tainaka、Kazuo Tanaka、Shuji Ikeda、Ken-ichiro Nishiza、Tomo Unzai、Yoshimasa Fujiwara、Isao Saito、Akimitsu Okamoto

  DOI：10.1021/ja069156a

  日期：2007.4.1

  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.