3'-O-<4''-((N-dansyl)-5'''-aminopent-1-yl-oxy)-5''-methoxy-2''-nitrophenylmethyl>thymidine | 221303-14-6

• 分子结构分类: 有机化合物 - 苯类化合物 - 萘
• 英文名称: 3'-O-<4''-((N-dansyl)-5'''-aminopent-1-yl-oxy)-5''-methoxy-2''-nitrophenylmethyl>thymidine
• 英文别名: 5-(dimethylamino)-N-[5-[4-[[(2R,3S,5R)-2-(hydroxymethyl)-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-3-yl]oxymethyl]-2-methoxy-5-nitrophenoxy]pentyl]naphthalene-1-sulfonamide
• CAS: 221303-14-6
• 化学式: C₃₅H₄₃N₅O₁₁S
• 分子量: 741.819
• InChiKey: FHRKNBANBXQBLN-RKKDRKJOSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  3.4
• 重原子数：
  52
• 可旋转键数：
  16
• 环数：
  5.0
• sp3杂化的碳原子比例：
  0.43
• 拓扑面积：
  210
• 氢给体数：
  3
• 氢受体数：
  13

反应信息

• 作为反应物：
  描述：

  3'-O-<4''-((N-dansyl)-5'''-aminopent-1-yl-oxy)-5''-methoxy-2''-nitrophenylmethyl>thymidine 生成 3'-O-<4''-((N-dansyl)-5'''-aminopent-1-yl-oxy)-5''-methoxy-2''-nitrophenylmethyl>thymidine 5'-O-triphosphate
  参考文献：
  名称：

  Synthesis of Fluorescent, Photolabile 3′-O-Protected Nucleoside Triphosphates for the Base Addition Sequencing Scheme

  摘要：

  The dansylated nucleoside triphosphates la and Ib were prepared as a prelude to investigating sequencing of DNA via a scheme that does not involve electrophoresis.

  DOI：

  10.1080/15257779908043067
• 作为产物：
  描述：

  5-Dimethylamino-naphthalene-1-sulfonic acid (5-{4-[(2R,3S,5R)-2-(tert-butyl-dimethyl-silanyloxymethyl)-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yloxymethyl]-2-methoxy-5-nitro-phenoxy}-pentyl)-amide 在 Bu₄BF 作用下， 以 四氢呋喃 为溶剂， 反应 0.18h， 生成 3'-O-<4''-((N-dansyl)-5'''-aminopent-1-yl-oxy)-5''-methoxy-2''-nitrophenylmethyl>thymidine
  参考文献：
  名称：

  Synthesis of Fluorescent, Photolabile 3′-O-Protected Nucleoside Triphosphates for the Base Addition Sequencing Scheme

  摘要：

  The dansylated nucleoside triphosphates la and Ib were prepared as a prelude to investigating sequencing of DNA via a scheme that does not involve electrophoresis.

  DOI：

  10.1080/15257779908043067

文献信息

• Syntheses of Nucleosides Designed for Combinatorial DNA Sequencing
  作者：Mike B. Welch、Carlos I. Martinez、Alex J. Zhang、Song Jin、Richard Gibbs、Kevin Burgess

  DOI：10.1002/(sici)1521-3765(19990301)5:3<951::aid-chem951>3.0.co;2-g

  日期：1999.3.1

  Nucleoside triphosphates I with 3'-O-blocking groups that are both photolabile and fluorescent were required to investigate the viability of a strategy for sequencing DNA in a combinatorial fashion (see Figure 1). Four compounds were prepared to realize this goal. Two of them, 14a and 14t, had dansyl-functionalized, 3'-O-(2"-nitrobenzyl) ether groups, while the other two, 18a and 18t, had similar pendant carbonate groups. Tests for incorporation of these analogues were performed by using five different DNA replicating enzymes, but the analogues were not incorporated. These results were surprising in view of the fact that previous studies had shown that 3'-O-(2"-nitrobenzyl)adenosine triphosphate II was incorporated by Bst DNA polymerase I. However, molecular simulations with the coordinates of a T7 polymerase crystal structure as a model demonstrates that analogues 14a, 14t, 18a and 18t are too large to fit into the enzyme active site, whereas accommodation of the unsubstituted 2-nitrobenzyl compound II is much less demanding. We conclude that both the nucleoside triphosphates and the DNA polymerase enzyme must be modified if the proposed DNA sequencing scheme is to be viable.