5-carboxymethyl-5'-O-dimethoxytrityl-2'-deoxyuridine | 209163-82-6

• 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-carboxymethyl-5'-O-dimethoxytrityl-2'-deoxyuridine
• 英文别名: 5-hydroxycarbamoyl methyl-5’-O-DMTr-2’-deoxyuridine；2-[1-[(2R,4S,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-hydroxyoxolan-2-yl]-2,4-dioxopyrimidin-5-yl]acetic acid
• CAS: 209163-82-6
• 化学式: C₃₂H₃₂N₂O₉
• 分子量: 588.614
• InChiKey: XVCSZTAHOUJMLL-UPRLRBBYSA-N

物化性质

• 密度：
  1.337±0.06 g/cm3(Predicted)

计算性质

• 辛醇/水分配系数(LogP)：
  2.5
• 重原子数：
  43
• 可旋转键数：
  11
• 环数：
  5.0
• sp3杂化的碳原子比例：
  0.28
• 拓扑面积：
  144
• 氢给体数：
  3
• 氢受体数：
  9

反应信息

• 作为反应物：
  描述：

  5-carboxymethyl-5'-O-dimethoxytrityl-2'-deoxyuridine 在 potassium carbonate 作用下， 以 六甲基磷酰三胺 为溶剂， 反应 6.0h， 生成
  参考文献：
  名称：

  Synthesis of a novel 2′-deoxyuridine derivative bearing a cyanomethoxycarbonylmethyl group at C-5 position and its use for versatile post-synthetic functionalization of oligodeoxyribonucleotides

  摘要：

  A novel 2'-deoxyuridine derivative bearing a cyanomethoxycarbonylmethyl group at the C-5 position (1) was synthesized and its use was examined as a convertible nucleoside for the versatile post-synthesis functionalization of oligodeoxyribonucleotides (ODNs). The ODNs containing 1 reacted with primary monoamines such as heptylamine, histamine, and tyramine as well as di- and polyamines under mild conditions, giving the corresponding derivatized ODNs. (C) 1998 Elsevier Science Ltd. AII rights reserved.

  DOI：

  10.1016/s0040-4039(98)00660-1
• 作为产物：
  描述：

  5'-O-(4,4'-dimethoxytrityl)-5-methoxycarbonylmethyl-2'-deoxyuridine 在 lithium hydroxide monohydrate 作用下， 以 四氢呋喃 为溶剂， 反应 2.0h， 生成 5-carboxymethyl-5'-O-dimethoxytrityl-2'-deoxyuridine
  参考文献：
  名称：

  Pseudo-Dumbbell-Type Molecular Beacon Probes Bearing Modified Deoxyuridine Derivatives and a Silylated Pyrene as a Fluorophore

  摘要：

  我们最近报告了一种新型伪哑铃型分子探针（探针1），它由聚胺连接的脱氧尿苷（U）和硅化的芘组成。探针在单独存在时显示出较弱的荧光信号。在存在互补DNA的情况下，探针的荧光信号增强。在本研究中，我们制备了新的分子探针，探针2和探针3，它们具有探针1的延长茎部分。此外，探针2中的一个U被含有蒽醌的脱氧尿苷残基（Y）替代了。在探针4中，基本上与探针1相同，但探针1环部分的一个脱氧鸟苷被探针4中的脱氧次黄嘌呤替代。在探针5中，探针3的3′末端脱氧胞苷被脱氧腺苷替代。这些探针在没有靶DNA的情况下，荧光信号有效淬灭。在所有探针中，探针3的淬灭效果最强。另一方面，在存在互补DNA的情况下，信号显著增强。探针3的信号与背景的比率最高。所有这些探针还以不同程度识别靶DNA中的单核苷酸变异。探针3的序列识别能力在所有探针中也是最高的。

  DOI：

  10.1246/bcsj.20140372

文献信息

• Termini-free Molecular Beacon Utilizing Silylated Perylene and Anthraquinone Attached to the C-5 Position of Pyrimidine Nucleobase
  作者：Yuzuru Sato、Tomohisa Moriguchi、Kazuo Shinozuka

  DOI：10.1246/cl.2012.420

  日期：2012.4.5

  A termini-free molecular beacon type of DNA bearing a novel silylated perylene and an anthraquinone both at the C-5 position of deoxyuridine residues exhibits prominent fluorescence upon mixing with complementary oligonucleotide (24- to 50-fold increase in comparison with a single-stranded state) along with one base mismatch discrimination ability.

  在脱氧尿苷残基的 C-5 位上含有一种新型硅烷化亚甲基和一种蒽醌的无末端分子信标型 DNA 与互补寡核苷酸混合后会发出明显的荧光（与单链状态相比，荧光增加了 24 至 50 倍），并具有一个碱基错配的识别能力。
• Development of the excimer probe responsible for DNA target bearing the silylated pyrenes at base moiety
  作者：Tomohisa Moriguchi、Mayumi Ichimura、Mitsuhisa Kato、Kenya Suzuki、Yuki Takahashi、Kazuo Shinozuka

  DOI：10.1016/j.bmcl.2014.08.018

  日期：2014.9

  For the development of the excimer probe responsible for DNA target, the deoxyuridine phosphoramidite derivative bearing the silylated pyrene attached at the C-5 position was prepared and incorporated into oligonucleotides. The modified oligonucleotides showed the excimer emission in the absence of the target DNA, on the other hands, the excimer emission was quenched in the presence of the target DNA. For the utilization of the fluorescence behavior, the novel molecular beacon probe containing the silylated pyrene-modified nucleoside at the stem region was designed and the fluorescence property of the probe found to show the responsibility for DNA target. (C) 2014 Elsevier Ltd. All rights reserved.
• Pseudo-Dumbbell-Type Molecular Beacon Probes Bearing Modified Deoxyuridine Derivatives and a Silylated Pyrene as a Fluorophore
  作者：Jakir Ahmed Chowdhury、Tomohisa Moriguchi、Kazuo Shinozuka

  DOI：10.1246/bcsj.20140372

  日期：2015.3.15

  We have recently reported a novel pseudo-dumbbell-type molecular beacon probe (Probe 1) possessing polyamine-connected deoxyuridine (U) and silylated pyrene. The probe showed weak fluorescence signal while it stayed alone. Fluorescence signal of the probe was increased in the presence of the complementary DNA. In this study, we prepared new molecular beacons, Probe 2 and Probe 3, possessing the elongated stem portion of Probe 1. In addition, one U in Probe 2 is substituted by anthraquinone-bearing deoxyuridine residue (Y) in Probe 3. Probe 4 is essentially the same as Probe 1 but one deoxyguanosine in the loop portion of Probe 1 is substituted by deoxyinosine in Probe 4. In Probe 5, 3′-terminal deoxycytidine of Probe 3 is substituted by deoxyadenosine. The fluorescence signal of these probes is effectively quenched in the absence of target DNA. Among all, Probe 3 shows the most effective quenching. On the other hand, the signal is substantially increased in the presence of complementary DNA. The ratio of signal to background in case of Probe 3 is the highest. All these probes also recognize single nucleotide alternation in the target DNA to a different extent. The sequence recognition ability of Probe 3 is also the highest among all the probes.

  我们最近报告了一种新型伪哑铃型分子探针（探针1），它由聚胺连接的脱氧尿苷（U）和硅化的芘组成。探针在单独存在时显示出较弱的荧光信号。在存在互补DNA的情况下，探针的荧光信号增强。在本研究中，我们制备了新的分子探针，探针2和探针3，它们具有探针1的延长茎部分。此外，探针2中的一个U被含有蒽醌的脱氧尿苷残基（Y）替代了。在探针4中，基本上与探针1相同，但探针1环部分的一个脱氧鸟苷被探针4中的脱氧次黄嘌呤替代。在探针5中，探针3的3′末端脱氧胞苷被脱氧腺苷替代。这些探针在没有靶DNA的情况下，荧光信号有效淬灭。在所有探针中，探针3的淬灭效果最强。另一方面，在存在互补DNA的情况下，信号显著增强。探针3的信号与背景的比率最高。所有这些探针还以不同程度识别靶DNA中的单核苷酸变异。探针3的序列识别能力在所有探针中也是最高的。
• Synthesis of a novel 2′-deoxyuridine derivative bearing a cyanomethoxycarbonylmethyl group at C-5 position and its use for versatile post-synthetic functionalization of oligodeoxyribonucleotides
  作者：Satoru Kohgo、Kazuo Shinozuka、Hiroaki Ozaki、Hiroaki Sawai

  DOI：10.1016/s0040-4039(98)00660-1

  日期：1998.6

  A novel 2'-deoxyuridine derivative bearing a cyanomethoxycarbonylmethyl group at the C-5 position (1) was synthesized and its use was examined as a convertible nucleoside for the versatile post-synthesis functionalization of oligodeoxyribonucleotides (ODNs). The ODNs containing 1 reacted with primary monoamines such as heptylamine, histamine, and tyramine as well as di- and polyamines under mild conditions, giving the corresponding derivatized ODNs. (C) 1998 Elsevier Science Ltd. AII rights reserved.