N²-(p-isopropylphenoxyacetyl)-5'-O-(p,p'-dimethoxytrityl)-2'-deoxyguanosine 3'-(2-cyanoethyl N,N-diisopropylphosphoramidite)

• 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: N²-(p-isopropylphenoxyacetyl)-5'-O-(p,p'-dimethoxytrityl)-2'-deoxyguanosine 3'-(2-cyanoethyl N,N-diisopropylphosphoramidite)
• 英文别名: N-[9-[(2R,4S,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxyoxolan-2-yl]-6-oxo-1H-purin-2-yl]-2-(4-propan-2-ylphenoxy)acetamide
• 化学式: C₅₁H₆₀N₇O₉P
• 分子量: 946.053
• InChiKey: BTWWAYGTCZANKL-JIRGUTPESA-N

计算性质

• 辛醇/水分配系数(LogP)：
  7.9
• 重原子数：
  68
• 可旋转键数：
  22
• 环数：
  7.0
• sp3杂化的碳原子比例：
  0.39
• 拓扑面积：
  180
• 氢给体数：
  2
• 氢受体数：
  13

反应信息

• 作为反应物：
  描述：

  N²-(p-isopropylphenoxyacetyl)-5'-O-(p,p'-dimethoxytrityl)-2'-deoxyguanosine 3'-(2-cyanoethyl N,N-diisopropylphosphoramidite) 在 甲胺 作用下， 以 四氢呋喃 为溶剂， 反应 2.0h， 以90%的产率得到5'-O-(4,4'-dimethoxytrityl)-2'-deoxyguanosine-3'-O-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite]
  参考文献：
  名称：

  N-未保护的脱氧核苷3'-亚磷酰胺构件的便捷合成，方法是将N-酰化的物种进行选择性脱酰并将其轻松转化为其他N-官能化的衍生物。

  摘要：

  [反应：见正文]描述了通过使用市售的N-酰化的脱氧核苷3'-亚磷酰胺的高度选择性N-脱酰作用来获得N-未保护的脱氧核苷3'-亚磷酰胺的基础的新途径。通过用酰化试剂进行容易的N-酰化，这些化合物可以容易地转化为其他类型的N-保护的物质。

  DOI：

  10.1021/ol051949z

文献信息

• Synthesis of Oligodeoxynucleotides Using Fully Protected Deoxynucleoside 3′-Phosphoramidite Building Blocks and Base Recognition of Oligodeoxynucleotides Incorporating N3-Cyano-Ethylthymine
  作者：Hirosuke Tsunoda、Tomomi Kudo、Akihiro Ohkubo、Kohji Seio、Mitsuo Sekine

  DOI：10.3390/molecules15117509

  日期：——

  Oligodeoxynucleotide (ODN) synthesis, which avoids the formation of side products, is of great importance to biochemistry-based technology development. One side reaction of ODN synthesis is the cyanoethylation of the nucleobases. We suppressed this reaction by synthesizing ODNs using fully protected deoxynucleoside 3'-phosphoramidite building blocks, where the remaining reactive nucleobase residues

  寡聚脱氧核苷酸 (ODN) 合成避免了副产物的形成，对于基于生物化学的技术开发具有重要意义。ODN 合成的一个副反应是核碱基的氰乙基化。我们通过使用完全受保护的脱氧核苷 3'-亚磷酰胺结构单元合成 ODN 来抑制该反应，其中剩余的反应性核碱基残基被酰基-、二酰基-和酰基-氧乙烯型基团完全保护。对核碱基位点氰乙基化的详细分析表明，胸腺嘧啶碱基的 N3 保护有效地抑制了丙烯腈的迈克尔加成。使用亚磷酰胺方法合成了包含 N3-氰乙基胸腺嘧啶的 ODN，并检查了涉及该 ODN 模板的引物延伸反应。其结果，
• Oligonucleotide−Oligospermine Conjugates (Zip Nucleic Acids): A Convenient Means of Finely Tuning Hybridization Temperatures
  作者：Régis Noir、Mitsuharu Kotera、Bénédicte Pons、Jean-Serge Remy、Jean-Paul Behr

  DOI：10.1021/ja804727a

  日期：2008.10.8

  allowed us to empirically derive a simple mathematical relation that is accurately predicting the T(m) of any oligonucleotide-oligospermine derivative. Zip nucleic acids (ZNA) are thus providing an interesting alternative to locked nucleic acids (LNA) or minor groove binders (MGB) for raising the stability of 8-12-mer oligonucleotides up to ca. 70 degrees C, the level required for quantitative PCR experiments

  寡核苷酸探针的合成及其杂交温度的控制是基于聚合酶链反应 (PCR) 的基因序列检测的关键方面。接近最后一个目标的直接方法是减少聚阴离子探针和目标链之间的排斥力。为此，我们开发了一种多功能的寡核苷酸-寡精胺衍生物自动合成方法，可以快速获取多种化合物。它们的杂交温度 T(m) 与总电荷的关系图提供了链间磷酸盐排斥（和精胺介导的吸引力）对双链体形成的主要驱动力（即碱基配对）的影响的衡量标准。结果表明，即使在高盐介质中，由过量阳离子电荷带来的稳定作用的绝对量级也大于链间排斥力。碱基序列和结合位点（3' 或 5'）几乎不影响精胺对 T(m) 的影响。在典型的 PCR 探针条件下，T(m) 随嫁接精胺的数量线性增加（例如，对于十核苷酸探针，每个精胺升高 6.2 摄氏度）。T(m) 与精胺数量和寡核苷酸长度的大数据集使我们能够凭经验得出一个简单的数学关系，该关系可以准确预测任何寡核苷酸-寡精胺衍生物的 T(m)。因此，Zip
• Independent Generation of the 5-Hydroxy-5,6-dihydrothymidin-6-yl Radical and Its Reactivity in Dinucleoside Monophosphates
  作者：Qibin Zhang、Yinsheng Wang

  DOI：10.1021/ja048492t

  日期：2004.10.1

  Hydroxyl radical is a major reactive oxygen species produced by gamma-radiolysis of water or Fenton reaction. It attacks pyrimidine bases and gives the 5-hydroxy-5,6-dihydropyrimidin-6-yl radical as the major product. Here we report the synthesis of all four stereoisomers of 5-hydroxy-6-phenylthio-5,6-dihydrothymidine (T*), which, upon 254 nm UV irradiation, give rise to the 5-hydroxy-5,6-dihydrothymidin-6-yl radical (1). We also incorporated the photolabile radical precursors into dinucleoside monophosphates d(GT*) and d(TT*) and characterized major products resulting from the 254-nm irradiation of these dinucleoside monophosphates. Our results showed that, under anaerobic conditions, the most abundant product emanating from the 254-nm irradiation of d(GT*) and d(TT*) is an abasic site lesion. Products with the thymine portion being modified to thymine glycol and 5-hydroxy-5,6-dihydrothymine were also observed. In addition, we demonstrated that radical I can attack the C8 carbon atom of its 5' neighboring guanine and give rise to a novel cross-link lesion. Moreover, LC-MS/MS results showed that gamma-radiation of d(GT) under anaerobic condition yielded the same type of cross-link lesions.
• Convenient Synthesis of <i>N</i>-Unprotected Deoxynucleoside 3‘-Phosphoramidite Building Blocks by Selective Deacylation of <i>N</i>-Acylated Species and Their Facile Conversion to Other <i>N</i>-Functionalized Derivatives
  作者：Akihiro Ohkubo、Kazushi Sakamoto、Ken-ichi Miyata、Haruhiko Taguchi、Kohji Seio、Mitsuo Sekine

  DOI：10.1021/ol051949z

  日期：2005.11.1

  highly selective N-deacylation of commercially available N-acylated deoxynucleoside 3'-phosphoramidites is described. These compounds could be readily converted to other types of N-protected species by facile N-acylations with acylating reagents.

  [反应：见正文]描述了通过使用市售的N-酰化的脱氧核苷3'-亚磷酰胺的高度选择性N-脱酰作用来获得N-未保护的脱氧核苷3'-亚磷酰胺的基础的新途径。通过用酰化试剂进行容易的N-酰化，这些化合物可以容易地转化为其他类型的N-保护的物质。