5-hydroxymethyl-2',3'-O-isopropylidenecytidine | 72472-12-9

• 分子结构分类: 有机化合物 - 有机杂环化合物 - 二嗪类
• 英文名称: 5-hydroxymethyl-2',3'-O-isopropylidenecytidine
• 英文别名: 5-hydroxymethyl-2’,3’-O-isopropylidenecytidine；5-hydroxymethyl-O^2'_,O3'-isopropylidene-cytidine；5-(Hydroxymethyl)-2',3'-O-(1-methylethylidene)cytidine；1-[(3aR,4R,6R,6aR)-6-(hydroxymethyl)-2,2-dimethyl-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3]dioxol-4-yl]-4-amino-5-(hydroxymethyl)pyrimidin-2-one
• CAS: 72472-12-9
• 化学式: C₁₃H₁₉N₃O₆
• 分子量: 313.31
• InChiKey: JKNVVCZBENODOV-TURQNECASA-N

计算性质

• 辛醇/水分配系数(LogP)：
  -1.27
• 重原子数：
  22.0
• 可旋转键数：
  3.0
• 环数：
  3.0
• sp3杂化的碳原子比例：
  0.69
• 拓扑面积：
  129.06
• 氢给体数：
  3.0
• 氢受体数：
  9.0

反应信息

• 作为反应物：
  描述：

  5-hydroxymethyl-2',3'-O-isopropylidenecytidine 在 manganese(IV) oxide 作用下， 以 甲醇 为溶剂， 以46 %的产率得到5-formyl-2’,3’-O-isopropylidenecytidine
  参考文献：
  名称：

  Photo‐Facilitated Detection and Sequencing of 5‐Formylcytidine RNA

  摘要：

  Abstract5‐Formylcytidine (f5C) is one of the epigenetic nucleotides in tRNA. Despite the evident importance of f5C in gene expression regulation, little is known about its exact amount and position. To capture this information, we developed a modification‐specific functionalization with a semi‐stabilized ylide. The chemical labelling exhibited a high selectivity towards f5C and allowed distinction from similar 5‐formyluridine. We realized a detection strategy based on the fluorescence signal of the cyclization product 4,5‐pyridin‐2‐amine‐cytidine paC, which exhibited a high quantum yield. The results clearly identified f5C with a limit of detection at 0.58 nM. This method altered the hydrogen bonding activities of f5C and modulated its reverse transcription signature in its sequencing profile. We showed that f5C can be detected from tRNA segments with a single‐base resolution. Taken together, this approach is a sensitive, antibody‐free, and applicable detection and sequencing method for f5C‐containing RNA.

  DOI：

  10.1002/anie.202210652
• 作为产物：
  描述：

  胞苷 在 硫酸 、 potassium hydroxide 作用下， 以 水 为溶剂， 反应 72.0h， 生成 5-hydroxymethyl-2',3'-O-isopropylidenecytidine
  参考文献：
  名称：

  Photo‐Facilitated Detection and Sequencing of 5‐Formylcytidine RNA

  摘要：

  Abstract5‐Formylcytidine (f5C) is one of the epigenetic nucleotides in tRNA. Despite the evident importance of f5C in gene expression regulation, little is known about its exact amount and position. To capture this information, we developed a modification‐specific functionalization with a semi‐stabilized ylide. The chemical labelling exhibited a high selectivity towards f5C and allowed distinction from similar 5‐formyluridine. We realized a detection strategy based on the fluorescence signal of the cyclization product 4,5‐pyridin‐2‐amine‐cytidine paC, which exhibited a high quantum yield. The results clearly identified f5C with a limit of detection at 0.58 nM. This method altered the hydrogen bonding activities of f5C and modulated its reverse transcription signature in its sequencing profile. We showed that f5C can be detected from tRNA segments with a single‐base resolution. Taken together, this approach is a sensitive, antibody‐free, and applicable detection and sequencing method for f5C‐containing RNA.

  DOI：

  10.1002/anie.202210652

文献信息

• Efficient Synthesis of 5-Hydroxymethyl Pyrimidines and their Nucleosides Using Microwave Irradiation
  作者：El S. El Ashry、Adel A.-H. Abdel-Rahman

  DOI：10.1055/s-2002-35592

  日期：——

  Hydroxymethylation of uracil (1), cytosine (3), 5-hydroxymethyl-2′,3′-O-isopropylideneuridine (5), 5′-O-tert-butyldiphenylsilyl-2′,3′-O-isopropylideneuridine (7), 2′,3′-O-isopropyl-idenecytidine (9) and 2′,3′-O-isopropylidene-5′-O-tritylcytidine (11) was efficiently carried out with paraformaldehyde in alkaline medium under microwave irradiation in very high yield.

  尿嘧啶（1）、胞嘧啶（3）、5-羟甲基-2′,3′-O-异亚丙基尿苷（5）、5′-O-叔丁基二苯基硅-2′,3′-O-异亚丙基尿苷（7）、2′、9）和 2′,3′-O-异亚丙基-5′-O-三苯甲基胞苷（11）。