1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-selenophen-2-ylpyrimidine-2,4-dione | 1447909-23-0

• 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: 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-selenophen-2-ylpyrimidine-2,4-dione
• CAS: 1447909-23-0
• 化学式: C₁₃H₁₄N₂O₆Se
• 分子量: 373.224
• InChiKey: KEUNWLYELMNROH-UGKPPGOTSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  -2.13
• 重原子数：
  22
• 可旋转键数：
  3
• 环数：
  3.0
• sp3杂化的碳原子比例：
  0.38
• 拓扑面积：
  119
• 氢给体数：
  4
• 氢受体数：
  6

反应信息

• 作为反应物：
  描述：

  三正丁胺 、 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-selenophen-2-ylpyrimidine-2,4-dione 、 三丁基焦磷酸铵 在 磷酸三甲酯 、 三氯氧磷 作用下， 以18%的产率得到
  参考文献：
  名称：

  Heavy Atom Containing Fluorescent Ribonucleoside Analog Probe for the Fluorescence Detection of RNA-Ligand Binding

  摘要：

  Although numerous biophysical tools have provided effective systems to study nucleic acids, our current knowledge on how RNA structure complements its function is limited. Therefore, development of robust tools to study the structure-function relationship of RNA is highly desired. Toward this endeavor, we have developed a new ribonucleoside analog, based on a (selenophen-2-yl)pyrimidine core, which could serve as a fluorescence probe to study the function of RNA in real time and as an anomalous scattering label (selenium atom) for the phase determination in X-ray crystallography. The fluorescent selenophene-modified uridine analog is minimally perturbing and exhibits probe-like properties such as sensitivity to microenvironment and conformation changes. Utilizing these properties and amicability of the corresponding ribonucleotide analog to enzymatic incorporation, we have synthesized a fluorescent bacterial ribosomal decoding site (A-site) RNA construct and have developed a fluorescence binding assay to effectively monitor the binding of aminoglycoside antibiotics to the A-site. Our results demonstrate that this simple approach of building a dual probe could provide new avenues to study the structure-function relationship of not only nucleic acids, but also other biomacromolecules.

  DOI：

  10.1021/bc400194g
• 作为产物：
  描述：

  5-碘尿苷 、 三丁基锡硒酚 在 bis-triphenylphosphine-palladium(II) chloride 作用下， 以 1,4-二氧六环 为溶剂， 以46%的产率得到1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-selenophen-2-ylpyrimidine-2,4-dione
  参考文献：
  名称：

  Heavy Atom Containing Fluorescent Ribonucleoside Analog Probe for the Fluorescence Detection of RNA-Ligand Binding

  摘要：

  Although numerous biophysical tools have provided effective systems to study nucleic acids, our current knowledge on how RNA structure complements its function is limited. Therefore, development of robust tools to study the structure-function relationship of RNA is highly desired. Toward this endeavor, we have developed a new ribonucleoside analog, based on a (selenophen-2-yl)pyrimidine core, which could serve as a fluorescence probe to study the function of RNA in real time and as an anomalous scattering label (selenium atom) for the phase determination in X-ray crystallography. The fluorescent selenophene-modified uridine analog is minimally perturbing and exhibits probe-like properties such as sensitivity to microenvironment and conformation changes. Utilizing these properties and amicability of the corresponding ribonucleotide analog to enzymatic incorporation, we have synthesized a fluorescent bacterial ribosomal decoding site (A-site) RNA construct and have developed a fluorescence binding assay to effectively monitor the binding of aminoglycoside antibiotics to the A-site. Our results demonstrate that this simple approach of building a dual probe could provide new avenues to study the structure-function relationship of not only nucleic acids, but also other biomacromolecules.

  DOI：

  10.1021/bc400194g