1'-deoxy-1'-(4-fluoro-1H-benzimidazol-1-yl)-β-D-ribofuranose | 304436-46-2

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 苯并咪唑核糖核苷和核糖核苷酸
• 英文名称: 1'-deoxy-1'-(4-fluoro-1H-benzimidazol-1-yl)-β-D-ribofuranose
• 英文别名: 1-deoxy-1-(4-fluoro-1H-benzimidazol-1-yl)-β-D-ribofuranose；1'-deoxy-1'-(4-fluorobenzimidazol-1-yl)-β-D-ribofuranose；(2R,3R,4S,5R)-2-(4-fluorobenzimidazol-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol
• CAS: 304436-46-2
• 化学式: C₁₂H₁₃FN₂O₄
• 分子量: 268.245
• InChiKey: PWPGTOQBEDOXKO-HJQYOEGKSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  -0.1
• 重原子数：
  19
• 可旋转键数：
  2
• 环数：
  3.0
• sp3杂化的碳原子比例：
  0.42
• 拓扑面积：
  87.7
• 氢给体数：
  3
• 氢受体数：
  6

反应信息

• 作为反应物：
  描述：

  1'-deoxy-1'-(4-fluoro-1H-benzimidazol-1-yl)-β-D-ribofuranose 在 silver nitrate 、 三乙胺 作用下， 以 四氢呋喃 、 吡啶 为溶剂， 反应 26.5h， 生成 3-O-[(tert-butyl)dimethylsilyl]-1-deoxy-5-O-(4,4'-dimethoxytrityl)-1-(4-fluoro-1H-benzimidazol-1-yl)-β-D-ribofuranose
  参考文献：
  名称：

  Synthesis of Fluorobenzene and Benzimidazole Nucleic-Acid Analogues and Their Influence on Stability of RNA Duplexes

  摘要：

  Six different ribonucleoside phosphoramidites with fluorobenzenes or fluorobenzimidazoles as base analogues, one abasic site, and inosine were synthesized and incorporated into oligoribonucleotides. The oligomers were investigated by means of UV and CD spectroscopy to assess the contribution of H-bonding, base stacking, and solvation to the stability of the RNA duplex. CD Spectra show that the incorporation of modified nucleosides does not lead to changes in the structure of RNA. The T-m differences determined are based on changes in base stacking and solvation. Individual contributions of base stacking and solvation of the modified nucleosides could be determined. In fluorobenzene . fluorobenzimidazole-modified base pairs, a duplex-stabilizing force was found that points to a weak F ... H H-bond.

  DOI：

  10.1002/1522-2675(20000809)83:8<1791::aid-hlca1791>3.0.co;2-k
• 作为产物：
  描述：

  四乙酰核糖 在 甲醇 、 N,O-双三甲硅基乙酰胺 、 氨 作用下， 以 乙腈 为溶剂， 反应 22.75h， 生成 1'-deoxy-1'-(4-fluoro-1H-benzimidazol-1-yl)-β-D-ribofuranose
  参考文献：
  名称：

  Synthesis of Fluorobenzene and Benzimidazole Nucleic-Acid Analogues and Their Influence on Stability of RNA Duplexes

  摘要：

  Six different ribonucleoside phosphoramidites with fluorobenzenes or fluorobenzimidazoles as base analogues, one abasic site, and inosine were synthesized and incorporated into oligoribonucleotides. The oligomers were investigated by means of UV and CD spectroscopy to assess the contribution of H-bonding, base stacking, and solvation to the stability of the RNA duplex. CD Spectra show that the incorporation of modified nucleosides does not lead to changes in the structure of RNA. The T-m differences determined are based on changes in base stacking and solvation. Individual contributions of base stacking and solvation of the modified nucleosides could be determined. In fluorobenzene . fluorobenzimidazole-modified base pairs, a duplex-stabilizing force was found that points to a weak F ... H H-bond.

  DOI：

  10.1002/1522-2675(20000809)83:8<1791::aid-hlca1791>3.0.co;2-k

文献信息

• Synthesis of Fluorobenzene and Benzimidazole Nucleic-Acid Analogues and Their Influence on Stability of RNA Duplexes
  作者：Jörg Parsch、Joachim W. Engels

  DOI：10.1002/1522-2675(20000809)83:8<1791::aid-hlca1791>3.0.co;2-k

  日期：2000.8.9

  Six different ribonucleoside phosphoramidites with fluorobenzenes or fluorobenzimidazoles as base analogues, one abasic site, and inosine were synthesized and incorporated into oligoribonucleotides. The oligomers were investigated by means of UV and CD spectroscopy to assess the contribution of H-bonding, base stacking, and solvation to the stability of the RNA duplex. CD Spectra show that the incorporation of modified nucleosides does not lead to changes in the structure of RNA. The T-m differences determined are based on changes in base stacking and solvation. Individual contributions of base stacking and solvation of the modified nucleosides could be determined. In fluorobenzene . fluorobenzimidazole-modified base pairs, a duplex-stabilizing force was found that points to a weak F ... H H-bond.
• RNA RECOGNITION BY FLUOR-AROMATIC SUBSTITUTED
  作者：A. Zivković、J. W. Engels

  DOI：10.1081/ncn-200059755

  日期：2005.4.1

  RNA exhibits a higher structural diversity than DNA and is an important molecule in the biology of life. It shows a number of secondary structures such as duplexes, hairpin loops, bulges, internal loops, etc. However, in natural RNA, bases are limited to the four Predominant structures Q, C, A, and G and so the number of compounds that can be used for investigation of parameters of base stacking, base pairing, and hydrogen bond is limited. We synthesized different fluoromodifications of RNA building blocks: 1'-deoxy- 1'-phenyl-beta-D-ribofuranose (B), 1'-deoxy- 1'-(4-fluorophenyl)-beta-D-ribofuranose (4 FB), 1'-deoxy- 1'-(2,4-difluorophenyl)-beta-D-ribofuranose (2,4 DFB), 1'-deoxy-1'-(2,4,5-trifluorophenyl)-beta-D-ribofuranose (2,4,5 TFB), 1'-deoxy-1'-(2,4,6-trifluorophenyl)-beta-D-ribofuranose, 1'-deoxy- 1'-(pentafluorophenyl)-beta-D-ribofuranose (PFB), 1'-deoxy-1'-(benzimidazol-1-yl)-beta-D-ribofuranose (BI), 1'-deoxy-1'-(4-fluoro- 1H-benzimidazol-1-yl)-beta-D-ribofuranose (4 FBI), 1'-deoxy-1'-(6-fluoro-1H-benzimidazol-1-y1)-beta-D-ribofuranose(6FBI), 1'-deoxy-1'-(4,6-difluoro-IH-benzimidazol-1-yl)-beta-D-ribofuranose(4,6 DFBI), 1'-deoxy-1'-(4-trifluoromethyl-1H-benzimidazol-1-yl)-beta-D-ribofuranose (4 TFM), 1'-deoxy-1'-(5-trifluoromethyl-1H-benzimidazol-1-yl)-beta-D-ribofuranose (5 TFM), and 1'-deoxy-1'-(6-trifluoromethyl- 1H-benzimidazol-1-yl)-beta-D-ribofuranose (6 TFM). These amidites were incorporated and tested in a defined A, U-rich RNA sequence (12-mer, 5'-CUU UUC XUU CUU-3' paired with 3'-GAA AAG YAA GAA-5'). Ono one position was modified, marked as X and Y, respectively. UV melting profiles of those oligonucleotides were measured.