5-(aminomethyl)-2'-deoxy-5'-O-pivaloyl-3'-O-(tetrahydro-2H-pyran-2-yl)uridine | 263712-25-0

• 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: 5-(aminomethyl)-2'-deoxy-5'-O-pivaloyl-3'-O-(tetrahydro-2H-pyran-2-yl)uridine
• 英文别名: [(2R,3S,5R)-5-[5-(aminomethyl)-2,4-dioxopyrimidin-1-yl]-3-(oxan-2-yloxy)oxolan-2-yl]methyl 2,2-dimethylpropanoate
• CAS: 263712-25-0
• 化学式: C₂₀H₃₁N₃O₇
• 分子量: 425.482
• InChiKey: PDLVBWRTUAPNNJ-BZZKYOCZSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  0.9
• 重原子数：
  30
• 可旋转键数：
  8
• 环数：
  3.0
• sp3杂化的碳原子比例：
  0.75
• 拓扑面积：
  129
• 氢给体数：
  2
• 氢受体数：
  8

反应信息

• 作为反应物：
  描述：

  5-(aminomethyl)-2'-deoxy-5'-O-pivaloyl-3'-O-(tetrahydro-2H-pyran-2-yl)uridine 在 吡啶 、 四氮唑 、 四丁基氟化铵 、 2,4,5,6-四甲基苯二磺酸氯 、 三乙胺 作用下， 以 四氢呋喃 、 N,N-二甲基甲酰胺 为溶剂， 反应 3.0h， 生成 2'-O-{2-{{{1-[2'-deoxy-5'-O-pivaloyl-3'-O-(tetrahydro-2H-pyran-2-yl)-β-D-ribofuranosyl]-1,2,3,4-tetrahydro-2,4-dioxopyrimidin-5-yl}methyl}amino}-2-oxoethyl}-5'-O-(4,4'-dimethoxytrityl)uridine 3'-(S,S'-diphenyl phosphorodithioate)
  参考文献：
  名称：

  Synthesis and Properties of Oligothymidylates Incorporating an Artificial Bend Motif

  摘要：

  The uridylyl-(3' --> 5')-thymidine dinucleotide block 14 (cUpdU), having a cyclic structure between the 2'-hydroxy of the upstream uridine and the 5-substituent of the downstream thymidine, was synthesized (Schemes 1 and 2). This cyclic structure is a stable mimic of the intraresidual H-bonding found in the anticodon loop of an E. coli minor tRNA(Arg). The spectroscopic and molecular-mechanics analyses of the cyclized dinucleotides predicted two major conformers, i.e., the turn and bent forms. The latter was expected to bend DNA oligomers when incorporated into them. This expectation was ascertained by incorporating the bent dimer motif into tetra-, deca-, or hexadecathymidylates by the conventional phosphoramidite method (see 18-20 in Scheme 4). The bending of oligonucleotides 18-20 was demonstrated by P-31-NMR and CD spectra and gel-electrophoretic studies. The duplex formation of these modified oligonucleotides with oligodeoxyadenylates was also studied. The decreased thermal stability of the duplexes when compared with unmodified ones indicates distorted structures of the modified duplexes. The 3D computer model of the duplexes showed a bend of cn. 30 degrees with a 'bulge-out' at the position of an adenosine residue facing the cyclized dimer. The artificially bent DNAs might become a new tool for the study of the effect of DNA bending induced in DNA/DNA-binding protein interactions.

  DOI：

  10.1002/(sici)1522-2675(20000119)83:1<162::aid-hlca162>3.0.co;2-y
• 作为产物：
  描述：

  5-羟甲基脱氧尿苷 在 palladium on activated charcoal 吡啶 、 三甲基氯硅烷 、 sodium azide 、 氢气 、 三氟乙酸 作用下， 以 1,4-二氧六环 、 甲醇 、 二氯甲烷 、 N,N-二甲基甲酰胺 为溶剂， 反应 28.25h， 生成 5-(aminomethyl)-2'-deoxy-5'-O-pivaloyl-3'-O-(tetrahydro-2H-pyran-2-yl)uridine
  参考文献：
  名称：

  Synthesis and Properties of Oligothymidylates Incorporating an Artificial Bend Motif

  摘要：

  The uridylyl-(3' --> 5')-thymidine dinucleotide block 14 (cUpdU), having a cyclic structure between the 2'-hydroxy of the upstream uridine and the 5-substituent of the downstream thymidine, was synthesized (Schemes 1 and 2). This cyclic structure is a stable mimic of the intraresidual H-bonding found in the anticodon loop of an E. coli minor tRNA(Arg). The spectroscopic and molecular-mechanics analyses of the cyclized dinucleotides predicted two major conformers, i.e., the turn and bent forms. The latter was expected to bend DNA oligomers when incorporated into them. This expectation was ascertained by incorporating the bent dimer motif into tetra-, deca-, or hexadecathymidylates by the conventional phosphoramidite method (see 18-20 in Scheme 4). The bending of oligonucleotides 18-20 was demonstrated by P-31-NMR and CD spectra and gel-electrophoretic studies. The duplex formation of these modified oligonucleotides with oligodeoxyadenylates was also studied. The decreased thermal stability of the duplexes when compared with unmodified ones indicates distorted structures of the modified duplexes. The 3D computer model of the duplexes showed a bend of cn. 30 degrees with a 'bulge-out' at the position of an adenosine residue facing the cyclized dimer. The artificially bent DNAs might become a new tool for the study of the effect of DNA bending induced in DNA/DNA-binding protein interactions.

  DOI：

  10.1002/(sici)1522-2675(20000119)83:1<162::aid-hlca162>3.0.co;2-y

文献信息

• Synthesis and Properties of Oligothymidylates Incorporating an Artificial Bend Motif
  作者：Kohji Seio、Takeshi Wada、Mitsuo Sekine

  DOI：10.1002/(sici)1522-2675(20000119)83:1<162::aid-hlca162>3.0.co;2-y

  日期：2000.1.19

  The uridylyl-(3' --> 5')-thymidine dinucleotide block 14 (cUpdU), having a cyclic structure between the 2'-hydroxy of the upstream uridine and the 5-substituent of the downstream thymidine, was synthesized (Schemes 1 and 2). This cyclic structure is a stable mimic of the intraresidual H-bonding found in the anticodon loop of an E. coli minor tRNA(Arg). The spectroscopic and molecular-mechanics analyses of the cyclized dinucleotides predicted two major conformers, i.e., the turn and bent forms. The latter was expected to bend DNA oligomers when incorporated into them. This expectation was ascertained by incorporating the bent dimer motif into tetra-, deca-, or hexadecathymidylates by the conventional phosphoramidite method (see 18-20 in Scheme 4). The bending of oligonucleotides 18-20 was demonstrated by P-31-NMR and CD spectra and gel-electrophoretic studies. The duplex formation of these modified oligonucleotides with oligodeoxyadenylates was also studied. The decreased thermal stability of the duplexes when compared with unmodified ones indicates distorted structures of the modified duplexes. The 3D computer model of the duplexes showed a bend of cn. 30 degrees with a 'bulge-out' at the position of an adenosine residue facing the cyclized dimer. The artificially bent DNAs might become a new tool for the study of the effect of DNA bending induced in DNA/DNA-binding protein interactions.