N-[2-(tert-butyl(dimethyl)silyloxy)-5-(9-phenylxanten-9-yloxy)cyclopentyl]-2-(N⁶-(p-methoxybenzoyl)adenin-1-yl)acetamide

• 分子结构分类: 有机化合物 - 有机杂环化合物 - 苯并吡喃
• 英文名称: N-[2-(tert-butyl(dimethyl)silyloxy)-5-(9-phenylxanten-9-yloxy)cyclopentyl]-2-(N⁶-(p-methoxybenzoyl)adenin-1-yl)acetamide
• 英文别名: N-[9-[2-[[(1S,2R,5R)-2-[tert-butyl(dimethyl)silyl]oxy-5-(9-phenylxanthen-9-yl)oxycyclopentyl]amino]-2-oxoethyl]purin-6-yl]-4-methoxybenzamide
• 化学式: C₄₅H₄₈N₆O₆Si
• 分子量: 796.998
• InChiKey: ASPVNYJIPUWDLB-BMJIQSQISA-N

计算性质

• 辛醇/水分配系数(LogP)：
  8.24
• 重原子数：
  58
• 可旋转键数：
  12
• 环数：
  8.0
• sp3杂化的碳原子比例：
  0.31
• 拓扑面积：
  139
• 氢给体数：
  2
• 氢受体数：
  9

反应信息

• 作为反应物：
  描述：

  N-[2-(tert-butyl(dimethyl)silyloxy)-5-(9-phenylxanten-9-yloxy)cyclopentyl]-2-(N⁶-(p-methoxybenzoyl)adenin-1-yl)acetamide 在 四丁基氟化铵 作用下， 以 四氢呋喃 为溶剂， 以98%的产率得到N-[2-hydroxy-5-(9-phenylxanten-9-yloxy)cyclopentyl]-2-(N⁶-(p-methoxybenzoyl)adenin-1-yl)acetamide
  参考文献：
  名称：

  Synthesis of Cyclopentane Amide DNA (cpa-DNA) and Its Pairing Properties

  摘要：

  We recently reported on the synthesis and pairing properties of the DNA analogue bicyclo[3.2.1]-amide DNA (bca-DNA). In this analogue the nucleobases are attached via a linear, 4-bond amide-linker to a structurally preorganized sugar-phosphate backbone unit. To define the importance of the degree of structural rigidity of the bca-backbone unit on the pairing properties, we designed the structurally simpler cyclopentane amide DNA (cpa-DNA), in which the bicyclo[3.2.1]-scaffold was reduced to a cyclopentane unit while the base-linker was left unchanged. Here we present a synthetic route to the enantiomerically pure cpa-DNA monomers and the corresponding phosphoramidites containing the bases A and T, starting from a known, achiral precursor in 9 and 12 steps, respectively. Fully modified oligodeoxynucleotides were synthesized by standard solid-phase oligonucleotide chemistry, and their base-pairing properties with complementary oligonucleotides of the DNA-, RNA-, bca-DNA-, and cpa-DNA-backbones were assessed by UV melting curves and CD-spectroscopic methods. We found that cpa-oligoadenylates form duplexes with complementary DNA that are less stable by -2.7 degreesC/mod. compared to DNA. The corresponding cpa-oligothymidylates do not participate in complementary base-pairing with any of the investigated backbone systems except with its own (homo-duplex). As its congener bca-DNA, cpa-DNA seems to prefer left-handed helical duplex structures with DNA or with itself as indicated by the CD spectra.

  DOI：

  10.1021/jo034143q
• 作为产物：
  描述：

  (2-环戊烯-1-氧基)二甲基(1,1-二甲基乙基)硅烷 在 palladium on activated charcoal 吡啶 、 咪唑 、 4-二甲氨基吡啶 、 氢氧化钾 、 phosphate buffer 、 pig liver esterase 、 四丁基氟化铵 、 氢气 、 sodium hydride 、 1-(3-二甲基氨基丙基)-3-乙基碳二亚胺 、 间氯过氧苯甲酸 作用下， 以 四氢呋喃 、 乙醇 、 二氯甲烷 、 水 、 二甲基亚砜 、 N,N-二甲基甲酰胺 、 甲苯 为溶剂， 20.0~95.0 ℃ 、1.01 MPa 条件下， 反应 69.0h， 生成 N-[2-(tert-butyl(dimethyl)silyloxy)-5-(9-phenylxanten-9-yloxy)cyclopentyl]-2-(N⁶-(p-methoxybenzoyl)adenin-1-yl)acetamide
  参考文献：
  名称：

  Synthesis of Cyclopentane Amide DNA (cpa-DNA) and Its Pairing Properties

  摘要：

  We recently reported on the synthesis and pairing properties of the DNA analogue bicyclo[3.2.1]-amide DNA (bca-DNA). In this analogue the nucleobases are attached via a linear, 4-bond amide-linker to a structurally preorganized sugar-phosphate backbone unit. To define the importance of the degree of structural rigidity of the bca-backbone unit on the pairing properties, we designed the structurally simpler cyclopentane amide DNA (cpa-DNA), in which the bicyclo[3.2.1]-scaffold was reduced to a cyclopentane unit while the base-linker was left unchanged. Here we present a synthetic route to the enantiomerically pure cpa-DNA monomers and the corresponding phosphoramidites containing the bases A and T, starting from a known, achiral precursor in 9 and 12 steps, respectively. Fully modified oligodeoxynucleotides were synthesized by standard solid-phase oligonucleotide chemistry, and their base-pairing properties with complementary oligonucleotides of the DNA-, RNA-, bca-DNA-, and cpa-DNA-backbones were assessed by UV melting curves and CD-spectroscopic methods. We found that cpa-oligoadenylates form duplexes with complementary DNA that are less stable by -2.7 degreesC/mod. compared to DNA. The corresponding cpa-oligothymidylates do not participate in complementary base-pairing with any of the investigated backbone systems except with its own (homo-duplex). As its congener bca-DNA, cpa-DNA seems to prefer left-handed helical duplex structures with DNA or with itself as indicated by the CD spectra.

  DOI：

  10.1021/jo034143q

文献信息

• Synthesis of Cyclopentane Amide DNA (cpa-DNA) and Its Pairing Properties
  作者：Dae-Ro Ahn、Markus Mosimann、Christian J. Leumann

  DOI：10.1021/jo034143q

  日期：2003.10.1

  We recently reported on the synthesis and pairing properties of the DNA analogue bicyclo[3.2.1]-amide DNA (bca-DNA). In this analogue the nucleobases are attached via a linear, 4-bond amide-linker to a structurally preorganized sugar-phosphate backbone unit. To define the importance of the degree of structural rigidity of the bca-backbone unit on the pairing properties, we designed the structurally simpler cyclopentane amide DNA (cpa-DNA), in which the bicyclo[3.2.1]-scaffold was reduced to a cyclopentane unit while the base-linker was left unchanged. Here we present a synthetic route to the enantiomerically pure cpa-DNA monomers and the corresponding phosphoramidites containing the bases A and T, starting from a known, achiral precursor in 9 and 12 steps, respectively. Fully modified oligodeoxynucleotides were synthesized by standard solid-phase oligonucleotide chemistry, and their base-pairing properties with complementary oligonucleotides of the DNA-, RNA-, bca-DNA-, and cpa-DNA-backbones were assessed by UV melting curves and CD-spectroscopic methods. We found that cpa-oligoadenylates form duplexes with complementary DNA that are less stable by -2.7 degreesC/mod. compared to DNA. The corresponding cpa-oligothymidylates do not participate in complementary base-pairing with any of the investigated backbone systems except with its own (homo-duplex). As its congener bca-DNA, cpa-DNA seems to prefer left-handed helical duplex structures with DNA or with itself as indicated by the CD spectra.