5-(6-N-(trifluoroacetyl)aminohexyl)-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyuridine | 149798-26-5

• 分子结构分类: 有机化合物 - 苯类化合物 - 三苯基化合物
• 英文名称: 5-(6-N-(trifluoroacetyl)aminohexyl)-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyuridine
• 英文别名: 5-[6-N-(trifluoroacetyl)aminohexyl]-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyuridine；N-[6-[1-[(2R,4S,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-hydroxyoxolan-2-yl]-2,4-dioxopyrimidin-5-yl]hexyl]-2,2,2-trifluoroacetamide
• CAS: 149798-26-5
• 化学式: C₃₈H₄₂F₃N₃O₈
• 分子量: 725.762
• InChiKey: IJXMQVZJHHIOLU-WIHCDAFUSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  5.8
• 重原子数：
  52
• 可旋转键数：
  16
• 环数：
  5.0
• sp3杂化的碳原子比例：
  0.39
• 拓扑面积：
  136
• 氢给体数：
  3
• 氢受体数：
  11

反应信息

• 作为反应物：
  描述：

  2-氰乙基N,N-二异丙基氯亚磷酰胺 、 5-(6-N-(trifluoroacetyl)aminohexyl)-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyuridine 在 N,N-二异丙基乙胺 作用下， 以 二氯甲烷 为溶剂， 反应 1.0h， 以93%的产率得到5-(6-N-(trifluoroacetyl)aminohexyl)-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyuridine 2-cyanoethyl N,N-diisopropylphosphoramidite
  参考文献：
  名称：

  Zwitterionic DNA

  摘要：

  As a strategy to make DNA net charge neutral, oligodeoxynucleotides bearing pyrimidine 5-omega-aminohexyl substituents have been synthesized and characterized. The resultant zwitterionic oligomers bind to natural DNA at low ionic strength as well or better than does natural DNA with itself, even when all of the nucleotides in a given single. strand are rendered zwitterionic. As would be expected, stabilities of duplexes bearing zwitterionic strands are relatively insensitive to changes in solution ionic strength as compared with natural DNA. Somewhat surprising, however, is the finding that a DNA duplex composed of a fully zwitterionic strand and a natural complementary strand exhibits no change in stability over a 20-fold change in ionic strength. Thus, double- and single-stranded states in this case have equivalent charge densities, consistent with the zwitterionic strand contributing no net charge. Stabilization due to the ammonium ions was verified by comparing free energies of DNA duplexes bearing hexyl tethered ammonium ions with those bearing simply hexyl groups devoid of ammonium ions. This comparison showed that without an added positive ammonium ion, the hexyl tether itself has a severe and cumulative unfavorable effect on duplex stability. Finally, zwitterionic nucleotides are found to distinguish matched from mismatched nucleotides in complementary DNA strands to a degree that rivals natural DNA.

  DOI：

  10.1021/ja00069a009
• 作为产物：
  描述：

  碘苷 在 palladium on activated charcoal 吡啶 、 copper(l) iodide 、 四(三苯基膦)钯 、 氢气 、 三乙胺 作用下， 以 甲醇 、 二氯甲烷 、 N,N-二甲基甲酰胺 为溶剂， 25.0 ℃ 、344.73 kPa 条件下， 反应 98.0h， 生成 5-(6-N-(trifluoroacetyl)aminohexyl)-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyuridine
  参考文献：
  名称：

  Zwitterionic DNA

  摘要：

  As a strategy to make DNA net charge neutral, oligodeoxynucleotides bearing pyrimidine 5-omega-aminohexyl substituents have been synthesized and characterized. The resultant zwitterionic oligomers bind to natural DNA at low ionic strength as well or better than does natural DNA with itself, even when all of the nucleotides in a given single. strand are rendered zwitterionic. As would be expected, stabilities of duplexes bearing zwitterionic strands are relatively insensitive to changes in solution ionic strength as compared with natural DNA. Somewhat surprising, however, is the finding that a DNA duplex composed of a fully zwitterionic strand and a natural complementary strand exhibits no change in stability over a 20-fold change in ionic strength. Thus, double- and single-stranded states in this case have equivalent charge densities, consistent with the zwitterionic strand contributing no net charge. Stabilization due to the ammonium ions was verified by comparing free energies of DNA duplexes bearing hexyl tethered ammonium ions with those bearing simply hexyl groups devoid of ammonium ions. This comparison showed that without an added positive ammonium ion, the hexyl tether itself has a severe and cumulative unfavorable effect on duplex stability. Finally, zwitterionic nucleotides are found to distinguish matched from mismatched nucleotides in complementary DNA strands to a degree that rivals natural DNA.

  DOI：

  10.1021/ja00069a009

文献信息

• Antisense oligonucleotides comprising 5-aminoalkyl pyrimidine nucleotides
  申请人：The Regents of the University of California

  公开号：US05596091A1

  公开（公告）日：1997-01-21

  Replacement of the natural nucleotides with unnatural zwitterionic nucleotides having a cationic moiety tethered to the base (or analog thereof) results in oligodeoxynucleotides with diminished charge but undiminished ability to complex with DNA at low ionic strengths. We have now discovered that DNA can be made fully zwitterionic by introducing tethered cationic moieties to the bases without affecting duplex formation. The resulting oligonucleotides have the further advantages of being nuclease resistant.

  将天然核苷酸替换为带有阳离子基团的非天然带电核苷酸（或其类似物）会导致寡脱氧核苷酸带有减少的电荷，但在低离子强度下与DNA结合的能力不减。我们现在发现，通过向碱基引入带有连接的阳离子基团，可以使DNA完全成为带电核酸，而不影响双链形成。由此产生的寡核苷酸具有耐核酸酶的额外优势。
• US5596091A
  申请人：——

  公开号：US5596091A

  公开（公告）日：1997-01-21
• US6031086A
  申请人：——

  公开号：US6031086A

  公开（公告）日：2000-02-29
• Zwitterionic DNA
  作者：Hiromasa Hashimoto、Marek G. Nelson、Christopher Switzer

  DOI：10.1021/ja00069a009

  日期：1993.8

  As a strategy to make DNA net charge neutral, oligodeoxynucleotides bearing pyrimidine 5-omega-aminohexyl substituents have been synthesized and characterized. The resultant zwitterionic oligomers bind to natural DNA at low ionic strength as well or better than does natural DNA with itself, even when all of the nucleotides in a given single. strand are rendered zwitterionic. As would be expected, stabilities of duplexes bearing zwitterionic strands are relatively insensitive to changes in solution ionic strength as compared with natural DNA. Somewhat surprising, however, is the finding that a DNA duplex composed of a fully zwitterionic strand and a natural complementary strand exhibits no change in stability over a 20-fold change in ionic strength. Thus, double- and single-stranded states in this case have equivalent charge densities, consistent with the zwitterionic strand contributing no net charge. Stabilization due to the ammonium ions was verified by comparing free energies of DNA duplexes bearing hexyl tethered ammonium ions with those bearing simply hexyl groups devoid of ammonium ions. This comparison showed that without an added positive ammonium ion, the hexyl tether itself has a severe and cumulative unfavorable effect on duplex stability. Finally, zwitterionic nucleotides are found to distinguish matched from mismatched nucleotides in complementary DNA strands to a degree that rivals natural DNA.