N4-Benzoyl-5'-O-DMT-5-methylcytidine | 160107-17-5

• 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: N4-Benzoyl-5'-O-DMT-5-methylcytidine
• 英文别名: N-[1-[(2R,3R,4S,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-3,4-dihydroxyoxolan-2-yl]-5-methyl-2-oxopyrimidin-4-yl]benzamide
• CAS: 160107-17-5
• 化学式: C₃₈H₃₇N₃O₈
• 分子量: 663.727
• InChiKey: QCKRNDPKDFQXCO-DHKUXYTCSA-N

物化性质

• 密度：
  1.30±0.1 g/cm3(Predicted)

计算性质

• 辛醇/水分配系数(LogP)：
  5.3
• 重原子数：
  49
• 可旋转键数：
  11
• 环数：
  6.0
• sp3杂化的碳原子比例：
  0.24
• 拓扑面积：
  139
• 氢给体数：
  3
• 氢受体数：
  8

反应信息

• 作为反应物：
  描述：

  N4-Benzoyl-5'-O-DMT-5-methylcytidine 在 吡啶 、 N-甲基咪唑 、 2,3,5-三甲基吡啶 、 silver nitrate 作用下， 以 四氢呋喃 为溶剂， 反应 6.0h， 生成 N-[1-[(2R,3R,4R,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-3-[tert-butyl(dimethyl)silyl]oxy-4-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxyoxolan-2-yl]-5-methyl-2-oxopyrimidin-4-yl]benzamide
  参考文献：
  名称：

  Recognition of RNA by triplex formation: Divergent effects of pyrimidine C-5 methylation

  摘要：

  In DNA triple helices, methylation at C-5 of thymine or cytosine is reported to have similar stabilizing effects for both bases. Here we show, however, that methylation of the same positions in RNA triplexes has distinctly different effects than in DNA. We have previously described the use of circular tripler-forming RNA oligonucleotides to recognize RNA sequences. Here it is shown that addition of C-5 methyl groups to uracils in these compounds very significantly increases not only affinity but also sequence selectivity in binding a purine-rich RNA target, as measured by thermal denaturation with various target RNAs. Surprisingly, however, addition of C-5 methyl groups to cytosines actually decreases affinity in binding RNA, while the same substitution in DNA is thermally stabilizing. possible sources of this divergent behavior are discussed. A synthesis of 5-methylcytidine ribonucleoside 2'-O-silyl-3'-O-phosphoramidite is also described. (C) 1997 Elsevier Science Ltd.

  DOI：

  10.1016/s0968-0896(97)00059-x
• 作为产物：
  描述：

  5-甲基-N-(三甲基甲硅烷基)-2-[(三甲基甲硅烷基)氧基]-4-嘧啶胺 在 吡啶 、 sodium hydroxide 、 sodium methylate 、 tin(ll) chloride 作用下， 以 甲醇 、 二氯甲烷 为溶剂， 反应 21.0h， 生成 N4-Benzoyl-5'-O-DMT-5-methylcytidine
  参考文献：
  名称：

  Recognition of RNA by triplex formation: Divergent effects of pyrimidine C-5 methylation

  摘要：

  In DNA triple helices, methylation at C-5 of thymine or cytosine is reported to have similar stabilizing effects for both bases. Here we show, however, that methylation of the same positions in RNA triplexes has distinctly different effects than in DNA. We have previously described the use of circular tripler-forming RNA oligonucleotides to recognize RNA sequences. Here it is shown that addition of C-5 methyl groups to uracils in these compounds very significantly increases not only affinity but also sequence selectivity in binding a purine-rich RNA target, as measured by thermal denaturation with various target RNAs. Surprisingly, however, addition of C-5 methyl groups to cytosines actually decreases affinity in binding RNA, while the same substitution in DNA is thermally stabilizing. possible sources of this divergent behavior are discussed. A synthesis of 5-methylcytidine ribonucleoside 2'-O-silyl-3'-O-phosphoramidite is also described. (C) 1997 Elsevier Science Ltd.

  DOI：

  10.1016/s0968-0896(97)00059-x

文献信息

• Oligonucleotides comprising a modified or non-natural nucleobase
  申请人：Manoharan Muthiah

  公开号：US20060035254A1

  公开（公告）日：2006-02-16

  One aspect of the present invention relates to a double-stranded oligonucleotide comprising at least one non-natural nucleobase. In certain embodiments, the non-natural nucleobase is difluorotolyl, nitroindolyl, nitropyrrolyl, or nitroimidazolyl. In a preferred embodiment, the non-natural nucleobase is difluorotolyl. In certain embodiments, only one of the two oligonucleotide strands comprising the double-stranded oligonucleotide contains a non-natural nucleobase. In certain embodiments, both of the oligonucleotide strands comprising the double-stranded oligonucleotide independently contain a non-natural nucleobase. In certain embodiments, the oligonucleotide strands comprise at least one modified sugar moiety. Another aspect of the present invention relates to a single-stranded oligonucleotide comprising at least one non-natural nucleobase. In a preferred embodiment, the non-natural nucleobase is difluorotolyl. In certain embodiments, the ribose sugar moiety that occurs naturally in nucleosides is replaced with a hexose sugar, polycyclic heteroalkyl ring, or cyclohexenyl group. In certain embodiments, at least one phosphate linkage in the oligonucleotide has been replaced with a phosphorothioate linkage.

  本发明的一个方面涉及含有至少一个非自然碱基的双链寡核苷酸。在某些实施例中，非自然碱基可以是二氟基甲苯基、硝基吲哚基、硝基吡咯基或硝基咪唑基。在一个首选实施例中，非自然碱基是二氟基甲苯基。在某些实施例中，双链寡核苷酸中的两个寡核苷酸链中只有一个含有非自然碱基。在某些实施例中，双链寡核苷酸中的两个寡核苷酸链都独立地含有非自然碱基。在某些实施例中，寡核苷酸链包含至少一个修饰的糖基。本发明的另一个方面涉及含有至少一个非自然碱基的单链寡核苷酸。在一个首选实施例中，非自然碱基是二氟基甲苯基。在某些实施例中，取代了核苷中天然存在的核糖糖基的是己糖糖基、多环杂烷基环或环己烯基团。在某些实施例中，寡核苷酸中的至少一个磷酸酯键被磷酸硫酯键取代。
• OLIGONUCLEOTIDES COMPRISING A MODIFIED OR NON-NATURAL NUCLEOBASE
  申请人：MANOHARAN Muthiah

  公开号：US20090281298A1

  公开（公告）日：2009-11-12

  One aspect of the present invention relates to a double-stranded oligonucleotide comprising at least one non-natural nucleobase. In certain embodiments, the non-natural nucleobase is difluorotolyl, nitroindolyl, nitropyrrolyl, or nitroimidazolyl. In a preferred embodiment, the non-natural nucleobase is difluorotolyl. In certain embodiments, only one of the two oligonucleotide strands comprising the double-stranded oligonucleotide contains a non-natural nucleobase. In certain embodiments, both of the oligonucleotide strands comprising the double-stranded oligonucleotide independently contain a non-natural nucleobase. In certain embodiments, the oligonucleotide strands comprise at least one modified sugar moiety. Another aspect of the present invention relates to a single-stranded oligonucleotide comprising at least one non-natural nucleobase. In a preferred embodiment, the non-natural nucleobase is difluorotolyl. In certain embodiments, the ribose sugar moiety that occurs naturally in nucleosides is replaced with a hexose sugar, polycyclic heteroalkyl ring, or cyclohexenyl group. In certain embodiments, at least one phosphate linkage in the oligonucleotide has been replaced with a phosphorothioate linkage.

  本发明的一个方面涉及至少包含一种非天然核碱基的双链寡核苷酸。在某些实施例中，非天然核碱基是二氟基甲苯基、硝基吲哚基、硝基吡咯基或硝基咪唑基。在一个首选实施例中，非天然核碱基是二氟基甲苯基。在某些实施例中，仅有双链寡核苷酸中的两个寡核苷酸链中的一个包含非天然核碱基。在某些实施例中，包含双链寡核苷酸的两个寡核苷酸链独立地包含非天然核碱基。在某些实施例中，寡核苷酸链包括至少一个修饰的糖基团。本发明的另一个方面涉及至少包含一种非天然核碱基的单链寡核苷酸。在一个首选实施例中，非天然核碱基是二氟基甲苯基。在某些实施例中，核苷中天然存在的核苷糖被替换为六碳糖、多环杂基烷基环或环己烯基团。在某些实施例中，寡核苷酸中的至少一个磷酸酯连接被替换为磷酸硫酯连接。
• US7579451B2
  申请人：——

  公开号：US7579451B2

  公开（公告）日：2009-08-25
• US7772387B2
  申请人：——

  公开号：US7772387B2

  公开（公告）日：2010-08-10
• [EN] OLIGONUCLEOTIDES COMPRISING A MODIFIED OR NON-NATURAL NUCLEOBASE<br/>[FR] OLIGONUCLEOTIDES COMPRENANT UNE NUCLEOBASE MODIFIEE OU NON NATURELLE
  申请人：ALNYLAM PHARMACEUTICALS

  公开号：WO2006093526A2

  公开（公告）日：2006-09-08

  (EN) One aspect of the present invention relates to a double-stranded oligonucleotide comprising at least one non-natural nucleobase. In certain embodiments, the non-natural nucleobase is difluorotolyl, nitroindolyl, nitropyrrolyl, or nitroimidazolyl. In a preferred embodiment, the non-natural nucleobase is difluorotolyl. In certain embodiments, only one of the two oligonucleotide strands comprising the double-stranded oligonucleotide contains a non-natural nucleobase. In certain e4mbodiments, both of the oligonucleotide strands comprising the double-stranded oligonucleotide independently contain a non-natural nucleobase. In certain embodiments, the oligonucleotide strands comprise at least one modified sugar moiety. Another aspect of the present invention relates to a single-stranded oligonucleotide comprising at least one non-natural nucleobase. In a preferred embodiment, the non-natural nucleobase is difluorotolyl. In certain embodiments, the ribose sugar moiety that occurs naturally in nucleosides is replaced with a hexose sugar, polycyclic heteroalkyl ring, or cyclohexenyl group. In certain embodiments, at least one phosphate linkage in the oligonucleotide has been replaced with a phosphrothioate linkage.(FR) Selon un aspect, l'invention concerne un oligonucléotide double brin qui comprend au moins une nucléobase non naturelle. Dans certains modes de réalisation, la nucléobase non naturelle est représentée par difluorotolyl, nitroindolyl, nitropyrrolyl, ou nitroimidazolyl. Dans un mode de réalisation préféré, la nucléobase non naturelle est représentée par difluorotolyl. Dans certains modes de réalisation, un seul des deux brins de l'oligonucléotide contient une nucléobase non naturelle. Dans certains modes de réalisation, les deux brins de l'oligonucléotide contiennent indépendamment une nucléobase non naturelle. Dans certains modes de réalisation, les brins de l'oligonucléotide comprennent au moins un fragment sucre modifié. Selon un autre aspect, l'invention concerne un oligonucléotide simple brin qui comprend au moins une nucléobase non naturelle. Dans un mode de réalisation préféré, la nucléobase non naturelle est représentée par difluorotolyl. Dans certains modes de réalisation, le fragment sucre de type ribose qui se forme naturellement dans des nucléosides est remplacé par du sucre de type hexose, un anneau hétéroalkyle polycyclique, ou un groupe cyclohexényle. Dans certains modes de réalisation, au moins une liaison phosphate dans l'oligonucléotide a été remplacée par une liaison phosphorothioate.