1-(2-deoxy-β-D-ribofuranosyl)-2-nitropyrrole | 940949-52-0

• 分子结构分类: 有机化合物 - 有机1,3-偶极化合物 - 烯丙基型1,3-偶极有机化合物
• 英文名称: 1-(2-deoxy-β-D-ribofuranosyl)-2-nitropyrrole
• 英文别名: (2R,3S,5R)-2-(hydroxymethyl)-5-(2-nitropyrrol-1-yl)oxolan-3-ol
• CAS: 940949-52-0
• 化学式: C₉H₁₂N₂O₅
• 分子量: 228.205
• InChiKey: LKCGPGBOPNIQFZ-LKEWCRSYSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  0.2
• 重原子数：
  16
• 可旋转键数：
  2
• 环数：
  2.0
• sp3杂化的碳原子比例：
  0.56
• 拓扑面积：
  100
• 氢给体数：
  2
• 氢受体数：
  5

反应信息

• 作为反应物：
  描述：

  1-(2-deoxy-β-D-ribofuranosyl)-2-nitropyrrole 在 bis-triphenylphosphine-palladium(II) chloride 、 N-碘代丁二酰亚胺 作用下， 以 N,N-二甲基甲酰胺 、 乙腈 为溶剂， 反应 1.5h， 生成 1-(2-deoxy-beta-D-ribofuranosyl)-4-propynyl-2-nitropyrrole
  参考文献：
  名称：

  Nucleic acid base analogs with quenching and fluorescent activities and applications thereof

  摘要：

  本发明的目的是提供淬灭或荧光核酸碱基类似物及其应用。本发明的淬灭剂具有由式I表示的2-硝基吡咯结构：[Formula 1]（在式I中，R1和R2是从以下组成的组中独立选择的基团：核糖和去氧核糖；氢、羟基和SH基团、卤素；取代或未取代的具有2到10个碳原子的烷基、烯基和炔基基团；一个或多个含氮或硫的五元杂环环、一个或多个含氮或硫的六元杂环环以及一个或多个融合的杂环环；糖、糖链、氨基酸和肽；以及通过连接物连接的荧光分子）。

  公开号：

  US09285319B2
• 作为产物：
  描述：

  ((2R,3S,5R)-3-((4-methylbenzoyl)oxy)-5-(2-nitro-1H-pyrrol-1-yl)tetrahydrofuran-2-yl)methyl 4-methylbenzoate 在 氨 作用下， 以 甲醇 为溶剂， 反应 12.0h， 以82%的产率得到1-(2-deoxy-β-D-ribofuranosyl)-2-nitropyrrole
  参考文献：
  名称：

  An Efficient Unnatural Base Pair for PCR Amplification

  摘要：

  Expansion of the genetic alphabet by an unnatural base pair system provides a powerful tool for modern biotechnology. As an alternative to previous unnatural base pairs, we have developed a new pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and 2-nitropyrrole (Pn), which functions in DNA amplification. Pn more selectively pairs with Ds in replication than another previously reported pairing partner, pyrrole-2-carbaldehyde (Pa). The nitro group of Pin efficiently prevented the mispairing with A. High efficiency and selectivity of the Ds-Pn pair in PCR amplification were achieved by using a substrate mixture of the gamma-amidotriphosphate of Ds and the usual triphosphates of Pn and the natural bases, with Vent DNA polymerase as a 3' to 5' exonuclease-proficient polymerase. After 20 cycles of PCR, the total mutation rate of the Ds-Pn site in an amplified DNA fragment was similar to 1%. PCR amplification of DNA fragments containing the unnatural Ds-Pn pair would be useful for expanded genetic systems in DNA-based biotechnology.

  DOI：

  10.1021/ja073830m

文献信息

• A New Unnatural Base Pair System between Fluorophore and Quencher Base Analogues for Nucleic Acid-Based Imaging Technology
  作者：Michiko Kimoto、Tsuneo Mitsui、Rie Yamashige、Akira Sato、Shigeyuki Yokoyama、Ichiro Hirao

  DOI：10.1021/ja1072383

  日期：2010.11.3

  selectivity in PCR amplification. Thus, this new unnatural base pair system would be suitable for detection methods of target nucleic acid sequences, and here we demonstrated the applications of the Dss-Pn and Dss-Px pairs as molecular beacons and in real-time PCR. The genetic alphabet expansion system with the replicable, unnatural fluorophore-quencher base pair will be a useful tool for sensing and diagnostic

  在开发用于扩展遗传字母表的正交额外碱基对的过程中，我们在荧光团和猝灭剂核碱基类似物之间创建了新的、非自然的碱基对。我们发现核碱基类似物 2-硝基吡咯（用 Pn 表示）及其 4-取代基，如 2-nitro-4-propynylpyrrole (Px) 和 4-[3-(6-aminohexanamido)-1-propynyl] -2-硝基吡咯 (NH(2)-hx-Px)，作为荧光猝灭剂。Pn 和 Px 碱基与其配对伙伴 7-(2,2'-bithien-5-yl)imidazo[4,5-b] 吡啶 (Dss) 特异性配对，后者具有强荧光。因此，这些非天然的 Dss-Pn 和 Dss-Px 碱基对起到报告基因-猝灭剂碱基对的作用，并通过聚合酶反应作为与天然 AT 和 GC 对结合的第三个碱基对互补整合到 DNA 中。由于静态接触淬火，Pn 和 Px 猝灭剂碱基通过 DNA 双链体中的非自然碱基配对显着降低了
• METHOD FOR REPLICATING NUCLEIC ACIDS AND NOVEL UNNATURAL BASE PAIRS
  申请人：Hirao Ichiro

  公开号：US20100036111A1

  公开（公告）日：2010-02-11

  The present invention relates to a method for nucleic acid replication and novel artificial base pairs. The method of the present invention for nucleic acid replication is characterized in that a deoxyribonucleoside 5′-triphosphate, in which the hydroxyl group of phosphoric acid at the γ-position is substituted with a group selected from the group consisting of an amino group, a methylamino group, a dimethylamino group, a mercapto group and a fluoro group, is used as a substrate during replication reaction. The novel artificial base pairs of the present invention are characterized in that 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) or an analog thereof forms a base pair with pyrrole-2-carbaldehyde (Pa) or an analog thereof.

  本发明涉及一种核酸复制方法和新型人工碱基对。本发明的核酸复制方法的特征在于，在复制反应过程中使用一种脱氧核苷酸5'-三磷酸作为底物，其中磷酸γ-位置的羟基被从以下群组中选择的一种群组所取代，所述群组包括氨基、甲基氨基、二甲基氨基、巯基和氟基。本发明的新型人工碱基对的特征在于，7-(2-噻吩基)-咪唑并[4,5-b]吡啶（Ds）或其类似物与吡咯-2-甲醛（Pa）或其类似物形成一对碱基。
• METHOD FOR NUCLEIC ACID REPLICATION AND NOVEL ARTIFICIAL BASE PAIRS
  申请人：Riken

  公开号：EP1970445A1

  公开（公告）日：2008-09-17

  The present invention relates to a method for nucleic acid replication and novel artificial base pairs. The method of the present invention for nucleic acid replication is characterized in that a deoxyribonucleoside 5'-triphosphate, in which the hydroxyl group of phosphoric acid at the γ-position is substituted with a group selected from the group consisting of an amino group, a methylamino group, a dimethylamino group, a mercapto group and a fluoro group, is used as a substrate during replication reaction. The novel artificial base pairs of the present invention are characterized in that 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) or an analog thereof forms a base pair with pyrrole-2-carbaldehyde (Pa) or an analog thereof.

  本发明涉及一种核酸复制方法和新型人工碱基对。 本发明的核酸复制方法的特征在于，在复制反应中使用脱氧核苷 5'-三磷酸作为底物，其中磷酸在 γ 位上的羟基被选自氨基、甲氨基、二甲氨基、巯基和氟基的基团取代。本发明的新型人工碱基对的特征在于，7-(2-噻吩基)-咪唑并[4,5-b]吡啶（Ds）或其类似物与吡咯-2-甲醛（Pa）或其类似物形成碱基对。
• NUCLEIC ACID BASE ANALOG WITH QUENCHING CHARACTERISTICS AND FLUORESCENCE AND APPLICATION THEREOF
  申请人：Riken

  公开号：EP2562255A1

  公开（公告）日：2013-02-27

  It is an object of the present invention to provide quenching or fluorescent nucleic acid base analogs and applications thereof. The quencher of the present invention has a 2-nitropyrrole structure represented by Formula I: (in Formula I, R1 and R2 are groups independently selected from the group consisting of: ribose and deoxyribose; hydrogen, hydroxyl and SH groups, and halogens; substituted or unsubstituted alkyl, alkenyl, and alkynyl groups each having 2 to 10 carbon atoms; one or more five-membered heterocyclic rings, one or more six-membered heterocyclic rings, and one or more fused heterocyclic rings, these heterocylic rings containing nitrogen or sulfur, and one or more aromatic rings; sugars, sugar chains, amino acids, and peptides; and fluorescent molecules linked via linkers).

  本发明的目的是提供淬灭或荧光核酸碱类似物及其应用。本发明的淬灭剂具有由式 I 表示的 2-硝基吡咯结构： (式 I 中，R1 和 R2 是独立选自以下组别的基团： 核糖和脱氧核糖； 氢、羟基、SH 基和卤素； 各自具有 2 至 10 个碳原子的取代或未取代的烷基、烯基和炔基； 一个或多个五元杂环、一个或多个六元杂环、一个或多个融合杂环（这些杂环含有氮或硫）以及一个或多个芳香环； 糖、糖链、氨基酸和肽；以及 通过连接体连接的荧光分子）。
• US8030478B2
  申请人：——

  公开号：US8030478B2

  公开（公告）日：2011-10-04