N-[9-[(2R,4S,5R)-5-(aminomethyl)-4-hydroxyoxolan-2-yl]purin-6-yl]benzamide | 289884-72-6

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 2 '，5'-二脱氧核苷
• 英文名称: N-[9-[(2R,4S,5R)-5-(aminomethyl)-4-hydroxyoxolan-2-yl]purin-6-yl]benzamide
• CAS: 289884-72-6
• 化学式: C₁₇H₁₈N₆O₃
• 分子量: 354.368
• InChiKey: LIUDNWWJDSKBNB-YNEHKIRRSA-N

物化性质

• 密度：
  1.61±0.1 g/cm3(Predicted)

计算性质

• 辛醇/水分配系数(LogP)：
  0
• 重原子数：
  26
• 可旋转键数：
  4
• 环数：
  4.0
• sp3杂化的碳原子比例：
  0.29
• 拓扑面积：
  128
• 氢给体数：
  3
• 氢受体数：
  7

反应信息

• 作为反应物：
  描述：

  N-[9-[(2R,4S,5R)-5-(aminomethyl)-4-hydroxyoxolan-2-yl]purin-6-yl]benzamide 在 吡啶 、 4-二甲氨基吡啶 作用下， 反应 12.0h， 生成 Succinic acid mono-[(2R,3S,5R)-5-(6-benzoylamino-purin-9-yl)-2-({[(4-methoxy-phenyl)-diphenyl-methyl]-amino}-methyl)-tetrahydro-furan-3-yl] ester
  参考文献：
  名称：

  Solid-Phase synthesis of positively charged deoxynucleic guanidine (DNG) oligonucleotide mixed sequences

  摘要：

  Positively charged DNG oligonucleotide mixed sequences containing A/T bases were prepared by solid-phase synthesis. Synthesis proceeds in 3'-->5' direction and involves coupling of 3'-Fmoc protected thiourea in the presence of HgCl2/TEA with the corresponding 5'-amine of the growing oligo chain. DNG binding characteristics with complementary DNA and with itself have been evaluated. (C) 2003 Elsevier Science Ltd. All rights reserved.

  DOI：

  10.1016/s0960-894x(03)00119-7
• 作为产物：
  描述：

  2'-脱氧腺苷 在 palladium on activated charcoal 吡啶 、 三甲基氯硅烷 、 叠氮化锂 、 氢气 作用下， 以 乙醇 、 N,N-二甲基甲酰胺 为溶剂， 反应 20.5h， 生成 N-[9-[(2R,4S,5R)-5-(aminomethyl)-4-hydroxyoxolan-2-yl]purin-6-yl]benzamide
  参考文献：
  名称：

  Solid-Phase synthesis of positively charged deoxynucleic guanidine (DNG) oligonucleotide mixed sequences

  摘要：

  Positively charged DNG oligonucleotide mixed sequences containing A/T bases were prepared by solid-phase synthesis. Synthesis proceeds in 3'-->5' direction and involves coupling of 3'-Fmoc protected thiourea in the presence of HgCl2/TEA with the corresponding 5'-amine of the growing oligo chain. DNG binding characteristics with complementary DNA and with itself have been evaluated. (C) 2003 Elsevier Science Ltd. All rights reserved.

  DOI：

  10.1016/s0960-894x(03)00119-7

文献信息

• A “Traceless” Staudinger Ligation for the Chemoselective Synthesis of Amide Bonds
  作者：Eliana Saxon、Joshua I. Armstrong、Carolyn R. Bertozzi

  DOI：10.1021/ol006054v

  日期：2000.7.1

  [reaction: see text] Here we report a novel modification of our previously reported "Staudinger ligation" that generates an amide bond from an azide and a specifically functionalized phosphine. This method for the selective formation of an amide bond, which does not require the orthogonal protection of distal functional groups, should find general utility in synthetic and biological chemistry.

  [反应：见正文]在这里，我们报告了对我们先前报道的“斯托丁格连接”的一种新颖修饰，该修饰从叠氮化物和经过特殊功能化的膦生成酰胺键。不需要远端官能团的正交保护的这种选择性形成酰胺键的方法应该在合成和生物化学中找到通用的用途。
• Porphyrin–DNA conjugates: porphyrin induced adenine–guanine homoduplex stabilization and interduplex assemblies
  作者：Gevorg Sargsyan、Milan Balaz

  DOI：10.1039/c2ob25710f

  日期：——

  DNA has found widespread uses as a nanosized scaffold for assembly of patterned multichomophoric nanostructures. Herein we report the synthesis, self-assembly, stability, and spectroscopic studies of short alternating non-self-complementary DNA sequences 5′-(dGdA)4 and 5′-(dAdG)4 with non-charged tetraarylporphyrins covalently linked to the 5′ position of deoxyadenosine or deoxyguanosine via a phosphate or amide linker. The linker, the metal in the porphyrin coordination center, and the neighboring nucleobase have very distinct effects on the duplex formation of porphyrin–deoxyguanosine–deoxyadenosine oligodeoxynucleotides. At ionic strength between 5 mM and 40 mM, free base trispyridylphenylporphyrin appended to the 5′ termini of 5′-(dAdG)4 oligonucleotide via short non-polar amide linker served as a hydrophobic molecular cap inducing deoxyadenosine–deoxyguanosine antiparallel homoduplex. At ionic strength of ≥60 mM, the free base porphyrin functioned as a molecular ‘glue’ and induced the formation of porphyrin–DNA inter-homoduplex assemblies with characteristic tetrasignate CD Cotton effects in the porphyrin Soret band region. When the porphyrin cap was covalently attached to 5′ position of deoxyguanosine or deoxyadenosine via charged phosphate linker, no significant deoxyadenosine–deoxyguanosine hybridization was observed even at elevated ionic strengths.

  DNA 已被广泛用作一种纳米支架，用于组装图案化多孔纳米结构。在此，我们报告了交替非自互补 DNA 短序列 5â²-(dGdA)4 和 5â²-(dAdG)4 的合成、自组装、稳定性和光谱研究，这些序列带有不带电的四芳基卟啉，通过磷酸或酰胺连接体共价连接到脱氧腺苷或脱氧鸟苷的 5â² 位。连接体、卟啉配位中心的金属和邻近的核碱基对卟啉-脱氧鸟苷-脱氧腺苷寡脱氧核苷酸的双链形成有非常明显的影响。在离子强度介于 5 mM 和 40 mM 之间时，游离碱基三(三吡啶基)苯基卟啉通过非极性短酰胺连接体附着在 5â²-(dAdG)4寡核苷酸的 5â²末端，成为疏水分子帽，诱导脱氧腺苷脱氧鸟苷反平行同源双链。在离子强度为±60 mM时，游离碱基卟啉起到分子 "胶合剂 "的作用，诱导形成卟啉-DNA间的同源双链体，并在卟啉索尔特带区域产生特征性的四木糖CD科顿效应。当卟啉帽通过带电磷酸盐连接体共价连接到脱氧鸟苷或脱氧腺苷的 5² 位时，即使在离子强度升高的情况下，也没有观察到明显的脱氧腺苷与脱氧鸟苷杂交。
• Development of gapmer antisense oligonucleotide with deoxyribonucleic guanidine (DNG) modifications
  作者：Naoshi Kojima、Ajaya R. Shrestha、Takuya Akisawa、Haishun Piao、Hideki Kizawa、Yoshihiro Ohmiya、Ryoji Kurita

  DOI：10.1080/15257770.2019.1668563

  日期：2020.2.20

  which has a positively charged internucleotide guanidinium linkage instead of negatively charged phosphodiester backbone linkage. We prepared a gapmer ASO containing DNG units at both wings of the sequence and compared its properties with 2′,4′-BNA/LNA gapmer ASOs with phosphorothioate (PS) backbone. Although DNG gapmer showed no stabilizing effect on the duplex formation with target RNA, the DNG modification

  摘要 为了在反义技术中的潜在应用，研究了侧接脱氧核糖核酸胍（DNG）的gapmer反义寡核苷酸（ASO）的性质。DNG 是一种独特的核苷酸类似物，它具有带正电荷的核苷酸间胍键，而不是带负电荷的磷酸二酯骨架键。我们在序列的两翼制备了含有 DNG 单元的 gapmer ASO，并将其特性与具有硫代磷酸酯 (PS) 骨架的 2',4'-BNA/LNA gapmer ASO 进行了比较。尽管 DNG gapmer 对与目标 RNA 的双链体形成没有稳定作用，但发现 DNG 修饰能够耐受外切核酸酶消化。此外，DNG gapmer 可以诱导 RNase H 介导的目标 RNA 分子裂解，这是反义策略的必要特性。所以，
• A Library Approach to the Generation of Bisubstrate Analogue Sulfotransferase Inhibitors
  作者：Joshua I. Armstrong、Xue Ge、Dawn E. Verdugo、Katharine A. Winans、Julie A. Leary、Carolyn R. Bertozzi

  DOI：10.1021/ol0162217

  日期：2001.8.1

  [GRAPHICS]A library of potential bisubstrate analogue inhibitors (1) targeting sulfotransferase enzymes was generated by the chemoselective ligation of the PAPS mimic 2 with a panel of 447 aldehydes. Preliminary screening has identified compounds that inhibit estrogen sulfotransferase (EST), an enzyme relevant to breast cancer.
• Sequence and linker dependent chiral dimerization of DNA–porphyrin conjugates
  作者：Gevorg Sargsyan、Brianna L. MacLeod、Urice Tohgha、Milan Balaz

  DOI：10.1016/j.tet.2012.01.021

  日期：2012.3

  Circular dichroism (CD), UV-vis absorption, fluorescence, and resonance light scattering (RLS) spectroscopies were used to elucidate the role of the DNA sequence, linkers between DNA and porphyrin, and metal in the porphyrin coordination center on the self-assembly of DNA-porphyrin conjugates. A series of eight non-self-complementary DNA-porphyrin conjugates have been synthesized with zinc and free-base porphyrins covalently attached to the short ODNs (A(8) or T-8) via amide or phosphate linker. A small structural modification (e.g., amide linker replaced by the phosphate linker) showed a dramatic effect on the aggregation properties of DNA-porphyrin conjugates and greatly altered their spectroscopic properties. At low ionic strength, porphyrin aggregation was not observed for any conjugate. An increase in the ionic strength caused two out of eight conjugates to form chiral porphyrin dimers. (C) 2012 Elsevier Ltd. All rights reserved.