7-deaza-2'-deoxy-7-nitroguanosine 5'-O-triphosphate

• 分子结构分类: 有机化合物 - 有机杂环化合物 - 吡咯并嘧啶类
• 英文名称: 7-deaza-2'-deoxy-7-nitroguanosine 5'-O-triphosphate
• 英文别名: 7-deaza-7-nitro-2'-deoxyadenosine 5'-triphosphate；[[[(2R,3S,5R)-5-(4-amino-5-nitropyrrolo[2,3-d]pyrimidin-7-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxy-oxidophosphaniumyl]oxy-hydroxyphosphoryl]oxyphosphonic acid
• 化学式: C₁₁H₁₆N₅O₁₄P₃
• 分子量: 535.194
• InChiKey: BFIWNNKVDWOAGE-XLPZGREQSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  -4.4
• 重原子数：
  33
• 可旋转键数：
  8
• 环数：
  3.0
• sp3杂化的碳原子比例：
  0.45
• 拓扑面积：
  304
• 氢给体数：
  6
• 氢受体数：
  17

反应信息

• 作为产物：
  描述：

  （2R，3S，5R）-5-（4-氨基-7H-吡咯[2,3-D]嘧啶-7-基-2 -（羟甲基）四氢呋喃-3-醇 在 吡啶 、 磷酸三甲酯 、 4-二甲氨基吡啶 、 三正丁胺 、 Proton-Sponge 、 sodium methylate 、 三丁基焦磷酸铵 、 三氯氧磷 作用下， 以 甲醇 、 N,N-二甲基甲酰胺 为溶剂， 反应 15.33h， 生成 7-deaza-2'-deoxy-7-nitroguanosine 5'-O-triphosphate
  参考文献：
  名称：

  7-硝基-7-脱氮嘌呤核苷和核苷酸的区域选择性合成，可用于有效的PCR掺入。

  摘要：

  嘌呤核苷酸的C（7）位置被强力的吸电子硝基取代，促进了碱性条件下糖苷键的裂解。该性质对于含有这些类似物的DNA的序列特异性切割是有用的。在这里，我们描述了从2'-脱氧腺苷和6-chloro-7开始使用两种不同方法制备7-deaza-7-NO（2）-dA和7-deaza-7-NO（2）-dG的方法。 -deaza-鸟嘌呤。这些修饰的核苷被转化为核苷酸三磷酸，每个核苷酸都可以代替相应的天然三磷酸以支持PCR扩增。[结构：见文字]

  DOI：

  10.1021/ol051144r

文献信息

• Synthesis and Application of Nitro-Substituted Nucleosides and Nucleotides
  作者：Jia Wolfe、Tomohiko Kawate、Bing Wang、Charles Allerson

  DOI：10.1055/s-2006-950218

  日期：——

  Protocols for the synthesis of C 7 -nitropurine nucleosides and nucleotides are described. Each of these nucleotides can completely replace its naturally occurring counterpart in polymerase chain reaction (PCR), generating amplified duplex DNA containing nitropurines. As predicted, the electron-withdrawing power of the nitro group rendered these modified oligonucleotides susceptible to chemoselective

  描述了用于合成 C 7 -硝基嘌呤核苷和核苷酸的方案。这些核苷酸中的每一个都可以在聚合酶链式反应 (PCR) 中完全取代其天然存在的对应物，从而产生含有硝基嘌呤的扩增双链 DNA。正如预测的那样，硝基的吸电子能力使这些修饰的寡核苷酸对修饰碱基的化学选择性切割敏感。在高温下用仲胺处理会在硝基嘌呤位点产生选择性 DNA 断裂。有趣的是，这种 Maxam-Gilbert 类型的 DNA 切割反应是通过添加强还原剂和亲核试剂三 (2-羧乙基) 膦 (TCEP) 促进的。质谱分析不仅证实了 DNA 裂解发生在硝基嘌呤上，但也揭示了片段化的 DNA 产物在其 3'-末端附加了一个 TCEP 部分。这一令人惊讶的结果为这种 DNA 切割反应的机制提供了新的见解。
• Template-Directed Interference Footprinting of Protein−Adenine Contacts
  作者：Changhee Min、Timothy D. Cushing、Gregory L. Verdine

  DOI：10.1021/ja953658z

  日期：1996.1.1

  Noncovalent contacts between amino acid residues and DNA bases are the principal contributors to sequence-specific recognition in most protein-DNA complexes. We have developed a method, template-directed interference (TDI) footprinting, which not only identifies DNA bases that are contacted by a protein upon formation of a specific complex but also reveals the groove location of the contacts and provides a rough gauge of their energetics. Previously, we demonstrated TDI footprinting of guanine (TDI-G), cytosine (TDI-C), and thymine (TDI-T) residues in the major groove of DNA. Here we report the development of a procedure for TDI footprinting of the fourth and final DNA base, adenine (TDI-A). The base-analog 7-deaza-7-nitroadenine (A*), present as the corresponding 2'-deoxynucleoside 5'-triphosphate, was found to undergo efficient incorporation into DNA during template-directed enzymatic polymerization. The analog exhibits the same base-pairing preference as its native counterpart (A), and could be selectively degraded, leading to DNA strand scission upon treatment with aqueous piperidine. To validate the use of A* as a probe of specific protein-DNA contacts, we carried out TDI-A footprinting of the bacteriophage 434 repressor/O(R)1 operator interaction. The observed interference by A* only at position-1 of the operator is consistent with the results of X-ray crystallographic analysis. Together with TDI-G, -C, and -T footprinting, the present TDI-A footprinting procedure now completes the series of four experiments required for the analysis of major groove contacts to all four DNA bases in solution.