DNA荧光探针前驱体,DNA小沟配体 | 537049-66-4

• 分子结构分类: 有机化合物 - 有机杂环化合物 - 唑类
• 中文名称: DNA荧光探针前驱体,DNA小沟配体
• 英文名称: 4-(1-methylpyrrole-2-carboxamido)-1-methylimidazole-2-carboxylic acid
• 英文别名: 1H-Imidazole-2-carboxylicacid,1-methyl-4-[[(1-methyl-1H-pyrrol-2-；1-methyl-4-[(1-methylpyrrole-2-carbonyl)amino]imidazole-2-carboxylic acid
• CAS: 537049-66-4
• 化学式: C₁₁H₁₂N₄O₃
• 分子量: 248.241
• InChiKey: QLCYJHRUUQJFLG-UHFFFAOYSA-N

物化性质

• 熔点：
  141.2-141.8 °C
• 密度：
  1.42±0.1 g/cm3(Predicted)

计算性质

• 辛醇/水分配系数(LogP)：
  0.1
• 重原子数：
  18
• 可旋转键数：
  3
• 环数：
  2.0
• sp3杂化的碳原子比例：
  0.18
• 拓扑面积：
  89.2
• 氢给体数：
  2
• 氢受体数：
  4

反应信息

• 作为反应物：
  描述：

  DNA荧光探针前驱体,DNA小沟配体 、 在 乙酰氯 、 sodium hydroxide 作用下， 以 甲醇 为溶剂， 生成
  参考文献：
  名称：

  通过合成接头分子将转录因子 SP1 重定向到 AT 富结合位点

  摘要：

  无处不在的转录因子 SP1 与富含 GC 的共有序列结合。在这里，我们描述了一种适配器分子，它介导 SP1 与富含 AT 的非同源 DNA 位点的结合。该接头由对富含 AT 的六聚体双链体具有高亲和力的Dervan型发夹聚酰胺组成。它还携带含有 SP1 共有序列的 27 聚体 DNA。报道了聚酰胺-DNA 偶联物的合成和纯化。Pulldown 实验和蛋白质印迹分析证明了接头介导的 SP1 与六聚体双链体 TTGTTA 的结合。

  DOI：

  10.1002/hlca.202100095
• 作为产物：
  描述：

  1-甲基-4-硝基-2-(三氟乙酰)-1H-咪唑 在 4-二甲氨基吡啶 、 palladium on activated charcoal 、 氢气 、 sodium hydroxide 作用下， 以 甲醇 、 乙酸乙酯 为溶剂， 生成 DNA荧光探针前驱体,DNA小沟配体
  参考文献：
  名称：

  通过合成接头分子将转录因子 SP1 重定向到 AT 富结合位点

  摘要：

  无处不在的转录因子 SP1 与富含 GC 的共有序列结合。在这里，我们描述了一种适配器分子，它介导 SP1 与富含 AT 的非同源 DNA 位点的结合。该接头由对富含 AT 的六聚体双链体具有高亲和力的Dervan型发夹聚酰胺组成。它还携带含有 SP1 共有序列的 27 聚体 DNA。报道了聚酰胺-DNA 偶联物的合成和纯化。Pulldown 实验和蛋白质印迹分析证明了接头介导的 SP1 与六聚体双链体 TTGTTA 的结合。

  DOI：

  10.1002/hlca.202100095

文献信息

• Facile Dimer Synthesis for DNA-Binding Polyamide Ligands
  作者：Modi Wetzler、David E. Wemmer

  DOI：10.1021/ol1013262

  日期：2010.8.6

  Pyrrole-imidazole polyamide ligands are highly sequence specific synthetic DNA-binding ligands that bind with high affinity. To counter the synthetic difficulties associated with coupling the electron-rich heterocyclic acids to the electron-deficient nucleophilic imidazole amine, a novel approach is described for synthesis of Fmoc-protected dimers for solid-phase peptide synthesis (SPPS). This method produces

  吡咯-咪唑聚酰胺配体是具有高亲和力的高度序列特异性合成DNA结合配体。为了解决与将富电子杂环酸偶联至缺电子亲核咪唑胺相关的合成难题，描述了一种用于固相肽合成（SPPS）的Fmoc保护的二聚体合成新方法。该方法以高收率生产二聚体，广泛适用于其他含杂环的聚酰胺，并提高了配体收率和合成时间。
• [EN] POLYAMIDES<br/>[FR] POLYAMIDES
  申请人：SPIROGEN LTD

  公开号：WO2009060215A1

  公开（公告）日：2009-05-14

  A polyamide moiety comprising at least one unit of formula I: -β1-X1-Y1-X3-X4-β3- (I) wherein: Y1 is either X2-β2 or β2-X2; β1 is -Rβ -CH2-NH- βa-, wherein βa is a β-alanine residue and Rβ is chosen from optionally substituted C1-7 alkylene, C1-7 alkenylene and C1-7 alkynylene groups; β2 and β3 are β-alanine residues; and X1, X2, X3 and X4 are independently fragments of formula (II): wherein E is an optionally substituted C5-6 heteroarylene group.

  一种聚酰胺基团，包括至少一个I式单位：-β1-X1-Y1-X3-X4-β3-（I），其中：Y1是X2-β2或β2-X2；β1是-Rβ-CH2-NH-βa-，其中βa是β-丙氨酸残基，Rβ选择自可选择取代的C1-7烷基，C1-7烯基和C1-7炔基；β2和β3是β-丙氨酸残基；X1、X2、X3和X4分别是式（II）的片段：其中E是可选择取代的C5-6杂芳烃基。
• Sequence specific and high affinity recognition of 5′-ACGCGT-3′ by rationally designed pyrrole-imidazole H-pin polyamides: Thermodynamic and structural studies
  作者：Hilary Mackay、Toni Brown、Peter B. Uthe、Laura Westrate、Alan Sielaff、Justin Jones、James P. Lajiness、Jerome Kluza、Caroline O’Hare、Binh Nguyen、Zach Davis、Chrystal Bruce、W. David Wilson、John A. Hartley、Moses Lee

  DOI：10.1016/j.bmc.2008.09.034

  日期：2008.10

  Imidazole (Im) and Pyrrole (Py)-containing polyamides that can form stacked dimers can be programmed to target specific sequences in the minor groove of DNA and control gene expression. Even though various designs of polyamides have been thoroughly investigated for DNA sequence recognition, the use of H-pin polyamides (covalently cross-linked polyamides) has not received as much attention. Therefore, experiments were designed to systematically investigate the DNA recognition properties of two symmetrical H-pin polyamides composed of PyImPyIm (5) or f-ImPyIm (3e, f = formamido) tethered with an ethylene glycol linker. These compounds were created to recognize the cognate 5 '-ACGCGT-3 ' through an overlapped and staggered binding motif, respectively. Results from DNaseI footprinting, thermal denaturation, circular dichroism, surface plasmon resonance and isothermal titration microcalorimetry studies demonstrated that both H-pin polyamides bound with higher afinity than their respective monomers. The binding afinity of formamido-containing H-pin 3e was more than a hundred times greater than that for the tetraamide H-pin 5, demonstrating the importance of having a formamido group and the staggered motif in enhancing affinity. However, compared to H-pin 3e, tetraamide H-pin 5 demonstrated superior binding preference for the cognate sequence over its non-cognates, ACCGGT and AAATTT. Data from SPR experiments yielded binding constants of 1.6 x 10(8) M (1) and 2.0 x 10(10) M (1) for PyImPyIm H-pin 5 and f-ImPyIm H-pin 3e, respectively. Both H-pins bound with significantly higher affinity (ca. 100-fold) than their corresponding unlinked PyImPyIm 4 and f-ImPyIm 2 counterparts. ITC analyses revealed modest enthalpies of reactions at 298 K (Delta H of -3.3 and -1.0 kcal mol (1) for 5 and 3e, respectively), indicating these were entropic-driven interactions. The heat capacities (Delta C(p)) were determined to be -116 and -499 cal mol (1) K (1), respectively. These results are in general agreement with Delta C(p) values determined from changes in the solvent accessible surface areas using complexes of the H-pins bound to (5 ' CCACGCGTGG)(2) . According to the models, the H-pins fit snugly in the minor groove and the linker comfortably holds both polyamide portions in place, with the oxygen atoms pointing into the solvent. In summary, the H-pin polyamide provides an important molecular design motif for the discovery of future generations of programmable small molecules capable of binding to target DNA sequences with high affinity and selectivity. 2008 Elsevier Ltd. All rights reserved.
• Redirection of the Transcription Factor SP1 to AT Rich Binding Sites by a Synthetic Adaptor Molecule
  作者：Mathias Bolz、Ute Scheffer、Elisabeth Kalden、Michael W. Göbel

  DOI：10.1002/hlca.202100095

  日期：2021.9

  The ubiquitous transcription factor SP1 binds to a GC rich consensus sequence. Here we describe an adaptor molecule that mediates binding of SP1 to a non-cognate DNA site rich in AT. The adaptor is comprised of a Dervan-type hairpin polyamide with high affinity to an AT rich hexamer duplex. It also carries a 27mer DNA that contains the SP1 consensus sequence. The synthesis and purification of the polyamide-DNA

  无处不在的转录因子 SP1 与富含 GC 的共有序列结合。在这里，我们描述了一种适配器分子，它介导 SP1 与富含 AT 的非同源 DNA 位点的结合。该接头由对富含 AT 的六聚体双链体具有高亲和力的Dervan型发夹聚酰胺组成。它还携带含有 SP1 共有序列的 27 聚体 DNA。报道了聚酰胺-DNA 偶联物的合成和纯化。Pulldown 实验和蛋白质印迹分析证明了接头介导的 SP1 与六聚体双链体 TTGTTA 的结合。