3′,5′-O-bis(tert-butyldimethylsilyl)-O⁶-(p-nitrophenylethyl)-2′-deoxy-2-fluoroguanosine | 190506-33-3

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 嘌呤核苷
• 英文名称: 3′,5′-O-bis(tert-butyldimethylsilyl)-O⁶-(p-nitrophenylethyl)-2′-deoxy-2-fluoroguanosine
• 英文别名: 3',5'-O-Di-tert-butyldimethylsilyl-6-O-[2-(4-nitrophenyl)ethyl]-2'-deoxy-2-fluoroinosine；tert-butyl-[[(2R,3S,5R)-3-[tert-butyl(dimethyl)silyl]oxy-5-[2-fluoro-6-[2-(4-nitrophenyl)ethoxy]purin-9-yl]oxolan-2-yl]methoxy]-dimethylsilane
• CAS: 190506-33-3
• 化学式: C₃₀H₄₆FN₅O₆Si₂
• 分子量: 647.895
• InChiKey: YTBQUPUTEIVNEC-RBZQAINGSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  7.19
• 重原子数：
  44
• 可旋转键数：
  12
• 环数：
  4.0
• sp3杂化的碳原子比例：
  0.63
• 拓扑面积：
  126
• 氢给体数：
  0
• 氢受体数：
  10

反应信息

• 作为反应物：
  描述：

  3′,5′-O-bis(tert-butyldimethylsilyl)-O⁶-(p-nitrophenylethyl)-2′-deoxy-2-fluoroguanosine 在 吡啶 、 triethylamine tris(hydrogen fluoride) 作用下， 以 四氢呋喃 为溶剂， 反应 37.0h， 生成 5'-O-(4,4'-Dimethoxytrityl)-6-O-[2-(4-nitrophenyl)ethyl]-2'-deoxy-2-fluoroinosine
  参考文献：
  名称：

  Synthesis and Hybridization Properties of Oligonucleotides Containing Polyamines at the C-2 Position of Purines: A Pre-synthetic Approach for the Incorporation of Spermine into Oligodeoxynucleotides Containing 2-(4,9,13-Triazatridecyl)-2′-deoxyguanosine

  摘要：

  We have developed a synthesis of spermine-containing oligonucleotides (ODN-sper) which allows incorporation of multiple polyamine residues. This approach was based on the pertrifluoroacetylated 5'DMT-dGsper phosphoramidite synthon. Its coupling yield with resin-bound ODN decreased dramatically when close to the 3'-end. Optimization of the coupling conditions allowed 22-mer ODNs containing up to six spermine residues to be synthesized. Several ODNs of different sequences with 1-4 pendent spermines could be purified and their hybridization properties were evaluated. Duplex melting temperatures increased linearly with the number of polyamine.residues (DeltaT(m)/sper = 3.0 +/- 0.2 degreesC in 100 mM NaCl). This compares very favorably with values reported for duplexes of similar initial stability containing other cation-substituted bases. Moreover, the stability increase was neither sequence nor position-dependent, and even contiguous spermine residues did not crosstalk. Extrapolation based on these findings leads to the conclusion that a duplex formed with a 22-mer oligonucleotide containing seven spermine residues would be as stable as genomic DNA, which highlights its potential for DNA strand invasion.

  DOI：

  10.1002/1521-3765(20001117)6:22<4188::aid-chem4188>3.0.co;2-n
• 作为产物：
  描述：

  2'-脱氧鸟苷 在 咪唑 、 亚硝酸特丁酯 、 poly[4-vinylpyridinium poly(hydrogen fluoride)] 、 三苯基膦 、 偶氮二甲酸二乙酯 作用下， 以 1,4-二氧六环 、 N,N-二甲基甲酰胺 、 甲苯 为溶剂， 反应 48.0h， 生成 3′,5′-O-bis(tert-butyldimethylsilyl)-O⁶-(p-nitrophenylethyl)-2′-deoxy-2-fluoroguanosine
  参考文献：
  名称：

  Synthesis and Hybridization Properties of Oligonucleotides Containing Polyamines at the C-2 Position of Purines: A Pre-synthetic Approach for the Incorporation of Spermine into Oligodeoxynucleotides Containing 2-(4,9,13-Triazatridecyl)-2′-deoxyguanosine

  摘要：

  We have developed a synthesis of spermine-containing oligonucleotides (ODN-sper) which allows incorporation of multiple polyamine residues. This approach was based on the pertrifluoroacetylated 5'DMT-dGsper phosphoramidite synthon. Its coupling yield with resin-bound ODN decreased dramatically when close to the 3'-end. Optimization of the coupling conditions allowed 22-mer ODNs containing up to six spermine residues to be synthesized. Several ODNs of different sequences with 1-4 pendent spermines could be purified and their hybridization properties were evaluated. Duplex melting temperatures increased linearly with the number of polyamine.residues (DeltaT(m)/sper = 3.0 +/- 0.2 degreesC in 100 mM NaCl). This compares very favorably with values reported for duplexes of similar initial stability containing other cation-substituted bases. Moreover, the stability increase was neither sequence nor position-dependent, and even contiguous spermine residues did not crosstalk. Extrapolation based on these findings leads to the conclusion that a duplex formed with a 22-mer oligonucleotide containing seven spermine residues would be as stable as genomic DNA, which highlights its potential for DNA strand invasion.

  DOI：

  10.1002/1521-3765(20001117)6:22<4188::aid-chem4188>3.0.co;2-n

文献信息

• N² -Substituted 2′-Deoxyguanosine Triphosphate Derivatives as Selective Substrates for Human DNA Polymerase κ
  作者：A. S. Prakasha Gowda、Marietta Lee、Thomas E. Spratt

  DOI：10.1002/anie.201611607

  日期：2017.3.1

  N2‐Alkyl‐2′‐deoxyguanosine triphosphate (N2‐alkyl‐dGTP) derivatives with methyl, butyl, benzyl, or 4‐ethynylbenzyl substituents were prepared and tested as substrates for human DNA polymerases. N2‐Benzyl‐dGTP was equal to dGTP as a substrate for DNA polymerase κ (pol κ), but was a poor substrate for pols β, δ, η, ι, or ν. In vivo reactivity was evaluated through incubation of N2‐4‐ethynylbenzyl‐dG

  Ñ 2 -烷基-2'-脱氧鸟苷三磷酸（N 2 -烷基的dGTP）制备具有甲基，丁基，苄基，或4-乙炔基苄基取代基的衍生物和作为用于人DNA聚合酶的底物进行测试。N 2-苄基-dGTP等于dGTP作为DNA聚合酶κ（polκ）的底物，但对于polsβ，δ，η，ι或ν则是较差的底物。体内的反应性是通过N个孵化评价2 -4-乙炔基苄基-dG的用野生型和polκ缺陷型小鼠胚胎成纤维细胞。CuAAC与5（6）-FAM-叠氮化物的反应表明，只有含有polκ的细胞才能掺入N 2-4-乙炔基苄基-dG进入细胞核。这是Y家族聚合酶特异性dNTP的第一个实例，该方法可用于探测体内polκ的活性。
• Formation of Pyrene Dimer Radical Cation at the Minor Groove of DNA
  作者：Kiyohiko Kawai、Takumi Kimura、Hiroko Yoshida、Akira Sugimoto、Sachiko Tojo、Mamoru Fujitsuka、Tetsuro Majima

  DOI：10.1246/bcsj.79.312

  日期：2006.2

  and the formation rates of the pyrene dimer radical cation were measured upon one-electron oxidation during pulse radiolysis. For all of the DNA studied here, the formation of a pyrene dimer radical cation was accomplished quickly, within 20 micro seconds after a 8-ns electron pulse during pulse radiolysis. The results show that the minor groove of DNA offers a good space for the formation of pyrene

  为了将芘排列在 DNA 的小沟中，我们合成了一种在鸟嘌呤 N2 上具有芘基团的核苷衍生物。合成了双芘修饰的双链 DNA，并在脉冲辐解过程中通过单电子氧化测量芘二聚体自由基阳离子的形成速率。对于这里研究的所有 DNA，芘二聚体自由基阳离子的形成是在脉冲辐射分解期间 8 ns 电子脉冲后 20 微秒内快速完成的。结果表明，DNA的小沟为芘二聚体自由基阳离子的形成提供了良好的空间。
• Postsynthetic Generation of a Major Acrolein Adduct of 2‘-Deoxyguanosine in Oligomeric DNA^†
  作者：Sonia Khullar、Chamakura V. Varaprasad、Francis Johnson

  DOI：10.1021/jm980605u

  日期：1999.3.1
• Monitoring of Microenvironmental Changes in the Major and Minor Grooves of DNA by Dan-Modified Oligonucleotides
  作者：Takumi Kimura、Kiyohiko Kawai、Tetsuro Majima

  DOI：10.1021/ol052473m

  日期：2005.12.1

  We describe the synthesis of new environmentally sensitive fluorescence probes to elucidate DNA structures. DNA oligonucleotides containing fluorophore dan (6-(dimethylamino)-2-acylnaphthalene)-modified dC or dG were able to monitor the microenvironmental changes in both the major and minor grooves of DNA with a B- to A-DNA conformational transition and RNA hybridization.
• Synthesis and properties of terthiophene-modified oligodeoxynucleotides
  作者：Kiyohiko Kawai、Akira Sugimoto、Hiroko Yoshida、Sachiko Tojo、Mamoru Fujitsuka、Tetsuro Majima

  DOI：10.1016/j.bmcl.2005.07.004

  日期：2005.10

  Synthesis and properties of oligodeoxynucleotides (ODNs) containing terthiophene (Thp) were described. One-electron oxidation of Thp-modified ODN resulted in the formation of Thp radical cation (Thp(.+)), which remained stable in the experimental time window up to 200 mu s, showing that charge may be carried along DNA by Thp as Thp(.+). (c) 2005 Elsevier Ltd. All rights reserved.