TBDMS(-3)[N(iPr)2P(OCH2CH2CN)(-5)]2-deoxy-D-eryPenf(b)-thymin-1-yl | 276679-09-5

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 核苷和核苷酸类似物
• 英文名称: TBDMS(-3)[N(iPr)2P(OCH2CH2CN)(-5)]2-deoxy-D-eryPenf(b)-thymin-1-yl
• 英文别名: 3-[[(2R,3S,5R)-3-[tert-butyl(dimethyl)silyl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-[di(propan-2-yl)amino]phosphanyl]oxypropanenitrile
• CAS: 276679-09-5
• 化学式: C₂₅H₄₅N₄O₆PSi
• 分子量: 556.715
• InChiKey: BCXFOCGCDFKSCR-NCNUMQTJSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  4.82
• 重原子数：
  37
• 可旋转键数：
  13
• 环数：
  2.0
• sp3杂化的碳原子比例：
  0.8
• 拓扑面积：
  113
• 氢给体数：
  1
• 氢受体数：
  8

反应信息

• 作为反应物：
  描述：

  TBDMS(-3)[N(iPr)2P(OCH2CH2CN)(-5)]2-deoxy-D-eryPenf(b)-thymin-1-yl 在 四氮唑 、 三乙胺 作用下， 以 四氯化碳 、 二氯甲烷 、 水 、 乙腈 为溶剂， 反应 1.0h， 生成 3-[[(2R,3aS,7R,7aS)-7-[bis(4-methoxyphenyl)-phenylmethoxy]-2-(5-methyl-2,4-dioxopyrimidin-1-yl)-3,3a,5,6,7,7a-hexahydro-2H-furo[3,2-b]pyridin-4-yl]-[[(2R,3S,5R)-3-[tert-butyl(dimethyl)silyl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl]oxypropanenitrile
  参考文献：
  名称：

  Conformationally Locked Nucleosides. Synthesis of Oligodeoxynucleotides Containing 3′-Amino-3′-deoxy-3′-N,5′(R)-C-ethylenethymidine

  摘要：

  3'-Amino-3'-deoxy-5'-O-(4,4'-dimethoxytrityl)-3'-N,5(R)-C-ethylenethymidine (6)was synthesized starting from 3'-azido-3'-deoxythymidine. Condensation of 6 with 5'-O-(H-phosphonyl)thymidine and 5'-O-(p-nitrophenoxycarbonyl)thymidine derivatives gave dinucleotide and dinucleoside derivatives, respectively, which were incorporated into oligodeoxynucleotides (ODNs). Tm data of the modified ODNs are also presented.

  DOI：

  10.1080/15257770008033851
• 作为产物：
  描述：

  2-氰乙基N,N-二异丙基氯亚磷酰胺 、 3'-O-(叔丁基二甲基硅烷基)胸苷 在 N,N-二异丙基乙胺 作用下， 反应 0.5h， 生成 TBDMS(-3)[N(iPr)2P(OCH2CH2CN)(-5)]2-deoxy-D-eryPenf(b)-thymin-1-yl
  参考文献：
  名称：

  Conformationally Locked Nucleosides. Synthesis of Oligodeoxynucleotides Containing 3′-Amino-3′-deoxy-3′-N,5′(R)-C-ethylenethymidine

  摘要：

  3'-Amino-3'-deoxy-5'-O-(4,4'-dimethoxytrityl)-3'-N,5(R)-C-ethylenethymidine (6)was synthesized starting from 3'-azido-3'-deoxythymidine. Condensation of 6 with 5'-O-(H-phosphonyl)thymidine and 5'-O-(p-nitrophenoxycarbonyl)thymidine derivatives gave dinucleotide and dinucleoside derivatives, respectively, which were incorporated into oligodeoxynucleotides (ODNs). Tm data of the modified ODNs are also presented.

  DOI：

  10.1080/15257770008033851

文献信息

• Synthesis of 3′-<i>S</i>-Phosphorothiolate Oligonucleotides for their Potential Use in RNA Interference
  作者：James W. Gaynor、John Brazier、Rick Cosstick

  DOI：10.1080/15257770701490753

  日期：2007.11.26

  The potency of RNA interference (RNAi) undoubtedly can be improved through chemical modifications to the small interfering RNAs (siRNA). By incorporation of the 3'-S-phosphorothiolate modification into strands of RNA, it is hoped that specific regions of a siRNA duplex can be stabilised to enhance the target binding affinity of a selected antisense strand into the activated RNA-induced silencing complex (RISC*). Oligonucleotides composed entirely of this modification are desirable so unconventional 5 -> 3' synthesis is investigated, with initial solution-phase testing proving successful. The phosphoroamidite monomer required for solid-phase synthesis has also been produced.
• Double Sugar and Phosphate Backbone-Constrained Nucleotides: Synthesis, Structure, Stability, and Their Incorporation into Oligodeoxynucleotides
  作者：Chuanzheng Zhou、Oleksandr Plashkevych、Jyoti Chattopadhyaya

  DOI：10.1021/jo900391n

  日期：2009.5.1

  Two diastereomerically pure carba-LNA dioxaphosphorinane nucleotides [(S-p)- or (R-p)-D-2-CNA], simultaneously conformationally locked at the sugar and the phosphate backbone, have been designed and synthesized. Structural studies by NMR as well as by ab initio calculations showed that in (S-p)- and (R-p)-D-2-CNA the Mowing occur: (i) the sugar is locked in extreme North-type conformation with P = 11 degrees and Phi(m) (ii) the six-membered 1,3,2-dioxaphosphorinane ring adopts a half-chair conformation; (iii) the fixed phosphate backbone delta, epsilon, and zeta torsions were found to be delta [gauch(+)], epsilon (cis), zeta[anticlinal(+)] for (S-p)-D-2-CNA, and delta [gaitche(+)], epsilon(cis), zeta[anticlittal(-)] for (R-p)-D-2-CNA. It has been found that F- ion can catalyze the isomerization of pure (S-p)-D-2-CNA or (R-p)-D-2-CNA to give an equilibrium mixture (K = 1.94). It turned out that at equilibrium concentration the (S-p)-D-2-CNA isomer is preferred over the (R-p)-D-2-CNA isomer by 0.39 kcal/mol. The chemical reactivity of the six-membered dioxaphosphorinane ring in D-2-CNA was found to be dependent on the internucleotidic phosphate stereochemistry. Thus, both (Sp)- and (Rp)-D2-CNA dimers (17a and 17b) were very labile toward nucleophile attack in concentrated aqueous ammonia [t(1/2) = 12 and 6 min, respectively] to give carba-LNA-6',5'-phosphodiester (21) approximate to 70-90%, carba-LNA-3',5'-phosphodiester (22) approximate to 10%, and carba-LNA-6',3'-phosphodiester (23) < 10%. In contrasts the (S-p)-D-2-CNA was about 2 times more stable than (Rp)-D2-CNA under hydrazine hydrate/pyficfine/AcOH (pH = 5.6) [t(1/2) = 178 and 99 h, respectively], which was exploited in the deprotection of pure (S-p)-D-2-CNA incorporated antisense oligodeoxynucleotides (AON). Thus, after removal of the solid supports from the (S-p)-D-2-CNA-modified AON by BDU/MeCN, they were treated with hydrazine hydrate in pyridine/AcOH to give pure AONs in 35-40% yield, which was unequivocally characterized by MALDI-TOF to show that they have an intact six-membered dioxaphosphorinane ring. The effect of pure (S-p)-D-2-CNA niodification in the AONs was estimated by complexing to the complementary RNA and DNA strands by the thermal denaturation studies. This showed that this cyclic phosphotriester modification destabilizes the AON/DNA and AON/RNA duplex by about -6 to -9 degrees C/modification. Treatment of (Sp)-D-2-CNA-modified AON with concentrated aqueous ammonia gave cwba-LNA-6',5'-phosphodiester modified AON (similar to 80%) plus a small amount of carba-LNA-3',5'-Phosphodiester-modified AON (similar to 20%). It is noteworthy that Carba-LNA-3',5'-phosphodiester modification stabilized the AON/RNA duplex by +4 degrees C/modificafion (J. Org. Chem. 2009, 74, 118), whereas carba-LNA-6', 5'-phosphodiester modification destabilizes both AON/RNA and AON/DNA significantly (by -10 to -19 degrees C/modification), which, as shown in our comparative CD studies, that the cyclic phosphotriester modified AONs as well as carba-LNA-6'.5'-phosphodiester modified AONs are much more weakly stacked than carba-LNA-3',5'-phosphodiester-modified AONs.