| 1221252-87-4

• 分子结构分类: 有机化合物 - 有机氧化合物
• CAS: 1221252-87-4
• 化学式: C₁₃H₁₈N₂O₆
• 分子量: 298.296
• InChiKey: RKGZORMBBBZDCA-CHNYTCMHSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  -1.91
• 重原子数：
  21.0
• 可旋转键数：
  2.0
• 环数：
  3.0
• sp3杂化的碳原子比例：
  0.69
• 拓扑面积：
  124.78
• 氢给体数：
  4.0
• 氢受体数：
  7.0

反应信息

• 作为反应物：
  描述：

  、 4,4'-双甲氧基三苯甲基氯 在 吡啶 作用下， 以424 mg的产率得到(1R,3R,4R,5S,6S,7S)-1-(4,4'-dimethoxytrityloxymethyl)-7-hydroxyl-5-methyl-6-tosylate-3-(thymin-1-yl)-2-oxabicyclo[2.2.1]heptane
  参考文献：
  名称：

  Double Sugar and Phosphate Backbone-Constrained Nucleotides: Synthesis, Structure, Stability, and Their Incorporation into Oligodeoxynucleotides

  摘要：

  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.

  DOI：

  10.1021/jo900391n
• 作为产物：
  描述：

  在 Crotalus adamanteus phosphodiesterase I 、 三羟甲基氨基甲烷盐酸盐 、 sodium chloride 、 magnesium chloride 作用下， 以 水 为溶剂， 生成
  参考文献：
  名称：

  Why Carba-LNA-Modified Oligonucleotides Show Considerably Improved 3′-Exonuclease Stability Compared to That of the LNA Modified or the Native Counterparts: A Michaelis−Menten Kinetic Analysis

  摘要：

  In this study, 12 different native or LNA, carba-LNA-modified dinucleoside phosphates were designed as simple chemical models to study how carba-LNA modifications improve the 3'-exonuclease (SVPDE in this study) resistance Of internucleotidic phosphate compared to those exhibited by LNA-modified and the native counterparts. Michaelis-Menten kinetic studies for dimers 3 - 7, in which the LNA or carba-LNA modifications are located at the 5'-end, showed that (i) increased 3'-exonuclease resistance of (5')[LNA-T](p)T (3) compared to the native (TpT)-T-5' (1) was mainly attributed to steric hindrance imposed by the LNA modification that retards the nuclease binding (K-M) and (ii) digestion of (5')[carba-LNA-dT](p)T (4) and (5')[LNA-T](p)T (3), however, exhibit similar K(M)s, whereas the former shows a 100x decrease in K-cat and is hence more stable than latter. By studying the correlation between log k(cat) and pK(a) of the departing 3'(or 6')-OHs for 3-7, we found the pK(a) of 3'-OH of carba-LNA-T was 1.4 pK(a) units higher than that of LNA-T, and this relatively less acidic character of the 3'-OH in the former leads to the 100x decrease in the catalytic efficiency for the digestion Of (5')[Carba-LNA-T](p)T (4). In contrast, Michaelis-Menten kinetic studies for dimers 9-12, with the LNA or carba-LNA modifications at the 3'-end, showed that the digestion of T-5'(p)[LNA-T] (9) exhibited similar K-M but k(cat) decreased around 40 times compared to that of the native (TpT)-T-5' (1). Similar k(cat) values have been observed for digestion of T-5'(p)[carba-LNA-T] (10) and T-5'(p)[LNA-T] (9). The higher stability of carba-LNA modified dimer 10 compared with LNA modified dimer 9 comes solely from the increased K-M.

  DOI：

  10.1021/jo100170g