N4-(N6-benzoyl-6-aminopyridin-2-yl)-5'-dimethoxytrityl-2'-deoxycytidine | 180476-69-1

• 分子结构分类: 有机化合物 - 苯类化合物 - 三苯基化合物
• 英文名称: N4-(N6-benzoyl-6-aminopyridin-2-yl)-5'-dimethoxytrityl-2'-deoxycytidine
• 英文别名: N⁴-(N⁶-benzoyl-6-aminopyridin-2-yl)-5'-dimethoxytrityl-2'-deoxycytidine
• CAS: 180476-69-1
• 化学式: C₄₂H₃₉N₅O₇
• 分子量: 725.801
• InChiKey: SHIBFWZBMNCWFZ-ABNQXDDGSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  6.31
• 重原子数：
  54.0
• 可旋转键数：
  13.0
• 环数：
  7.0
• sp3杂化的碳原子比例：
  0.19
• 拓扑面积：
  146.06
• 氢给体数：
  3.0
• 氢受体数：
  11.0

反应信息

• 作为反应物：
  描述：

  2-氰乙基N,N-二异丙基氯亚磷酰胺 、 N4-(N6-benzoyl-6-aminopyridin-2-yl)-5'-dimethoxytrityl-2'-deoxycytidine 在 吡啶 、 N,N-二异丙基乙胺 作用下， 以 二氯甲烷 为溶剂， 反应 1.0h， 以73%的产率得到N⁴-(N⁶-benzoyl-6-aminopyridin-2-yl)-5'-dimethoxytrityl-2'-deoxycytidine 3'-O-(2-cyanoethyl-N,N-diisopropylaminophosphoramidite)
  参考文献：
  名称：

  The Synthesis ofN⁴-(6-Aminopyridin-2-yl)-2′-deoxycytidine for Recognizing the CG Base Pair at Neutral pH by Oligodeoxyribonucleotide-Directed Triple Helix Formation

  摘要：

  AbstractThe sequence‐specific recognition of double‐helical DNA by oligodeoxyribonucleotide‐directed triple helix (triplex) formation is limited mostly to purine tracts. To interrupt the purine tract in a target sequence, a non‐natural deoxyribonucleoside N4‐(6‐aminopyridin‐2‐yl)‐2′‐deoxycytidine (pC) was designed to interact with the C base in the CG base pair. The protected phosphoramidite synthon of pC was synthesized in seven steps and then was incorporated into an oligodeoxyribonucleotide by an automatic DNA synthesizer. Two 22‐mers, designated as C2 and P, with a common sequence of 5′‐d‐TmCTXTmCTTCTGTCTCCAGACAG were synthesized in this study. mC is 5‐methyl‐2′‐deoxycytidine and X is either 2′‐deoxycytidine (C) or pC for C2 and P, respectively. C2 is able to form a paper clip type triplex with one C · CG mismatched base triad in slightly acidic conditions but not at the neutral pH. On the other hand, P forms a stable triplex under both acidic and neutral conditions. This indicates that pC is able to form a pC · CG base triad in the triplex. Their physical properties were studied by UV thermal melting experiments and circular dichorism spectroscopy (CD). The thermal melting results imply that the pC · CG base triad is as stable as the C+ · GC triad at pH 6.0, and pC helps the triplex formation preferably at neutral to acidic pH. In addition to the hydrogen bonding interaction with the CG base pair, the hydrophobic interaction of pC may also play an important role in stabilizing the triplex formation of oligodeoxyribonucleotides. In the presence of spermine at either pH 5.0 or pH 6.0, the melting temperature of the third strand of P was elevated about 30 and 21 °C, respectively. Thus, spermine can enhance the stability of the triple‐helical structure.

  DOI：

  10.1002/jccs.199900103
• 作为产物：
  描述：

  二乙酰基-2'脱氧尿苷 在 吡啶 、 胍 、 三乙胺 、 三氯氧磷 作用下， 以 乙醇 、 二氯甲烷 、 乙腈 为溶剂， 反应 168007.83h， 生成 N4-(N6-benzoyl-6-aminopyridin-2-yl)-5'-dimethoxytrityl-2'-deoxycytidine
  参考文献：
  名称：

  The Synthesis ofN⁴-(6-Aminopyridin-2-yl)-2′-deoxycytidine for Recognizing the CG Base Pair at Neutral pH by Oligodeoxyribonucleotide-Directed Triple Helix Formation

  摘要：

  AbstractThe sequence‐specific recognition of double‐helical DNA by oligodeoxyribonucleotide‐directed triple helix (triplex) formation is limited mostly to purine tracts. To interrupt the purine tract in a target sequence, a non‐natural deoxyribonucleoside N4‐(6‐aminopyridin‐2‐yl)‐2′‐deoxycytidine (pC) was designed to interact with the C base in the CG base pair. The protected phosphoramidite synthon of pC was synthesized in seven steps and then was incorporated into an oligodeoxyribonucleotide by an automatic DNA synthesizer. Two 22‐mers, designated as C2 and P, with a common sequence of 5′‐d‐TmCTXTmCTTCTGTCTCCAGACAG were synthesized in this study. mC is 5‐methyl‐2′‐deoxycytidine and X is either 2′‐deoxycytidine (C) or pC for C2 and P, respectively. C2 is able to form a paper clip type triplex with one C · CG mismatched base triad in slightly acidic conditions but not at the neutral pH. On the other hand, P forms a stable triplex under both acidic and neutral conditions. This indicates that pC is able to form a pC · CG base triad in the triplex. Their physical properties were studied by UV thermal melting experiments and circular dichorism spectroscopy (CD). The thermal melting results imply that the pC · CG base triad is as stable as the C+ · GC triad at pH 6.0, and pC helps the triplex formation preferably at neutral to acidic pH. In addition to the hydrogen bonding interaction with the CG base pair, the hydrophobic interaction of pC may also play an important role in stabilizing the triplex formation of oligodeoxyribonucleotides. In the presence of spermine at either pH 5.0 or pH 6.0, the melting temperature of the third strand of P was elevated about 30 and 21 °C, respectively. Thus, spermine can enhance the stability of the triple‐helical structure.

  DOI：

  10.1002/jccs.199900103