5-<3-<(9-phenylxanthen-9-yl)amino>prop-1-yn-1-yl>-5'-O-(9-phenylxanthen-9-yl)-2'-deoxyuridine

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 嘧啶核苷
• 英文名称: 5-<3-<(9-phenylxanthen-9-yl)amino>prop-1-yn-1-yl>-5'-O-(9-phenylxanthen-9-yl)-2'-deoxyuridine
• 英文别名: 5-{3-[(9-phenylxanthen-9-yl)amino]prop-1-yn-1-yl}-5'-O-(9-phenylxanthen-9-yl)-2'-deoxyuridine；1-[(2R,4S,5R)-4-hydroxy-5-[(9-phenylxanthen-9-yl)oxymethyl]oxolan-2-yl]-5-[3-[(9-phenylxanthen-9-yl)amino]prop-1-ynyl]pyrimidine-2,4-dione
• 化学式: C₅₀H₃₉N₃O₇
• 分子量: 793.876
• InChiKey: RIOLZJKYMMBWAK-OIAACSHNSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  7
• 重原子数：
  60
• 可旋转键数：
  9
• 环数：
  10.0
• sp3杂化的碳原子比例：
  0.16
• 拓扑面积：
  119
• 氢给体数：
  3
• 氢受体数：
  8

反应信息

• 作为产物：
  描述：

  碘苷 在 4-二甲氨基吡啶 、 四(三苯基膦)钯 吡啶 、 copper(l) iodide 、 三乙胺 作用下， 以 N,N-二甲基甲酰胺 为溶剂， 反应 6.0h， 生成 5-<3-<(9-phenylxanthen-9-yl)amino>prop-1-yn-1-yl>-5'-O-(9-phenylxanthen-9-yl)-2'-deoxyuridine
  参考文献：
  名称：

  The synthesis of oligonucleotide-polyamide conjugate molecules suitable as PCR primers

  摘要：

  A new class of oligonucleotide-polyamide conjugates having free 3'-termini has been developed. These molecules have the potential to act as multiply-labeled nonradioactive polymerase chain reaction (PCR) primers. The linkage between the oligonucleotide and the polyamide is via a C5-modified deoxyuridine, synthesized in three steps from 5-iodo-2'-deoxyuridine (6). Subsequent palladium-catalyzed coupling of the 5'-O-protected deoxyuridine derivative 7 and the N-protected propargylamines 11 and 12 gave the alkynyl nucleosides 3 and 4, respectively. Both of these were then incorporated onto succinyl-CPG resin by diisopropylcarbodiimide/DMAP-mediated esterifications to give 18 and 19, respectively. Acidolytic removal of all protecting groups, selective acylation at the C5 pendant amine by an activated N(alpha)-(9-fluorenylmethoxycarbonyl) (Fmoc)-protected amino acid followed by reprotection of the 5'-hydroxyl by tritylation with 4,4'-dimethoxytrityl chloride gave the solid support 22. Standard Fmoc solid-phase peptide synthesis on the C5 pendant arm of 22 followed by oligonucleotide synthesis using standard phosphoramidite chemistry on the 5'-hydroxyl gave the desired oligonucleotide-polyamide conjugate 5. A single biotin label was incorporated into the polyamide using the biotinylated lysine synthon 29; this method is expected to be readily applicable for the attachment of multiple biotin residues in a facile and highly-controlled manner. The conjugate 5 was characterized by UV spectroscopy, amino acid analysis, 5'-end labeling with P-32 and reversed-phase C18 HPLC analysis of enzymatic digests. Preliminary experiments with 5 have shown that it is an efficient PCR primer.

  DOI：

  10.1021/jo00060a044

文献信息

• The synthesis of oligonucleotide-polyamide conjugate molecules suitable as PCR primers
  作者：Glenn Tong、John M. Lawlor、Geoffrey W. Tregear、Jim Haralambidis

  DOI：10.1021/jo00060a044

  日期：1993.4

  A new class of oligonucleotide-polyamide conjugates having free 3'-termini has been developed. These molecules have the potential to act as multiply-labeled nonradioactive polymerase chain reaction (PCR) primers. The linkage between the oligonucleotide and the polyamide is via a C5-modified deoxyuridine, synthesized in three steps from 5-iodo-2'-deoxyuridine (6). Subsequent palladium-catalyzed coupling of the 5'-O-protected deoxyuridine derivative 7 and the N-protected propargylamines 11 and 12 gave the alkynyl nucleosides 3 and 4, respectively. Both of these were then incorporated onto succinyl-CPG resin by diisopropylcarbodiimide/DMAP-mediated esterifications to give 18 and 19, respectively. Acidolytic removal of all protecting groups, selective acylation at the C5 pendant amine by an activated N(alpha)-(9-fluorenylmethoxycarbonyl) (Fmoc)-protected amino acid followed by reprotection of the 5'-hydroxyl by tritylation with 4,4'-dimethoxytrityl chloride gave the solid support 22. Standard Fmoc solid-phase peptide synthesis on the C5 pendant arm of 22 followed by oligonucleotide synthesis using standard phosphoramidite chemistry on the 5'-hydroxyl gave the desired oligonucleotide-polyamide conjugate 5. A single biotin label was incorporated into the polyamide using the biotinylated lysine synthon 29; this method is expected to be readily applicable for the attachment of multiple biotin residues in a facile and highly-controlled manner. The conjugate 5 was characterized by UV spectroscopy, amino acid analysis, 5'-end labeling with P-32 and reversed-phase C18 HPLC analysis of enzymatic digests. Preliminary experiments with 5 have shown that it is an efficient PCR primer.