3'-TBDMS-rU 亚磷酰胺单体 | 129451-77-0

• 分子结构分类: 有机化合物 - 苯类化合物 - 三苯基化合物
• 中文名称: 3'-TBDMS-rU 亚磷酰胺单体
• 中文别名: 3'-TBDMS-RU亚磷酰胺单体
• 英文名称: 5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-2'-O-[P-(2-cyanethoxy)-P-(N,N-diisopropylamino)phosphino]-3'-O-[dimethyl(tert-butyl)silyl]uridine
• 英文别名: 3′-O-(tert-butyldimethylsilyl)-5′-O-(4,4′-dimethoxytrityl)uridine-2′-O-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite；5'-O-DMT-3'-O-tert-Butyldimethylsilyl-uridine-2'-CE phosphoramidite；3-[[(2R,3R,4R,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-[tert-butyl(dimethyl)silyl]oxy-2-(2,4-dioxopyrimidin-1-yl)oxolan-3-yl]oxy-[di(propan-2-yl)amino]phosphanyl]oxypropanenitrile
• CAS: 129451-77-0
• 化学式: C₄₅H₆₁N₄O₉PSi
• 分子量: 861.06
• InChiKey: UZVSHRLVIXPYEZ-ZMHKPELYSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  8.51
• 重原子数：
  60
• 可旋转键数：
  20
• 环数：
  5.0
• sp3杂化的碳原子比例：
  0.49
• 拓扑面积：
  141
• 氢给体数：
  1
• 氢受体数：
  11

反应信息

• 作为反应物：
  描述：

  N³,2',3'-O-tribenzoyluridine 、 3'-TBDMS-rU 亚磷酰胺单体 在 四氮唑 、 叔丁基过氧化氢 作用下， 生成 [(2R,3R,4R,5R)-5-(3-benzoyl-2,4-dioxopyrimidin-1-yl)-4-benzoyloxy-2-[[[(2R,3R,4R,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-[tert-butyl(dimethyl)silyl]oxy-2-(2,4-dioxopyrimidin-1-yl)oxolan-3-yl]oxy-(2-cyanoethoxy)phosphoryl]oxymethyl]oxolan-3-yl] benzoate
  参考文献：
  名称：

  Kinetics and Mechanism of Facile and Selective Dephosphorylation of 2‘-Phosphorylated and 2‘-Thiophosphorylated Dinucleotides:  Neighboring 3‘−5‘ Phosphodiester Promotes 2‘-Dephosphorylation

  摘要：

  2'-phosphorylated and 2'-thiophosphorylated dinucleotides U(2'-p)pU (1) and U(2'-ps)pU (2) were found to undergo facile 2'-specific dephosphorylation at 90 degrees C in neutral aqueous solution to give UpU, and the first-order rate constants of these reactions were determined by HPLC. Particularly, U(2'-ps)pU (2, k = 1.38 +/- 0.4 x 10(-3) s(-1), t(comp) = 1 h) was cleanly dephosphorylated ca. 100 times more rapidly than U(2'-p)pU (1, k = 1.41 +/- 0.05 x 10(-5) s(-1), t(comp) = 72 h). Dephosphorylations of 1 and 2 were faster than those of thymidine 3'-phosphate (8) and thymidine 3'-thiophosphate (9), respectively. The kinetic data observed were independent of the 2'- or 3'-position of the phosphate group and the kind of base moiety. The neighboring 3'-5' phosphodiester function most probably promotes the 2'-dephosphorylation efficiently. A branched trimer, U(2'-pU)pU (3), and related compounds having a substituent on the 2'-phosphoryl group, such as U(2'-pp-biotin)pU (4) and U(2'-ps-bimane)pU (5), were rather resistant to hydrolysis. The addition of divalent metal ions (Mg2+, Mn2+, Zn2+, Ca2+, Co2+, and Cd2+) remarkably decreased the rate of 2'-de(thio)phosphorylation of 1 or 2. Among these metal ions, Zn2+ most significantly inhibited the dephosphorylation. On the contrary, trivalent metal ions considerably accelerated the 2'-de(thio)phosphorylation of 1 or 2. The mechanism of 2'-dephosphorylation in the presence and absence of various metal ions is also discussed.

  DOI：

  10.1021/jo970021k
• 作为产物：
  描述：

  5'-O-[二(4-甲氧基苯基)苯基甲基]-3'-O-[(叔丁基)二甲基硅烷基]尿苷 、 2-(Cyanethoxy)-bis-N,N-(diisopropylamino)phosphane 在 4-二甲氨基吡啶 、 N,N-二异丙基乙胺 作用下， 以 四氢呋喃 为溶剂， 反应 4.0h， 以86%的产率得到3'-TBDMS-rU 亚磷酰胺单体
  参考文献：
  名称：

  关于事实和伪像：评估人工核酸酶的困难

  摘要：

  近年来，已经开发出许多有希望的用于RNA水解降解的合成催化剂。其中一些对嘧啶核苷酸显示出显着的选择性。所有这些研究的普遍问题是区分由天然核糖核酸污染痕迹引起的真实效果和伪像。我们证明了代表当前技术水平的方法（焦碳酸二乙酯处理，灭菌，超滤等）。）不能充分防止严重的伪影。但是，通过比较RNA的裂解及其镜像，可以发现一种可靠的检测方法。对映异构体RNA完全抗酶促降解，而非对称非手性催化剂，通过基本的对称定律，无法区分对映异构体，并且会在两种底物上诱导出完全相同的裂解模式。

  DOI：

  10.1002/hlca.200390316

文献信息

• Synthesis and compositions of 2'-terminator nucleotides
  申请人：Bodepudi Veeraiah

  公开号：US20050037991A1

  公开（公告）日：2005-02-17

  The invention provides compositions the comprise nucleotides and/or nucleosides having blocking groups at 2′-positions of sugar moieties. Methods of synthesizing these nucleic acids are also provided.

  该发明提供了含有在糖基的2′-位置具有阻断基团的核苷酸和/或核苷的组合物。同时还提供了合成这些核酸的方法。
• Solid-Phase Synthesis and Hybrization Behavior of Partially 2′/3′-<i>O</i>-Acetylated RNA Oligonucleotides
  作者：Jianfeng Xu、Colm D. Duffy、Christopher K. W. Chan、John D. Sutherland

  DOI：10.1021/jo5002824

  日期：2014.4.18

  Synthesis of partially 2'/3'-O-acetylated oligoribonucleotides has been accomplished by using a 2'/3'-O-acetyl orthogonal protecting group strategy in which nonnucleophilic strong-base (DBU) labile nucleobase protecting groups and a LTV-light cleavable linker were used. Strong-base stability of the photolabile linker allowed on-column nucleobase and phosphate deprotection, followed by a mild cleavage of the acetylated oligonucleotides from the solid support with UV light. Two 17nt oligonucleotides, which were synthesized possessing one specific internal 2' or 3'-acetyl group, were used as synthetic standards in a recent report from this laboratory detailing the prebiotically plausible ligation of RNA oligonucleotides. In order to further investigate the effect of 2'/3'-O-acetyl groups on the stability of RNA duplex structure, two complementary bis-acetylated RNA oligonucleotides were also expediently obtained with the newly developed protocols. UV melting curves of 2'-O-acetylated RNA duplexes showed a consistent similar to 3.1 degrees C decrease in T-m per 2'-O-acetyl group.
• MILECKI, JAN;DEMBEK, PIOTR;ANTKOWIAK, WIESLAW Z.;GDANIEC, ZOFIA;MIELEWCZY+, NUCLEOSIDES AND NUCLEOTIDES, 8,(1989) N, C. 463-474
  作者：MILECKI, JAN、DEMBEK, PIOTR、ANTKOWIAK, WIESLAW Z.、GDANIEC, ZOFIA、MIELEWCZY+

  DOI：——

  日期：——
• Kinetics and Mechanism of Facile and Selective Dephosphorylation of 2‘-Phosphorylated and 2‘-Thiophosphorylated Dinucleotides:  Neighboring 3‘−5‘ Phosphodiester Promotes 2‘-Dephosphorylation
  作者：Hiroyuki Tsuruoka、Koh-ichiroh Shohda、Takeshi Wada、Mitsuo Sekine

  DOI：10.1021/jo970021k

  日期：1997.5.1

  2'-phosphorylated and 2'-thiophosphorylated dinucleotides U(2'-p)pU (1) and U(2'-ps)pU (2) were found to undergo facile 2'-specific dephosphorylation at 90 degrees C in neutral aqueous solution to give UpU, and the first-order rate constants of these reactions were determined by HPLC. Particularly, U(2'-ps)pU (2, k = 1.38 +/- 0.4 x 10(-3) s(-1), t(comp) = 1 h) was cleanly dephosphorylated ca. 100 times more rapidly than U(2'-p)pU (1, k = 1.41 +/- 0.05 x 10(-5) s(-1), t(comp) = 72 h). Dephosphorylations of 1 and 2 were faster than those of thymidine 3'-phosphate (8) and thymidine 3'-thiophosphate (9), respectively. The kinetic data observed were independent of the 2'- or 3'-position of the phosphate group and the kind of base moiety. The neighboring 3'-5' phosphodiester function most probably promotes the 2'-dephosphorylation efficiently. A branched trimer, U(2'-pU)pU (3), and related compounds having a substituent on the 2'-phosphoryl group, such as U(2'-pp-biotin)pU (4) and U(2'-ps-bimane)pU (5), were rather resistant to hydrolysis. The addition of divalent metal ions (Mg2+, Mn2+, Zn2+, Ca2+, Co2+, and Cd2+) remarkably decreased the rate of 2'-de(thio)phosphorylation of 1 or 2. Among these metal ions, Zn2+ most significantly inhibited the dephosphorylation. On the contrary, trivalent metal ions considerably accelerated the 2'-de(thio)phosphorylation of 1 or 2. The mechanism of 2'-dephosphorylation in the presence and absence of various metal ions is also discussed.
• On Facts and Artefacts: The Difficulty to Evaluate an Artificial Nuclease
  作者：Stefan Pitsch、Ute Scheffer、Markus Hey、Andreas Strick、Michael W. Göbel

  DOI：10.1002/hlca.200390316

  日期：2003.11

  general problem of all these studies is to distinguish between real effects and artefacts caused by traces of contaminating natural ribonucleases. We show that methods representing the current state of the art (diethylpyrocarbonate treatment, sterilization, ultrafiltration, etc.) do not sufficiently protect against severe artefacts. However, an incorruptible assay could be found by comparing the cleavage

  近年来，已经开发出许多有希望的用于RNA水解降解的合成催化剂。其中一些对嘧啶核苷酸显示出显着的选择性。所有这些研究的普遍问题是区分由天然核糖核酸污染痕迹引起的真实效果和伪像。我们证明了代表当前技术水平的方法（焦碳酸二乙酯处理，灭菌，超滤等）。）不能充分防止严重的伪影。但是，通过比较RNA的裂解及其镜像，可以发现一种可靠的检测方法。对映异构体RNA完全抗酶促降解，而非对称非手性催化剂，通过基本的对称定律，无法区分对映异构体，并且会在两种底物上诱导出完全相同的裂解模式。