5-(2-nitrobenzyloxy)methyl-2'-deoxyuridine | 1028383-70-1

• 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-(2-nitrobenzyloxy)methyl-2'-deoxyuridine
• 英文别名: 5-[(1-(2-nitrobenzyl)oxy)methyl]-2'-deoxyuridine；1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-[(2-nitrophenyl)methoxymethyl]pyrimidine-2,4-dione
• CAS: 1028383-70-1
• 化学式: C₁₇H₁₉N₃O₈
• 分子量: 393.353
• InChiKey: XEQNWUPODWCTAB-RRFJBIMHSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  -0.6
• 重原子数：
  28
• 可旋转键数：
  6
• 环数：
  3.0
• sp3杂化的碳原子比例：
  0.41
• 拓扑面积：
  154
• 氢给体数：
  3
• 氢受体数：
  8

反应信息

• 作为反应物：
  描述：

  5-(2-nitrobenzyloxy)methyl-2'-deoxyuridine 在 咪唑 、 4-二甲氨基吡啶 、 四丁基氟化铵 、 氨 、 三乙胺 作用下， 以 四氢呋喃 、 1,4-二氧六环 、 二氯甲烷 、 N,N-二甲基甲酰胺 为溶剂， 反应 4.0h， 生成 5-(2-nitrobenzyloxy)methyl-2'-deoxycytidine
  参考文献：
  名称：

  苄基碳取代的立体化学与 2-硝基苄基的环修饰作为快速裂解可逆终止子的关键决定因素

  摘要：

  已经开发出一套完整的 2-硝基苄基修饰的可逆终止剂，它们在暴露于紫外线下时会产生天然的羟甲基核苷酸（见方案）。苄基碳上的立体特异性 ( S )-叔丁基 (R) 和 2-硝基苄基环上的 5-OMe 基团 (R') 的组合显着提高了光化学裂解的速率。对于 7-deaza-7-hydroxymethyl-2'-deoxyguanosine，这些修饰导致速率增加超过一个数量级。

  DOI：

  10.1002/anie.201106516
• 作为产物：
  描述：

  N³-tert-butyloxycarbonyl-5-bromomethyl-3',5'-bis-O-tert-butyldimethylsilyl-2'-deoxyuridine 在 2,2,6,6-四甲基哌啶 、 silver trifluoromethanesulfonate 、 碳酸氢钠 、 triethylamine tris(hydrogen fluoride) 作用下， 以 四氢呋喃 、 甲醇 、 乙腈 为溶剂， 反应 2.17h， 生成 5-(2-nitrobenzyloxy)methyl-2'-deoxyuridine
  参考文献：
  名称：

  带有可见光可裂解基团的受保护的5-（羟甲基）尿嘧啶核苷酸是光笼DNA聚合酶合成的基础†

  摘要：

  制备了含有被光裂解基团（2-硝基苄基，6-硝基哌啶基或9-蒽甲基）保护的5-（羟甲基）尿嘧啶的核苷，核苷酸和2'-脱氧核糖核苷三磷酸酯（dNTP），并作为光笼聚合酶合成的基础材料进行了测试寡核苷酸和DNA。在模型核苷单磷酸上详细研究了光脱保护（光释放）反应，并确定了它们的光反应量子产率。然后测试了光笼dNTPs，并将其用作引物延伸或PCR中DNA聚合酶的底物。制备了在限制性内切核酸酶的识别序列中包含光笼或游离5-羟甲基U的DNA探针，并用于研究笼罩DNA通过不同波长的紫外线或可见光的光释放。

  DOI：

  10.1039/c8ob00160j

文献信息

• [EN] 5-METHOXY. 3'-OH UNBLOCKED, FAST PHOTOCLEAVABLE TERMINATING NUCLEOTIDES AND METHODS FOR NUCLEIC ACID SEQUENCING<br/>[FR] 5-MÉTHOXY-NUCLÉOTIDES À TERMINAISON RAPIDEMENT PHOTOCLIVABLE NON BLOQUÉS EN 3'OH ET PROCÉDÉS DE SÉQUENÇAGE D'ACIDE NUCLÉIQUE
  申请人：LASERGEN INC

  公开号：WO2013040257A1

  公开（公告）日：2013-03-21

  The present invention relates generally to 3'-OH unblocked nucleotides and nucleosides labeled and unlabeled with 5-methoxy-substituted nitrobenzyl-based photocleavable terminating groups for use in methods and systems related to DNA and RNA sequencing and analysis. These compounds may be used as reversible terminators as they exhibit fast nucleotide incorporation kinetics, single-base termination, high nucleotide selectivity, and rapid terminating group cleavage that results in a naturally occurring nucleotide.

  本发明通常涉及用于DNA和RNA测序和分析方法及系统中的3'-OH未阻断核苷酸和核苷的标记和未标记的5-甲氧基取代硝基苯基光致裂解终止基团。这些化合物可用作可逆终止剂，因为它们表现出快速的核苷酸结合动力学、单碱基终止、高核苷酸选择性和快速的终止基团裂解，导致自然发生的核苷酸。
• Polymerase Synthesis of Photocaged DNA Resistant against Cleavage by Restriction Endonucleases
  作者：Zuzana Vaníková、Michal Hocek

  DOI：10.1002/anie.201402370

  日期：2014.6.23

  5‐[(2‐Nitrobenzyl)oxymethyl]‐2′‐deoxyuridine 5′‐O‐triphosphate was used for polymerase (primer extension or PCR) synthesis of photocaged DNA that is resistant to the cleavage by restriction endonucleases. Photodeprotection of the caged DNA released 5‐hydroxymethyluracil‐modified nucleic acids, which were fully recognized and cleaved by restriction enzymes.

  5-（（2-硝基苄基）氧基甲基] -2 -′-脱氧尿苷5′- O-三磷酸酯用于聚合酶（引物延伸或PCR）合成的光笼DNA，该DNA对限制性核酸内切酶具有抗性。笼中DNA的光脱保护释放了5-羟甲基尿嘧啶修饰的核酸，这些核酸被限制酶完全识别和切割。
• PHOTOCLEAVABLE LABELED NUCLEOTIDES AND NUCLEOSIDES AND METHODS FOR THEIR USE IN DNA SEQUENCING
  申请人：Wu Weidong

  公开号：US20090081686A1

  公开（公告）日：2009-03-26

  Provided are novel nucleotides, nucleoside, and their derivatives described herein, that can be used in DNA sequencing technology and other types of DNA analysis. In one embodiment, the nucleotide or nucleoside with an unprotected 3′-OH group is derivatized at the nucleobase to include a fluorescent dye attached via a linker to a photocleavable terminating group. The photocleavable-fluorescent group is designed to terminate DNA synthesis as well as be cleaved so that DNA oligomers can be sequenced efficiently in a parallel format. The design of such rapidly cleavable fluorescent groups on nucleotides and nucleosides can enhance the speed and accuracy of sequencing of large oligomers of DNA in parallel, to allow rapid whole genome sequencing, and the identification of polymorphisms and other valuable genetic information, as well as allowing further manipulation and analysis of nucleic acid molecules in their native state following cleavage of the fluorescent group.

  本文介绍了一些新型的核苷酸、核苷和它们的衍生物，可以用于DNA测序技术和其他类型的DNA分析。在一个实施例中，带有未保护的3'-OH基团的核苷酸或核苷在核碱基处衍生化，包括通过连接剂连接的荧光染料和光解终止基团。光解荧光基团旨在终止DNA合成，同时被裂解，以便在并行格式中高效地测序DNA寡聚物。在核苷酸和核苷上设计这种快速可裂解的荧光基团可以增强大型DNA寡聚物并行测序的速度和准确性，以实现快速的全基因组测序，并识别多态性和其他有价值的遗传信息，同时在裂解荧光基团后允许进一步操作和分析核酸分子的自然状态。
• Photocleavable labeled nucleotides and nucleosides and methods for their use in DNA sequencing
  申请人：Wu Weidong

  公开号：US20080132692A1

  公开（公告）日：2008-06-05

  Provided are novel nucleotides, nucleoside, and their derivatives described herein, that can be used in DNA sequencing technology and other types of DNA analysis. In one embodiment, the nucleotide or nucleoside with an unprotected 3′-OH group is derivatized at the nucleobase to include a fluorescent dye attached via a linker to a photocleavable terminating group. The photocleavable-fluorescent group is designed to terminate DNA synthesis as well as be cleaved so that DNA oligomers can be sequenced efficiently in a parallel format. The design of such rapidly cleavable fluorescent groups on nucleotides and nucleosides can enhance the speed and accuracy of sequencing of large oligomers of DNA in parallel, to allow rapid whole genome sequencing, and the identification of polymorphisms and other valuable genetic information, as well as allowing further manipulation and analysis of nucleic acid molecules in their native state following cleavage of the fluorescent group.

  本文提供了新型核苷酸、核苷和它们的衍生物，可以用于DNA测序技术和其他类型的DNA分析。在一种实施方式中，核苷酸或核苷的3'-OH基团未保护，通过连接剂连接到光致解终止基团的荧光染料，衍生化到核碱基上。光致解荧光基团被设计成能够终止DNA合成，并被裂解，以便在并行格式下高效地测序DNA寡聚物。在核苷酸和核苷上设计这种快速可裂解的荧光基团，可以增强大型DNA寡聚物并行测序的速度和准确性，以实现快速全基因组测序和多态性等有价值的遗传信息的识别，同时在裂解荧光基团后，还可以对核酸分子进行进一步的操作和分析。
• 3'OH-UNBLOCKED, NUCLEOTIDES AND NUCLEOSIDES BASE MODIFIED WITH LABELS AND PHOTOCLEAVABLE, TERMINATING GROUPS AND METHODS FOR THEIR USE IN DNA SEQUENCING
  申请人：Wu Weidong

  公开号：US20110287427A1

  公开（公告）日：2011-11-24

  Provided are novel nucleotides, nucleoside, and their derivatives described herein, that can be used in DNA sequencing technology and other types of DNA analysis. In one embodiment, the nucleotide or nucleoside with an unprotected 3′-OH group is derivatized at the nucleobase to include a fluorescent dye attached via a linker to a photocleavable terminating group. The photocleavable-fluorescent group is designed to terminate DNA synthesis as well as be cleaved so that DNA oligomers can be sequenced efficiently in a parallel format. The design of such rapidly cleavable fluorescent groups on nucleotides and nucleosides can enhance the speed and accuracy of sequencing of large oligomers of DNA in parallel, to allow rapid whole genome sequencing, and the identification of polymorphisms and other valuable genetic information, as well as allowing further manipulation and analysis of nucleic acid molecules in their native state following cleavage of the fluorescent group.

  本文介绍了新型核苷酸、核苷和其衍生物，可用于DNA测序技术和其他类型的DNA分析。在一种实施例中，具有未保护的3'-OH基团的核苷酸或核苷在核碱基上被衍生化，包括通过连接剂连接的荧光染料附着的光解终止基团。光解荧光基团旨在终止DNA合成，并被裂解，以便在并行格式中高效测序DNA寡聚体。在核苷酸和核苷上设计这种快速裂解的荧光基团可以提高大型DNA寡聚体并行测序的速度和准确性，从而实现快速全基因组测序，并识别多态性和其他有价值的遗传信息，同时允许在裂解荧光基团后对核酸分子进行进一步的操作和分析。