脲氨基酸氧羰基肼-d-生物素 | 139585-03-8

• 分子结构分类: 有机化合物 - 有机杂环化合物 - 生物素及其衍生物
• 中文名称: 脲氨基酸氧羰基肼-d-生物素
• 英文名称: N-(aminooxyacetyl)-N'-(D-biotinoyl)hydrazine
• 英文别名: N'-aminoxymethylcarbonylhydrazino D-biotin；O-(biotinylcarbazoylmethyl)hydroxylamine；aldehyde reactive probe；5-[(3aS,4S,6aR)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]-N'-(2-aminooxyacetyl)pentanehydrazide
• CAS: 139585-03-8
• 化学式: C₁₂H₂₁N₅O₄S
• 分子量: 331.396
• InChiKey: KYHUBFIOWQTECH-LAEOZQHASA-N

物化性质

• 沸点：
  772.9±55.0 °C(Predicted)
• 密度：
  1.309±0.06 g/cm3(Predicted)

计算性质

• 辛醇/水分配系数(LogP)：
  -1.3
• 重原子数：
  22
• 可旋转键数：
  7
• 环数：
  2.0
• sp3杂化的碳原子比例：
  0.75
• 拓扑面积：
  160
• 氢给体数：
  5
• 氢受体数：
  6

反应信息

• 作为反应物：
  描述：

  、 脲氨基酸氧羰基肼-d-生物素 在 尿素 作用下， 生成
  参考文献：
  名称：

  Chemoenzymatic Probes for Detecting and Imaging Fucose-α(1-2)-galactose Glycan Biomarkers

  摘要：

  The disaccharide motif fucose-alpha(1-2)-galactose (Fuc alpha(1-2)Gal) is involved in many important physiological processes, such as learning and memory, inflammation, asthma, and tumorigenesis. However, the size and structural complexity of Fuc alpha(1-2) Gal-containing glycans have posed a significant challenge to their detection. We report a new chemoenzymatic strategy for the rapid, sensitive detection of Fuc alpha(1-2)Gal glycans. We demonstrate that the approach is highly selective for the Fuc alpha(1-2)Gal motif, detects a variety of complex glycans and glycoproteins, and can be used to profile the relative abundance of the motif on live cells, discriminating malignant from normal cells. This approach represents a new potential strategy for biomarker detection and expands the technologies available for understanding the roles of this important class of carbohydrates in physiology and disease.

  DOI：

  10.1021/ja211312u

文献信息

• Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
  作者：William A. Pastor、Utz J. Pape、Yun Huang、Hope R. Henderson、Ryan Lister、Myunggon Ko、Erin M. McLoughlin、Yevgeny Brudno、Sahasransu Mahapatra、Philipp Kapranov、Mamta Tahiliani、George Q. Daley、X. Shirley Liu、Joseph R. Ecker、Patrice M. Milos、Suneet Agarwal、Anjana Rao

  DOI：10.1038/nature10102

  日期：2011.5.19

  The modified DNA base 5-hydroxymethylcytosine (5hmC), sometimes called the sixth base, is present in the mammalian genome where it is generated by oxidation of 5-methylcytosine (5mC; the fifth base) by enzymes of the Tet family. Four papers in this issue, from the Helin, Zhang, Rao and Reik laboratories, respectively, report on the genome-wide distribution of Tet1 and/or 5hmC in mouse embryonic stem cells using the ChIP-seq technique. Links between Tet1 and transcription regulation — both activation and repression — are revealed. Anjana Rao and colleagues also describe two alternative methods with increased sensitivity for mapping single 5hmC bases. In the associated News & Views, Nathalie Véron and Antoine H. F. M. Peters discuss what these and other recent papers reveal about the role of Tet proteins in regulating DNA methylation and gene expression. 5-hydroxymethylcytosine (5hmC) is a modified base present at low levels in diverse cell types in mammals1,2,3,4,5. 5hmC is generated by the TET family of Fe(II) and 2-oxoglutarate-dependent enzymes through oxidation of 5-methylcytosine (5mC)1,2,4,5,6,7. 5hmC and TET proteins have been implicated in stem cell biology and cancer1,4,5,8,9, but information on the genome-wide distribution of 5hmC is limited. Here we describe two novel and specific approaches to profile the genomic localization of 5hmC. The first approach, termed GLIB (glucosylation, periodate oxidation, biotinylation) uses a combination of enzymatic and chemical steps to isolate DNA fragments containing as few as a single 5hmC. The second approach involves conversion of 5hmC to cytosine 5-methylenesulphonate (CMS) by treatment of genomic DNA with sodium bisulphite, followed by immunoprecipitation of CMS-containing DNA with a specific antiserum to CMS5. High-throughput sequencing of 5hmC-containing DNA from mouse embryonic stem (ES) cells showed strong enrichment within exons and near transcriptional start sites. 5hmC was especially enriched at the start sites of genes whose promoters bear dual histone 3 lysine 27 trimethylation (H3K27me3) and histone 3 lysine 4 trimethylation (H3K4me3) marks. Our results indicate that 5hmC has a probable role in transcriptional regulation, and suggest a model in which 5hmC contributes to the ‘poised’ chromatin signature found at developmentally-regulated genes in ES cells.

  经修饰的DNA碱基——5-羟甲基胞嘧啶(5hmC),有时被称为第六种碱基——存在于哺乳动物基因组中,它是由Ten结构的酶将第五种碱基5-甲基胞嘧啶(5mC)氧化而生成的。在最近的一期杂志中,来自Helin、Zhang、Rao和Reik实验室的四篇文章,分别报道了小鼠胚胎干细胞内Tet1和/或5hmC的全基因组分布,研究中使用的技术是染色质免疫沉淀-测序法(ChIP-seq)。文章揭示了Tet1与转录调控的关联——既包括活化也包括抑制,Anjana Rao与同事还提出了两种灵敏度更高的检测方法,用以对单碱基5hmC进行定位。在同期杂志的新闻与观点栏目中,Nathalie Véron和Antoine H. F. M. Peters对之前和这些文章一起发表的论文进行了讨论,论述了Tet蛋白在调控DNA甲基化和基因表达过程中所起的作用。5-羟甲基胞嘧啶(5hmC)是一种处于低水平的修饰碱基,在各类哺乳动物细胞中都有发现。5hmC是由TET家族的Fe(II)依赖型、2-氧戊二酸依赖型酶类通过氧化作用由5-甲基胞嘧啶(5mC)生成的。5hmC和TET蛋白已经被证明与干细胞生物学和癌症的发生具有关联,但关于5hmC全基因组分布的信息还不多。这里我们描述了两种全新且具有针对性的研究5hmC在基因组上位置的方法。第一种方法称为GLIB(葡糖基化,高碘酸盐氧化,生物素化),利用一系列酶法和化学手段,分离仅含少量5hmC的DNA短链。第二种方法是用亚硫酸氢盐处理基因组DNA,使其中的5hmC转化为胞嘧啶-5-亚甲砜(CMS),再利用特异性抗血清对含有CMS的DNA作免疫共沉淀。对含有5hmC的小鼠胚胎干细胞(ES)基因组进行高通量测序后我们发现,测序结果强烈富集于外显子位置和转录起始位点附近。在携带有组蛋白3赖氨酸27三甲基化(H3K27me3)和组蛋白3赖氨酸4三甲基化(H3K4me3)标记的基因上游启动子区,5hmC高度富集。我们的结果显示,5hmC很可能具有调控转录的功能,并提出了一种假设,即5hmC能够参与到ES干细胞中,赋予那些受发育调控的基因以"预备"的组蛋白特征。
• Analysis of M₁G-dR in DNA by Aldehyde Reactive Probe Labeling and Liquid Chromatography Tandem Mass Spectrometry
  作者：Yo-Chan Jeong、Ramiah Sangaiah、Jun Nakamura、Brian F. Pachkowski、Asoka Ranasinghe、Avram Gold、Louise M. Ball、James A. Swenberg

  DOI：10.1021/tx049853l

  日期：2005.1.1

  aldehydic form can result from loss of the adduct during analysis by its reaction with amines or proteins. We utilized the aldehyde reactive probe (ARP) to produce a stable ARP-M1G-deoxyribose (ARP-M1G-dR) conjugate to minimize adduct loss. This conjugate has increased the hydrophobicity that enhances separation of ARP-M1G-dR from unmodified DNA nucleosides by using solid phase extraction. In addition

  开发了一种测定嘧啶并[1,2-a]嘌呤-10（3H）one（M1G）的新方法。由于该病灶存在于闭环形式和开环醛形式之间的平衡中，因此混淆了分析M1G的先前方法。醛形式的检测灵敏度差可能是由于加合物在与胺或蛋白质的反应过程中分析过程中加合物的损失。我们利用醛反应探针（ARP）产生稳定的ARP-M1G-脱氧核糖（ARP-M1G-dR）共轭物，以最大程度地减少加合物损失。通过使用固相萃取，该结合物增加了疏水性，从而增强了ARP-M1G-dR从未修饰的DNA核苷中的分离。此外，通过[ARP-M1G-dR + H] +（635）的选择性反应监测（SRM）测量ARP-M1G-dR-> [M1G + H] +（188）跃迁相对于SRM对M1G-dR的测量将检测灵敏度提高了近一个数量级。为了进行准确的测量，使用了分析标准品（AS）DNA和内标（IS）DNA。从已在含有（15NH4）2SO4的最低盐培养基中
• Selective Chemical Labeling of Natural T Modifications in DNA
  作者：Robyn E. Hardisty、Fumiko Kawasaki、Aleksandr B. Sahakyan、Shankar Balasubramanian

  DOI：10.1021/jacs.5b03730

  日期：2015.7.29

  We present a chemical method to selectively tag and enrich thymine modifications, 5-formyluracil (5-fU) and 5-hydroxymethyluracil (5-hmU), found naturally in DNA. Inherent reactivity differences have enabled us to tag 5-fU chemoselectively over its C modification counterpart, 5-formylcytosine (5-fC). We rationalized the enhanced reactivity of 5-fU compared to 5-fC via ab initio quantum mechanical calculations

  我们提出了一种化学方法来选择性标记和丰富胸腺嘧啶修饰，5-甲酰尿嘧啶 (5-fU) 和 5-羟甲基尿嘧啶 (5-hmU)，天然存在于 DNA 中。固有的反应性差异使我们能够在其 C 修饰对应物 5-甲酰胞嘧啶 (5-fC) 上化学选择性地标记 5-fU。我们通过 ab initio 量子力学计算将 5-fU 与 5-fC 相比增强的反应性合理化。我们利用这种化学标记反应为从含有 5-fC 或未修饰的池中富集含有 5-fU 的 DNA 提供概念证明。我们进一步证明 5-hmU 可以被化学氧化为 5-fU，为 5-hmU 的富集提供了策略。这些方法将使基因组 DNA 中 5-fU 和 5-hmU 的映射成为可能，从而深入了解它们在生物学中的功能作用和动力学。
• New Role for an Old Probe:  Affinity Labeling of Oxylipid Protein Conjugates by <i>N</i>‘-Aminooxymethylcarbonylhydrazino <scp>d</scp>-biotin
  作者：Juan Chavez、Jianyong Wu、Bingnan Han、Woon-Gye Chung、Claudia S. Maier

  DOI：10.1021/ac0607257

  日期：2006.10.1

  carbonyl-modified proteins, namely, oxylipid peptide and protein conjugates formed by Michael addition-type conjugation reactions of alpha,beta-unsaturated aldehydic lipid peroxidation products with nucleophilic peptide side chains. This new application of an "old" probe, which has been used for the detection of abasic sites in DNA strands, introduces a biotin moiety into the oxylipid peptide conjugate

  自由基，亲电试剂和内源性反应中间体是在正常的生理过程中产生的，能够修饰DNA，脂质和蛋白质。但是，由反应性物种引起的蛋白质氧化修饰水平的升高与氧化应激介导的疾病，神经变性和衰老的病因和病理学有关。据报道，基于质谱的方法有助于羰基修饰蛋白的鉴定和表征。该方法使用N'-氨氧基甲基羰基肼基d-生物素，一种生物素化的羟胺衍生物，与氧化修饰的蛋白质中的醛/酮基形成肟衍生物。在本文中，该方法针对一类经羰基修饰的蛋白质进行了验证，即 脂质肽和蛋白质共轭物，是由具有亲核肽侧链的α，β-不饱和醛脂质过氧化产物的迈克尔加成型共轭反应形成的。“旧”探针的这种新应用已用于检测DNA链中的无碱基位点，将生物素部分引入了脂质肽结合物中。然后使用抗生物素蛋白亲和捕获使生物素修饰的脂质肽缀合物富集。所描述的方法代表了用于氧化肽和蛋白质的肼基衍生化方法的一种有吸引力的替代方法，因为可以省去bond键转化为化学上更稳定的肼键
• Palladium‐Catalyzed Oxidation of Glucose in Glycopeptides**
  作者：Niels R. M. Reintjens、Liubov Yakovlieva、Nittert Marinus、Johan Hekelaar、Francesca Nuti、Anna Maria Papini、Martin D. Witte、Adriaan J. Minnaard、Marthe T. C. Walvoort

  DOI：10.1002/ejoc.202200677

  日期：2022.7.7

  The development of selective labeling methods to investigate protein glycosylation is a current challenge in glycobiology. This work reports the Pd-catalyzed oxidation of glucosides in pure glucopeptides and tryptic digest mixtures by using a previously reported method to selectively oxidize the C3-position of unprotected carbohydrates with [(neocuproine)PdOAc]2OTf2 as catalyst. The obtained keto-group

  开发用于研究蛋白质糖基化的选择性标记方法是糖生物学的当前挑战。这项工作报告了 Pd 催化的葡萄糖苷在纯糖肽和胰蛋白酶消化混合物中的氧化，方法是使用先前报道的方法以 [(neocuproine)PdOAc] 2 OTf 2作为催化剂选择性氧化未保护碳水化合物的 C3 位。获得的酮基通过肟连接用生物素手柄进一步官能化。