tert-butyl 3-(2-(benzyloxy)-2-oxoethyl)-5-methyl-2,6-dioxo-2,3-dihydropyrimidine-1(6H)-carboxylate | 1354832-37-3

• 分子结构分类: 有机化合物 - 有机酸及其衍生物 - 羧酸及其衍生物
• 英文名称: tert-butyl 3-(2-(benzyloxy)-2-oxoethyl)-5-methyl-2,6-dioxo-2,3-dihydropyrimidine-1(6H)-carboxylate
• 英文别名: benzyl N3-Boc-thymin-1-ylacetate；Tert-butyl 5-methyl-2,6-dioxo-3-(2-oxo-2-phenylmethoxyethyl)pyrimidine-1-carboxylate
• CAS: 1354832-37-3
• 化学式: C₁₉H₂₂N₂O₆
• 分子量: 374.393
• InChiKey: OFSKORLYDQMSKR-UHFFFAOYSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  2.3
• 重原子数：
  27
• 可旋转键数：
  7
• 环数：
  2.0
• sp3杂化的碳原子比例：
  0.37
• 拓扑面积：
  93.2
• 氢给体数：
  0
• 氢受体数：
  6

反应信息

• 作为反应物：
  描述：

  tert-butyl 3-(2-(benzyloxy)-2-oxoethyl)-5-methyl-2,6-dioxo-2,3-dihydropyrimidine-1(6H)-carboxylate 在 四氢呋喃 、 aluminum oxide 作用下， 反应 5.0h， 以43.5%的产率得到(9H-fluoren-9-yl)methyl (hydroxymethyl)carbamate
  参考文献：
  名称：

  SPECIFIC SYNTHETIC CHIMERIC XENONUCLEIC ACID GUIDE RNA; s(XNA-gRNA) FOR ENHANCING CRISPR MEDIATED GENOME EDITING EFFICIENCY

  摘要：

  该发明提供了xenonucleic acids和合成嵌合xenonucleic acid guide RNA；s(XNA-gRNA)，用于增强crispr介导的基因组编辑效率。该发明还提供了诱导CRISPR/Cas基因编辑/调控（例如基因组编辑或基因表达）靶向核酸（例如靶向DNA或靶向RNA）在细胞中的方法和组合物。这些方法包括使用已经经过化学修饰的xeno核酸的单导RNA（sgRNAs），这些核酸增强了原代细胞中靶向核酸的基因调控，用于体外治疗或用于体内治疗中的受体细胞。此外，本文提供了通过向受体注射已经经过化学修饰的xeno核酸的足够数量的sgRNA来预防或治疗受体的遗传疾病的方法，以纠正与该遗传疾病相关的靶基因的突变。

  公开号：

  US20190330621A1
• 作为产物：
  描述：

  二碳酸二叔丁酯 、 benzyl 1,2,3,4-tetrahydro-5-methyl-2,4-dioxopyrimidine-1-acetate 在 4-二甲氨基吡啶 作用下， 以 四氢呋喃 为溶剂， 反应 18.5h， 以95%的产率得到tert-butyl 3-(2-(benzyloxy)-2-oxoethyl)-5-methyl-2,6-dioxo-2,3-dihydropyrimidine-1(6H)-carboxylate
  参考文献：
  名称：

  Fmoc / Boc保护的2,6-二氨基嘌呤，2-氨基嘌呤和胸腺嘧啶的PNA单体的合成和低聚†

  摘要：

  已经开发了基于Fmoc的PNA（肽核酸）寡聚化的Boc保护基策略，用于 胸腺嘧啶， 2,6-二氨基嘌呤（DAP）和2-氨基嘌呤（2AP）。单体可与标准Fmoc PNA单体互换使用。在DAP单体掺入PNA，并且发现其选择性结合Ť（Δ Ť米在互补DNA链≥6℃）。的2AP单体显示出极好的区分Ť（Δ Ť米≥12℃）比其他的核碱基。2AP还充当PNA：DNA双链体的荧光探针，并显示依赖于相反碱基的荧光猝灭。

  DOI：

  10.1039/c1ob06582c

文献信息

• DNA mutation detection employing enrichment of mutant polynucleotide sequences and minimally invasive sampling
  申请人：Powell Michael J

  公开号：US11208689B2

  公开（公告）日：2021-12-28

  The invention relates to a method for enriching a target polynucleotide sequence containing a genetic variation said method comprising: (a) providing two primers targeted to said target polynucleotide sequence; (b) providing a target specific xenonucleic acid clamp oligomer specific for a wildtype polynucleotide sequence; (c) generating multiple amplicons using PCR under specific temperature cycling conditions; and (d) detecting said amplicons. We introduce a novel molecule, Xenonucleic Acid (XNA) for the NGS library preparation. XNA is able to selectively suppress amplification of DNA with wild type alleles and amplify DNA containing mutant alleles. Mutants with low allelic frequency will be easily detectable without deep sequencing after enrichment by adding XNA in multiplex PCR. The 17 actionable mutants related to lung or colorectal cancer diseases at different variant allelic frequency (VAF) % were investigated. Clinical sensitivity is significantly improved with XNA in various types of samples.

  本发明涉及一种富集含有遗传变异的目标多核苷酸序列的方法，所述方法包括：(a) 提供针对所述目标多核苷酸序列的两个引物；(b) 提供针对野生型多核苷酸序列的目标特异性异种核酸钳夹寡聚体；(c) 在特定温度循环条件下使用 PCR 生成多个扩增子；以及 (d) 检测所述扩增子。我们为 NGS 文库制备引入了一种新型分子--Xenonucleic Acid（XNA）。XNA 能够选择性地抑制野生型等位基因 DNA 的扩增，而扩增含有突变等位基因的 DNA。在多重 PCR 中加入 XNA 进行富集后，等位基因频率较低的突变体无需深度测序即可轻松检测到。我们研究了与肺癌或结直肠癌疾病相关的 17 种可操作突变体，其变异等位基因频率（VAF）各不相同。在各种类型的样本中，使用 XNA 可明显提高临床灵敏度。
• DNA MUTATION DETECTION EMPLOYING ENRICHMENT OF MUTANT POLYNUCLEOTIDE SEQUENCES AND MINIMALLY INVASIVE SAMPLING
  申请人：Powell Michael J

  公开号：US20190330692A1

  公开（公告）日：2019-10-31

  The invention relates to a method for enriching a target polynucleotide sequence containing a genetic variation said method comprising: (a) providing two primers targeted to said target polynucleotide sequence; (b) providing a target specific xenonucleic acid clamp oligomer specific for a wildtype polynucleotide sequence; (c) generating multiple amplicons using PCR under specific temperature cycling conditions; and (d) detecting said amplicons. We introduce a novel molecule, Xenonucleic Acid (XNA) for the NGS library preparation. XNA is able to selectively suppress amplification of DNA with wild type alleles and amplify DNA containing mutant alleles. Mutants with low allelic frequency will be easily detectable without deep sequencing after enrichment by adding XNA in multiplex PCR. The 17 actionable mutants related to lung or colorectal cancer diseases at different variant allelic frequency (VAF)% were investigated. Clinical sensitivity is significantly improved with XNA in various types of samples.
• XENONUCLEIC ACID-MEDIATED MULTIPLEX QPCR CLAMPING TECHNOLOGY FOR LUNG CANCER MUTATION DETECTION
  申请人：Sha Michael Y

  公开号：US20220025453A1

  公开（公告）日：2022-01-27

  The invention provides a multiplex method for enriching a plurality of target polynucleotide sequences containing genetic mutations associated with lung cancer comprising: (a) providing a biological sample; (b) isolating DNA from said sample; said DNA including said plurality of target polynucleotide sequences containing genetic mutations; (c) providing a plurality of primer probes targeted to said target polynucleotide sequences said primer probes allowing formation of a PCR product; (d) providing a plurality of target specific xenonucleic acid clamps oligomer probes specific for wildtype polynucleotide sequences; so that during the qPCR process only mutant templates are amplified: (e) admixing the plurality of primer probes and the plurality of xenonucleic clamping probes with the target nucleic acid sample; (f) performing a PCR amplification process in reaction solution under hybridization conditions thereby generating multiple amplicons; and (g) detecting said amplicons and wherein said xenonucleic acid clamps have aza-aza, thio-aza and oxy-aza chemical functionality.
• NOVEL METHOD OF COMBINED MOLECULAR CLAMPING AND ALLELE SPECIFIC qPCR TECHNOLOGY FOR KRAS G12C MUTATION DETECTION
  申请人：Sun Qing

  公开号：US20220025437A1

  公开（公告）日：2022-01-27

  The invention provides a method for detecting KRAS mutations at one or more of codons, said method comprising the steps of: (a) extracting DNA from a biological sample; (b) assaying the DNA via PCR for KRAS mutations at one or more of codons with at least one set of oligonucleotides, wherein the at least one set of oligonucleotides comprises an allele specific forward primer, a reverse primer, a probe and a xenonucleic acid clamp to block amplification of wild type DNA. The xenonucleic acid clamps have aza-aza, thio-aza and oxy-aza chemical functionality.
• SPECIFIC SYNTHETIC CHIMERIC XENONUCLEIC ACID GUIDE RNA; s(XNA-gRNA) FOR ENHANCING CRISPR MEDIATED GENOME EDITING EFFICIENCY
  申请人：Powell Michael J

  公开号：US20190330621A1

  公开（公告）日：2019-10-31

  The invention provides xenonucleic acids and synthetic chimeric xenonucleic acid guide RNA; s(XNA-gRNA) for enhancing crispr mediated genome editing efficiency. The invention also provides methods and compositions for inducing CRISPR/Cas-based gene editing/regulation (e.g., genome editing or gene expression) of a target nucleic acid (e.g., target DNA or target RNA) in a cell. The methods include using single guide RNAs (sgRNAs) that have been chemically modified with xeno nucleic acids which enhance gene regulation of the target nucleic acid in a primary cell for use in ex vivo therapy or in a cell in a subject for use in in vivo therapy. Additionally, provided herein are methods for preventing or treating a genetic disease in a subject by administering a sufficient amount of a sgRNA that has been chemically modified with xeno nucleic acids to correct a mutation in a target gene associated with the genetic disease.

  该发明提供了xenonucleic acids和合成嵌合xenonucleic acid guide RNA；s(XNA-gRNA)，用于增强crispr介导的基因组编辑效率。该发明还提供了诱导CRISPR/Cas基因编辑/调控（例如基因组编辑或基因表达）靶向核酸（例如靶向DNA或靶向RNA）在细胞中的方法和组合物。这些方法包括使用已经经过化学修饰的xeno核酸的单导RNA（sgRNAs），这些核酸增强了原代细胞中靶向核酸的基因调控，用于体外治疗或用于体内治疗中的受体细胞。此外，本文提供了通过向受体注射已经经过化学修饰的xeno核酸的足够数量的sgRNA来预防或治疗受体的遗传疾病的方法，以纠正与该遗传疾病相关的靶基因的突变。