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化学进展 2020, Vol. 32 Issue (11): 1634-1650 DOI: 10.7536/PC200606 前一篇   后一篇

• •

DNA中醛基嘧啶的化学检测

周倩1,2, 李娜2, 李坤2, 余孝其1,2,**()   

  1. 1. 西华大学化学系 成都 610039
    2. 四川大学化学学院 绿色化学与技术教育部重点实验室 成都 610064
  • 收稿日期:2020-06-02 修回日期:2020-06-18 出版日期:2020-11-24 发布日期:2020-09-01
  • 通讯作者: 余孝其
  • 作者简介:

    余孝其

    在生物荧光探针和荧光成像方面开展了系统的研究工作,开发了修饰核酸检测以及线粒体、溶酶体、细胞膜等细胞器靶向的分子荧光探针,并实现了对细胞内活性氧和活性硫等气体信号分子的选择性成像和定量检测。

    ** Corresponding author e-mail:
  • 基金资助:
    *国家自然科学基金项目(21877082)

Detection of 5-Formylpyrimidines in DNA Based on Chemoselective Labeling

Qian Zhou1,2, Na Li2, Kun Li2, Xiaoqi Yu1,2,**()   

  1. 1. Department of Chemistry, Xihua University, Chengdu 610039, China
    2. Laboratory of Green Chemistry and Technology(Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, China
  • Received:2020-06-02 Revised:2020-06-18 Online:2020-11-24 Published:2020-09-01
  • Contact: Xiaoqi Yu
  • Supported by:
    the National Natural Science Foundation of China(21877082)

基因组DNA除A、G、T、C四大经典碱基外,还存在上百种稀有碱基。其中,醛基嘧啶(5-醛基胞嘧啶和5-醛基尿嘧啶)是DNA中天然存在的嘧啶类修饰碱基,在哺乳动物细胞中广泛分布。5-醛基胞嘧啶除参与DNA主动去甲基化过程外,还具备独立的表观遗传功能;而5-醛基尿嘧啶通常被认为是一种基因毒性很高的DNA氧化损伤。根据醛基嘧啶的特征结构,有针对性地开发准确、灵敏和简便的检测方法,从全基因组范围内对他们进行定性、定量和区域定位,是进一步明确这类碱基修饰物调控机制的基础和前提。本文从选择性化学标记的角度总结了近年来醛基嘧啶检测方法的研究进展。

In addition to the four canonical nucleobases of A, G, T and C, hundreds of chemical modifications have been identified in genome DNA. Among them, 5-formylpyrimidines, including 5-formylcytosine(5fC) and 5-formyluracil(5fU), are naturally occurring pyrimidine-covalent-modifications and are widely distributed in mammalian cells. Emerging evidence indicates that 5fC not only serves as a key intermediate in active DNA demethylation but also carry independent epigenetic significance; while 5fU was always considered to be an oxidative DNA lesion with high genotoxicity. In order to further understand their regulatory functions, it is necessary to develop accurate, sensitive and facile methods for qualitative, quantitative, and localized detection of 5-formylpyrimidines in the whole genome. In this review, we summarized the recent progress in detecting 5-formylpyrimidines from the perspective of selective chemical labeling.

Contents

1 Introduction

1.1 DNA methylation and demethylation

1.2 5-Formylcytosine and 5-formyluracil

1.3 Detection methods of 5-formylpyrimidines

2 Detection of 5-formyluracil based on chemoselective modification

2.1 Fluorescent labelling of 5-formyluracil

2.2 Enrichment and sequencing of 5-formyluracil

3 Detection of 5-formylcytosine based on chemoselective modification

3.1 Fluorescent labelling of 5-formylcytosine

3.2 Enrichment and sequencing of 5-formylcytosine

4 Conclusion and outlook

()
图1 DNA甲基化和去甲基化过程[4]
Fig.1 DNA methylation and demethylation[4]
图2 邻氨基苯硫酚衍生物1荧光标记DNA中的5fU[69]
Fig.2 Fluorescent labeling of 5fU in DNA with 2-aminothiophenol derivative 1[69]
图3 邻苯二胺衍生物荧光衍生5fU核苷[70]
Fig.3 Fluorescent derivatization of 5fU with o-phenylenediamine derivatives[70]
图4 具有富集功能的邻苯二胺衍生物Biotin-lys(3)荧光标记DNA中的5fU[71]
Fig.4 Fluorescent labelling and enrichment of 5fU with Biotin-lys(3)[71]
图5 肼衍生物NBDH(4)比色法、荧光法检测DNA中的5fU[72]
Fig.5 Detection of 5fU in DNA with NBDH(4) by colorimetry and fluorescence[72]
图6 肼衍生物5标记DNA中的5fU及PAGE定量分析[73]
Fig.6 Detection of 5fU in DNA with hydrazine derivative 5 by PAGE and fluorescence[73]. Copyright 2018, Royal Society of Chemistry.
图7 羟胺衍生物6同时标记DNA中的5fC、5fU及AP位点(反应条件:NaOAc缓冲液,pH=5.0,37 ℃,5 h)[74]
Fig.7 Simultaneously labelling 5fU, 5fC and AP sites in DNA with hydroxylamine derivative 6(Conditions: NaOAc buffer, pH=5.0, 37 ℃, 5 h)[74]
图8 吲哚衍生物7、8及9对DNA/RNA中5fU的荧光标记[75]
Fig.8 Fluorescent labelling 5fU in DNA/RNA with Indole derivatives 7, 8 and 9[75]
图9 Wittig试剂10对DNA中5fU的荧光标记[76]
Fig.9 Fluorescent labelling 5fU in DNA with Wittig reagent 10[76]. Copyright 2018, Royal Society of Chemistry.
图10 具有富集功能的氨基衍生物11、12、13及选择性标记5fU的反应条件[77]
Fig.10 Selective enrichment of 5fU with amino derivatives 11, 12 and 13[77]. Copyright 2015, American Chemical Society.
图11 活性亚甲基试剂azi-BIAN(14)对5fU的亲和性富集测序[48]
Fig.11 Selective 5fU labeling and genome-wide mapping with azi-BIAN(14)[48]
图12 5fU的错配性质及其在单碱基分辨率测序中的应用[78]
Fig.12 5fU:G mispairing and its application in single-base resolution sequencing[78]
图13 烷基伯胺15、16荧光标记DNA中的5fC[80]
Fig.13 Fluorescent labelling 5fC in DNA with primary amines 15 and 16[80]
图14 羟胺衍生物荧光标记DNA中的5fC[74, 81~83]
Fig.14 Fluorescent labelling 5fC in DNA with hydroxylamine derivatives[74, 81~83]
图15 羟胺衍生物17基于“CCP-FRET”策略检测5fC[84]
Fig.15 Principle of the CCP-FRET-based assay to detect 5fC with hydroxylamine derivatives 17[84]. Copyright 2019, American Chemical Society.
图16 吖啶修饰的肼衍生物HMA(20) 标记DNA中的5fC及其功能调控[85]
Fig.16 Acridine-modified hydrazine derivative(HMA, 20) label 5fC in DNA and its functional regulation[85]. Copyright 2013, Royal Society of Chemistry.
图17 芘修饰的肼衍生物区分DNA中对称5fCpG与非对称5fCpG[86]
Fig.17 Pyrene-modified hydrazine derivatives distinguish symmetric from asymmetric 5fCpG sites in dsDNA[86]. Copyright 2014, John Wiley and Sons.
图18 肼衍生物5选择性荧光标记DNA中的5fC[73]
Fig.18 Chemoselective fluorescent labelling 5fC in DNA with hydrazine derivative 5[73]
图19 吲哚衍生物7对DNA/RNA中5fC的荧光标记[75]
Fig.19 Fluorescent labelling 5fC in DNA/RNA with indole derivatives 7[75]
图20 Wittig试剂YC-CN(24)对5fC的选择性荧光标记[87]
Fig.20 Selective fluorescent labelling of 5fC with Wittig reagent YC-CN(24)[87]. Copyright 2019, American Chemical Society.
图21 兼具富集及单碱基分辨率测序功能的1,3-茚满二酮衍生物[88]
Fig.21 Enrichment and single-base resolution sequencing of 5fC with 1,3-indanedione derivative[88]
图22 单细胞、单碱基分辨率水平的5fC全基因组测序技术(CLEVER-seq)[90]
Fig.22 Single-cell 5fC landscapes of mammalian early embryos and ESCs at single-base resolution[90]
图23 兼具荧光定量及单碱基分辨率测序功能的活性亚甲基化合物CBAN(27)[91]
Fig.23 Fluorescent labelling and single-base resolution sequencing of 5fC with CBAN(27)[91]
图24 兼具qPCR定量及单碱基分辨率测序功能的活性亚甲基化合物azi-BP(28)[92]
Fig.24 Gene specific-loci quantitative and single-base resolution analysis of 5fC by qPCR with azi-BP(28)[92]
图25 具有富集功能的5fC捕获剂11及其可剪切变体29[33, 93]
Fig.25 Enrichment of 5fC with aldehyde reactive probe 11 and its cleavable version 29[33, 93]
图26 基于NaBH4还原的富集测序技术(fC-Seal)[94]
Fig.26 Enrichment and sequencing of 5fC based on NaBH4 reduction[94]
图27 亚硫酸氢盐辅助的单碱基分辨率测序[95]
Fig.27 Bisulfite sequencing of 5fC at single-base resolution[95]
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摘要

DNA中醛基嘧啶的化学检测