Suppr超能文献

由DNA甲基转移酶翻转出的胸腺嘧啶残基的化学展示。

Chemical display of thymine residues flipped out by DNA methyltransferases.

作者信息

Serva S, Weinhold E, Roberts R J, Klimasauskas S

机构信息

Institute of Biotechnology, Laboratory of Biological DNA Modification, Graiciuno 8, LT-2028 Vilnius, Lithuania.

出版信息

Nucleic Acids Res. 1998 Aug 1;26(15):3473-9. doi: 10.1093/nar/26.15.3473.

DOI:10.1093/nar/26.15.3473
PMID:9671807
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC147733/
Abstract

The DNA cytosine-C5 methyltransferase M. Hha I flips its target base out of the DNA helix during interaction with the substrate sequence GCGC. Binary and ternary complexes between M. Hha I and hemimethylated DNA duplexes were used to examine the suitability of four chemical methods to detect flipped-out bases in protein-DNA complexes. These methods probe the structural peculiarities of pyrimidine bases in DNA. We find that in cases when the target cytosine is replaced with thymine (GTGC), KMnO4proved an efficient probe for positive display of flipped-out thymines. The generality of this procedure was further verified by examining a DNA adenine-N6 methyltransferase, M. Taq I, in which case an enhanced reactivity of thymine replacing the target adenine (TCGT) in the recognition sequence TCGA was also observed. Our results support the proposed base-flipping mechanism for adenine methyltransferases, and offer a convenient laboratory tool for detection of flipped-out thymines in protein-DNA complexes.

摘要

DNA胞嘧啶 - C5甲基转移酶Hha I在与底物序列GCGC相互作用时，会将其目标碱基翻转出DNA螺旋。利用Hha I与半甲基化DNA双链体之间的二元和三元复合物，研究了四种化学方法检测蛋白质 - DNA复合物中翻转碱基的适用性。这些方法探测DNA中嘧啶碱基的结构特性。我们发现，当目标胞嘧啶被胸腺嘧啶取代（GTGC）时，高锰酸钾被证明是一种有效的探针，可用于阳性显示翻转出的胸腺嘧啶。通过研究DNA腺嘌呤 - N6甲基转移酶Taq I进一步验证了该方法的通用性，在这种情况下，还观察到在识别序列TCGA中，胸腺嘧啶取代目标腺嘌呤（TCGT）时反应性增强。我们的结果支持所提出的腺嘌呤甲基转移酶的碱基翻转机制，并为检测蛋白质 - DNA复合物中翻转出的胸腺嘧啶提供了一种便捷的实验室工具。

相似文献

1
Chemical display of thymine residues flipped out by DNA methyltransferases.
Nucleic Acids Res. 1998 Aug 1;26(15):3473-9. doi: 10.1093/nar/26.15.3473.
2
Chemical mapping of cytosines enzymatically flipped out of the DNA helix.
Nucleic Acids Res. 2008 Jun;36(10):e57. doi: 10.1093/nar/gkn200. Epub 2008 May 1.
3
2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases.
Nucleic Acids Res. 1998 Feb 15;26(4):1076-83. doi: 10.1093/nar/26.4.1076.
4
M.HhaI binds tightly to substrates containing mismatches at the target base.
Nucleic Acids Res. 1995 Apr 25;23(8):1388-95. doi: 10.1093/nar/23.8.1388.
5
The cytosine N4-methyltransferase M.PvuII also modifies adenine residues.
Biol Chem. 2001 Apr;382(4):707-10. doi: 10.1515/BC.2001.084.
6
Structure and function of DNA methyltransferases.
Annu Rev Biophys Biomol Struct. 1995;24:293-318. doi: 10.1146/annurev.bb.24.060195.001453.
7
Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
Nucleic Acids Res. 1997 Jul 15;25(14):2702-15. doi: 10.1093/nar/25.14.2702.
8
On the substrate specificity of DNA methyltransferases. adenine-N6 DNA methyltransferases also modify cytosine residues at position N4.
J Biol Chem. 1999 Jul 9;274(28):19538-44. doi: 10.1074/jbc.274.28.19538.
9
Identification of the binding site for the extrahelical target base in N6-adenine DNA methyltransferases by photo-cross-linking with duplex oligodeoxyribonucleotides containing 5-iodouracil at the target position.
J Biol Chem. 1999 May 21;274(21):15066-72. doi: 10.1074/jbc.274.21.15066.
10
Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution.
EMBO J. 1998 Jan 2;17(1):317-24. doi: 10.1093/emboj/17.1.317.

引用本文的文献

1
Small molecule-based regulation of gene expression in human astrocytes switching on and off the G-quadruplex control systems.
J Biol Chem. 2025 Jan;301(1):108040. doi: 10.1016/j.jbc.2024.108040. Epub 2024 Nov 29.
2
High-precision mapping reveals rare N-deoxyadenosine methylation in the mammalian genome.
Cell Discov. 2022 Dec 27;8(1):138. doi: 10.1038/s41421-022-00484-1.
3
DNA base flipping analytical pipeline.
Biol Methods Protoc. 2017 Aug 11;2(1):bpx010. doi: 10.1093/biomethods/bpx010. eCollection 2017 Jan.
4
Chemical display of pyrimidine bases flipped out by modification-dependent restriction endonucleases of MspJI and PvuRts1I families.
PLoS One. 2014 Dec 8;9(12):e114580. doi: 10.1371/journal.pone.0114580. eCollection 2014.
5
Direct observation of cytosine flipping and covalent catalysis in a DNA methyltransferase.
Nucleic Acids Res. 2011 May;39(9):3771-80. doi: 10.1093/nar/gkq1329. Epub 2011 Jan 17.
6
Base flipping in tn10 transposition: an active flip and capture mechanism.
PLoS One. 2009 Jul 10;4(7):e6201. doi: 10.1371/journal.pone.0006201.
7
Chemical mapping of cytosines enzymatically flipped out of the DNA helix.
Nucleic Acids Res. 2008 Jun;36(10):e57. doi: 10.1093/nar/gkn200. Epub 2008 May 1.
8
Base-flipping dynamics in a DNA hairpin processing reaction.
Nucleic Acids Res. 2007;35(8):2584-95. doi: 10.1093/nar/gkm186. Epub 2007 Apr 4.
9
Molecular architecture of a eukaryotic DNA replication terminus-terminator protein complex.
Mol Cell Biol. 2006 Nov;26(21):8061-74. doi: 10.1128/MCB.01102-06. Epub 2006 Aug 28.
10
KpnI restriction endonuclease and methyltransferase exhibit contrasting mode of sequence recognition.
Nucleic Acids Res. 2004 Jun 10;32(10):3148-55. doi: 10.1093/nar/gkh638. Print 2004.

本文引用的文献

1
2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases.
Nucleic Acids Res. 1998 Feb 15;26(4):1076-83. doi: 10.1093/nar/26.4.1076.
2
Direct real time observation of base flipping by the EcoRI DNA methyltransferase.
J Biol Chem. 1998 Jan 23;273(4):2368-73. doi: 10.1074/jbc.273.4.2368.
3
Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution.
EMBO J. 1998 Jan 2;17(1):317-24. doi: 10.1093/emboj/17.1.317.
4
The role of base flipping in damage recognition and catalysis by T4 endonuclease V.
J Biol Chem. 1997 Oct 24;272(43):27210-7. doi: 10.1074/jbc.272.43.27210.
5
Role of TrfA and DnaA proteins in origin opening during initiation of DNA replication of the broad host range plasmid RK2.
J Biol Chem. 1997 Aug 8;272(32):20173-8. doi: 10.1074/jbc.272.32.20173.
6
Potassium permanganate and tetraethylammonium chloride are a safe and effective substitute for osmium tetroxide in solid-phase fluorescent chemical cleavage of mismatch.
Nucleic Acids Res. 1997 Aug 15;25(16):3377-8. doi: 10.1093/nar/25.16.3377.
7
Footprint analysis of the bsp RI DNA methyltransferase-DNA interaction.
Nucleic Acids Res. 1997 Jul 15;25(14):2841-6. doi: 10.1093/nar/25.14.2841.
8
Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
Nucleic Acids Res. 1997 Jul 15;25(14):2702-15. doi: 10.1093/nar/25.14.2702.
9
Solution structure as a function of pH of two central mismatches, C . T and C . C, in the 29 to 39 K-ras gene sequence, by nuclear magnetic resonance and molecular dynamics.
J Mol Biol. 1997 May 2;268(2):331-47. doi: 10.1006/jmbi.1997.0975.
10
DNA-repair enzymes.
Curr Opin Struct Biol. 1997 Feb;7(1):103-9. doi: 10.1016/s0959-440x(97)80013-9.

文献AI研究员

20分钟写一篇综述，助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型，支持多种主流文档格式。

立即体验