转录因子使DNA弯曲的立体化学基础。
Stereochemical basis of DNA bending by transcription factors.
作者信息
Suzuki M, Yagi N
机构信息
MRC Laboratory of Molecular Biology, Cambridge, UK.
出版信息
Nucleic Acids Res. 1995 Jun 25;23(12):2083-91. doi: 10.1093/nar/23.12.2083.
Abstract
Superstructure-formation of DNA plays an important role in transcription regulation as well as in chromatin formation. To understand the stereochemical basis of DNA bending by proteins we analysed the structural characteristics of dinucleotide steps which occur at the site where DNA is bent upon binding a transcription factor. When DNA is considerably bent in a crystal structure the bending is not spread smoothly over a length, but the DNA is kinked at a pair of crucial steps which are highly rolled and untwisted. These rolled steps are spaced 6-10 bp apart and are predominantly occupied by pyrimidine-purine sequences. In association with another dinucleotide step at the centre, which combines 6 bp-spaced rolled steps towards the same side of the DNA, these produce two essentially different types of DNA bending.
摘要
DNA的超结构形成在转录调控以及染色质形成中起着重要作用。为了理解蛋白质使DNA弯曲的立体化学基础，我们分析了二核苷酸步的结构特征，这些二核苷酸步出现在DNA结合转录因子时发生弯曲的位点。当DNA在晶体结构中大幅弯曲时，弯曲并非在一段长度上平滑扩展，而是在一对高度卷曲且解旋的关键步处发生扭结。这些卷曲步相隔6 - 10个碱基对，且主要由嘧啶 - 嘌呤序列占据。与中心的另一个二核苷酸步相关联，该二核苷酸步将相隔6个碱基对的卷曲步组合到DNA的同一侧，这些产生了两种本质上不同类型的DNA弯曲。
相似文献
1
Stereochemical basis of DNA bending by transcription factors.转录因子使DNA弯曲的立体化学基础。
Nucleic Acids Res. 1995 Jun 25;23(12):2083-91. doi: 10.1093/nar/23.12.2083.
2
DNA bending: the prevalence of kinkiness and the virtues of normality.DNA弯曲：弯曲现象的普遍性与正常状态的优势
Nucleic Acids Res. 1998 Apr 15;26(8):1906-26. doi: 10.1093/nar/26.8.1906.
3
DNA bending is an important component of site-specific recognition by the TATA binding protein.DNA弯曲是TATA结合蛋白进行位点特异性识别的一个重要组成部分。
J Mol Biol. 1995 Jul 21;250(4):434-46. doi: 10.1006/jmbi.1995.0388.
4
Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein.TATA 重要吗？对其与 TATA 盒结合蛋白复合物中选择性决定因素的结构探索。
Biophys J. 1997 Aug;73(2):640-52. doi: 10.1016/S0006-3495(97)78099-8.
5
Analysis of co-crystal structures to identify the stereochemical determinants of the orientation of TBP on the TATA box.对共晶体结构进行分析，以确定TBP在TATA盒上取向的立体化学决定因素。
Nucleic Acids Res. 1996 Jul 15;24(14):2767-73. doi: 10.1093/nar/24.14.2767.
6
Signals for TBP/TATA box recognition.TBP/TATA框识别信号。
J Mol Biol. 2000 Jun 16;299(4):965-77. doi: 10.1006/jmbi.2000.3797.
7
Binding mechanisms of TATA box-binding proteins: DNA kinking is stabilized by specific hydrogen bonds.TATA 框结合蛋白的结合机制：特定氢键稳定 DNA 弯曲。
Biophys J. 2000 Apr;78(4):1988-96. doi: 10.1016/S0006-3495(00)76746-4.
8
Bending of DNA in solution caused by a protein from Arabidopsis that binds to a TATA element.拟南芥中一种与TATA元件结合的蛋白质导致溶液中DNA弯曲。
Biosci Biotechnol Biochem. 1994 May;58(5):916-20. doi: 10.1271/bbb.58.916.
9
In simple synthetic promoters YY1-induced DNA bending is important in transcription activation and repression.在简单的合成启动子中，YY1诱导的DNA弯曲在转录激活和抑制中起重要作用。
Nucleic Acids Res. 1996 Nov 1;24(21):4341-8. doi: 10.1093/nar/24.21.4341.
10
Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor.启动子序列的预弯曲可增强对TATA结合因子的亲和力。
Nature. 1995 Feb 23;373(6516):724-7. doi: 10.1038/373724a0.
引用本文的文献
1
A high-throughput single-molecule platform to study DNA supercoiling effect on protein-DNA interactions.一种用于研究DNA超螺旋对蛋白质-DNA相互作用影响的高通量单分子平台。
Nucleic Acids Res. 2025 Jun 20;53(12). doi: 10.1093/nar/gkaf581.
2
A high throughput single molecule platform to study DNA supercoiling effect on protein-DNA interactions.一种用于研究DNA超螺旋对蛋白质-DNA相互作用影响的高通量单分子平台。
bioRxiv. 2024 Oct 25:2024.10.24.620099. doi: 10.1101/2024.10.24.620099.
3
DNAcycP: a deep learning tool for DNA cyclizability prediction.DNAcycP：一种用于 DNA 环化能力预测的深度学习工具。
Nucleic Acids Res. 2022 Apr 8;50(6):3142-3154. doi: 10.1093/nar/gkac162.
4
A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences.锌指蛋白 Kaiso 中的构象转换介导特定和甲基化 DNA 序列的差异读取。
Biochemistry. 2020 May 26;59(20):1909-1926. doi: 10.1021/acs.biochem.0c00253. Epub 2020 May 12.
5
Strong deformations of DNA: Effect on the persistence length.DNA的强烈变形：对持久长度的影响。
Eur Phys J E Soft Matter. 2018 Sep 28;41(9):114. doi: 10.1140/epje/i2018-11722-8.
6
Key determinants of target DNA recognition by retroviral intasomes.逆转录病毒整合体识别靶DNA的关键决定因素。
Retrovirology. 2015 Apr 30;12:39. doi: 10.1186/s12977-015-0167-3.
7
DNA Recognition by a Novel Bis-Intercalator, Potent Anticancer Drug XR5944.新型双嵌入剂、强效抗癌药物XR5944对DNA的识别
Curr Top Med Chem. 2015;15(14):1385-97. doi: 10.2174/1568026615666150413155608.
8
Solution structure of a 2:1 complex of anticancer drug XR5944 with TFF1 estrogen response element: insights into DNA recognition by a bis-intercalator.抗癌药物 XR5944 与 TFF1 雌激素反应元件 2:1 复合物的溶液结构：双嵌入剂对 DNA 识别的深入了解。
Nucleic Acids Res. 2014 May;42(9):6012-24. doi: 10.1093/nar/gku219. Epub 2014 Apr 7.
9
Residue correlation networks in nuclear receptors reflect functional specialization and the formation of the nematode-specific P-box.核受体中的残基相关网络反映了功能专业化和线虫特异性 P 盒的形成。
BMC Genomics. 2013;14 Suppl 6(Suppl 6):S1. doi: 10.1186/1471-2164-14-S6-S1. Epub 2013 Oct 25.
10
Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.通过核磁共振 (13)C 弛豫和分子动力学模拟探测 a-链段和嘧啶-嘌呤步中的序列特异性 DNA 柔性。
Biochemistry. 2012 Oct 30;51(43):8654-64. doi: 10.1021/bi3009517. Epub 2012 Oct 18.
本文引用的文献
1
A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend.一个含有腺嘌呤序列的DNA十二聚体以独特的晶格形式结晶，并呈现出一种新的弯曲形态。
J Mol Biol. 1993 Jun 20;231(4):1024-39. doi: 10.1006/jmbi.1993.1349.
2
High resolution crystal structure of the A-DNA decamer d(CCCGGCCGGG). Novel intermolecular base-paired G*(G.C) triplets.A-DNA 十聚体 d(CCCGGCCGGG)的高分辨率晶体结构。新型分子间碱基配对的 G*(G.C)三联体。
J Mol Biol. 1993 May 20;231(2):431-44. doi: 10.1006/jmbi.1993.1292.
3
Sequence-dependent DNA structure. The role of base stacking interactions.序列依赖性DNA结构。碱基堆积相互作用的作用。
J Mol Biol. 1993 Apr 5;230(3):1025-54. doi: 10.1006/jmbi.1993.1217.
4
Crystal structure of CATGGCCATG and its implications for A-tract bending models.CATGGCCATG的晶体结构及其对A序列弯曲模型的影响。
Proc Natl Acad Sci U S A. 1993 Apr 1;90(7):2930-4. doi: 10.1073/pnas.90.7.2930.
5
Evidence for opposite groove-directed curvature of GGGCCC and AAAAA sequence elements.
Nucleic Acids Res. 1993 Feb 25;21(4):1025-9. doi: 10.1093/nar/21.4.1025.
6
Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility of B-DNA.两种不同空间群中B-DNA十聚体C-C-A-A-C-I-T-T-G-G的结构：B-DNA的构象灵活性
Biochemistry. 1993 Feb 9;32(5):1373-89. doi: 10.1021/bi00056a024.
7
Co-crystal structure of TBP recognizing the minor groove of a TATA element.TBP识别TATA元件小沟的共晶体结构。
Nature. 1993 Oct 7;365(6446):520-7. doi: 10.1038/365520a0.
8
Crystal structure of a yeast TBP/TATA-box complex.酵母TBP/TATA盒复合物的晶体结构。
Nature. 1993 Oct 7;365(6446):512-20. doi: 10.1038/365512a0.
9
Transcription. Opening the gateway.转录。打开通道。
Nature. 1993 Oct 7;365(6446):486-7. doi: 10.1038/365486a0.
10
Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers.一种五指GLI-DNA复合物的晶体结构：锌指结构的新视角
Science. 1993 Sep 24;261(5129):1701-7. doi: 10.1126/science.8378770.
Zotero 插件