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Hydroxyl radical footprints reveal novel structural features around the NF I binding site in adenovirus DNA.

作者信息

Zorbas H, Rogge L, Meisterernst M, Winnacker E L

机构信息

Institut für Biochemie, Universität München, FRG.

出版信息

Nucleic Acids Res. 1989 Oct 11;17(19):7735-48. doi: 10.1093/nar/17.19.7735.

DOI:10.1093/nar/17.19.7735
PMID:2552414
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC334881/
Abstract

We have identified a number of as yet unknown structural abnormalities of the NF I-DNA binding site within the inverted terminal repetition of adenovirus DNA by probing it with a hydroxyl radical footprinting technique. NF I binding alters the accessibility of the deoxyribose moieties to hydroxyl radicals both at the 3' and at the 5' side of the recognition sequence 5'-TGG(N)6GCCAA-3'. A smooth bend at the 5' side of the binding sequence is already present in naked linear DNA and it is further enhanced by protein binding. This could be demonstrated not only by hydroxyl radical footprinting but also by studying the temperature dependent mobility during gel electrophoresis of DNA fragments carrying the NF I binding site at circularly permutated positions. We propose that the bent conformation at this site is responsible for facilitating protein/DNA interactions.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5e27/334881/666bdb28c711/nar00136-0177-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5e27/334881/896ba80039b8/nar00136-0172-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5e27/334881/3a3a47329b5b/nar00136-0173-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5e27/334881/666bdb28c711/nar00136-0177-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5e27/334881/896ba80039b8/nar00136-0172-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5e27/334881/3a3a47329b5b/nar00136-0173-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5e27/334881/666bdb28c711/nar00136-0177-a.jpg

相似文献

1
Hydroxyl radical footprints reveal novel structural features around the NF I binding site in adenovirus DNA.
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2
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3
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Hydroxyl radical footprinting.羟基自由基足迹法
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10
[In vitro formation of multimers of specific DNA-protein complexes with nuclear factor I (NF I)].[特定DNA-蛋白质复合物与核因子I（NF I）的多聚体的体外形成]
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引用本文的文献

1
NFI and Oct-1 bend the Ad5 origin in the same direction leading to optimal DNA replication.NFI和Oct-1使腺病毒5型（Ad5）的起始点向同一方向弯曲，从而实现最佳的DNA复制。
Nucleic Acids Res. 2004 Dec 1;32(21):6218-25. doi: 10.1093/nar/gkh944. Print 2004.
2
Bending of adenovirus origin DNA by nuclear factor I as shown by scanning force microscopy is required for optimal DNA replication.扫描力显微镜显示，腺病毒起源DNA被核因子I弯曲是最佳DNA复制所必需的。
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3
CopR binds and bends its target DNA: a footprinting and fluorescence resonance energy transfer study.

本文引用的文献

1
Bent helical structure in kinetoplast DNA.动基体 DNA 的弯曲螺旋结构。
Proc Natl Acad Sci U S A. 1982 Dec;79(24):7664-8. doi: 10.1073/pnas.79.24.7664.
2
The pitch of chromatin DNA is reflected in its nucleotide sequence.染色质DNA的螺距反映在其核苷酸序列中。
Proc Natl Acad Sci U S A. 1980 Jul;77(7):3816-20. doi: 10.1073/pnas.77.7.3816.
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Heteronomous DNA.异源DNA
CopR与它的靶DNA结合并使其弯曲：足迹法和荧光共振能量转移研究。
Nucleic Acids Res. 2002 May 1;30(9):2052-60. doi: 10.1093/nar/30.9.2052.
4
Two regions within the DNA binding domain of nuclear factor I interact with DNA and stimulate adenovirus DNA replication independently.核因子I的DNA结合域内的两个区域与DNA相互作用，并独立刺激腺病毒DNA复制。
Mol Cell Biol. 1996 Aug;16(8):4073-80. doi: 10.1128/MCB.16.8.4073.
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In vivo footprinting of the IRF-1 promoter: inducible occupation of a GAS element next to a persistent structural alteration of the DNA.
Nucleic Acids Res. 1994 Aug 11;22(15):3033-7. doi: 10.1093/nar/22.15.3033.
6
A new interference footprinting method for analysing simultaneously protein contacts to phosphate and guanine residues on DNA.一种用于同时分析蛋白质与DNA上磷酸基团和鸟嘌呤残基相互作用的新型干涉足迹法。
Nucleic Acids Res. 1995 Apr 25;23(8):1443-4. doi: 10.1093/nar/23.8.1443.
7
A novel type of interaction between cruciform DNA and a cruciform binding protein from HeLa cells.一种来自人宫颈癌（HeLa）细胞的十字形DNA与十字形结合蛋白之间新型的相互作用。
EMBO J. 1995 Apr 3;14(7):1571-80. doi: 10.1002/j.1460-2075.1995.tb07143.x.
8
Hydroxyl radical footprint analysis of human immunodeficiency virus reverse transcriptase-template.primer complexes.
Proc Natl Acad Sci U S A. 1993 Jul 1;90(13):5909-13. doi: 10.1073/pnas.90.13.5909.
9
The NF-kappa B transcription factor induces DNA bending which is modulated by its 65-kD subunit.核因子κB转录因子可诱导DNA弯曲，这种弯曲由其65-kD亚基调节。
Nucleic Acids Res. 1990 Nov 25;18(22):6497-502. doi: 10.1093/nar/18.22.6497.
10
Transfer-RNA interferes with the uniform cleavage pattern of DNA by hydroxyl radicals.转运核糖核酸通过羟基自由基干扰DNA的均匀切割模式。
Nucleic Acids Res. 1990 Oct 25;18(20):6160. doi: 10.1093/nar/18.20.6160.
Nucleic Acids Res. 1983 Jun 25;11(12):4141-55. doi: 10.1093/nar/11.12.4141.
4
Rapid and quantitative recovery of DNA fragments from gels by displacement electrophoresis (isotachophoresis).通过置换电泳（等速电泳）从凝胶中快速定量回收DNA片段。
Biochim Biophys Acta. 1984 Jun 16;782(2):120-6. doi: 10.1016/0167-4781(84)90014-9.
5
A bent helix in kinetoplast DNA.动质体DNA中的弯曲螺旋
Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:279-83. doi: 10.1101/sqb.1983.047.01.033.
6
Specific binding of a cellular DNA replication protein to the origin of replication of adenovirus DNA.一种细胞DNA复制蛋白与腺病毒DNA复制起点的特异性结合。
Proc Natl Acad Sci U S A. 1983 Oct;80(20):6177-81. doi: 10.1073/pnas.80.20.6177.
7
The TGGCA-binding protein: a eukaryotic nuclear protein recognizing a symmetrical sequence on double-stranded linear DNA.TGGCA结合蛋白：一种识别双链线性DNA上对称序列的真核细胞核蛋白。
Nucleic Acids Res. 1984 May 25;12(10):4295-311. doi: 10.1093/nar/12.10.4295.
8
DNA structural variations in the E. coli tyrT promoter.大肠杆菌tyrT启动子中的DNA结构变异
Cell. 1984 Jun;37(2):491-502. doi: 10.1016/0092-8674(84)90379-9.
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The locus of sequence-directed and protein-induced DNA bending.序列导向和蛋白质诱导的DNA弯曲位点。
Nature. 1984;308(5959):509-13. doi: 10.1038/308509a0.
10
Sequencing end-labeled DNA with base-specific chemical cleavages.通过碱基特异性化学切割对末端标记的DNA进行测序。
Methods Enzymol. 1980;65(1):499-560. doi: 10.1016/s0076-6879(80)65059-9.