Effect of flanking bases on the DNA specificity of EmBP-1

De Jong A.T.

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Effect of flanking bases on the DNA specificity of EmBP-1

机译：侧翼碱基对EmBP-1 DNA特异性的影响

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EmBP-1 is a basic region leucine zipper (bZIP) protein found in many types of plants. In general, plant bZIP proteins bind selectively to DNA sequences containing ACGT core sequences with different immediate flanking nucleotides preferred by different proteins. I report that the distant flanking sequence also has a strong effect on the preference of EmBP-1 for internal bases and determine the residue governing this effect. EmBP-1 binds selectively to the 10 bp gcG-box palindrome GCCACGTGGC 18-fold more tightly than the gcC-box GTGACGTCAC, but when the outer flanking G/C residues were changed to A/T (i.e., ACCACGTGGT and ATGACGTCAT), an only 1.2-fold preference for G-box binding was observed. Analysis of a series of single-residue alanine mutants of EmBP-1 revealed that this effect is mediated by arginine 10. Mutation of this residue to alanine greatly reduces the affinity for the gcG-box while leaving the affinity for other sequences relatively unchanged. Partial retention of G-box specificity upon mutation of R10 to lysine indicates that the effect is reliant on the basic nature of the residue. Additional studies with other EmBP-1 protein mutants and with oligonucleotides containing the T/A and C/G flanking sequences demonstrate the complexity of the protein-DNA interaction and demonstrate that the mechanism of sequence selective DNA binding is highly dependent on the flanking sequence.

机译：EmBP-1是在许多类型的植物中发现的基本区域亮氨酸拉链（bZIP）蛋白。通常，植物bZIP蛋白选择性结合包含ACGT核心序列的DNA序列，所述ACGT核心序列具有不同蛋白质优选的不同的直接侧翼核苷酸。我报告说，遥远的侧翼序列对EmBP-1对内部碱基的偏好也有很强的影响，并确定控制这种作用的残基。 EmBP-1与10 bp gcG-box回文序列GCCACGTGGC的选择性比gcC-box GTGACGTCAC高18倍，但是当外侧的G / C残基变为A / T（即ACCACGTGGT和ATGACGTCAT）时，仅观察到1.2倍的G-box结合偏好。对EmBP-1的一系列单残基丙氨酸突变体的分析表明，这种作用是由精氨酸10介导的。此残基突变为丙氨酸会大大降低对gcG-box的亲和力，而对其他序列的亲和力却相对不变。 R10突变为赖氨酸后，G-box特异性的部分保留表明该作用依赖于残基的基本性质。对其他EmBP-1蛋白突变体和含有T / A和C / G侧翼序列的寡核苷酸的其他研究证明了蛋白质与DNA相互作用的复杂性，并证明了序列选择性DNA结合的机制高度依赖于侧翼序列。

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《Biochemistry》 |2013年第5期|共9页
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De Jong A.T.;
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1. Effect of flanking bases on the DNA specificity of EmBP-1 [J] . De Jong A.T. Biochemistry . 2013,第5期

机译：侧翼碱基对EmBP-1 DNA特异性的影响
2. Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation [J] . Gregory Fishberger, Grant A. Challen, Andrew Martens, Biology Open . 2016,第6期

机译：基于可重新编程的CRISPR / Cas9的系统，用于诱导特定位点的DNA甲基化基于可重新编程的CRISPR / Cas9的系统，用于诱导特定位点的DNA甲基化
3. Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation [J] . Gregory Fishberger, Grant A. Challen, Andrew Martens, Biology Open . 2016,第6期

机译：基于可重新编程的CRISPR / Cas9的系统，用于诱导特定位点的DNA甲基化基于可重新编程的CRISPR / Cas9的系统，用于诱导特定位点的DNA甲基化
4. Examining Flanking Sequence Specificity and Topological Specificity in the Binding of Various Molecular Types to DNAs Using Restriction Endonuclease Activity Assays [C] . S. A. Winkle, E. Duran, J. Pulido, Symposium on frontiers in nucleic acids . 2011

机译：使用限制性内切核酸酶活性测定检查各种分子类型与DNA的结合中的侧翼序列特异性和拓扑特异性
5. NMR structural studies on multi-stranded DNA formed by guanine -rich sequences and duplex DNA containing a carcinogenic benzo[a]pyrene guanine adduct flanked by methylated cytosine. [D] . Zhang, Na. 2006

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6. Sequence specific generation of a DNA panhandle permits PCR amplification of unknown flanking DNA. [O] . D H Jones, S C Winistorfer 1992

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7. Distant conserved sequences flanking endothelial-specific promoters contain tissue-specific DNase-hypersensitive sites and over-represented motifs [O] . John A. Bernat, Gregory E. Crawford, Aleksey Y. Ogurtsov, 2006

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8. Critical DNA flanking sequences of a CpG Oligodeoxynucleotide, but not the 6 base CpG motif, can be replaced with RNA without quantitative or qualitative changes in Toll-like receptor 9-mediated activity [R] . Sen, G., Flora, M., Chattopadhyay, G., 2004

机译：CpG寡脱氧核苷酸的关键DNa侧翼序列，但不是6碱基CpG基序，可被RNa取代，而Toll样受体9介导的活性无定量或定性变化

Effect of flanking bases on the DNA specificity of EmBP-1

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