A simple motif for protein recognition in DNA secondary structures
A simple motif for protein recognition in DNA secondary structures
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DOI：
10.1016/j.jmb.2005.07.001
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发表时间：
2005-09-02
影响因子：
5.6
通讯作者：
Frankel, AD
中科院分区：
文献类型：
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作者：
Landt, SG;Ramirez, A;Frankel, AD
单链形式的DNA （ssDNA）在细胞内短暂存在，包括线性染色体的端粒和一些DNA病毒的基因组。与RNA一样，在单链状态下，一些DNA序列能够折叠成复杂的二级和三级结构，这些结构可能被蛋白质识别并参与基因调控。为了更好地了解这些DNA元件如何折叠并与蛋白质相互作用，并将识别特征与结构化RNA的识别特征进行比较，我们使用体外选择来鉴定具有高亲和力和特异性的结合HIV Rev蛋白RNA结合肽的ssdna。大多数选择的结合物包含一个非沃森-克里克G- t碱基对和一个相邻的C:G碱基对，两者都是结合所必需的。这种GT基序可以出现在不同的DNA环境中，包括近乎完美的双链结构和分支的三螺旋结构，并且似乎在很大程度上被a-螺旋旋转分离的精氨酸残基所识别。有趣的是，一个非常相似的GT基序对于蛋白质结合和来自proenkephalin启动子的一个特征良好的模型ssDNA调控元件的功能也是必需的。(c) 2005 Elsevier Ltd版权所有。
DNA in a single-stranded form (ssDNA) exists transiently within the cell and comprises the telomeres of linear chromosomes and the genomes of some DNA viruses. As with RNA, in the single-stranded state, some DNA sequences are able to fold into complex secondary and tertiary structures that may be recognized by proteins and participate in gene regulation. To better understand how such DNA elements might fold and interact with proteins, and to compare recognition features to those of a structured RNA, we used in vitro selection to identify ssDNAs that bind an RNA-binding peptide from the HIV Rev protein with high affinity and specificity. The large majority of selected binders contain a non-Watson-Crick G-T basepair and an adjacent C:G base-pair and both are essential for binding. This GT motif can be presented in different DNA contexts, including a nearly perfect duplex and a branched three-helix structure, and appears to be recognized in large part by arginine residues separated by one turn of an a-helix. Interestingly, a very similar GT motif is necessary also for protein binding and function of a well-characterized model ssDNA regulatory element from the proenkephalin promoter. (c) 2005 Elsevier Ltd. All rights reserved.