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首页> 外文期刊>Journal of Molecular Biology >A simple motif for protein recognition in DNA secondary structures
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A simple motif for protein recognition in DNA secondary structures

机译：DNA二级结构中蛋白质识别的简单基序

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摘要

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.
机译：单链形式的DNA（ssDNA）瞬时存在于细胞内，并包含线性染色体的端粒和某些DNA病毒的基因组。与RNA一样，在单链状态下，某些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。为了更好地了解此类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与HIV Rev蛋白中的RNA结合肽具有高亲和力的单链DNA结合，特异性。选定的粘合剂中绝大多数都包含一个非Watson-Crick 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。该GT基序可以呈现在不同的DNA上下文中，包括近乎完美的双链体和分支的三螺旋结构，并且似乎在很大程度上被被一螺旋a螺旋隔开的精氨酸残基所识别。有趣的是，对于原脑啡肽启动子中的蛋白质结合和功能完备的模型ssDNA调控元件的功能，非常相似的GT基序也是必需的。 （c）2005 Elsevier Ltd.保留所有权利。

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