RecA通过检测五或六个核苷酸匹配序列并使第二个DNA变形来动态选择同源DNA。

IF 7.2 2区 生物学 Q1 BIOPHYSICS Quarterly Reviews of Biophysics Pub Date : 2018-01-01 DOI:10.1017/S0033583518000094
Masayuki Takahashi
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引用次数: 1

摘要

在同源重组过程中,RecA家族蛋白对具有相同序列的两个dna进行配对以促进链交换。为了了解RecA蛋白如何寻找和识别同源性,我们试图确定允许RecA开始反应的同源序列的长度。具体来说,我们分析了序列异质性对同源DNA与RecA/单链DNA复合体关联率的影响。我们假设反应可以在DNA的任何点上以相同的可能性开始,并且序列异质性消除了一些可能的起始位点。分析表明,RecA的有效识别大小为5 - 6个核苷酸,比RecA单体识别的3个核苷酸要大。由于每三个碱基插入RecA的氨基酸残基,第一个DNA被拉长1.5倍,因此第二个结合的DNA必须被拉长才能与第一个DNA配对。由于该长度与基于链交换反应或DNA对形成的估计相似,因此同源性测试可能主要发生在结合步骤。由于缺乏氢键而产生的能量差异太小,无法在5个或6个核苷酸序列中区分单核苷酸的异质性。这种选择很可能是动力学上的,而且可能涉及到沃森-克里克氢键以外的一些结构因素。确定其他涉及DNA碱基互补的生物反应(如复制、转录和翻译)是否也是如此,将是有价值的。
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RecA kinetically selects homologous DNA by testing a five- or six-nucleotide matching sequence and deforming the second DNA.

RecA family proteins pair two DNAs with the same sequence to promote strand exchange during homologous recombination. To understand how RecA proteins search for and recognize homology, we sought to determine the length of homologous sequence that permits RecA to start its reaction. Specifically, we analyzed the effect of sequence heterogeneity on the association rate of homologous DNA with RecA/single-stranded DNA complex. We assumed that the reaction can start with equal likelihood at any point in the DNA, and that sequence heterogeneity abolishes some possible initiation sites. This analysis revealed that the effective recognition size is five or six nucleotides, larger than the three nucleotides recognized by a RecA monomer. Because the first DNA is elongated 1.5-fold by intercalation of amino acid residues of RecA every three bases, the second bound DNA must be elongated to pair with the first. Because this length is similar to estimates based on the strand-exchange reaction or DNA pair formation, the homology test is likely to occur primarily at the association step. The energetic difference due to the absence of hydrogen bonding is too small to discriminate single-nucleotide heterogeneity over a five- or six-nucleotide sequence. The selection is very likely to be made kinetically, and probably involves some structural factor other than Watson-Crick hydrogen bonding. It would be valuable to determine whether this is also the case for other biological reactions involving DNA base complementarity, such as replication, transcription, and translation.

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来源期刊
Quarterly Reviews of Biophysics
Quarterly Reviews of Biophysics 生物-生物物理
CiteScore
12.90
自引率
1.60%
发文量
16
期刊介绍: Quarterly Reviews of Biophysics covers the field of experimental and computational biophysics. Experimental biophysics span across different physics-based measurements such as optical microscopy, super-resolution imaging, electron microscopy, X-ray and neutron diffraction, spectroscopy, calorimetry, thermodynamics and their integrated uses. Computational biophysics includes theory, simulations, bioinformatics and system analysis. These biophysical methodologies are used to discover the structure, function and physiology of biological systems in varying complexities from cells, organelles, membranes, protein-nucleic acid complexes, molecular machines to molecules. The majority of reviews published are invited from authors who have made significant contributions to the field, who give critical, readable and sometimes controversial accounts of recent progress and problems in their specialty. The journal has long-standing, worldwide reputation, demonstrated by its high ranking in the ISI Science Citation Index, as a forum for general and specialized communication between biophysicists working in different areas. Thematic issues are occasionally published.
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