A unified model for the origin of DNA sequence-directed curvature
A unified model for the origin of DNA sequence-directed curvature
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DOI：
10.1002/bip.10364
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发表时间：
2003-05-01
期刊：
影响因子：
2.9
通讯作者：
Plavec, J
中科院分区：
文献类型：
--
作者：
Hud, NV;Plavec, J
DNA双螺旋的精细结构及其许多物理性质取决于核苷酸序列。这包括小沟宽度、经历B-型到A-型转变的倾向、序列导向曲率和阳离子定位。尽管对DNA进行了大量的研究，但仍然很难理解这些基本性质是如何在核苷酸序列水平上相互联系的。我们表明，DNA的几个序列依赖性的属性可以归因于，至少在部分，在主要和次要凹槽的阳离子的序列特异性本地化。我们还表明，阳离子定位对DNA结构的影响更容易理解，如果我们把所有的DNA序列分为三个主要群体：A-tracts，G-tracts，和通用的DNA。序列的A道组具有独特的螺旋结构（即，B* 型），具有异常狭窄的小沟和高基对螺旋桨扭转。实验和理论研究都提供了证据表明，B* 型螺旋结构的A-道需要阳离子定位在小沟。另一方面，随着离子强度的增加，胃肠道倾向于经历B型到A型的转变。G-道的这种性质与阳离子优先定位于G-道序列的大沟中的观察直接相关。代表绝大多数DNA序列的通用DNA具有比A区或G区更平衡的阳离子对大沟和小沟的占据，从而稳定在典型的B型螺旋中。因此，DNA二级结构可以被视为阳离子大沟和小沟之间的拉锯战，A区和G区各有一个沟，在阳离子定位方面主导另一个沟。最后，在这两种情况下，由A束和G束引起的序列定向弯曲可以通过A束和G束螺旋结构与通用DNA的典型B型螺旋的阳离子依赖性错配来解释（即，阳离子依赖性结模型）。(C)2003 Wiley Periodicals，Inc.
The fine structure of the DNA double helix and a number of its physical properties depend upon nucleotide sequence. This includes minor groove width, the propensity to undergo the B-form to A-form transition, sequence-directed curvature, and cation localization. Despite the multitude of studies conducted on DNA, it is still difficult to appreciate how these fundamental properties are linked to each other at the level of nucleotide sequence. We demonstrate that several sequence-dependent properties of DNA can be attributed, at least in part, to the sequence-specific localization of cations in the major and minor grooves. We also show that effects of cation localization on DNA structure are easier to understand if we divide all DNA sequences into three principal groups: A-tracts, G-tracts, and generic DNA. The A-tract group of sequences has a peculiar helical structure (i.e., B*-form) with an unusually narrow minor groove and high base-pair propeller twist. Both experimental and theoretical studies have provided evidence that the B*-form helical structure of A-tracts requires cations to be localized in the minor groove. G-tracts, on the other hand, have a propensity to undergo the B-form to A-form transition with increasing ionic strength. This property of G-tracts is directly connected to the observation that cations are preferentially localized in the major groove of G-tract sequences. Generic DNA, which represents the vast majority of DNA sequences, has a more balanced occupation of the major and minor grooves by cations than A-tracts or G-tracts and is thereby stabilized in the canonical B-form helix. Thus, DNA secondary structure can be viewed as a tug of war between the major and minor grooves for cations, with A-tracts and G-tracts each having one groove that dominates the other for cation localization. Finally, the sequence-directed curvature caused by A-tracts and G-tracts can, in both cases, be explained by the cation-dependent mismatch of A-tract and G-tract helical structures with the canonical B-form helix of generic DNA (i.e., a cation-dependent junction model). (C) 2003 Wiley Periodicals, Inc.