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基因组长程相关性对 DNA 持久长度的影响:从理论到单分子实验。

Effect of genomic long-range correlations on DNA persistence length: from theory to single molecule experiments.

机构信息

Université de Lyon, F-69000 Lyon, France.

出版信息

J Phys Chem B. 2010 Apr 22;114(15):5125-43. doi: 10.1021/jp911031y.

Abstract

Sequence dependency of DNA intrinsic bending properties has been emphasized as a possible key ingredient to in vivo chromatin organization. We use atomic force microscopy (AFM) in air and liquid to image intrinsically straight (synthetic), uncorrelated (hepatitis C RNA virus) and persistent long-range correlated (human) DNA fragments in various ionic conditions such that the molecules freely equilibrate on the mica surface before being captured in a particular conformation. 2D thermodynamic equilibrium is experimentally verified by a detailed statistical analysis of the Gaussian nature of the DNA bend angle fluctuations. We show that the worm-like chain (WLC) model, commonly used to describe the average conformation of long semiflexible polymers, reproduces remarkably well the persistence length estimates for the first two molecules as consistently obtained from (i) mean square end-to-end distance measurement and (ii) mean projection of the end-to-end vector on the initial orientation. Whatever the operating conditions (air or liquid, concentration of metal cations Mg(2+) and/or Ni(2+)), the persistence length found for the uncorrelated viral DNA underestimates the value obtained for the straight DNA. We show that this systematic difference is the signature of the presence of an uncorrelated structural intrinsic disorder in the hepatitis C virus (HCV) DNA fragment that superimposes on local curvatures induced by thermal fluctuations and that only the entropic disorder depends upon experimental conditions. In contrast, the WLC model fails to describe the human DNA conformations. We use a mean-field extension of the WLC model to account for the presence of long-range correlations (LRC) in the intrinsic curvature disorder of human genomic DNA: the stronger the LRC, the smaller the persistence length. The comparison of AFM imaging of human DNA with LRC DNA simulations confirms that the rather small mean square end-to-end distance observed, particularly for G+C-rich human DNA molecules, more likely results from a large-scale intrinsic curvature due to a persistent distribution of DNA curvature sites than from some increased flexibility.

摘要

DNA 内在弯曲特性的序列依赖性已被强调为体内染色质组织的可能关键因素。我们使用原子力显微镜(AFM)在空气和液体中成像内在笔直(合成)、不相关(丙型肝炎 RNA 病毒)和持久长程相关(人类)的 DNA 片段,在各种离子条件下,使分子在被捕获到特定构象之前可以在云母表面上自由平衡。通过对 DNA 弯曲角度波动的高斯性质进行详细的统计分析,实验验证了二维热力学平衡。我们表明,普遍用于描述长半柔性聚合物平均构象的蠕虫链(WLC)模型非常好地再现了前两个分子的持久性长度估计值,这是通过(i)均方末端到末端距离的测量和(ii)末端到末端向量在初始方向上的平均投影一致获得的。无论操作条件(空气或液体,金属阳离子 Mg(2+)和/或 Ni(2+)的浓度)如何,未相关病毒 DNA 的持久性长度都低估了笔直 DNA 的值。我们表明,这种系统差异是丙型肝炎病毒(HCV)DNA 片段中存在无相关结构内在无序的特征,这种无序与热波动引起的局部曲率叠加,并且只有熵无序取决于实验条件。相比之下,WLC 模型无法描述人类 DNA 构象。我们使用 WLC 模型的平均场扩展来解释人类基因组 DNA 中内在曲率无序的长程相关性(LRC):LRC 越强,持久性长度越小。与 LRC DNA 模拟的 AFM 成像相比,人类 DNA 的比较证实,观察到的特别是富含 G+C 的人类 DNA 分子的相当小的均方末端到末端距离更可能是由于大尺度内在曲率导致的,而不是由于某些增加的灵活性。

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