DNA knots reveal a chiral organization of DNA in phage capsids
DNA knots reveal a chiral organization of DNA in phage capsids
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DOI：
10.1073/pnas.0409323102
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发表时间：
2005-06-28
影响因子：
11.1
通讯作者：
Roca, J
中科院分区：
文献类型：
--
作者：
Arsuaga, J;Vazquez, M;Roca, J
二十面体噬菌体将其双链 DNA 基因组包装到接近晶体的密度，并实现了自然界中发现的最高水平的 DNA 浓缩之一。尽管进行了大量研究，但噬菌体衣壳内 DNA 包装几何形状的一些基本特性仍然未知。我们提出了一种不同的方法来解决包装 DNA 的随机性和手性问题。我们最近发现，大多数从噬菌体 P4 中提取的 DNA 分子由于限制在噬菌体衣壳中的线性 DNA 分子环化而高度打结。在这里，我们证明这些结提供了有关衣壳内 DNA 整体排列的信息。首先，我们通过高分辨率凝胶电泳分析病毒 DNA 结的分布。接下来，我们对限制在球形体积内的自由连接多边形进行随机打结的蒙特卡罗计算机模拟。通过两种技术获得的结分布的比较产生了病毒 DNA 非随机包装的拓扑证明。此外，我们的模拟表明，在 DNA 结的病毒分布中观察到的非手性结 4(1) 的稀缺性和环面结 5(1) 相对于扭结 5(2) 的优势不能仅通过限制来获得，而必须包括构象采样中的扭曲偏差。这些结果表明病毒衣壳内 DNA 的包装几何形状是扭曲定向的。
Icosahedral bacteriophages pack their double-stranded DNA genomes to near-crystalline density and achieve one of the highest levels of DNA condensation found in nature. Despite numerous studies, some essential properties of the packaging geometry of the DNA inside the phage capsid are still unknown. We present a different approach to the problems of randomness and chirality of the packed DNA. We recently showed that most DNA molecules extracted from bacteriophage P4 are highly knotted because of the cyclization of the linear DNA molecule confined in the phage capsid. Here, we show that these knots provide information about the global arrangement of the DNA inside the capsid. First, we analyze the distribution of the viral DNA knots by high-resolution gel electrophoresis. Next, we perform Monte Carlo computer simulations of random knotting for freely jointed polygons confined to spherical volumes. Comparison of the knot distributions obtained by both techniques produces a topological proof of nonrandom packaging of the viral DNA. Moreover, our simulations show that the scarcity of the achiral knot 4(1) and the predominance of the torus knot 5(1) over the twist knot 5(2) observed in the viral distribution of DNA knots cannot be obtained by confinement alone but must include writhe bias in the conformation sampling. These results indicate that the packaging geometry of the DNA inside the viral capsid is writhe-directed.