Double-stranded DNA is under extreme confinement when packed in phage phi29 with osmotic pressures approaching 60 atm and densities near liquid crystalline. The shape of the capsid determined from experiment is elongated. We consider the effects of the capsid shape and volume on the DNA distribution. We propose simple models for the capsid of phage phi29 to capture volume, shape, and wall flexibility, leading to an accurate DNA density profile. The effect of the packaging motor twisting the DNA on the resulting density distribution has been explored. We find packing motor induced twisting leads to a greater numbers of defects formed. The emergence of defects such as bubbles or large roll angles along the DNA shows a sequence dependence, and the resulting flexibility leads to an inhomogeneous distribution of defects occurring more often at TpA steps and AT-rich regions. In conjunction with capsid elongation, this has effects on the global DNA packing structures.

中文翻译：

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模型形状、体积和外壳柔软度对 phi29 DNA 包装的影响

当渗透压接近 60 atm 且密度接近液晶时，双链 DNA 在包装在 phi29 噬菌体中时处于极端限制状态。由实验确定的衣壳的形状是拉长的。我们考虑衣壳形状和体积对 DNA 分布的影响。我们为噬菌体 phi29 的衣壳提出了简单的模型，以捕获体积、形状和壁的灵活性，从而获得准确的 DNA 密度分布。已经探索了包装电机扭曲 DNA 对产生的密度分布的影响。我们发现包装电机引起的扭曲会导致形成更多的缺陷。DNA 上出现的缺陷（如气泡或大滚动角）显示出序列依赖性，并且由此产生的灵活性导致缺陷的不均匀分布更频繁地发生在 TpA 步骤和富含 AT 的区域。结合衣壳伸长，这对整体 DNA 包装结构有影响。