Córdoba Andrés, Hinckley Daniel M, Lequieu Joshua, de Pablo Juan J
Institute for Molecular Engineering, University of Chicago, Chicago, Illinois.
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin.
Biophys J. 2017 Apr 11;112(7):1302-1315. doi: 10.1016/j.bpj.2017.02.015.
Genome packing in viruses and prokaryotes relies on positively charged ions to reduce electrostatic repulsions, and induce attractions that can facilitate DNA condensation. Here we present molecular dynamics simulations spanning several microseconds of dsDNA packing inside nanometer-sized viral capsids. We use a detailed molecular model of DNA that accounts for molecular structure, basepairing, and explicit counterions. The size and shape of the capsids studied here are based on the 30-nanometer-diameter gene transfer agents of bacterium Rhodobacter capsulatus that transfer random 4.5-kbp (1.5 μm) DNA segments between bacterial cells. Multivalent cations such as spermidine and magnesium induce attraction between packaged DNA sites that can lead to DNA condensation. At high concentrations of spermidine, this condensation significantly increases the shear stresses on the packaged DNA while also reducing the pressure inside the capsid. These effects result in an increase in the packing velocity and the total amount of DNA that can be packaged inside the nanometer-sized capsids. In the simulation results presented here, high concentrations of spermidine did not produce the premature stalling observed in experiments. However, a small increase in the heterogeneity of packing velocities was observed in the systems with magnesium and spermidine ions compared to the system with only salt. The results presented here indicate that the effect of multivalent cations and of spermidine, in particular, on the dynamics of DNA packing, increases with decreasing packing velocities.
病毒和原核生物中的基因组包装依赖带正电荷的离子来减少静电排斥，并诱导能促进DNA凝聚的吸引力。在此，我们展示了跨越数微秒的双链DNA在纳米级病毒衣壳内包装的分子动力学模拟。我们使用了一个详细的DNA分子模型，该模型考虑了分子结构、碱基配对和明确的抗衡离子。这里研究的衣壳的大小和形状基于红假单胞菌直径为30纳米的基因转移因子，它们在细菌细胞之间转移随机的4.5千碱基对（1.5微米）DNA片段。多价阳离子如亚精胺和镁会诱导包装好的DNA位点之间产生吸引力，从而导致DNA凝聚。在高浓度亚精胺的情况下，这种凝聚会显著增加包装好的DNA上的剪切应力，同时也会降低衣壳内的压力。这些效应导致包装速度加快，以及能够包装在纳米级衣壳内的DNA总量增加。在本文展示的模拟结果中，高浓度亚精胺并未产生实验中观察到的过早停滞现象。然而，与仅含盐的系统相比，在含有镁离子和亚精胺离子的系统中，观察到包装速度的异质性略有增加。本文展示的结果表明，多价阳离子，尤其是亚精胺，对DNA包装动力学的影响会随着包装速度的降低而增加。
