Role of DNA-DNA sliding friction and nonequilibrium dynamics in viral genome ejection and packaging.
Role of DNA-DNA sliding friction and nonequilibrium dynamics in viral genome ejection and packaging.
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DOI：
10.1093/nar/gkad582
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发表时间：
2023-08-25
影响因子：
14.9
通讯作者：
中科院分区：
文献类型：
--
作者：
许多病毒通过病毒外壳中的纳米通道排出它们的DNA，这是由高密度基因组包装产生的内力驱动的。DNA退出的速度是由限制分子流动性的摩擦力控制的，但这种摩擦的性质是未知的。我们介绍了一种方法来探测紧密限制的DNA的流动性，通过测量DNA退出噬菌体phi 29衣壳与光镊。我们测量极低的初始出口速度，一个政权的指数增长的速度，随机暂停，占主导地位的动力学和大的动态异质性。与变量施加的力的测量提供的证据表明，初始速度是由DNA-DNA滑动摩擦控制，符合Frenkel-Kontorova模型的纳米级摩擦。我们确认了几个方面的理论模型预测的弹射动力学。暂停的特征表明，它与软物质系统中的“堵塞”现象有关。我们的研究结果提供的证据表明，DNA-DNA摩擦和堵塞控制的DNA退出动力学，但这种摩擦并不显着影响DNA包装。
Many viruses eject their DNA via a nanochannel in the viral shell, driven by internal forces arising from the high-density genome packing. The speed of DNA exit is controlled by friction forces that limit the molecular mobility, but the nature of this friction is unknown. We introduce a method to probe the mobility of the tightly confined DNA by measuring DNA exit from phage phi29 capsids with optical tweezers. We measure extremely low initial exit velocity, a regime of exponentially increasing velocity, stochastic pausing that dominates the kinetics and large dynamic heterogeneity. Measurements with variable applied force provide evidence that the initial velocity is controlled by DNA–DNA sliding friction, consistent with a Frenkel–Kontorova model for nanoscale friction. We confirm several aspects of the ejection dynamics predicted by theoretical models. Features of the pausing suggest that it is connected to the phenomenon of ‘clogging’ in soft matter systems. Our results provide evidence that DNA–DNA friction and clogging control the DNA exit dynamics, but that this friction does not significantly affect DNA packaging.
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影响因子：
4
作者：
delToro, Damian;Smith, Douglas E.
通讯作者：
Smith, Douglas E.
影响因子：
14.9
作者：
Fuller, DN;Gemmen, GJ;Smith, DE
通讯作者：
Smith, DE
影响因子：
7.7
作者：
Brandariz-Nunez, Alberto;Liu, Ting;Evilevitch, Alex
通讯作者：
Evilevitch, Alex
影响因子：
3.4
作者：
Berndsen, Zachary T.;Keller, Nicholas;Smith, Douglas E.
通讯作者：
Smith, Douglas E.
DOI：
10.1073/pnas.0409323102
发表时间：
2005-06-28
影响因子：
11.1
作者：
Arsuaga, J;Vazquez, M;Roca, J
通讯作者：
Roca, J