DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size.
DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size.
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DOI：
10.1093/nar/gkx1282
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发表时间：
2018-02-16
影响因子：
14.9
通讯作者：
Nir E
中科院分区：
文献类型：
--
作者：
Khara DC;Schreck JS;Tomov TE;Berger Y;Ouldridge TE;Doye JPK;Nir E
我们对 DNA 双足马达在 DNA 折纸上迈步的行走动力学和机制进行了详细的粗粒度计算机模拟和单分子荧光研究。特别是，我们研究了步行效率和步进动力学对步长的依赖性。模拟准确地捕捉并解释了三种不同的实验观察结果。这些包括对最大可能步长的描述、短距离行走效率的降低以及效率对相对于折纸轨道的行走方向的依赖性。前两个观察结果是出乎意料的并且是重要的。基于这项研究，我们建议进行三项设计修改，以改进未来的 DNA 步行器。我们的研究证明了 oxDNA 模型解决复杂 DNA 机器动力学的能力，及其作为设计在三个空间维度运行的 DNA 机器的工程工具的有用性。
We present a detailed coarse-grained computer simulation and single molecule fluorescence study of the walking dynamics and mechanism of a DNA bipedal motor striding on a DNA origami. In particular, we study the dependency of the walking efficiency and stepping kinetics on step size. The simulations accurately capture and explain three different experimental observations. These include a description of the maximum possible step size, a decrease in the walking efficiency over short distances and a dependency of the efficiency on the walking direction with respect to the origami track. The former two observations were not expected and are non-trivial. Based on this study, we suggest three design modifications to improve future DNA walkers. Our study demonstrates the ability of the oxDNA model to resolve the dynamics of complex DNA machines, and its usefulness as an engineering tool for the design of DNA machines that operate in the three spatial dimensions.
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影响因子：
14.9
作者：
Kim DN;Kilchherr F;Dietz H;Bathe M
通讯作者：
Bathe M
影响因子：
15
作者：
Ke, Yonggang;Douglas, Shawn M.;Liu, Minghui;Sharma, Jaswinder;Cheng, Anchi;Leung, Albert;Liu, Yan;Shih, William M.;Yan, Hao
通讯作者：
Yan, Hao
影响因子：
14.9
作者：
Douglas SM;Marblestone AH;Teerapittayanon S;Vazquez A;Church GM;Shih WM
通讯作者：
Shih WM
影响因子：
17.1
作者：
Ouldridge, Thomas E.;Hoare, Rollo L.;Turberfield, Andrew J.
通讯作者：
Turberfield, Andrew J.
影响因子：
13.3
作者：
Bath, Jonathan;Green, Simon J.;Turberfield, Andrew J.
通讯作者：
Turberfield, Andrew J.