Ben-Gurion University of the Negev, Beer-Sheva and the Ilse Katz Institute for Nanoscale Science and Technology, P.O. Box 653, Beer-Sheva, 8410501, Israel.
Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA.
Nucleic Acids Res. 2018 Feb 16;46(3):1553-1561. doi: 10.1093/nar/gkx1282.
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.
我们提出了一个详细的粗粒计算机模拟和单分子荧光研究，研究了在 DNA 折纸结构上行走的 DNA 双足马达的行走动力学和机制。特别是，我们研究了行走效率和步动力学对步长的依赖性。模拟准确地捕捉和解释了三个不同的实验观察结果。这些结果包括对最大可能步长的描述，短距离内行走效率的降低，以及行走效率对相对于 origami 轨道的行走方向的依赖性。前两个观察结果是出乎意料的，也不是微不足道的。基于这项研究，我们提出了三种设计修改建议，以改进未来的 DNA 步行者。我们的研究表明，oxDNA 模型能够解决复杂 DNA 机器的动力学问题，并且它可以作为在三个空间维度上运行的 DNA 机器设计的工程工具。
