Mechanistic Understanding of Surface Migration Dynamics with DNA Walkers
Mechanistic Understanding of Surface Migration Dynamics with DNA Walkers
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DOI：
10.1021/acs.jpcb.0c09048
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发表时间：
2021-01-11
影响因子：
3.3
通讯作者：
Choi, Jong Hyun
中科院分区：
文献类型：
--
作者：
Du, Yancheng;Pan, Jing;Choi, Jong Hyun
动态DNA步行者可以通过各种机制在表面上移动货物，包括酶促反应和链置换。虽然它们表现出高的持续合成能力和速度，但它们的运动动力学还没有得到很好的理解。在这里，我们利用酶动力的DNA步行者作为模型系统，并采用随机行走模型，以提供新的见解迁移动力学。四个不同的迁移模式（弹道，利维，自我回避，扩散运动）被确定。每种模式显示出独特的步长时间和速度分布，这是相关的均方位移（MSD）缩放。实验结果与理论预测非常吻合。随着对动力学的更好理解，我们进行了机械研究，阐明了货物类型和大小，步行者序列设计和环境条件的影响。最后，本研究提供了一套设计原则，调整的DNA步行者的行为。这项工作的DNA步行者可以作为数学研究的多功能平台，并为生物工程开辟新的机会。
Dynamic DNA walkers can move cargoes on a surface through various mechanisms including enzymatic reactions and strand displacement. While they have demonstrated high processivity and speed, their motion dynamics are not well understood. Here, we utilize an enzyme-powered DNA walker as a model system and adopt a random walk model to provide new insight into migration dynamics. Four distinct migration modes (ballistic, Levy, self-avoiding, and diffusive motions) are identified. Each mode shows unique step time and velocity distributions, which are related to mean-squared displacement (MSD) scaling. Experimental results are in excellent agreement with the theoretical predictions. With a better understanding of the dynamics, we performed a mechanistic study, elucidating the effects of cargo types and sizes, walker sequence designs, and environmental conditions. Finally, this study provides a set of design principles for tuning the behaviors of DNA walkers. The DNA walkers from this work could serve as a versatile platform for mathematical studies and open new opportunities for bioengineering.