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Mechanistic Understanding of Surface Migration Dynamics with DNA Walkers

preprint
submitted on 23.09.2020 and posted on 23.09.2020 by yancheng Du, Jing Pan, Hengming Qiu, Chengde Mao, Jong Hyun Choi

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 on migration dynamics. Four distinct migration modes (ballistic, Lévy, 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.

History

Email Address of Submitting Author

jchoi@purdue.edu

Institution

Purdue University

Country

United States

ORCID For Submitting Author

0000-0002-0507-3052

Declaration of Conflict of Interest

No competing financial interest

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