An enzyme-powered, three-dimensional lame DNA walker.

Jie Fang, Changjing Yuan, Junjie Li, Junlong Li, Tingyan Yang, Yongcan Guo, Ding Wang, Jianjiang Xue, WeiLing Fu, Guoming Xie

Biosensors & bioelectronics 2021 Apr 01

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Molecular machines constructed by three-dimensional (3-D) DNA walker have emerged as a hot topic in applications such as novel biosensors, cargo delivery platforms and intracellular imaging. Herein, we first propose a lame DNA walker that can randomly and autonomously move on microsphere-based 3-D track. The stochastic lame walker has a long leg mainly responsible for persistent movement and a short leg cutting substrates rapidly. Its motion is propelled by a nicking endonuclease cleavage of hybridized DNA tracks. Kinetic and persistent study show that the lame DNA walker enables reaction equilibrium at 30 min, need a cleat domain of at least 14 nucleotides and can persistently move on 3-D tracks with an average rate of 6.467 × 10-11 M s-1. We also demonstrate that the lame walker can be used to detect target DNA in the detection range of 10 pM-5 nM with high specificity by toehold exchange mechanism. This work will further expand the performance of 3-D DNA walkers and substantially contributes to the improved understanding of DNA walking systems. Copyright © 2021 Elsevier B.V. All rights reserved.

Citation

Jie Fang, Changjing Yuan, Junjie Li, Junlong Li, Tingyan Yang, Yongcan Guo, Ding Wang, Jianjiang Xue, WeiLing Fu, Guoming Xie. An enzyme-powered, three-dimensional lame DNA walker. Biosensors & bioelectronics. 2021 Apr 01;177:112981