Exploring the speed limit of toehold exchange with a cartwheeling DNA acrobat
Exploring the speed limit of toehold exchange with a cartwheeling DNA acrobat
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DOI：
10.1038/s41565-018-0130-2
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发表时间：
2018-08-01
影响因子：
38.3
通讯作者：
Walter, Nils G.
中科院分区：
文献类型：
--
作者：
Li, Jieming;Johnson-Buck, Alexander;Walter, Nils G.
动态DNA纳米技术已经产生了不平凡的自主行为，如刺激引导的移动、计算和可编程的分子组装。尽管取得了这些成功，但基于DNA的纳米机器动力学缓慢，需要几分钟或更长时间才能进行几个操作。在这里，我们通过对一种新型的DNA步行器进行单分子优化，来追求DNA纳米技术中一类重要反应的速度限制-脚趾交换-这种新型DNA步行器在一系列互补的寡核苷酸上经历侧翻运动。在为快速移动优化了这个DNA‘杂技’之后，我们测量了接近1s(-1)的步速常数，这比以前的DNA步行者快了10到100倍。最后，我们使用单粒子跟踪来演示步行器在10分钟内超过数百纳米的运动，这与步进动力学的预测定量一致。这些结果表明，利用链置换的广泛类别的DNA纳米机器的运行率有可能大幅提高。
Dynamic DNA nanotechnology has yielded nontrivial autonomous behaviours such as stimulus-guided locomotion, computation and programmable molecular assembly. Despite these successes, DNA-based nanomachines suffer from slow kinetics, requiring several minutes or longer to carry out a handful of operations. Here, we pursue the speed limit of an important class of reactions in DNA nanotechnology-toehold exchange-through the single-molecule optimization of a novel class of DNA walker that undergoes cartwheeling movements over a field of complementary oligonucleotides. After optimizing this DNA 'acrobat' for rapid movement, we measure a stepping rate constant approaching 1s(-1), which is 10- to 100-fold faster than prior DNA walkers. Finally, we use single-particle tracking to demonstrate movement of the walker over hundreds of nanometres within 10 min, in quantitative agreement with predictions from stepping kinetics. These results suggest that substantial improvements in the operating rates of broad classes of DNA nanomachines utilizing strand displacement are possible.