State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China.
ACS Nano. 2018 Apr 24;12(4):3341-3350. doi: 10.1021/acsnano.7b08673. Epub 2018 Mar 30.
DNA/RNA strand displacement is one of the most fundamental reactions in DNA and RNA circuits and nanomachines. In this work, we reported an exploration of the dynamic process of the toehold-mediated strand displacement via core-satellite plasmon rulers at the single-molecule level. Applying plasmon rulers with unlimited lifetime, single-strand displacement triggered by the invader that resulted in stepwise leaving of satellite from the core was continuously monitored by changes of scattering signal for hours. The kinetics of strand displacement in vitro with three different toehold lengths have been investigated. Also, the study revealed the difference in the kinetics of strand displacement between DNA/RNA and DNA/DNA duplexes. For the kinetics study in vivo, influence from the surrounding medium has been evaluated using both phosphate buffer and cell lysate. Applying core-satellite plasmon rulers with high signal/noise ratio, kinetics study in living cells proceeded for the first time, which was not possible by conventional methods with a fluorescent reporter. The plasmon rulers, which are flexible, easily constructed, and robust, have proven to be effective tools in exploring the dynamical behaviors of biochemical reactions in vivo.
DNA/RNA 链置换是 DNA 和 RNA 电路和纳米机器中最基本的反应之一。在这项工作中，我们在单分子水平上报告了通过核心-卫星等离子体尺子探索引发物介导的链置换的动态过程。通过应用具有无限寿命的等离子体尺子，通过入侵物触发的单链置换导致卫星从核心逐步离开，通过散射信号的变化可以连续监测数小时。已经研究了具有三种不同的连接子长度的体外链置换的动力学。此外，该研究揭示了 DNA/RNA 和 DNA/DNA 双链之间链置换动力学的差异。为了进行体内动力学研究，已经使用磷酸盐缓冲液和细胞裂解物评估了周围介质的影响。通过应用具有高信噪比的核心-卫星等离子体尺子，首次在活细胞中进行了动力学研究，这是使用荧光报告器的传统方法不可能实现的。事实证明，等离子体尺子灵活、易于构建且坚固耐用，是探索体内生化反应动态行为的有效工具。
