Investigating the dynamics of surface-immobilized DNA nanomachines.
Investigating the dynamics of surface-immobilized DNA nanomachines.
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DOI：
10.1038/srep29581
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发表时间：
2016-07-08
影响因子：
4.6
通讯作者：
Tyrrell AM
中科院分区：
文献类型：
--
作者：
Dunn KE;Trefzer MA;Johnson S;Tyrrell AM
分子的表面固定可以对其结构、功能和动力学产生深远的影响。立足点介导的链置换通常在溶液中用于驱动由 DNA 制成的合成纳米机器，但表面固定对该反应的机制和动力学的影响尚未完全阐明。在这里，我们表明，表面固定纳米机器中链位移的动力学与溶液相反应的动力学显着不同，我们将其归因于 DNA 层内分子间相互作用的影响。我们证明，可以通过改变链长度、浓度和 G/C 含量来控制链位移的动态。通过插入不匹配的碱基，还可以独立地调节成分置换过程（立足点结合和分支迁移）的速率，并且可以根据整个反应的时间依赖性对信息进行编码。我们的研究结果将促进表面固定动态 DNA 纳米机器的合理设计，包括计算设备和轨道电机。
Surface-immobilization of molecules can have a profound influence on their structure, function and dynamics. Toehold-mediated strand displacement is often used in solution to drive synthetic nanomachines made from DNA, but the effects of surface-immobilization on the mechanism and kinetics of this reaction have not yet been fully elucidated. Here we show that the kinetics of strand displacement in surface-immobilized nanomachines are significantly different to those of the solution phase reaction, and we attribute this to the effects of intermolecular interactions within the DNA layer. We demonstrate that the dynamics of strand displacement can be manipulated by changing strand length, concentration and G/C content. By inserting mismatched bases it is also possible to tune the rates of the constituent displacement processes (toehold-binding and branch migration) independently, and information can be encoded in the time-dependence of the overall reaction. Our findings will facilitate the rational design of surface-immobilized dynamic DNA nanomachines, including computing devices and track-based motors.