Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement
Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement
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DOI：
10.1038/s41467-020-16353-y
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发表时间：
2020-05-22
影响因子：
16.6
通讯作者：
Turberfield, Andrew J.
中科院分区：
文献类型：
--
作者：
Haley, Natalie E. C.;Ouldridge, Thomas E.;Turberfield, Andrew J.
近年来，合成自组装分子系统的研究取得了很大进展。然而，设计非平衡结构需要对反应的热力学和动力学进行更精细的控制。我们提出了一种机制来增强DNA链位移反应的热力学驱动，同时几乎不干扰正向反应速率：在初始双相中引入不匹配。通过实验和仿真相结合，我们证明了位移速率对失配位置非常敏感，并且可以通过合理的设计进行调整。通过在远离双端的地方放置不匹配，可以在不显著影响正向反应速率的情况下改变链位移反应的热力学驱动。这种隐藏的热力学驱动动机是理想的非平衡系统的工程，依赖于催化控制，必须是稳健的泄漏反应。合成分子系统需要对其热力学和反应动力学进行微妙的控制，以实现催化等特性。在这里，作者建议在DNA双链中使用错配来推动催化反应，同时保持严格的催化控制。
Recent years have seen great advances in the development of synthetic self-assembling molecular systems. Designing out-of-equilibrium architectures, however, requires a more subtle control over the thermodynamics and kinetics of reactions. We propose a mechanism for enhancing the thermodynamic drive of DNA strand-displacement reactions whilst barely perturbing forward reaction rates: the introduction of mismatches within the initial duplex. Through a combination of experiment and simulation, we demonstrate that displacement rates are strongly sensitive to mismatch location and can be tuned by rational design. By placing mismatches away from duplex ends, the thermodynamic drive for a strand-displacement reaction can be varied without significantly affecting the forward reaction rate. This hidden thermodynamic driving motif is ideal for the engineering of non-equilibrium systems that rely on catalytic control and must be robust to leak reactions. Synthetic molecular systems require subtle control over their thermodynamics and reaction kinetics to implement features such as catalysis. Here the authors propose using mismatches in a DNA duplex to drive catalytic reactions forward whilst maintaining tight catalytic control.