Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA.
Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA.
Nucleic Acids Res. 2019 Nov 18;47(20):10968-10975. doi: 10.1093/nar/gkz844.
DNA-based devices often operate through a series of toehold-mediated strand-displacement reactions. To achieve cycling, fluidic mixing can be used to introduce 'recovery' strands to reset the system. However, such mixing can be cumbersome, non-robust, and wasteful of materials. Here we demonstrate mixing-free thermal cycling of DNA devices that operate through associative strand-displacement cascades. These cascades are favored at low temperatures due to the primacy of a net increase in base pairing, whereas rebinding of 'recovery' strands is favored at higher temperatures due to the primacy of a net release of strands. The temperature responses of the devices could be modulated by adjustment of design parameters such as the net increase of base pairs and the concentrations of strands. Degradation of function was not observable even after 500 thermal cycles. We experimentally demonstrated simple digital-logic circuits that evaluate at 35°C and reset after transient heating to 65°C. Thus associative strand displacement enables robust thermal cycling of DNA-based devices in a closed system.
基于 DNA 的器件通常通过一系列的链置换反应来实现。为了实现循环，通常使用流体混合来引入“恢复”链以重置系统。然而，这种混合可能很繁琐、不稳定且浪费材料。在这里，我们展示了通过缔合链置换级联反应进行无混合的 DNA 器件热循环。这些级联在低温下是有利的，因为碱基配对的净增加占主导地位，而“恢复”链的重新结合在较高温度下是有利的，因为链的净释放占主导地位。通过调整设计参数（如碱基对的净增加和链的浓度）可以调节器件的温度响应。即使在 500 次热循环后，也没有观察到功能退化。我们通过实验演示了在 35°C 下进行评估、在短暂加热至 65°C 后重置的简单数字逻辑电路。因此，缔合链置换使基于 DNA 的器件在封闭系统中能够进行稳健的热循环。
