DNA Logic Gate Based on Metallo-Toehold Strand Displacement

DNA is increasingly being used as an ideal material for the construction of nanoscale structures, circuits, and machines. Toehold-mediated DNA strand displacement reactions play a very important role in these enzyme-free constructions. In this study, the concept of metallo-toehold was utilized to further develop a mechanism for strand displacement driven by Ag+ ions, in which the intercalation of cytosine–cytosine mismatched base pairs on the toeholds provides additional control by varying of the concentration of Ag+ ions. The characteristics of displacement reaction in response to different concentration of Ag+ ions are investigated by fluorescence spectral and non-denaturing polyacrylamide gel electrophoresis. The reaction can successfully occur when the concentration of Ag+ ions is suitabe; excess Ag+ ions block the reaction. Furthermore, the displacement reaction can be tuned and controlled most efficiently under the condition of two C:C mismatched base pairs placed on the six-nt toehold. Based on our research, a mechanism was developed to construct Boolean logic gate AND and OR by employing strand displacement reaction as a tool, Ag+ and Hg2+ as input.

脱氧核糖核酸（DNA）正日益被用作构建纳米级结构、电路与机器的理想材料。托荷（Toehold）介导的DNA链置换反应在这类无酶构建体系中发挥着至关重要的作用。本研究利用金属托荷（metallo-toehold）概念，进一步开发了由银离子（Ag+）驱动的链置换反应机制：托荷区域上的胞嘧啶-胞嘧啶错配碱基对可通过改变银离子浓度实现额外的反应调控。本研究通过荧光光谱法与非变性聚丙烯酰胺凝胶电泳，探究了链置换反应对不同银离子浓度的响应特性。当银离子浓度适宜时，该反应可顺利发生；而过量银离子则会阻断反应进程。此外，当6 nt长度的托荷区域引入两处C:C错配碱基对时，链置换反应可被最高效地调控与控制。基于本研究成果，我们开发了一种以链置换反应为工具、银离子与汞离子（Hg2+）为输入信号，构建布尔逻辑与门（AND）与或门（OR）的机制。