Abstract
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.
Highlights
The remarkable specificity and strength of interactions between complementary nucleotides make DNA a useful material [1] for structuring nanoscale device [2,3,4], circuits [5,6], and machines [7,8]
We explore the effects of the length of toehold, the numbers of cytosine-cytosine mismatched, and the concentration of Ag+ ions on the control of strand displacement reaction
The concept of metallo-toeholds is utilized to further propose a mechanism that Ag+ ions which insert into mismatched base pair (C:C) to form C–Ag(I)–C structure can be used to trigger the DNA strand displacement reaction
Summary
The remarkable specificity and strength of interactions between complementary nucleotides make DNA a useful material [1] for structuring nanoscale device [2,3,4], circuits [5,6], and machines [7,8]. The concept of toehold-mediated DNA strand displace- ment first used by Yurke [9] attracted a lot of interest, which occurs when hybridization of an invading strand starts at a short single strand attached to another single-stranded sticky end called as ‘‘toehold’’ domain of a double-stranded complex, resulting in a branch migration reaction [10] that the invading strand displaces the target strand from the double-stranded complex along with the production of a new complex with the help of a short sequence of contiguous complementary bases This concept has been proved to be a powerful tool that allows control over the building of nucleic acid tweezers [11], DNA walkers [12], molecular gears [13] as well as the constructing of DNA-based logic gates [14]. We revealed a strategy for the assembly and logic operation of gold nanoparticles driven by a dynamic DNA-fueled molecular machine [19]
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