Research Article: DNA Logic Gate Based on Metallo-Toehold Strand Displacement

Date Published: November 3, 2014

Publisher: Public Library of Science

Author(s): Wei Deng, Huaguo Xu, Wei Ding, Haojun Liang, Gayle E. Woloschak.

http://doi.org/10.1371/journal.pone.0111650

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.

Partial Text

The remarkable specificity and strength of interactions between complementary nucleotides make DNA a useful material [1] for structuring nanoscale device [2]–[4], circuits [5], [6], and machines [7], [8]. Recently, 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]. Moreover, the Winfree group reported that toehold-mediated strand displacement can be applied to the construction of entropy-driven catalytic circuit reactions [15], digital logic circuit [16], and neural network computation [17]. The kinetics of DNA strand displacement has also been elaborately studied [18]. In previous papers, we also revealed a strategy for the assembly and logic operation of gold nanoparticles driven by a dynamic DNA-fueled molecular machine [19].

In summary, the concept of metallo-toeholds is utilized to further propose a mechanism that Ag+ ions which specifically insert into mismatched base pair (C:C) to form C–Ag(I)–C structure can be used to trigger the DNA strand displacement reaction. The Ag+ ions serve as a regulator, and can tune the DNA strand displacement reaction through metallo-toehold. Through detailed discussions on the influences of toehold length and C:C mismatched numbers on the toehold, we confirmed that the strand displacement reaction can be tuned and controlled most efficiently under the condition of two C:C mismatched placed on a six-nt toehold. By introducing the completely complementary strand, we clarified that excessive Ag+ ions obstructed the dis- placement reaction. Moreover, a mechanism for constructing Boolean logic gate AND and OR by employing strand displacement reaction as a tool, Ag+ and Hg2+ as input is deveploed. Besides, such logic gates work well. It has been reported that other metal ions, such as Cu2+ and Ni2+, can specifically interact with nucleoside bases to form metal-ion-mediated base pairs [46], [47]. Therefore, our strategy extends the application between metal ions and nucleic acids. Moreover, this strategy can be further used to construct new logic gate with other metal ions as input and complicated logic circuits. We hope that the concept of metallo-toehold formed by metal ions (e.g., Ag+ and Hg2+) can be further used in DNA nanotechnology.

 

Source:

http://doi.org/10.1371/journal.pone.0111650