Metal-Ion-Triggered Exonuclease III Activity for the Construction of DNA Colorimetric Logic Gates

Abstract

The logic system is obtained by using a series of double-stranded (ds) DNA templates with mismatched base pairs (T-T or C-C) and ion-modulated exonuclease III (Exo III) activity, in which the Exo III cofactors, Hg(2+) and Ag(+) ions, are used as inputs for the activation of the respective scission of Exo III based on the formation of T-Hg(2+) -T or C-Ag(+) -C base pairs. Additionally, two kinds of signal probes are utilized to transduce the logic operations. One is the two split G-rich DNA strands that are used to design the OR, AND, INHIBIT, and XOR gates, whereas the other is the self-assembled split G-quadruplex structure to construct NOR, NAND, IMPLICATION, and XNOR operations based on DNA hybridization and strand displacement. In the presence of hemin, the split G-quadruplex biocatalyzes the formation of a colored product, which is an output signal for the different logic gates. Thus, we have constructed a complete set of colorimetric DNA logic gates based on the Exo III and split G-quadruplex for the first time. In addition, we are able to effortlessly recognize the logic output signals by the naked eye and their simplicity and cost-effective design is the most apparent feature for the logic gates developed in this work.

Keywords: DNA; G-quadruplexes; biocatalysis; enzymes; molecular electronics; silver.