Reconfigurable DNA triplex structure for pH responsive logic gates

Abstract

The DNA triplex is a special DNA structure often used as a logic gate substrate due to its high stability, programmability, and pH responsiveness. However, multiple triplex structures with different C-G-C⁺ proportions must be introduced into existing triplex logic gates due to the numerous logic calculations involved. This requirement complicates circuit design and results in many reaction by-products, greatly restricting the construction of large-scale logic circuits. Thus, we designed a new reconfigurable DNA triplex structure (RDTS) and constructed the pH-responsive logic gates through its conformational change that uses two types of logic calculations, 'AND' and 'OR'. The use of these logic calculations necessitates fewer substrates, further enhancing the extensibility of the logic circuit. This result is expected to promote the development of the triplex in molecular computing and facilitate the completion of large-scale computing networks.

Fig. 1. (A) Scheme of DNA triplex assembly and separation in response to pH changes. The modified fluorescence groups in the figure are respectively Cy5 (red), BHQ-2 (black) and quenched Cy5 (gray). (B) PAGE analysis of DNA triplex at pH 5 (left) and pH 8 (right).

Fig. 2. (A) Corresponding fitted pH-dependent curve. The black dots represent normalized fluorescence measurements at pH, and the red curve is the fitting curve. (B) Normalized fluorescence kinetic measurements of DNA triplex cyclic pH-jump experiments. The experiments were performed at 25 °C.

Fig. 3. (A and B) Scheme of the RDTS assembled under acidic condition and alkaline condition. (C and D) Fluorescence kinetics measurements of RDTS assembled at pH 5 (C) and at pH 8 (D). Strands L2, O, and input are added at the arrow marks in the figure.

Fig. 4. Scheme of pH responsive logic gates. The logic gate substrate is state 1 at pH 5, showing as ‘AND’ gate; the logic gate substrate transforms into state 2 at pH 8, presenting itself as ‘OR’ gate. The corresponding reactions of the two logic gates are also shown in this figure, the truth tables of ‘AND’ gate and ‘OR’ gate are given.

Fig. 5. (A and B) PAGE analysis of pH responsive logic gates: ‘AND’ gate (pH 5) and ‘OR’ gate (pH 8). (C and D) Fluorescence kinetics measurements of pH responsive logic gates: ‘AND’ gate (pH 5) and ‘OR’ gate (pH 8). We take normalized fluorescence intensity 0.4 as the threshold value.