DNA Computing Systems Activated by Electrochemically-triggered DNA Release from a Polymer-brush-modified Electrode Array

Abstract

An array of four independently wired indium tin oxide (ITO) electrodes was used for electrochemically stimulated DNA release and activation of DNA-based Identity, AND and XOR logic gates. Single-stranded DNA molecules were loaded on the mixed poly(N,N-di-methylaminoethyl methacrylate) (PDMAEMA)/poly-(methacrylic acid) (PMAA) brush covalently attached to the ITO electrodes. The DNA deposition was performed at pH 5.0 when the polymer brush is positively charged due to protonation of tertiary amino groups in PDMAE-MA, thus resulting in electrostatic attraction of the negatively charged DNA. By applying electrolysis at -1.0 V(vs. Ag/AgCl reference) electrochemical oxygen reduction resulted in the consumption of hydrogen ions and local pH increase near the electrode surface. The process resulted in recharging the polymer brush to the negative state due to dissociation of carboxylic groups of PMAA, thus repulsing the negatively charged DNA and releasing it from the electrode surface. The DNA release was performed in various combinations from different electrodes in the array assembly. The released DNA operated as input signals for activation of the Boolean logic gates. The developed system represents a step forward in DNA computing, combining for the first time DNA chemical processes with electronic input signals.

Keywords: DNA computing; DNA release; Electrochemical signal; Logic gate; Modified electrode; Polymer brush.

Fig. 1

Modification of the ITO electrode with the mixed polymer brush. Note that the same procedure was used for modification of a single-ITO-coated glass slide electrode used for the AFM characterization as well as for modification of individual ITO electrodes in the electrode array used for the electrochemical study and DNA load/release. The following abbreviations are used in the scheme: BPS=(3-Bromopropyl)trimethoxysilane; APBMA=amino terminated poly(t-butyl methacrylate); PDMAEMA=poly(N,N-dimethylaminoethyl methacrylate); PMAA=poly(methacrylic acid).

Fig. 2

Impedance spectra measured on the mixed-polymer-brush modified ITO electrode (one of the electrodes in the array) in the presence of 1 mM [Fe(CN)₆]^3−/4− redox probe. The experiments were performed at pH 5.0 and 9.0 (curves a and b, respectively), when the mixed-polymer brush is positively and negatively charged, respectively. The bias potential is +0.25 V vs. Ag/AgCl reference.

Fig. 3

Schematic representation of the electrostatic loading of DNA on the negatively charged polymer brush at pH 5.0 (A), electro-chemically generated pH increase in course of O₂ reduction (B), and electrostatic repulsion and release of DNA from the negatively charged electrode at pH ca. 9.9 locally produced at the electrode surface (C).

Fig. 4

AFM characterization of the mixed polymer brush thickness: (A) before deposition of FAM-DNA, (C) after deposition of FAM-DNA, 200 pmol, and (E) after removing FAM-DNA from the electrode surface upon its washing with a lactate solution, 1 mM, with pH 9.9. Plots B, D and F show the corresponding scratch profiles. Note that the AFM measurements were performed on the ITO-coated glass slide in air by scanning in tapping mode.

Fig. 5

Time-dependent fluorescence measured at λ =520 nm in 1 mM lactic solution containing 100 mM Na₂SO₄, pH 5.0, upon leakage and electrochemically stimulated FAM-DNA release. The FAM-DNA load and release were performed on one of the ITO electrodes in the array. The structure of the FAM fluorescent label attached to the DNA molecule is shown at the right. The process can be considered as a model of the DNA-based Identity gate where the input signal (potential applied on the electrode) is directly copied to the output signal (fluorescence measured in the solution).

Fig. 6

The operation of the DNA-based AND logic gate activated by Input A and Input B signals released from two electrodes in the array upon application of −1.0 V to the electrodes in different combinations. The output signal was measured in the solution as the fluorescence of the FAM dye. The exact solution composition and other experimental details are given in the Supporting Information.

Fig. 7

(A) Truth table of the Boolean AND gate. (B) Fluorescence spectra measured in the solution upon application of −1.0 V to two DNA-loaded electrodes and Input A and Input B release in different combinations. (C) The bar chart demonstrating the output signal for different combinations of the input signals.

Fig. 8

The operation of the DNA-based XOR logic gate activated by Input C and Input D signals released from two electrodes in the array upon application of −1.0 V to the electrodes in different combinations. The output signal was measured in the solution as the fluorescence of the Qz6 dye (shown in the scheme as F). The exact solution composition and other experimental details are given in the Supporting Information.

Fig. 9

(A) Truth table of the Boolean XOR gate. (B) Fluorescence spectra measured in the solution upon application of −1.0 V to two DNA-loaded electrodes and Input C and Input D release in different combinations. (C) The bar chart demonstrating the output signal for different combinations of the input signals.