Voltammetric oxidation behavior of single-stranded DNA on carbon screen printed electrodes: From short oligonucleotides to ultralong amplification products

To deeper understand the electrochemical behavior of nucleic acids, the synthetic DNA oligonucleotides of general formula (ACTG)n, where n = 1-12, as well as 16-mer DNA oligonucleotides varying in the number of guanine (dG; G-n, n = 0-7) or adenine (dA; A-n, n = 0-8) residues, and single-stranded DNA (ssDNA) amplification products were employed to systematically investigate their oxidation in the 'dissolved' and 'adsorbed' forms on carbon screen printed electrodes by square wave and cycling voltammetry in the potential range of 0.5-1.5 V (vs. Ag/AgCl). Two signals at 0.9-1.0 V and 1.1-1.2 V, attributed to the oxidation of dG and dA, respectively, were registered for the most of oligonucleotides. The oxidation process of 'dissolved' (ACTG)n with n = 1-2 via dG was found diffusion-controlled, while (ACTG)3 has demonstrated a mixed mechanism of oxidation reaction. At the same time, 'adsorbed' oligonucleotides demonstrated adsorption-limited responses, except for (ACTG)1 showing a mixed reaction mechanism. At a constant nucleotide or oligonucleotide molar concentration, the registered signals for (ACTG)n exponentially decreased with the molecule length. The signals of all studied oligonucleotides after pre-adsorption on electrode surface were up to 10-fold higher than those in the soluble form, except for (ACTG)1. The dG oxidation signal for G-n oligonucleotides, registered at about 0.9 V, was practically insensitive to the position of a single dG (at the end or in the middle of polynucleotide chain), while demonstrating a bell-shaped dependence on the dG amount with a maximum at n = 3-4. The dG oxidation signal for A-n oligonucleotides with a constant portion of dG also increased with the number of dA residues in the bell-shaped fashion with a maximum at n = 5. The folding of oligonucleotides into hairpins with a stem formed via dG/dC pairing resulted in a shift of the peak potential for dG oxidation to higher values. Finally, ultralong ssDNA products generated by rolling circle amplification (RCA) were found to produce strong non-Faradaic current masking the dG and dA oxidation signals. The electrochemical detection of RCA products via dG and dA oxidation was found possible if ultralong ssDNA is fragmented by carrying out RCA in the presence of an appropriate restrictase.

Automated summary

In this study, the electrochemical behavior of nucleic acids was investigated using synthetic DNA oligonucleotides and single-stranded DNA amplification products. The oxidation of guanine (dG) and adenine (dA) residues in the oligonucleotides was studied by square wave and cycling voltammetry. The results showed that the oxidation process of dissolved oligonucleotides was diffusion-controlled, while adsorbed oligonucleotides demonstrated adsorption-limited responses. The signal intensity of the oligonucleotides exponentially decreased with the molecule length at a constant concentration. The oxidation signal of dG in G-n oligonucleotides was insensitive to the position of dG, but showed a bell-shaped dependence on the amount of dG. The oxidation signal of dG in A-n oligonucleotides increased with the number of dA residues in a bell-shaped fashion. Folding the oligonucleotides into hairpins shifted the peak potential for dG oxidation to higher values.