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

• Published in: Microchemical journal 2023-08, Vol.191, p.108800, Article 108800
• Main Authors: Suprun, Elena V., Kutdusova, Gulnaz R., Khmeleva, Svetlana A., Ptitsyn, Konstantin G., Kurbatov, Leonid K., Radko, Sergey P.
• Format: Article
• Language: English
• Subjects: Adenine; DNA oligonucleotide; Guanine; Nucleic acid; Rolling circle amplification
• ISSN: 0026-265X; 1095-9149
• DOI: 10.1016/j.microc.2023.108800

[Display omitted] •The oxidation signal of dG in ssDNA exponentially decreases with the oligonucleotide length.•The oxidation signal of dG in 16-mer ssDNA has a bell-shaped dependence on the dG amount.•The oxidation of a single dG is insensitive to its terminal or middle position in 16-mer ssDNA.•The folding of DNA into a hairpin structure leads to about 100 mV shift of the dG oxidation peak.•The oxidation of ultralong ssDNA produced by RCA is masked by a strong non-Faradaic current. 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