Adsorption and electrochemical oxidation of purine bases in intact and acid-treated oligodeoxynucleotides at graphite-based electrodes. Effects of pyrimidine fraction and electrode surface oxidation

Abstract

In this work we performed a detailed study (using voltammetry and capacitance-time measurements) of the interfacial behavior of intact and acid-treated oligodeoxynucleotides (ODNs) of homopurine, homopyrimidine, or combined sequences, on the surfaces of a basal-plane pyrolytic graphite electrode (BPGE). Although the studied ODNs (d(A)5; d(G)5; d(GA)5; and d(G5A5T7C7)) contained an identical number of guanine (G) and/or adenine (A) residues, the intensities (and shapes) of their oxidation signals differed. These differences reflected variations in the relative proportions of the given purine content to the rest of the ODN, and also variations in the accessibility of electroactive sites of purine bases in the adsorbed intact ODNs. When we performed acid treatment of the ODNs in 0.5 M perchloric acid, the homopurine bases were completely removed, as evidenced by polyacrylamide gel electrophoresis (PAGE). The homopyrimidine ODNs appeared to be stable during the treatment in 0.5 M perchloric acid. Mixed sequence ODNs after acidic treatment contained short homopyrimidine ODN fragments, as shown by PAGE. These non-hydrolyzable fractions strongly adsorb onto the BPGE, significantly interfering with the voltammetric determination of released purines by blocking the surface. Interference of the pyrimidine fraction was observed even when 15 M sulfuric acid was used for the hydrolysis. Modification of the BPGE surface with graphite oxides (GrO) resulted in a strong suppression of the ODN adsorption, likely due to water clusters occupying the GrO-modified BPGE surface structure. By eliminating interference from non-hydrolyzable fractions, we attained substantial improvement in the determination of free (released) purines on GrO, as demonstrated through the detection of acid-treated plasmid DNA on a disposable, low-cost pencil graphite electrode modified with GrO.