Influence of the lengths of thymine, cytosine, and adenine stretches on the two-dimensional condensation of oligodeoxynucleotides at mercury and silver amalgam electrode surfaces

Abstract

Two-dimensional (2D) condensation of nucleic acid components at mercury electrodes around the potential of zero charge has been known for decades. In our previous pilot study, we reported on 2D condensation of homopyrimidine oligodeoxynucleotides (ODNs) at the hanging mercury drop electrode (HMDE) in negative potential region. In this work we focused in detail on the effect of the homopyrimidine ODN length (from 3- to 50-mers) on the formation and properties of 2D condensed films at the HMDE. To elicit possible orientation of the homopyrimidine ODN molecules in their 2D condensed layers (i.e. surface concentration of the ODN molecules and the cross-section areas per adsorbed ODN molecules) we used a model in which the maximum surface concentration of the adsorbed ODN molecules is determined from linear dependences of the square of capacitance pit width on temperature. Effect of the length of homoadenine ODNs on their adsorption/desorption processes were studied for comparison, as well as effects of ionic strength and base protonation. Further we focused on the effects of the length of periodically repeated homothymine/homocytosine stretches in 30-mer ODNs on their interfacial behavior at the negatively charged HMDE. Experiments with binary mixtures of non-complementary and complementary 15-mer homo-ODNs revealed dominance of the homopyrimidine, particularly cytosine, ODN responses in such competitive arrangement. The usefulness of solid silver amalgam electrode for this type of studies is demonstrated. Finally, potential applications of our results in label-free electrochemical analysis of alternative DNA structures are briefly discussed.