Interfacial behaviour of oligodeoxynucleotides prone to G-quadruplex formation on negatively charged electrode surface monitored by electrochemical probes

Development of analytical tools enabling discrimination amongst various structures of nucleic acids attracts interest due to diverse biological functions and prospective biotechnological applications of the latter. In this work, two electrochemically active compounds, copper porphyrin complex Cu-TMPy2PP and base-modified deoxyguanosine triphosphate conjugate bearing 3-nitrophenyl moiety (dGNPTP), were used as probes to study electrode potential effects on oligodeoxynucleotides (ODNs) of various sequences and abilities to form secondary structures (including unstructured single strands, duplexes, guanine quadruplexes, i-motifs) at the surface of hanging mercury drop electrode (HMDE). Our experiments revealed formation of less dense adsorbed layers by G-rich ODNs with the propensity to fold into G-quadruplexes (G4), compared to layers formed by other studied sequences. Strikingly, the G4-forming ODNs were significantly more susceptible to desorption from the HMDE surface during its polarization to highly negative potentials compared to other ODNs. Negative potential-induced desorption of the ODNs from HMDE was further confirmed by gel electrophoresis. Application of the electro-chemical probes offers a useful method for further research of DNA conformations and transitions taking place in solution and at electrically charged surfaces.

Automated summary

In this study, two electrochemically active compounds, Cu-TMPy2PP and dGNPTP, were used as probes to investigate the effects of electrode potential on ODNs and their abilities to form secondary structures at the HMDE surface. The results showed that G-rich ODNs with the potential to form G-quadruplexes formed less dense adsorbed layers compared to other sequences. Additionally, the G4-forming ODNs were more easily desorbed from the HMDE surface at highly negative potentials, as confirmed by gel electrophoresis. This application of electrochemical probes provides a useful method for studying DNA conformations and transitions.