Electrochemical and circular dichroism spectroscopic evidence of two types of interaction between [Ru(NH3)6]3+ and an elongated thrombin binding aptamer G-quadruplex

In the field of electrochemical biosensing based on DNA probes immobilised at electrode surfaces the [Ru(NH3)6]3+ redox marker is commonly used for quantitative characterisation and/or detection purposes. Although it is generally assumed that the interactions between the hexaammineruthenium(III) cation and DNA are solely of electrostatic nature, and thus non-specific in essence, it is shown herein that this is not the case for a sequence containing a G-quadruplex part. The present work investigates the interactions of [Ru(NH3)6]3+ with an oligonucleotide (21-mer) consisting of the thrombin binding aptamer sequence (a G-quadruplex) elongated by a 5’-overhang of six nucleotides. Combining circular dichroism and electrochemical analyses by differential pulse voltammetry, alternating current voltammetry and cyclic voltammetry, it is demonstrated that the overall interaction stoichiometry (number of [Ru(NH3)6]3+ bound to one DNA strand) is lower than the 7 [Ru(NH3)6]3+ per strand expected for a total charge compensation. Our results indicate that two types of interaction take place between [Ru(NH3)6]3+ and the elongated TBA sequence: one is the conventional electrostatic binding of the positively charged redox marker with the negatively charged phosphate groups, while the other is connected with the G-quadruplex part of the sequence. This latter interaction influences the DNA conformation in solution and involves 2 [Ru(NH3)6]3+ per strand, both in solution and with DNA immobilised at gold electrodes. In this configuration, the electron transfer rate constant is evaluated at 37 ± 5 s-1 on the basis of a Laviron plot.