Electrochemical behavior of 7-deazaguanine- and 7-deazaadenine-modified DNA at the hanging mercury drop electrode

Abstract

DNA modification with synthetic analogs of natural nucleotides and/or their conjugates with external redox active groups is applied in the development of electrochemical DNA sensors or assay for DNA hybridization, SNP typing, DNA damage and so forth. 7-Deazapurines (Pu*) are analogs of natural purine bases in which N7 atom is replaced by CH group. The Pu* bases retain Watson-Crick base pairing of their parent purines (and the ability to form duplex DNA) but are incapable of Hoogsteen pairing (and thus cannot be involved in triplex or quadruples DNA structures). Previously, we studied electrochemical oxidation of Pu* residues in DNA fragments (prepared by PCR in the presence of Pu* deoxynucleoside triphosphates) at a carbon electrode and reported on significantly lower potentials of oxidation of both 7-deazaguanine (G*) and 7-deazaadenine (A*), compared to natural guanine (G) and adenine (A), respectively. In this work, we studied faradaic and tensammetric responses of G*-or A*-modified DNA on the hanging mercury drop electrode (HMDE). While A* was reduced at the HMDE, giving rise to a similar irreversible cathodic peak as the natural A, G* did not yield any peak analogous to the peak G due to guanine, in agreement with a loss of corresponding redox site in G*. Responses of DNA modified with A* were relatively similar to those of unmodified DNA (albeit we observed certain differences in tensammetric peak currents). Effects of G substitution by G* were more pronounced, being reflected in diminution of peak due to guanine, decrease of the peak CA (due to cytosine and adenine reduction) and in significantly changed shape of tensammetric DNA signals, indicating altered adsorption/desorption processes. While substitution of A by A* resulted in certain destabilization of the DNA duplex at the negatively charged HMDE surface (in qualitative agreement with significantly decreased melting temperature of the same DNA duplexes in solution), G*-modified duplex DNA displayed apparently lower susceptibility to surface denaturation. Graphical abstract -1.5 -1.2 -0.9 -0.6 -0.3 0.0 -0.9 -0.6 -0.3 0.0

Butylacrylate‐nucleobase Conjugates as Targets for Two‐step Redox Labeling of DNA with an Osmium Tetroxide Complex

“…At 37 °C even the natural DNA got partially modified. Increased reactivity of the dA*‐dsDNA at 25 °C, compared to the natural dsDNA, can be attributed to a reduced stability of duplex DNA in which A residues were substituted with A* (in agreement with our recent electrochemical study ). Inspection of the peak potentials resulting from these modification experiments (Table ) brought further support for the conclusion that it is the BA moiety what is preferentially modified in the ds DNA: at all temperatures these samples gave peak α at −0.570–−0.575 V, which is in a perfect agreement with the value obtained for the dA BA TdT tailing product (Table ).…”

Label‐free Voltammetric Detection of Products of Terminal Deoxynucleotidyl Transferase Tailing Reaction

“…This fact is utilized, for example, in PCR amplification of G‐rich sequences where the quadruplex formation could affect the amplification process. For analysis of the A 30 +G* tailing reaction products (Figure C and 3D), only oxidation at PGE was used since, with HMDE, G* does not yield any peak analogous to the G HMDE peak, in agreement with absence of the corresponding redox site in G* . Both voltammetric and PAGE analysis showed that, unlike in the case of A 30 +G tailing products, the length of the tailing products grew gradually with the rising dG*TP:primer ratio, with the average tail length much higher than in the case of dGTP, especially for the 20 : 1 and 50 : 1 ratios and the G* OX signal for the 50 : 1 ratio being ∼10‐fold higher than that for the 1 : 1 ratio.…”

Preparation of a New Copper/Mercury‐Based Amalgam Electrode with Minimal Mercury Content and Its Application for the Determination of Azathioprine in Biological Fluids

“…Mercury drop electrode usually shows better performance for electrochemical reduction of a wide range of organic and inorganic species, compared to the other electrodes because of exhibiting considerable overpotential for hydrogen ion reduction [19–21] . However, the toxicity of mercury electrode encourages the researchers to replace it with less toxic amalgam electrodes which are the mixture of metal and mercury [22–25] …”