N-methyl mesoporphyrin IX (NMM) as electrochemical probe for detection of guanine quadruplexes

G-quadruplexes (G4) are stable alternative secondary structures of nucleic acids. With increasing understanding of their roles in biological processes and their application in bio- and nanotechnology, the exploration of novel methods for the analysis of these structures is becoming important. In this work, N-methyl mesoporphyrin IX (NMM) was used as a voltammetric probe for an easy electrochemical detection of G4s. Cyclic voltammetry on a hanging mercury drop electrode (HMDE) was used to detect NMM with a limit of detection (LOD) of 40 nM. Characteristic reduction signal of NMM was found to be substantially higher in the presence of G4 oligodeoxynucleotides (ODNs) than in the presence of single- or double-stranded ODNs and even ODNs susceptible to form G4s but in their unfolded, single-stranded forms. Gradual transition from unstructured single strand to G4, induced by increasing concentrations of the G4 stabilizing K+ ions, was detected by an electrochemical method for the first time. All obtained results were supported by circular dichroism spectroscopy. This work expands on the concept of electrochemical probes utilization in DNA secondary structure recognition and offers a proof of principle that can be potentially employed in the development of novel electroanalytical methods for nucleic acid structure studies.

Automated summary

In this study, N-methyl mesoporphyrin IX (NMM) was utilized as a voltammetric probe for the electrochemical detection of G4s. The detection of NMM was achieved by cyclic voltammetry on a hanging mercury drop electrode (HMDE) with a limit of detection (LOD) of 40 nM. The reduction signal of NMM was found to be significantly higher when G4 oligodeoxynucleotides (G4 ODNs) were present compared to single- or double-stranded ODNs or unfolded ODNs capable of forming G4s. Gradual transition from unstructured single strand to G4, induced by increasing concentrations of the G4 stabilizing K+ ions, was detected for the first time using electrochemical methods. Circular dichroism spectroscopy provided support for the obtained results. This work expands on the utilization of electrochemical probes for DNA secondary structure recognition and offers a proof of principle for the development of novel electroanalytical methods for nucleic acid structure studies.