DNA Interaction of Methylene Green and Fast Green with dsDNA and ssDNA and G-quadruplex DNA

DNA plays an active role in cellular processes not only through the transport of genetic information through its base sequence but also through the secondary structures revealed by folding. In recent years, investigating the interaction of DNA-targeting ligands has emerged as an important area of research, especially considering the importance of these structures in processes such as cancer. The current study investigated the interaction of MG and FG ligands with DNA. The main motivation for the study was to investigate whether these structures, known to interact with DNA, have a specific affinity for ctDNA, ssDNA, and G-quadruplex DNA. The interaction of FG with DNA species did not cause any significant spectral changes, thus concluding that the affinity was very low. Competitive dialysis experiments confirmed the affinity results. Significant spectral changes were observed in the MG-DNA interaction. The interaction of MG with DNA species caused a hypochromic effect of up to 52%, while a bathochromic shift of up to 17 nm was observed. Kb values ​​calculated from the data were also found to be higher than 106 M-1. The interaction stoichiometry with G-quadruplex DNAs was determined to be 1:2, indicating an end-stacking mechanism. Competitive dialysis experiments also confirmed that MG exhibited high affinity for DNA species.