Investigation of the interactions between methylene blue and intramolecular G-quadruplexes: an explicit distinction in electrochemical behavior

Abstract

G-quadruplex sequences exist in eukaryotic organisms and prokaryotes, and the investigation of interactions between Gquadruplexes and small molecule ligands is important for gene therapy, biosensor fabrication, fluorescence imaging and so on. Here, we investigated the behaviour of methylene blue (MB), an electroactive molecule, in the presence of different intramolecular G-quadruplexes by electrochemical method using a miniaturized electrochemical device based on its intrinsic electrochemical property. Although the effects of MB on different intramolecular G-quadruplex structures are not obvious by circular dichroism spectroscopy, distinct differences in binding affinities of MB with different intramolecular Gquadruplexes were fast and easily observed by the electrochemical technique. At the same time, for the human telomerase G-rich sequence (HT), the diffusion current of MB changed sensitively under different ion conditions due to the formation of different conformations of HT, which indicated that our electrochemical method has the potential to study the influence of metal ions on the conformations of the G-quadruplexes with simplicity, rapid response and low cost. From all these, new stacking mechanism and rule were obtained, which were also validated by docking studies and isothermal titration calorimetry (ITC).

Magic-angle spinning NMR spectroscopy provides insight into the impact of small molecule uptake by G-quartet hydrogels

“…59 These upfield shifts associated with 1 H signals of MB in gels (i.e., Dd = 0.3, 0.3 and 0.7 ppm for the signals at 7.7, 6.8 and 6.2 ppm, respectively) can be attributed to the p-p stacking and CH-p interactions that occur between MB and G4 fibrils. In addition, various binding interactions, such as end stacking, side stacking and parallel stacking of MB molecules to G4-rich DNA, have been previously proposed, 55 and those same types of interactions may be relevant here in the context of MB binding to the G4ÁK + gels. Also, a priori, ionic interactions between cationic MB and borate anions in the G4ÁK + borate gels are certainly important.…”

“…The cationic and planar dye, methylene blue (MB), is well known to bind to G-quadruplex DNA fibrils. [54][55][56][57] We have previously studied the physical absorption of MB by these anionic GB gels, using both UV-Vis spectroscopy and 11 B NMR spectroscopy. 21,22 In particular, we found that G4ÁK + gels (72 mM in G) were able to quantitatively absorb 12.5 mM MB after soaking the hydrogel in a KCl solution of the dye for 24 h, as determined by UV-Vis spectroscopy.…”

G-Quadruplexes in the Regulation of Viral Gene Expressions and Their Impacts on Controlling Infection

“…However, further investigation in infected cells is required to assess whether berberine effectively reduces SARS-CoV-2 infectivity. Methylene blue (M-Blue), a tricyclic phenothiazine compound, has been shown to have G4-stabilizing properties [255]. M-Blue has been previously approved by the FDA for the treatment of methemoglobinemia and other medical applications [256].…”

A Homogeneous Label-Free Electrochemical microRNA Biosensor Coupling With G-Triplex/Methylene Blue Complex and λ-Exonuclease-Assisted Recycling Amplification

“…For example, the hemin/G4, a known horseradish peroxidase mimicking DNAzyme, has been widely used in the construction of various electrochemical biosensors ( Wu et al, 2017 ; Liu et al, 2017b ; Chen et al, 2018 ; Sun et al, 2018 ; Ji et al, 2019 ; Wu et al, 2021a ). The discovery that the combination of G4 and MB can cause a great reduction in MB diffusion current has further expanded its biosensing application scope ( Zhang et al, 2014 ; Cao et al, 2017 ; Zhao et al, 2020b ). Subsequently, it was found that G-triplex (G3), as a folding intermediate of G4, has an even stronger affinity to MB than G4.…”