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Interactions between a Bioflavonoid and c-MYC Promoter G-Quadruplex DNA: Ensemble and Single-Molecule Investigations

Paul, Sneha, Hossain, Sk Saddam, M, Bala Divya, Samanta, Anunay
TheJournal of physical chemistry 2019 v.123 no.9 pp. 2022-2031
DNA, computer simulation, dissociation, energy transfer, enzymes, fluorescence, fluorescence correlation spectroscopy, gene overexpression, hypersensitivity, kaempferol, oncogenes
Small molecules capable of stabilizing the G-quadruplex structure of the nuclease hypersensitivity element III₁ (NHE III₁) are useful in controlling the overexpression of the c-MYC oncogene. In this study, we have probed the interactions of a 22-mer c-MYC promoter quadruplex-forming sequence (Pu22) with a bioflavonoid 3,4′,5,7-tetrahydroxyflavone, commonly known as kaempferol (KF). Ensemble fluorescence resonance energy transfer experiments on labeled Pu22 indicate that KF decreases the affinity of the former toward its complimentary strand, suggesting the stabilization of the quadruplex structure of Pu22. Considering that binding dynamics plays an important role in supramolecular interactions, there is hardly any information on this aspect for quadruplex–flavonoid systems; we have studied the kinetics of KF–Pu22 complexation and decomplexation processes on the single-molecule level by employing fluorescence correlation spectroscopy technique. The binding dynamics is characterized by a fast relaxation time of 10–50 μs. This leads to a high association rate constant (k₊) of ∼10⁹ M–¹ s–¹, which is close to the pure diffusion controlled limit. However, it is the low dissociation rate constant (k–) of ∼10⁴ s–¹ that is mainly responsible for the stability of the KF–Pu22 complex. Molecular docking study shows that KF binds near the 3′-end of Pu22 by forming several H-bonds with the bases. These findings suggest that KF is a potential binder of the c-MYC promoter quadruplex DNA and can be useful in anticancer therapies.