Photophysical and thermodynamic landscape of interaction of a styryl-based dye with DNA duplex: effect of medium ionic strength and live cell imaging.

Abstract

A red-emitting excited-state intramolecular charge transfer pyridinium dye, [4-((1E,3E)-4-(4-(dimethylamino)phenyl)buta-1,3-dien-1-yl)-1-methylpyridin-1-ium] (DAPBMP), was synthesized and characterized using NMR and ESIMS studies. Binding interaction between dye DAPBMP and genomic DNA were investigated using steady-state and time-resolved spectroscopic methods. The thermodynamics of the interaction process were characterized using isothermal titration calorimetry (ITC) which reveals the key role of the hydrophobic effect and electrostatic interaction between the positive charged dye and the negatively charged polyphosphate of DNA backbone. The binding of dye to the minor groove of the DNA double helix is confirmed by circular dichroism spectroscopy and molecular docking simulation study. The binding interaction is found to be strongly dependent on the ionic strength of the medium as demonstrated by a systematic study in the presence of various concentrations of NaCl. A detailed calorimetric study shows that polyelectrolytic contribution, ΔGpe, (a measure of the role of electrostatic force) to the total free energy change (ΔG) of interaction progressively decreases with increasing ionic strength of the medium due to weakening of the DAPBMP:DNA binding by screening of the electrostatic charges. The fluorescence of DAPBMP exhibits a remarkable emission enhancement of almost 15 times when the viscosity of the water-propylene glycol system increases. Fluorescent microscopy was performed with C2C12 mouse skeletal myoblast and A549 lung cancer cells in the presence of DAPBMP dye. The dye passed through the C2C12 cell membrane and binds the negatively charged nucleic acids, essentially double-stranded DNA which made the nuclear puncta along with perinuclear located mitochondria.