Do cationic surfactants like gemini, bolaamphiphiles etc intercalate DNA ? If not, how can they displace ethidium bromide from intercalating site of plasmid DNA that causing decrease in fluorescence? I am not getting proper reference regarding binding mode and forces of interaction between plasmid DNA and cationic surfactant.
DNA intercalating agents need planar (usually sp2 hybridized) geometry. Since cationic surfactants are used to complex pDNA and siRNA/miRNA for transfection purposes, I would expect the decreased ethidium bromide fluorescence signal to be possibly the result of blocking ethidium bromide by steric hindrance or more likely through absorption of the light used for excitation (ethidium bromide shows strong absorption at and below ~300 nm).
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