Spectra of the Supramolecular Interaction of Neutral Red with Double-stranded DNA in a Neutral Medium

Abstract

With the spectral measurements of molecular absorption, fluorescence, and resonance light scattering, the binding mode of neutral red (NR) with double stranded DNA has been characterized in a neutral aqueous medium. Depending on the molar ratio R of NR: DNA, it was found that the binding involves in two processes at pH 7.63 and ionic strength lower than 0.01. The first process occurs in R > 2.22, where enhanced resonance light scattering was found, indicating the aggregation of NR molecules on the molecular surface of double stranded DNA. Scatchard plot was used to discuss the aggregation features based on the measurements of RLS data. The second process occurs in R < 2.22, characterized by bathochromic and hyperchromic molecular absorption of the interacting system, indicating the intercalative binding of NR into the base pairs of the double stranded DNA molecules. Energy transfer from DNA to NR molecules in the second interacting process occurs, resulting in strong enhancement of fluorescence, which proves NR can be used as a fluorescent probe as DNA structure.