Improving the understanding of DNA-propanediyl-1,3-bis(dodecyldimethylammonium) dibromide interaction using thermodynamic, structural and kinetic approaches

A kinetic, thermodynamic and structural study of the interaction of the gemini surfactant propanediyl-1,3-bis(dimethyldodecylammonium dibromide) (12-3-12.2Br) with calf thymus DNA was carried out at several ionic strengths (NaCl) in aqueous solutions. A new 12-3-12(2+)-selective membrane was prepared in order to gain insight into the factors that control the binding of 12-3-12.2Br to DNA. We used ethidium bromide (EB) as a fluorescence probe to follow the kinetics of the interaction by using the stopped-flow fluorescence technique. The results can be explained in terms of a reaction mechanism involving two consecutive reversible (fast and slow) steps. The fast step was attributed to the union/separation of the surfactant with/from the DNA polynucleotide. Changes in the kinetic constants in the forward and backward directions were discussed in terms of the Bronsted-Pitzer equation and of the increase in hydrophobic interactions of the surfactant tails as a consequence of salting-out effects, respectively. The slow step corresponds to a conformational change of the surfactant-DNA complex to a more compacted form. The equilibrium constant, calculated from the forward and reverse rate constants of these steps, agrees with the results obtained from potentiometric titration using a 12-3-12-(2+) selective electrode.