An insight into the interaction of phenanthridine dyes with polyriboadenylic acid: spectroscopic and thermodynamic...

Interaction of two phenanthridine dyes, namely ethidium bromide (EB) and propidium iodide (PI) with polyriboadenylic acid was investigated using various spectroscopic techniques. They were found to bind only with the single stranded form of the polymer, while no affinity was observed for the double stranded form. Enhanced binding observed for PI compared to EB may be attributed to the presence of external alkyl chain in PI. Thermodynamic studies showed negative enthalpy and negative entropy changes for the binding of both the dyes. Salt dependent studies revealed a lesser electrolytic contribution compared to the nonelectrolytic contribution to the total Gibbs free energy change in each case. This indicated importance of hydrophobic and van der Waal's interaction for the binding process. Overall, the binding data and detail energetics of interaction presented here would be helpful in the design of phenanthridine based molecules that interact with specific RNA structure.